Starting phenix.real_space_refine on Fri Mar 22 08:26:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Bad SHEET records, were skipped: SHEET 1 AA3126 ASP A 83 GLN A 85 0 SHEET 3 AA3126 PHE A 120 ARG A 153 -1 O ASN A 148 N SER A 89 SHEET 4 AA3126 GLY A 197 GLY A 231 -1 O LYS A 216 N LEU A 133 SHEET 5 AA3126 GLY A 234 ARG A 262 -1 O ARG A 262 N ARG A 203 SHEET 9 AA3126 PHE C 120 ARG C 153 -1 O ASN C 148 N SER C 89 SHEET 10 AA3126 GLY C 197 GLY C 231 -1 O LYS C 216 N LEU C 133 SHEET 11 AA3126 GLY C 234 ARG C 262 -1 O ARG C 262 N ARG C 203 SHEET 15 AA3126 PHE D 120 ARG D 153 -1 O ASN D 148 N SER D 89 SHEET 16 AA3126 GLY D 197 GLY D 231 -1 O LYS D 216 N LEU D 133 SHEET 17 AA3126 GLY D 234 ARG D 262 -1 O ARG D 262 N ARG D 203 SHEET 21 AA3126 PHE E 120 ARG E 153 -1 O ASN E 148 N SER E 89 SHEET 22 AA3126 GLY E 197 GLY E 231 -1 O LYS E 216 N LEU E 133 SHEET 23 AA3126 GLY E 234 ARG E 262 -1 O ARG E 262 N ARG E 203 SHEET 27 AA3126 PHE F 120 ARG F 153 -1 O ASN F 148 N SER F 89 SHEET 28 AA3126 GLY F 197 GLY F 231 -1 O LYS F 216 N LEU F 133 SHEET 29 AA3126 GLY F 234 ARG F 262 -1 O ARG F 262 N ARG F 203 SHEET 33 AA3126 PHE G 120 ARG G 153 -1 O ASN G 148 N SER G 89 SHEET 34 AA3126 GLY G 197 GLY G 231 -1 O LYS G 216 N LEU G 133 SHEET 35 AA3126 GLY G 234 ARG G 262 -1 O ARG G 262 N ARG G 203 SHEET 39 AA3126 PHE H 120 ARG H 153 -1 O ASN H 148 N SER H 89 SHEET 40 AA3126 GLY H 197 GLY H 231 -1 O LYS H 216 N LEU H 133 SHEET 41 AA3126 GLY H 234 ARG H 262 -1 O ARG H 262 N ARG H 203 SHEET 45 AA3126 PHE I 120 ARG I 153 -1 O ASN I 148 N SER I 89 SHEET 46 AA3126 GLY I 197 GLY I 231 -1 O LYS I 216 N LEU I 133 SHEET 47 AA3126 GLY I 234 ARG I 262 -1 O ARG I 262 N ARG I 203 SHEET 51 AA3126 PHE J 120 ARG J 153 -1 O ASN J 148 N SER J 89 SHEET 52 AA3126 GLY J 197 GLY J 231 -1 O LYS J 216 N LEU J 133 SHEET 53 AA3126 GLY J 234 ARG J 262 -1 O ARG J 262 N ARG J 203 SHEET 57 AA3126 PHE K 120 ARG K 153 -1 O ASN K 148 N SER K 89 SHEET 58 AA3126 GLY K 197 GLY K 231 -1 O LYS K 216 N LEU K 133 SHEET 59 AA3126 GLY K 234 ARG K 262 -1 O ARG K 262 N ARG K 203 SHEET 63 AA3126 PHE L 120 ARG L 153 -1 O ASN L 148 N SER L 89 SHEET 64 AA3126 GLY L 197 GLY L 231 -1 O LYS L 216 N LEU L 133 SHEET 65 AA3126 GLY L 234 ARG L 262 -1 O ARG L 262 N ARG L 203 SHEET 69 AA3126 PHE M 120 ARG M 153 -1 O ASN M 148 N SER M 89 SHEET 70 AA3126 GLY M 197 GLY M 231 -1 O LYS M 216 N LEU M 133 SHEET 71 AA3126 GLY M 234 ARG M 262 -1 O ARG M 262 N ARG M 203 SHEET 75 AA3126 PHE N 120 ARG N 153 -1 O ASN N 148 N SER N 89 SHEET 76 AA3126 GLY N 197 GLY N 231 -1 O LYS N 216 N LEU N 133 SHEET 77 AA3126 GLY N 234 ARG N 262 -1 O ARG N 262 N ARG N 203 SHEET 81 AA3126 PHE O 120 ARG O 153 -1 O ASN O 148 N SER O 89 SHEET 82 AA3126 GLY O 197 GLY O 231 -1 O LYS O 216 N LEU O 133 SHEET 83 AA3126 GLY O 234 ARG O 262 -1 O ARG O 262 N ARG O 203 SHEET 87 AA3126 PHE P 120 ARG P 153 -1 O ASN P 148 N SER P 89 SHEET 88 AA3126 GLY P 197 GLY P 231 -1 O LYS P 216 N LEU P 133 SHEET 89 AA3126 GLY P 234 ARG P 262 -1 O ARG P 262 N ARG P 203 SHEET 93 AA3126 PHE Q 120 ARG Q 153 -1 O ASN Q 148 N SER Q 89 SHEET 94 AA3126 GLY Q 197 GLY Q 231 -1 O LYS Q 216 N LEU Q 133 SHEET 95 AA3126 GLY Q 234 ARG Q 262 -1 O ARG Q 262 N ARG Q 203 SHEET 99 AA3126 PHE R 120 ARG R 153 -1 O ASN R 148 N SER R 89 SHEET 100 AA3126 GLY R 197 GLY R 231 -1 O LYS R 216 N LEU R 133 SHEET 101 AA3126 GLY R 234 ARG R 262 -1 O ARG R 262 N ARG R 203 SHEET 105 AA3126 PHE S 120 ARG S 153 -1 O ASN S 148 N SER S 89 SHEET 106 AA3126 GLY S 197 GLY S 231 -1 O LYS S 216 N LEU S 133 SHEET 107 AA3126 GLY S 234 ARG S 262 -1 O ARG S 262 N ARG S 203 SHEET 111 AA3126 PHE T 120 ARG T 153 -1 O ASN T 148 N SER T 89 SHEET 112 AA3126 GLY T 197 GLY T 231 -1 O LYS T 216 N LEU T 133 SHEET 113 AA3126 GLY T 234 ARG T 262 -1 O ARG T 262 N ARG T 203 SHEET 117 AA3126 PHE U 120 ARG U 153 -1 O ASN U 148 N SER U 89 SHEET 118 AA3126 GLY U 197 GLY U 231 -1 O LYS U 216 N LEU U 133 SHEET 119 AA3126 GLY U 234 ARG U 262 -1 O ARG U 262 N ARG U 203 SHEET 123 AA3126 PHE V 120 ARG V 153 -1 O ASN V 148 N SER V 89 SHEET 124 AA3126 GLY V 197 GLY V 231 -1 O LYS V 216 N LEU V 133 SHEET 125 AA3126 GLY V 234 ARG V 262 -1 O ARG V 262 N ARG V 203 Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6w_15883/03_2024/8b6w_15883.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6w_15883/03_2024/8b6w_15883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6w_15883/03_2024/8b6w_15883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6w_15883/03_2024/8b6w_15883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6w_15883/03_2024/8b6w_15883.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6w_15883/03_2024/8b6w_15883.pdb" } resolution = 2.6 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= 0.001 sd= 0.022 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: 6 Type Number sf(0) Gaussians Mg 21 5.21 5 S 189 5.16 5 C 46788 2.51 5 N 12558 2.21 5 O 14469 1.98 5 H 71274 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 139": "OE1" <-> "OE2" Residue "I TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 139": "OE1" <-> "OE2" Residue "K TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "L TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 139": "OE1" <-> "OE2" Residue "M TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 139": "OE1" <-> "OE2" Residue "N TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 139": "OE1" <-> "OE2" Residue "O TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 139": "OE1" <-> "OE2" Residue "P TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 139": "OE1" <-> "OE2" Residue "Q TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 139": "OE1" <-> "OE2" Residue "R TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 139": "OE1" <-> "OE2" Residue "S TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T GLU 139": "OE1" <-> "OE2" Residue "T TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U GLU 139": "OE1" <-> "OE2" Residue "U TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V GLU 139": "OE1" <-> "OE2" Residue "V TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 145299 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "C" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "D" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "E" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "F" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "G" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "H" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "I" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "J" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "K" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "L" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "M" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "N" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "O" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "P" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "Q" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "R" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "S" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "T" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "U" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "V" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 6918 Classifications: {'peptide': 454} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 45.12, per 1000 atoms: 0.31 Number of scatterers: 145299 At special positions: 0 Unit cell: (260.348, 259.281, 144.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 189 16.00 Mg 21 11.99 O 14469 8.00 N 12558 7.00 C 46788 6.00 H 71274 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 84.81 Conformation dependent library (CDL) restraints added in 11.8 seconds 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17472 Finding SS restraints... Bad SHEET records, were skipped: SHEET 1 AA3126 ASP A 83 GLN A 85 0 SHEET 3 AA3126 PHE A 120 ARG A 153 -1 O ASN A 148 N SER A 89 SHEET 4 AA3126 GLY A 197 GLY A 231 -1 O LYS A 216 N LEU A 133 SHEET 5 AA3126 GLY A 234 ARG A 262 -1 O ARG A 262 N ARG A 203 SHEET 9 AA3126 PHE C 120 ARG C 153 -1 O ASN C 148 N SER C 89 SHEET 10 AA3126 GLY C 197 GLY C 231 -1 O LYS C 216 N LEU C 133 SHEET 11 AA3126 GLY C 234 ARG C 262 -1 O ARG C 262 N ARG C 203 SHEET 15 AA3126 PHE D 120 ARG D 153 -1 O ASN D 148 N SER D 89 SHEET 16 AA3126 GLY D 197 GLY D 231 -1 O LYS D 216 N LEU D 133 SHEET 17 AA3126 GLY D 234 ARG D 262 -1 O ARG D 262 N ARG D 203 SHEET 21 AA3126 PHE E 120 ARG E 153 -1 O ASN E 148 N SER E 89 SHEET 22 AA3126 GLY E 197 GLY E 231 -1 O LYS E 216 N LEU E 133 SHEET 23 AA3126 GLY E 234 ARG E 262 -1 O ARG E 262 N ARG E 203 SHEET 27 AA3126 PHE F 120 ARG F 153 -1 O ASN F 148 N SER F 89 SHEET 28 AA3126 GLY F 197 GLY F 231 -1 O LYS F 216 N LEU F 133 SHEET 29 AA3126 GLY F 234 ARG F 262 -1 O ARG F 262 N ARG F 203 SHEET 33 AA3126 PHE G 120 ARG G 153 -1 O ASN G 148 N SER G 89 SHEET 34 AA3126 GLY G 197 GLY G 231 -1 O LYS G 216 N LEU G 133 SHEET 35 AA3126 GLY G 234 ARG G 262 -1 O ARG G 262 N ARG G 203 SHEET 39 AA3126 PHE H 120 ARG H 153 -1 O ASN H 148 N SER H 89 SHEET 40 AA3126 GLY H 197 GLY H 231 -1 O LYS H 216 N LEU H 133 SHEET 41 AA3126 GLY H 234 ARG H 262 -1 O ARG H 262 N ARG H 203 SHEET 45 AA3126 PHE I 120 ARG I 153 -1 O ASN I 148 N SER I 89 SHEET 46 AA3126 GLY I 197 GLY I 231 -1 O LYS I 216 N LEU I 133 SHEET 47 AA3126 GLY I 234 ARG I 262 -1 O ARG I 262 N ARG I 203 SHEET 51 AA3126 PHE J 120 ARG J 153 -1 O ASN J 148 N SER J 89 SHEET 52 AA3126 GLY J 197 GLY J 231 -1 O LYS J 216 N LEU J 133 SHEET 53 AA3126 GLY J 234 ARG J 262 -1 O ARG J 262 N ARG J 203 SHEET 57 AA3126 PHE K 120 ARG K 153 -1 O ASN K 148 N SER K 89 SHEET 58 AA3126 GLY K 197 GLY K 231 -1 O LYS K 216 N LEU K 133 SHEET 59 AA3126 GLY K 234 ARG K 262 -1 O ARG K 262 N ARG K 203 SHEET 63 AA3126 PHE L 120 ARG L 153 -1 O ASN L 148 N SER L 89 SHEET 64 AA3126 GLY L 197 GLY L 231 -1 O LYS L 216 N LEU L 133 SHEET 65 AA3126 GLY L 234 ARG L 262 -1 O ARG L 262 N ARG L 203 SHEET 69 AA3126 PHE M 120 ARG M 153 -1 O ASN M 148 N SER M 89 SHEET 70 AA3126 GLY M 197 GLY M 231 -1 O LYS M 216 N LEU M 133 SHEET 71 AA3126 GLY M 234 ARG M 262 -1 O ARG M 262 N ARG M 203 SHEET 75 AA3126 PHE N 120 ARG N 153 -1 O ASN N 148 N SER N 89 SHEET 76 AA3126 GLY N 197 GLY N 231 -1 O LYS N 216 N LEU N 133 SHEET 77 AA3126 GLY N 234 ARG N 262 -1 O ARG N 262 N ARG N 203 SHEET 81 AA3126 PHE O 120 ARG O 153 -1 O ASN O 148 N SER O 89 SHEET 82 AA3126 GLY O 197 GLY O 231 -1 O LYS O 216 N LEU O 133 SHEET 83 AA3126 GLY O 234 ARG O 262 -1 O ARG O 262 N ARG O 203 SHEET 87 AA3126 PHE P 120 ARG P 153 -1 O ASN P 148 N SER P 89 SHEET 88 AA3126 GLY P 197 GLY P 231 -1 O LYS P 216 N LEU P 133 SHEET 89 AA3126 GLY P 234 ARG P 262 -1 O ARG P 262 N ARG P 203 SHEET 93 AA3126 PHE Q 120 ARG Q 153 -1 O ASN Q 148 N SER Q 89 SHEET 94 AA3126 GLY Q 197 GLY Q 231 -1 O LYS Q 216 N LEU Q 133 SHEET 95 AA3126 GLY Q 234 ARG Q 262 -1 O ARG Q 262 N ARG Q 203 SHEET 99 AA3126 PHE R 120 ARG R 153 -1 O ASN R 148 N SER R 89 SHEET 100 AA3126 GLY R 197 GLY R 231 -1 O LYS R 216 N LEU R 133 SHEET 101 AA3126 GLY R 234 ARG R 262 -1 O ARG R 262 N ARG R 203 SHEET 105 AA3126 PHE S 120 ARG S 153 -1 O ASN S 148 N SER S 89 SHEET 106 AA3126 GLY S 197 GLY S 231 -1 O LYS S 216 N LEU S 133 SHEET 107 AA3126 GLY S 234 ARG S 262 -1 O ARG S 262 N ARG S 203 SHEET 111 AA3126 PHE T 120 ARG T 153 -1 O ASN T 148 N SER T 89 SHEET 112 AA3126 GLY T 197 GLY T 231 -1 O LYS T 216 N LEU T 133 SHEET 113 AA3126 GLY T 234 ARG T 262 -1 O ARG T 262 N ARG T 203 SHEET 117 AA3126 PHE U 120 ARG U 153 -1 O ASN U 148 N SER U 89 SHEET 118 AA3126 GLY U 197 GLY U 231 -1 O LYS U 216 N LEU U 133 SHEET 119 AA3126 GLY U 234 ARG U 262 -1 O ARG U 262 N ARG U 203 SHEET 123 AA3126 PHE V 120 ARG V 153 -1 O ASN V 148 N SER V 89 SHEET 124 AA3126 GLY V 197 GLY V 231 -1 O LYS V 216 N LEU V 133 SHEET 125 AA3126 GLY V 234 ARG V 262 -1 O ARG V 262 N ARG V 203 Secondary structure from input PDB file: 189 helices and 105 sheets defined 18.5% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.78 Creating SS restraints... Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.836A pdb=" N LEU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 159 through 164' Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 179 through 191 Processing helix chain 'A' and resid 265 through 272 removed outlier: 3.593A pdb=" N GLY A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 276 through 290 Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 311 through 325 Processing helix chain 'A' and resid 325 through 334 Processing helix chain 'C' and resid 159 through 164 removed outlier: 3.836A pdb=" N LEU C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 164' Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 179 through 191 Processing helix chain 'C' and resid 265 through 272 removed outlier: 3.594A pdb=" N GLY C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 272 " --> pdb=" O LYS C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 275 No H-bonds generated for 'chain 'C' and resid 273 through 275' Processing helix chain 'C' and resid 276 through 290 Processing helix chain 'C' and resid 306 through 309 Processing helix chain 'C' and resid 311 through 325 Processing helix chain 'C' and resid 325 through 334 Processing helix chain 'D' and resid 159 through 164 removed outlier: 3.835A pdb=" N LEU D 163 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 159 through 164' Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 179 through 191 Processing helix chain 'D' and resid 265 through 272 removed outlier: 3.594A pdb=" N GLY D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL D 272 " --> pdb=" O LYS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 275 No H-bonds generated for 'chain 'D' and resid 273 through 275' Processing helix chain 'D' and resid 276 through 290 Processing helix chain 'D' and resid 306 through 309 Processing helix chain 'D' and resid 311 through 325 Processing helix chain 'D' and resid 325 through 334 Processing helix chain 'E' and resid 159 through 164 removed outlier: 3.836A pdb=" N LEU E 163 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET E 164 " --> pdb=" O LEU E 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 159 through 164' Processing helix chain 'E' and resid 165 through 174 Processing helix chain 'E' and resid 179 through 191 Processing helix chain 'E' and resid 265 through 272 removed outlier: 3.594A pdb=" N GLY E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL E 272 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 275 No H-bonds generated for 'chain 'E' and resid 273 through 275' Processing helix chain 'E' and resid 276 through 290 Processing helix chain 'E' and resid 306 through 309 Processing helix chain 'E' and resid 311 through 325 Processing helix chain 'E' and resid 325 through 334 Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.836A pdb=" N LEU F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET F 164 " --> pdb=" O LEU F 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 164' Processing helix chain 'F' and resid 165 through 174 Processing helix chain 'F' and resid 179 through 191 Processing helix chain 'F' and resid 265 through 272 removed outlier: 3.594A pdb=" N GLY F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL F 272 " --> pdb=" O LYS F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 275 No H-bonds generated for 'chain 'F' and resid 273 through 275' Processing helix chain 'F' and resid 276 through 290 Processing helix chain 'F' and resid 306 through 309 Processing helix chain 'F' and resid 311 through 325 Processing helix chain 'F' and resid 325 through 334 Processing helix chain 'G' and resid 159 through 164 removed outlier: 3.835A pdb=" N LEU G 163 " --> pdb=" O SER G 159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET G 164 " --> pdb=" O LEU G 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 159 through 164' Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 179 through 191 Processing helix chain 'G' and resid 265 through 272 removed outlier: 3.594A pdb=" N GLY G 271 " --> pdb=" O ALA G 267 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL G 272 " --> pdb=" O LYS G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 275 No H-bonds generated for 'chain 'G' and resid 273 through 275' Processing helix chain 'G' and resid 276 through 290 Processing helix chain 'G' and resid 306 through 309 Processing helix chain 'G' and resid 311 through 325 Processing helix chain 'G' and resid 325 through 334 Processing helix chain 'H' and resid 159 through 164 removed outlier: 3.836A pdb=" N LEU H 163 " --> pdb=" O SER H 159 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET H 164 " --> pdb=" O LEU H 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 159 through 164' Processing helix chain 'H' and resid 165 through 174 Processing helix chain 'H' and resid 179 through 191 Processing helix chain 'H' and resid 265 through 272 removed outlier: 3.594A pdb=" N GLY H 271 " --> pdb=" O ALA H 267 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL H 272 " --> pdb=" O LYS H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 275 No H-bonds generated for 'chain 'H' and resid 273 through 275' Processing helix chain 'H' and resid 276 through 290 Processing helix chain 'H' and resid 306 through 309 Processing helix chain 'H' and resid 311 through 325 Processing helix chain 'H' and resid 325 through 334 Processing helix chain 'I' and resid 159 through 164 removed outlier: 3.835A pdb=" N LEU I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET I 164 " --> pdb=" O LEU I 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 159 through 164' Processing helix chain 'I' and resid 165 through 174 Processing helix chain 'I' and resid 179 through 191 Processing helix chain 'I' and resid 265 through 272 removed outlier: 3.594A pdb=" N GLY I 271 " --> pdb=" O ALA I 267 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL I 272 " --> pdb=" O LYS I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 275 No H-bonds generated for 'chain 'I' and resid 273 through 275' Processing helix chain 'I' and resid 276 through 290 Processing helix chain 'I' and resid 306 through 309 Processing helix chain 'I' and resid 311 through 325 Processing helix chain 'I' and resid 325 through 334 Processing helix chain 'J' and resid 159 through 164 removed outlier: 3.835A pdb=" N LEU J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET J 164 " --> pdb=" O LEU J 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 159 through 164' Processing helix chain 'J' and resid 165 through 174 Processing helix chain 'J' and resid 179 through 191 Processing helix chain 'J' and resid 265 through 272 removed outlier: 3.594A pdb=" N GLY J 271 " --> pdb=" O ALA J 267 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL J 272 " --> pdb=" O LYS J 268 " (cutoff:3.500A) Processing helix chain 'J' and resid 273 through 275 No H-bonds generated for 'chain 'J' and resid 273 through 275' Processing helix chain 'J' and resid 276 through 290 Processing helix chain 'J' and resid 306 through 309 Processing helix chain 'J' and resid 311 through 325 Processing helix chain 'J' and resid 325 through 334 Processing helix chain 'K' and resid 159 through 164 removed outlier: 3.835A pdb=" N LEU K 163 " --> pdb=" O SER K 159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET K 164 " --> pdb=" O LEU K 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 159 through 164' Processing helix chain 'K' and resid 165 through 174 Processing helix chain 'K' and resid 179 through 191 Processing helix chain 'K' and resid 265 through 272 removed outlier: 3.594A pdb=" N GLY K 271 " --> pdb=" O ALA K 267 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL K 272 " --> pdb=" O LYS K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 273 through 275 No H-bonds generated for 'chain 'K' and resid 273 through 275' Processing helix chain 'K' and resid 276 through 290 Processing helix chain 'K' and resid 306 through 309 Processing helix chain 'K' and resid 311 through 325 Processing helix chain 'K' and resid 325 through 334 Processing helix chain 'L' and resid 159 through 164 removed outlier: 3.836A pdb=" N LEU L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET L 164 " --> pdb=" O LEU L 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 159 through 164' Processing helix chain 'L' and resid 165 through 174 Processing helix chain 'L' and resid 179 through 191 Processing helix chain 'L' and resid 265 through 272 removed outlier: 3.594A pdb=" N GLY L 271 " --> pdb=" O ALA L 267 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL L 272 " --> pdb=" O LYS L 268 " (cutoff:3.500A) Processing helix chain 'L' and resid 273 through 275 No H-bonds generated for 'chain 'L' and resid 273 through 275' Processing helix chain 'L' and resid 276 through 290 Processing helix chain 'L' and resid 306 through 309 Processing helix chain 'L' and resid 311 through 325 Processing helix chain 'L' and resid 325 through 334 Processing helix chain 'M' and resid 159 through 164 removed outlier: 3.836A pdb=" N LEU M 163 " --> pdb=" O SER M 159 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET M 164 " --> pdb=" O LEU M 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 159 through 164' Processing helix chain 'M' and resid 165 through 174 Processing helix chain 'M' and resid 179 through 191 Processing helix chain 'M' and resid 265 through 272 removed outlier: 3.593A pdb=" N GLY M 271 " --> pdb=" O ALA M 267 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL M 272 " --> pdb=" O LYS M 268 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 275 No H-bonds generated for 'chain 'M' and resid 273 through 275' Processing helix chain 'M' and resid 276 through 290 Processing helix chain 'M' and resid 306 through 309 Processing helix chain 'M' and resid 311 through 325 Processing helix chain 'M' and resid 325 through 334 Processing helix chain 'N' and resid 159 through 164 removed outlier: 3.836A pdb=" N LEU N 163 " --> pdb=" O SER N 159 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET N 164 " --> pdb=" O LEU N 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 159 through 164' Processing helix chain 'N' and resid 165 through 174 Processing helix chain 'N' and resid 179 through 191 Processing helix chain 'N' and resid 265 through 272 removed outlier: 3.593A pdb=" N GLY N 271 " --> pdb=" O ALA N 267 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL N 272 " --> pdb=" O LYS N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 273 through 275 No H-bonds generated for 'chain 'N' and resid 273 through 275' Processing helix chain 'N' and resid 276 through 290 Processing helix chain 'N' and resid 306 through 309 Processing helix chain 'N' and resid 311 through 325 Processing helix chain 'N' and resid 325 through 334 Processing helix chain 'O' and resid 159 through 164 removed outlier: 3.836A pdb=" N LEU O 163 " --> pdb=" O SER O 159 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET O 164 " --> pdb=" O LEU O 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 159 through 164' Processing helix chain 'O' and resid 165 through 174 Processing helix chain 'O' and resid 179 through 191 Processing helix chain 'O' and resid 265 through 272 removed outlier: 3.594A pdb=" N GLY O 271 " --> pdb=" O ALA O 267 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL O 272 " --> pdb=" O LYS O 268 " (cutoff:3.500A) Processing helix chain 'O' and resid 273 through 275 No H-bonds generated for 'chain 'O' and resid 273 through 275' Processing helix chain 'O' and resid 276 through 290 Processing helix chain 'O' and resid 306 through 309 Processing helix chain 'O' and resid 311 through 325 Processing helix chain 'O' and resid 325 through 334 Processing helix chain 'P' and resid 159 through 164 removed outlier: 3.835A pdb=" N LEU P 163 " --> pdb=" O SER P 159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET P 164 " --> pdb=" O LEU P 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 159 through 164' Processing helix chain 'P' and resid 165 through 174 Processing helix chain 'P' and resid 179 through 191 Processing helix chain 'P' and resid 265 through 272 removed outlier: 3.593A pdb=" N GLY P 271 " --> pdb=" O ALA P 267 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL P 272 " --> pdb=" O LYS P 268 " (cutoff:3.500A) Processing helix chain 'P' and resid 273 through 275 No H-bonds generated for 'chain 'P' and resid 273 through 275' Processing helix chain 'P' and resid 276 through 290 Processing helix chain 'P' and resid 306 through 309 Processing helix chain 'P' and resid 311 through 325 Processing helix chain 'P' and resid 325 through 334 Processing helix chain 'Q' and resid 159 through 164 removed outlier: 3.836A pdb=" N LEU Q 163 " --> pdb=" O SER Q 159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET Q 164 " --> pdb=" O LEU Q 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 159 through 164' Processing helix chain 'Q' and resid 165 through 174 Processing helix chain 'Q' and resid 179 through 191 Processing helix chain 'Q' and resid 265 through 272 removed outlier: 3.594A pdb=" N GLY Q 271 " --> pdb=" O ALA Q 267 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL Q 272 " --> pdb=" O LYS Q 268 " (cutoff:3.500A) Processing helix chain 'Q' and resid 273 through 275 No H-bonds generated for 'chain 'Q' and resid 273 through 275' Processing helix chain 'Q' and resid 276 through 290 Processing helix chain 'Q' and resid 306 through 309 Processing helix chain 'Q' and resid 311 through 325 Processing helix chain 'Q' and resid 325 through 334 Processing helix chain 'R' and resid 159 through 164 removed outlier: 3.835A pdb=" N LEU R 163 " --> pdb=" O SER R 159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 159 through 164' Processing helix chain 'R' and resid 165 through 174 Processing helix chain 'R' and resid 179 through 191 Processing helix chain 'R' and resid 265 through 272 removed outlier: 3.593A pdb=" N GLY R 271 " --> pdb=" O ALA R 267 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL R 272 " --> pdb=" O LYS R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 275 No H-bonds generated for 'chain 'R' and resid 273 through 275' Processing helix chain 'R' and resid 276 through 290 Processing helix chain 'R' and resid 306 through 309 Processing helix chain 'R' and resid 311 through 325 Processing helix chain 'R' and resid 325 through 334 Processing helix chain 'S' and resid 159 through 164 removed outlier: 3.836A pdb=" N LEU S 163 " --> pdb=" O SER S 159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET S 164 " --> pdb=" O LEU S 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 159 through 164' Processing helix chain 'S' and resid 165 through 174 Processing helix chain 'S' and resid 179 through 191 Processing helix chain 'S' and resid 265 through 272 removed outlier: 3.593A pdb=" N GLY S 271 " --> pdb=" O ALA S 267 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL S 272 " --> pdb=" O LYS S 268 " (cutoff:3.500A) Processing helix chain 'S' and resid 273 through 275 No H-bonds generated for 'chain 'S' and resid 273 through 275' Processing helix chain 'S' and resid 276 through 290 Processing helix chain 'S' and resid 306 through 309 Processing helix chain 'S' and resid 311 through 325 Processing helix chain 'S' and resid 325 through 334 Processing helix chain 'T' and resid 159 through 164 removed outlier: 3.836A pdb=" N LEU T 163 " --> pdb=" O SER T 159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET T 164 " --> pdb=" O LEU T 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 159 through 164' Processing helix chain 'T' and resid 165 through 174 Processing helix chain 'T' and resid 179 through 191 Processing helix chain 'T' and resid 265 through 272 removed outlier: 3.593A pdb=" N GLY T 271 " --> pdb=" O ALA T 267 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL T 272 " --> pdb=" O LYS T 268 " (cutoff:3.500A) Processing helix chain 'T' and resid 273 through 275 No H-bonds generated for 'chain 'T' and resid 273 through 275' Processing helix chain 'T' and resid 276 through 290 Processing helix chain 'T' and resid 306 through 309 Processing helix chain 'T' and resid 311 through 325 Processing helix chain 'T' and resid 325 through 334 Processing helix chain 'U' and resid 159 through 164 removed outlier: 3.835A pdb=" N LEU U 163 " --> pdb=" O SER U 159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET U 164 " --> pdb=" O LEU U 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 159 through 164' Processing helix chain 'U' and resid 165 through 174 Processing helix chain 'U' and resid 179 through 191 Processing helix chain 'U' and resid 265 through 272 removed outlier: 3.593A pdb=" N GLY U 271 " --> pdb=" O ALA U 267 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL U 272 " --> pdb=" O LYS U 268 " (cutoff:3.500A) Processing helix chain 'U' and resid 273 through 275 No H-bonds generated for 'chain 'U' and resid 273 through 275' Processing helix chain 'U' and resid 276 through 290 Processing helix chain 'U' and resid 306 through 309 Processing helix chain 'U' and resid 311 through 325 Processing helix chain 'U' and resid 325 through 334 Processing helix chain 'V' and resid 159 through 164 removed outlier: 3.836A pdb=" N LEU V 163 " --> pdb=" O SER V 159 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET V 164 " --> pdb=" O LEU V 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 159 through 164' Processing helix chain 'V' and resid 165 through 174 Processing helix chain 'V' and resid 179 through 191 Processing helix chain 'V' and resid 265 through 272 removed outlier: 3.594A pdb=" N GLY V 271 " --> pdb=" O ALA V 267 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL V 272 " --> pdb=" O LYS V 268 " (cutoff:3.500A) Processing helix chain 'V' and resid 273 through 275 No H-bonds generated for 'chain 'V' and resid 273 through 275' Processing helix chain 'V' and resid 276 through 290 Processing helix chain 'V' and resid 306 through 309 Processing helix chain 'V' and resid 311 through 325 Processing helix chain 'V' and resid 325 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 69 Processing sheet with id=AA4, first strand: chain 'A' and resid 340 through 347 removed outlier: 3.612A pdb=" N TYR A 340 " --> pdb=" O GLN A 383 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS A 381 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU A 344 " --> pdb=" O CYS A 379 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N CYS A 379 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL A 346 " --> pdb=" O TYR A 377 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR A 377 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 401 removed outlier: 6.073A pdb=" N VAL A 394 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU A 433 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP A 396 " --> pdb=" O LYS A 431 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 443 through 449 Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43 Processing sheet with id=AA8, first strand: chain 'C' and resid 67 through 69 Processing sheet with id=AA9, first strand: chain 'C' and resid 340 through 347 removed outlier: 3.612A pdb=" N TYR C 340 " --> pdb=" O GLN C 383 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N HIS C 381 " --> pdb=" O ASP C 342 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU C 344 " --> pdb=" O CYS C 379 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS C 379 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL C 346 " --> pdb=" O TYR C 377 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR C 377 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 392 through 401 removed outlier: 6.074A pdb=" N VAL C 394 " --> pdb=" O GLU C 433 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU C 433 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP C 396 " --> pdb=" O LYS C 431 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 443 through 449 Processing sheet with id=AB3, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB4, first strand: chain 'D' and resid 67 through 69 Processing sheet with id=AB5, first strand: chain 'D' and resid 340 through 347 removed outlier: 3.612A pdb=" N TYR D 340 " --> pdb=" O GLN D 383 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS D 381 " --> pdb=" O ASP D 342 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU D 344 " --> pdb=" O CYS D 379 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS D 379 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL D 346 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR D 377 " --> pdb=" O VAL D 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 392 through 401 removed outlier: 6.074A pdb=" N VAL D 394 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU D 433 " --> pdb=" O VAL D 394 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP D 396 " --> pdb=" O LYS D 431 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 443 through 449 Processing sheet with id=AB8, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB9, first strand: chain 'E' and resid 67 through 69 Processing sheet with id=AC1, first strand: chain 'E' and resid 340 through 347 removed outlier: 3.612A pdb=" N TYR E 340 " --> pdb=" O GLN E 383 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N HIS E 381 " --> pdb=" O ASP E 342 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU E 344 " --> pdb=" O CYS E 379 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS E 379 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL E 346 " --> pdb=" O TYR E 377 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR E 377 " --> pdb=" O VAL E 346 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 392 through 401 removed outlier: 6.074A pdb=" N VAL E 394 " --> pdb=" O GLU E 433 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU E 433 " --> pdb=" O VAL E 394 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP E 396 " --> pdb=" O LYS E 431 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 443 through 449 Processing sheet with id=AC4, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC5, first strand: chain 'F' and resid 67 through 69 Processing sheet with id=AC6, first strand: chain 'F' and resid 340 through 347 removed outlier: 3.612A pdb=" N TYR F 340 " --> pdb=" O GLN F 383 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N HIS F 381 " --> pdb=" O ASP F 342 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU F 344 " --> pdb=" O CYS F 379 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N CYS F 379 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL F 346 " --> pdb=" O TYR F 377 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR F 377 " --> pdb=" O VAL F 346 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 392 through 401 removed outlier: 6.074A pdb=" N VAL F 394 " --> pdb=" O GLU F 433 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU F 433 " --> pdb=" O VAL F 394 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP F 396 " --> pdb=" O LYS F 431 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 443 through 449 Processing sheet with id=AC9, first strand: chain 'G' and resid 42 through 43 Processing sheet with id=AD1, first strand: chain 'G' and resid 67 through 69 Processing sheet with id=AD2, first strand: chain 'G' and resid 340 through 347 removed outlier: 3.612A pdb=" N TYR G 340 " --> pdb=" O GLN G 383 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N HIS G 381 " --> pdb=" O ASP G 342 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU G 344 " --> pdb=" O CYS G 379 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS G 379 " --> pdb=" O LEU G 344 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL G 346 " --> pdb=" O TYR G 377 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR G 377 " --> pdb=" O VAL G 346 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 392 through 401 removed outlier: 6.074A pdb=" N VAL G 394 " --> pdb=" O GLU G 433 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU G 433 " --> pdb=" O VAL G 394 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP G 396 " --> pdb=" O LYS G 431 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 443 through 449 Processing sheet with id=AD5, first strand: chain 'H' and resid 42 through 43 Processing sheet with id=AD6, first strand: chain 'H' and resid 67 through 69 Processing sheet with id=AD7, first strand: chain 'H' and resid 340 through 347 removed outlier: 3.613A pdb=" N TYR H 340 " --> pdb=" O GLN H 383 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS H 381 " --> pdb=" O ASP H 342 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU H 344 " --> pdb=" O CYS H 379 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS H 379 " --> pdb=" O LEU H 344 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL H 346 " --> pdb=" O TYR H 377 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR H 377 " --> pdb=" O VAL H 346 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 392 through 401 removed outlier: 6.074A pdb=" N VAL H 394 " --> pdb=" O GLU H 433 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU H 433 " --> pdb=" O VAL H 394 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP H 396 " --> pdb=" O LYS H 431 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 443 through 449 Processing sheet with id=AE1, first strand: chain 'I' and resid 42 through 43 Processing sheet with id=AE2, first strand: chain 'I' and resid 67 through 69 Processing sheet with id=AE3, first strand: chain 'I' and resid 340 through 347 removed outlier: 3.612A pdb=" N TYR I 340 " --> pdb=" O GLN I 383 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N HIS I 381 " --> pdb=" O ASP I 342 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU I 344 " --> pdb=" O CYS I 379 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS I 379 " --> pdb=" O LEU I 344 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL I 346 " --> pdb=" O TYR I 377 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR I 377 " --> pdb=" O VAL I 346 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 392 through 401 removed outlier: 6.074A pdb=" N VAL I 394 " --> pdb=" O GLU I 433 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU I 433 " --> pdb=" O VAL I 394 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP I 396 " --> pdb=" O LYS I 431 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 443 through 449 Processing sheet with id=AE6, first strand: chain 'J' and resid 42 through 43 Processing sheet with id=AE7, first strand: chain 'J' and resid 67 through 69 Processing sheet with id=AE8, first strand: chain 'J' and resid 340 through 347 removed outlier: 3.612A pdb=" N TYR J 340 " --> pdb=" O GLN J 383 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS J 381 " --> pdb=" O ASP J 342 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU J 344 " --> pdb=" O CYS J 379 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS J 379 " --> pdb=" O LEU J 344 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL J 346 " --> pdb=" O TYR J 377 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR J 377 " --> pdb=" O VAL J 346 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 392 through 401 removed outlier: 6.074A pdb=" N VAL J 394 " --> pdb=" O GLU J 433 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU J 433 " --> pdb=" O VAL J 394 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP J 396 " --> pdb=" O LYS J 431 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 443 through 449 Processing sheet with id=AF2, first strand: chain 'K' and resid 42 through 43 Processing sheet with id=AF3, first strand: chain 'K' and resid 67 through 69 Processing sheet with id=AF4, first strand: chain 'K' and resid 340 through 347 removed outlier: 3.612A pdb=" N TYR K 340 " --> pdb=" O GLN K 383 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N HIS K 381 " --> pdb=" O ASP K 342 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU K 344 " --> pdb=" O CYS K 379 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS K 379 " --> pdb=" O LEU K 344 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL K 346 " --> pdb=" O TYR K 377 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR K 377 " --> pdb=" O VAL K 346 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 392 through 401 removed outlier: 6.074A pdb=" N VAL K 394 " --> pdb=" O GLU K 433 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU K 433 " --> pdb=" O VAL K 394 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP K 396 " --> pdb=" O LYS K 431 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 443 through 449 Processing sheet with id=AF7, first strand: chain 'L' and resid 42 through 43 Processing sheet with id=AF8, first strand: chain 'L' and resid 67 through 69 Processing sheet with id=AF9, first strand: chain 'L' and resid 340 through 347 removed outlier: 3.612A pdb=" N TYR L 340 " --> pdb=" O GLN L 383 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS L 381 " --> pdb=" O ASP L 342 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU L 344 " --> pdb=" O CYS L 379 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS L 379 " --> pdb=" O LEU L 344 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL L 346 " --> pdb=" O TYR L 377 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR L 377 " --> pdb=" O VAL L 346 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 392 through 401 removed outlier: 6.073A pdb=" N VAL L 394 " --> pdb=" O GLU L 433 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU L 433 " --> pdb=" O VAL L 394 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP L 396 " --> pdb=" O LYS L 431 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 443 through 449 Processing sheet with id=AG3, first strand: chain 'M' and resid 42 through 43 Processing sheet with id=AG4, first strand: chain 'M' and resid 67 through 69 Processing sheet with id=AG5, first strand: chain 'M' and resid 340 through 347 removed outlier: 3.612A pdb=" N TYR M 340 " --> pdb=" O GLN M 383 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS M 381 " --> pdb=" O ASP M 342 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU M 344 " --> pdb=" O CYS M 379 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS M 379 " --> pdb=" O LEU M 344 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL M 346 " --> pdb=" O TYR M 377 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR M 377 " --> pdb=" O VAL M 346 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 392 through 401 removed outlier: 6.074A pdb=" N VAL M 394 " --> pdb=" O GLU M 433 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU M 433 " --> pdb=" O VAL M 394 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP M 396 " --> pdb=" O LYS M 431 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 443 through 449 Processing sheet with id=AG8, first strand: chain 'N' and resid 42 through 43 Processing sheet with id=AG9, first strand: chain 'N' and resid 67 through 69 Processing sheet with id=AH1, first strand: chain 'N' and resid 340 through 347 removed outlier: 3.612A pdb=" N TYR N 340 " --> pdb=" O GLN N 383 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N HIS N 381 " --> pdb=" O ASP N 342 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU N 344 " --> pdb=" O CYS N 379 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS N 379 " --> pdb=" O LEU N 344 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL N 346 " --> pdb=" O TYR N 377 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR N 377 " --> pdb=" O VAL N 346 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 392 through 401 removed outlier: 6.073A pdb=" N VAL N 394 " --> pdb=" O GLU N 433 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU N 433 " --> pdb=" O VAL N 394 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP N 396 " --> pdb=" O LYS N 431 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 443 through 449 Processing sheet with id=AH4, first strand: chain 'O' and resid 42 through 43 Processing sheet with id=AH5, first strand: chain 'O' and resid 67 through 69 Processing sheet with id=AH6, first strand: chain 'O' and resid 340 through 347 removed outlier: 3.612A pdb=" N TYR O 340 " --> pdb=" O GLN O 383 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N HIS O 381 " --> pdb=" O ASP O 342 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU O 344 " --> pdb=" O CYS O 379 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS O 379 " --> pdb=" O LEU O 344 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL O 346 " --> pdb=" O TYR O 377 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR O 377 " --> pdb=" O VAL O 346 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 392 through 401 removed outlier: 6.074A pdb=" N VAL O 394 " --> pdb=" O GLU O 433 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU O 433 " --> pdb=" O VAL O 394 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP O 396 " --> pdb=" O LYS O 431 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 443 through 449 Processing sheet with id=AH9, first strand: chain 'P' and resid 42 through 43 Processing sheet with id=AI1, first strand: chain 'P' and resid 67 through 69 Processing sheet with id=AI2, first strand: chain 'P' and resid 340 through 347 removed outlier: 3.611A pdb=" N TYR P 340 " --> pdb=" O GLN P 383 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS P 381 " --> pdb=" O ASP P 342 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU P 344 " --> pdb=" O CYS P 379 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS P 379 " --> pdb=" O LEU P 344 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL P 346 " --> pdb=" O TYR P 377 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR P 377 " --> pdb=" O VAL P 346 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'P' and resid 392 through 401 removed outlier: 6.074A pdb=" N VAL P 394 " --> pdb=" O GLU P 433 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU P 433 " --> pdb=" O VAL P 394 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP P 396 " --> pdb=" O LYS P 431 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'P' and resid 443 through 449 Processing sheet with id=AI5, first strand: chain 'Q' and resid 42 through 43 Processing sheet with id=AI6, first strand: chain 'Q' and resid 67 through 69 Processing sheet with id=AI7, first strand: chain 'Q' and resid 340 through 347 removed outlier: 3.613A pdb=" N TYR Q 340 " --> pdb=" O GLN Q 383 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS Q 381 " --> pdb=" O ASP Q 342 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU Q 344 " --> pdb=" O CYS Q 379 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS Q 379 " --> pdb=" O LEU Q 344 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL Q 346 " --> pdb=" O TYR Q 377 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR Q 377 " --> pdb=" O VAL Q 346 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'Q' and resid 392 through 401 removed outlier: 6.074A pdb=" N VAL Q 394 " --> pdb=" O GLU Q 433 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU Q 433 " --> pdb=" O VAL Q 394 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP Q 396 " --> pdb=" O LYS Q 431 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'Q' and resid 443 through 449 Processing sheet with id=AJ1, first strand: chain 'R' and resid 42 through 43 Processing sheet with id=AJ2, first strand: chain 'R' and resid 67 through 69 Processing sheet with id=AJ3, first strand: chain 'R' and resid 340 through 347 removed outlier: 3.612A pdb=" N TYR R 340 " --> pdb=" O GLN R 383 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS R 381 " --> pdb=" O ASP R 342 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU R 344 " --> pdb=" O CYS R 379 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS R 379 " --> pdb=" O LEU R 344 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL R 346 " --> pdb=" O TYR R 377 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR R 377 " --> pdb=" O VAL R 346 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'R' and resid 392 through 401 removed outlier: 6.074A pdb=" N VAL R 394 " --> pdb=" O GLU R 433 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU R 433 " --> pdb=" O VAL R 394 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP R 396 " --> pdb=" O LYS R 431 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'R' and resid 443 through 449 Processing sheet with id=AJ6, first strand: chain 'S' and resid 42 through 43 Processing sheet with id=AJ7, first strand: chain 'S' and resid 67 through 69 Processing sheet with id=AJ8, first strand: chain 'S' and resid 340 through 347 removed outlier: 3.612A pdb=" N TYR S 340 " --> pdb=" O GLN S 383 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS S 381 " --> pdb=" O ASP S 342 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU S 344 " --> pdb=" O CYS S 379 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS S 379 " --> pdb=" O LEU S 344 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL S 346 " --> pdb=" O TYR S 377 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR S 377 " --> pdb=" O VAL S 346 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'S' and resid 392 through 401 removed outlier: 6.073A pdb=" N VAL S 394 " --> pdb=" O GLU S 433 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU S 433 " --> pdb=" O VAL S 394 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP S 396 " --> pdb=" O LYS S 431 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'S' and resid 443 through 449 Processing sheet with id=AK2, first strand: chain 'T' and resid 42 through 43 Processing sheet with id=AK3, first strand: chain 'T' and resid 67 through 69 Processing sheet with id=AK4, first strand: chain 'T' and resid 340 through 347 removed outlier: 3.612A pdb=" N TYR T 340 " --> pdb=" O GLN T 383 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS T 381 " --> pdb=" O ASP T 342 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU T 344 " --> pdb=" O CYS T 379 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS T 379 " --> pdb=" O LEU T 344 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL T 346 " --> pdb=" O TYR T 377 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR T 377 " --> pdb=" O VAL T 346 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'T' and resid 392 through 401 removed outlier: 6.074A pdb=" N VAL T 394 " --> pdb=" O GLU T 433 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU T 433 " --> pdb=" O VAL T 394 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP T 396 " --> pdb=" O LYS T 431 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'T' and resid 443 through 449 Processing sheet with id=AK7, first strand: chain 'U' and resid 42 through 43 Processing sheet with id=AK8, first strand: chain 'U' and resid 67 through 69 Processing sheet with id=AK9, first strand: chain 'U' and resid 340 through 347 removed outlier: 3.611A pdb=" N TYR U 340 " --> pdb=" O GLN U 383 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N HIS U 381 " --> pdb=" O ASP U 342 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU U 344 " --> pdb=" O CYS U 379 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS U 379 " --> pdb=" O LEU U 344 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL U 346 " --> pdb=" O TYR U 377 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR U 377 " --> pdb=" O VAL U 346 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'U' and resid 392 through 401 removed outlier: 6.074A pdb=" N VAL U 394 " --> pdb=" O GLU U 433 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU U 433 " --> pdb=" O VAL U 394 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP U 396 " --> pdb=" O LYS U 431 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'U' and resid 443 through 449 Processing sheet with id=AL3, first strand: chain 'V' and resid 42 through 43 Processing sheet with id=AL4, first strand: chain 'V' and resid 67 through 69 Processing sheet with id=AL5, first strand: chain 'V' and resid 340 through 347 removed outlier: 3.612A pdb=" N TYR V 340 " --> pdb=" O GLN V 383 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS V 381 " --> pdb=" O ASP V 342 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU V 344 " --> pdb=" O CYS V 379 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS V 379 " --> pdb=" O LEU V 344 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL V 346 " --> pdb=" O TYR V 377 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR V 377 " --> pdb=" O VAL V 346 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'V' and resid 392 through 401 removed outlier: 6.074A pdb=" N VAL V 394 " --> pdb=" O GLU V 433 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU V 433 " --> pdb=" O VAL V 394 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP V 396 " --> pdb=" O LYS V 431 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'V' and resid 443 through 449 1533 hydrogen bonds defined for protein. 4221 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: 51.60 Time building geometry restraints manager: 89.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 71190 1.03 - 1.23: 89 1.23 - 1.42: 32839 1.42 - 1.61: 42567 1.61 - 1.81: 294 Bond restraints: 146979 Sorted by residual: bond pdb=" N THR C 31 " pdb=" H1 THR C 31 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N THR N 31 " pdb=" H1 THR N 31 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N THR A 31 " pdb=" H1 THR A 31 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N THR T 31 " pdb=" H1 THR T 31 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR O 31 " pdb=" H1 THR O 31 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 146974 not shown) Histogram of bond angle deviations from ideal: 81.71 - 92.18: 63 92.18 - 102.65: 126 102.65 - 113.12: 168718 113.12 - 123.59: 83896 123.59 - 134.06: 11524 Bond angle restraints: 264327 Sorted by residual: angle pdb=" CG2 VAL D 358 " pdb=" CB VAL D 358 " pdb=" HB VAL D 358 " ideal model delta sigma weight residual 108.00 81.71 26.29 3.00e+00 1.11e-01 7.68e+01 angle pdb=" CG2 VAL G 358 " pdb=" CB VAL G 358 " pdb=" HB VAL G 358 " ideal model delta sigma weight residual 108.00 81.72 26.28 3.00e+00 1.11e-01 7.67e+01 angle pdb=" CG2 VAL S 358 " pdb=" CB VAL S 358 " pdb=" HB VAL S 358 " ideal model delta sigma weight residual 108.00 81.73 26.27 3.00e+00 1.11e-01 7.67e+01 angle pdb=" CG2 VAL A 358 " pdb=" CB VAL A 358 " pdb=" HB VAL A 358 " ideal model delta sigma weight residual 108.00 81.73 26.27 3.00e+00 1.11e-01 7.67e+01 angle pdb=" CG2 VAL K 358 " pdb=" CB VAL K 358 " pdb=" HB VAL K 358 " ideal model delta sigma weight residual 108.00 81.73 26.27 3.00e+00 1.11e-01 7.67e+01 ... (remaining 264322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 64108 16.67 - 33.34: 4331 33.34 - 50.01: 1071 50.01 - 66.69: 462 66.69 - 83.36: 126 Dihedral angle restraints: 70098 sinusoidal: 37359 harmonic: 32739 Sorted by residual: dihedral pdb=" CA MET T 200 " pdb=" C MET T 200 " pdb=" N GLY T 201 " pdb=" CA GLY T 201 " ideal model delta harmonic sigma weight residual 180.00 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA MET D 200 " pdb=" C MET D 200 " pdb=" N GLY D 201 " pdb=" CA GLY D 201 " ideal model delta harmonic sigma weight residual -180.00 -151.08 -28.92 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA MET C 200 " pdb=" C MET C 200 " pdb=" N GLY C 201 " pdb=" CA GLY C 201 " ideal model delta harmonic sigma weight residual -180.00 -151.08 -28.92 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 70095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.285: 11109 0.285 - 0.570: 0 0.570 - 0.855: 0 0.855 - 1.140: 0 1.140 - 1.425: 21 Chirality restraints: 11130 Sorted by residual: chirality pdb=" CB VAL O 358 " pdb=" CA VAL O 358 " pdb=" CG1 VAL O 358 " pdb=" CG2 VAL O 358 " both_signs ideal model delta sigma weight residual False -2.63 -1.20 -1.42 2.00e-01 2.50e+01 5.07e+01 chirality pdb=" CB VAL U 358 " pdb=" CA VAL U 358 " pdb=" CG1 VAL U 358 " pdb=" CG2 VAL U 358 " both_signs ideal model delta sigma weight residual False -2.63 -1.21 -1.42 2.00e-01 2.50e+01 5.07e+01 chirality pdb=" CB VAL I 358 " pdb=" CA VAL I 358 " pdb=" CG1 VAL I 358 " pdb=" CG2 VAL I 358 " both_signs ideal model delta sigma weight residual False -2.63 -1.21 -1.42 2.00e-01 2.50e+01 5.06e+01 ... (remaining 11127 not shown) Planarity restraints: 22596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 92 " -0.007 2.00e-02 2.50e+03 1.23e-02 4.55e+00 pdb=" CG TYR F 92 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR F 92 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR F 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 92 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR F 92 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 92 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR F 92 " -0.024 2.00e-02 2.50e+03 pdb=" HD1 TYR F 92 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR F 92 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR F 92 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR F 92 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 92 " -0.006 2.00e-02 2.50e+03 1.23e-02 4.53e+00 pdb=" CG TYR M 92 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR M 92 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR M 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR M 92 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR M 92 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR M 92 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR M 92 " -0.024 2.00e-02 2.50e+03 pdb=" HD1 TYR M 92 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR M 92 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR M 92 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR M 92 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 92 " -0.007 2.00e-02 2.50e+03 1.23e-02 4.52e+00 pdb=" CG TYR G 92 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR G 92 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR G 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR G 92 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR G 92 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR G 92 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR G 92 " -0.024 2.00e-02 2.50e+03 pdb=" HD1 TYR G 92 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR G 92 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR G 92 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR G 92 " 0.000 2.00e-02 2.50e+03 ... (remaining 22593 not shown) Histogram of nonbonded interaction distances: 0.93 - 1.66: 350 1.66 - 2.40: 68115 2.40 - 3.13: 443334 3.13 - 3.87: 592852 3.87 - 4.60: 957428 Warning: very small nonbonded interaction distances. Nonbonded interactions: 2062079 Sorted by model distance: nonbonded pdb=" HA ASP L 265 " pdb=" OD2 ASP M 88 " model vdw 0.930 2.620 nonbonded pdb=" HA ASP T 265 " pdb=" OD2 ASP U 88 " model vdw 0.936 2.620 nonbonded pdb=" HA ASP I 265 " pdb=" OD2 ASP J 88 " model vdw 0.937 2.620 nonbonded pdb=" OD2 ASP A 88 " pdb=" HA ASP V 265 " model vdw 0.940 2.620 nonbonded pdb=" HA ASP D 265 " pdb=" OD2 ASP E 88 " model vdw 0.940 2.620 ... (remaining 2062074 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 '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 'U' selection = chain 'V' } 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: 4.340 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: 1.570 Extract box with map and model: 22.050 Check model and map are aligned: 1.560 Set scattering table: 0.980 Process input model: 333.510 Find NCS groups from input model: 6.260 Set up NCS constraints: 1.180 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: 0.020 Load rotamer database and sin/cos tables:9.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 380.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 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 : 0.004 0.032 75705 Z= 0.289 Angle : 0.722 10.779 102795 Z= 0.415 Chirality : 0.077 1.425 11130 Planarity : 0.007 0.076 13503 Dihedral : 11.924 76.220 27321 Min Nonbonded Distance : 1.192 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.42 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: -0.28 (0.08), residues: 9492 helix: -0.74 (0.11), residues: 1512 sheet: 1.28 (0.07), residues: 3591 loop : -1.27 (0.08), residues: 4389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 150 HIS 0.004 0.001 HIS G 167 PHE 0.017 0.002 PHE A 293 TYR 0.024 0.005 TYR F 92 ARG 0.014 0.003 ARG M 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Evaluate side-chains 1934 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1934 time to evaluate : 7.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 GLN cc_start: 0.7602 (pt0) cc_final: 0.7237 (pt0) REVERT: A 173 ASP cc_start: 0.8074 (p0) cc_final: 0.7849 (p0) REVERT: A 304 GLU cc_start: 0.6834 (mp0) cc_final: 0.6483 (mp0) REVERT: A 316 GLU cc_start: 0.6851 (tp30) cc_final: 0.6563 (tp30) REVERT: A 320 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7717 (ttmt) REVERT: A 323 ASP cc_start: 0.7154 (t0) cc_final: 0.6856 (t70) REVERT: A 324 ASP cc_start: 0.7207 (m-30) cc_final: 0.6938 (m-30) REVERT: C 68 ARG cc_start: 0.7560 (ptm-80) cc_final: 0.7274 (ptt-90) REVERT: C 320 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7376 (ttmt) REVERT: C 323 ASP cc_start: 0.7331 (t0) cc_final: 0.7123 (t0) REVERT: D 170 GLN cc_start: 0.7472 (pt0) cc_final: 0.7253 (pt0) REVERT: D 320 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7593 (ttmt) REVERT: D 324 ASP cc_start: 0.7215 (m-30) cc_final: 0.6960 (m-30) REVERT: D 441 ILE cc_start: 0.6967 (mt) cc_final: 0.6729 (mp) REVERT: E 181 LYS cc_start: 0.8277 (mmmt) cc_final: 0.7958 (mmmm) REVERT: E 318 MET cc_start: 0.8071 (mtp) cc_final: 0.7796 (mtp) REVERT: E 324 ASP cc_start: 0.7043 (m-30) cc_final: 0.6827 (m-30) REVERT: F 175 LEU cc_start: 0.8486 (tp) cc_final: 0.8259 (tt) REVERT: F 257 THR cc_start: 0.7493 (t) cc_final: 0.7210 (m) REVERT: F 316 GLU cc_start: 0.6920 (tp30) cc_final: 0.6507 (tm-30) REVERT: F 320 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7760 (ttmt) REVERT: F 330 GLN cc_start: 0.7987 (mm110) cc_final: 0.7773 (mm-40) REVERT: G 37 GLU cc_start: 0.7203 (pm20) cc_final: 0.6950 (pm20) REVERT: G 181 LYS cc_start: 0.8114 (mmmt) cc_final: 0.7827 (mppt) REVERT: G 320 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7768 (ttmt) REVERT: G 324 ASP cc_start: 0.7334 (m-30) cc_final: 0.7094 (m-30) REVERT: G 330 GLN cc_start: 0.7978 (mm110) cc_final: 0.7733 (mm-40) REVERT: H 37 GLU cc_start: 0.7185 (pm20) cc_final: 0.6956 (pm20) REVERT: H 181 LYS cc_start: 0.8073 (mmmt) cc_final: 0.7865 (mmmm) REVERT: H 320 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7837 (ttmt) REVERT: H 324 ASP cc_start: 0.7181 (m-30) cc_final: 0.6898 (m-30) REVERT: H 330 GLN cc_start: 0.8243 (mm110) cc_final: 0.7776 (mm-40) REVERT: H 332 GLU cc_start: 0.6928 (tp30) cc_final: 0.6659 (tp30) REVERT: I 37 GLU cc_start: 0.7353 (pm20) cc_final: 0.7072 (pm20) REVERT: I 68 ARG cc_start: 0.7688 (ptm-80) cc_final: 0.7324 (ptt180) REVERT: I 219 TYR cc_start: 0.6360 (p90) cc_final: 0.5782 (p90) REVERT: I 246 GLU cc_start: 0.5955 (tt0) cc_final: 0.5593 (tt0) REVERT: I 324 ASP cc_start: 0.7245 (m-30) cc_final: 0.6945 (m-30) REVERT: I 333 LYS cc_start: 0.7883 (tttp) cc_final: 0.7640 (tttt) REVERT: I 441 ILE cc_start: 0.6968 (mt) cc_final: 0.6642 (mp) REVERT: J 36 VAL cc_start: 0.8194 (p) cc_final: 0.7887 (t) REVERT: J 37 GLU cc_start: 0.7267 (pm20) cc_final: 0.6936 (pm20) REVERT: J 181 LYS cc_start: 0.7831 (mmmt) cc_final: 0.7609 (mmmm) REVERT: J 320 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7608 (ttmt) REVERT: J 324 ASP cc_start: 0.7243 (m-30) cc_final: 0.6982 (m-30) REVERT: K 57 VAL cc_start: 0.8560 (p) cc_final: 0.8247 (t) REVERT: K 316 GLU cc_start: 0.6960 (tp30) cc_final: 0.6519 (tp30) REVERT: K 320 LYS cc_start: 0.7917 (ttmt) cc_final: 0.7388 (ttmt) REVERT: K 330 GLN cc_start: 0.8090 (mm110) cc_final: 0.7844 (mm-40) REVERT: K 441 ILE cc_start: 0.6890 (mt) cc_final: 0.6554 (mp) REVERT: L 181 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7886 (mmmm) REVERT: L 316 GLU cc_start: 0.6865 (tp30) cc_final: 0.6562 (tp30) REVERT: L 320 LYS cc_start: 0.7789 (ttmt) cc_final: 0.7291 (tppp) REVERT: L 441 ILE cc_start: 0.6678 (mt) cc_final: 0.6476 (mp) REVERT: M 304 GLU cc_start: 0.7090 (mp0) cc_final: 0.6821 (mp0) REVERT: M 311 SER cc_start: 0.6234 (m) cc_final: 0.5629 (t) REVERT: M 330 GLN cc_start: 0.7976 (mm110) cc_final: 0.7744 (mm-40) REVERT: M 441 ILE cc_start: 0.6729 (mt) cc_final: 0.6447 (mp) REVERT: N 68 ARG cc_start: 0.7540 (ptm-80) cc_final: 0.7312 (ptt-90) REVERT: N 254 TYR cc_start: 0.5975 (t80) cc_final: 0.5747 (t80) REVERT: N 320 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7442 (ttmt) REVERT: N 333 LYS cc_start: 0.7713 (tttp) cc_final: 0.7511 (tttt) REVERT: N 441 ILE cc_start: 0.6891 (mt) cc_final: 0.6599 (mp) REVERT: O 181 LYS cc_start: 0.7956 (mmmt) cc_final: 0.7718 (mmmm) REVERT: O 219 TYR cc_start: 0.6060 (p90) cc_final: 0.5746 (p90) REVERT: O 320 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7663 (ttmt) REVERT: O 324 ASP cc_start: 0.7221 (m-30) cc_final: 0.6882 (m-30) REVERT: P 36 VAL cc_start: 0.8277 (p) cc_final: 0.8026 (t) REVERT: P 170 GLN cc_start: 0.7622 (pt0) cc_final: 0.7345 (pt0) REVERT: P 479 CYS cc_start: 0.6690 (m) cc_final: 0.5891 (p) REVERT: Q 47 ILE cc_start: 0.8203 (tt) cc_final: 0.7973 (tt) REVERT: Q 80 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6550 (mt-10) REVERT: Q 170 GLN cc_start: 0.7671 (pt0) cc_final: 0.7389 (pt0) REVERT: Q 174 GLU cc_start: 0.7146 (pt0) cc_final: 0.6937 (pt0) REVERT: Q 189 ARG cc_start: 0.8419 (mmm160) cc_final: 0.8092 (mmt180) REVERT: Q 304 GLU cc_start: 0.6877 (mp0) cc_final: 0.6635 (mp0) REVERT: Q 320 LYS cc_start: 0.8205 (ttmt) cc_final: 0.7496 (ttmt) REVERT: Q 324 ASP cc_start: 0.7340 (m-30) cc_final: 0.7105 (m-30) REVERT: R 316 GLU cc_start: 0.6997 (tp30) cc_final: 0.6675 (tp30) REVERT: S 219 TYR cc_start: 0.6298 (p90) cc_final: 0.5947 (p90) REVERT: S 304 GLU cc_start: 0.6917 (mp0) cc_final: 0.6485 (mp0) REVERT: S 320 LYS cc_start: 0.8384 (ttmt) cc_final: 0.7971 (ttpp) REVERT: S 324 ASP cc_start: 0.7093 (m-30) cc_final: 0.6685 (m-30) REVERT: T 37 GLU cc_start: 0.7269 (pm20) cc_final: 0.6919 (pm20) REVERT: T 68 ARG cc_start: 0.7467 (ptm-80) cc_final: 0.7186 (ptt180) REVERT: T 179 ASP cc_start: 0.6952 (t0) cc_final: 0.6749 (t0) REVERT: T 181 LYS cc_start: 0.7989 (mmmt) cc_final: 0.7718 (mmmm) REVERT: T 292 ASP cc_start: 0.7291 (m-30) cc_final: 0.6704 (m-30) REVERT: T 316 GLU cc_start: 0.7036 (tp30) cc_final: 0.6598 (tp30) REVERT: T 320 LYS cc_start: 0.8289 (ttmt) cc_final: 0.7657 (ttmt) REVERT: T 324 ASP cc_start: 0.7390 (m-30) cc_final: 0.7127 (m-30) REVERT: U 47 ILE cc_start: 0.8391 (tt) cc_final: 0.8187 (tt) REVERT: U 162 GLU cc_start: 0.6853 (mp0) cc_final: 0.6637 (mp0) REVERT: U 181 LYS cc_start: 0.7726 (mmmt) cc_final: 0.7381 (mtmm) REVERT: U 254 TYR cc_start: 0.5824 (t80) cc_final: 0.5374 (t80) REVERT: U 286 SER cc_start: 0.7954 (p) cc_final: 0.7752 (p) REVERT: U 320 LYS cc_start: 0.8380 (ttmt) cc_final: 0.7697 (ttmm) REVERT: U 324 ASP cc_start: 0.7291 (m-30) cc_final: 0.7073 (m-30) REVERT: U 333 LYS cc_start: 0.7779 (tttp) cc_final: 0.7574 (tttt) REVERT: V 43 TYR cc_start: 0.8785 (t80) cc_final: 0.8482 (t80) REVERT: V 170 GLN cc_start: 0.7606 (pt0) cc_final: 0.7161 (pt0) REVERT: V 174 GLU cc_start: 0.7064 (pt0) cc_final: 0.6833 (pt0) REVERT: V 178 ASN cc_start: 0.8014 (m-40) cc_final: 0.7780 (m110) REVERT: V 181 LYS cc_start: 0.8049 (mmmt) cc_final: 0.7843 (mmmm) REVERT: V 285 ASP cc_start: 0.7210 (m-30) cc_final: 0.6972 (m-30) REVERT: V 307 THR cc_start: 0.7957 (m) cc_final: 0.7656 (p) REVERT: V 320 LYS cc_start: 0.8307 (ttmt) cc_final: 0.7776 (ttmt) REVERT: V 324 ASP cc_start: 0.7338 (m-30) cc_final: 0.7117 (m-30) outliers start: 0 outliers final: 3 residues processed: 1934 average time/residue: 3.4256 time to fit residues: 8658.4837 Evaluate side-chains 1643 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1640 time to evaluate : 7.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain M residue 176 ASN Chi-restraints excluded: chain V residue 219 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 797 optimal weight: 0.7980 chunk 716 optimal weight: 4.9990 chunk 397 optimal weight: 0.5980 chunk 244 optimal weight: 0.4980 chunk 483 optimal weight: 7.9990 chunk 382 optimal weight: 1.9990 chunk 740 optimal weight: 0.2980 chunk 286 optimal weight: 1.9990 chunk 450 optimal weight: 1.9990 chunk 551 optimal weight: 1.9990 chunk 858 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 86 GLN A 253 GLN ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN C 53 ASN C 58 GLN C 86 GLN C 87 ASN C 144 GLN C 253 GLN ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 ASN D 256 ASN ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 455 ASN E 53 ASN E 86 GLN E 170 GLN ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 ASN F 53 ASN F 86 GLN F 170 GLN F 176 ASN F 178 ASN F 256 ASN ** F 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 ASN G 53 ASN G 86 GLN G 87 ASN ** G 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 455 ASN H 53 ASN H 86 GLN H 144 GLN H 170 GLN H 178 ASN ** H 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 455 ASN I 53 ASN I 86 GLN I 87 ASN I 256 ASN ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 455 ASN J 53 ASN J 86 GLN J 170 GLN J 256 ASN ** J 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 455 ASN K 53 ASN K 86 GLN K 87 ASN K 170 GLN ** K 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 455 ASN L 53 ASN L 86 GLN L 87 ASN ** L 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 455 ASN M 53 ASN ** M 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 ASN ** M 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 455 ASN N 53 ASN N 86 GLN N 87 ASN ** N 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 455 ASN O 53 ASN O 86 GLN O 87 ASN O 178 ASN O 253 GLN ** O 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 455 ASN P 53 ASN P 86 GLN P 87 ASN P 171 GLN P 253 GLN P 303 GLN ** P 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 455 ASN Q 53 ASN Q 86 GLN Q 87 ASN Q 144 GLN Q 253 GLN ** Q 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 455 ASN R 53 ASN R 86 GLN R 87 ASN R 170 GLN R 253 GLN ** R 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 455 ASN S 53 ASN ** S 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN S 170 GLN ** S 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 455 ASN T 86 GLN T 87 ASN T 144 GLN T 170 GLN T 253 GLN ** T 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 455 ASN ** U 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 144 GLN U 170 GLN U 178 ASN U 253 GLN ** U 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 455 ASN ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 253 GLN ** V 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 455 ASN Total number of N/Q/H flips: 103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 75705 Z= 0.213 Angle : 0.632 11.604 102795 Z= 0.329 Chirality : 0.081 1.560 11130 Planarity : 0.004 0.048 13503 Dihedral : 5.905 22.432 10422 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.19 % Allowed : 10.03 % Favored : 88.78 % 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: -0.22 (0.08), residues: 9492 helix: 0.29 (0.13), residues: 1701 sheet: 0.79 (0.07), residues: 3927 loop : -1.34 (0.09), residues: 3864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 283 HIS 0.005 0.001 HIS C 167 PHE 0.015 0.002 PHE M 128 TYR 0.019 0.001 TYR I 92 ARG 0.006 0.001 ARG N 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Evaluate side-chains 1773 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1679 time to evaluate : 8.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8026 (p0) cc_final: 0.7711 (p0) REVERT: A 304 GLU cc_start: 0.6840 (mp0) cc_final: 0.6454 (mp0) REVERT: A 316 GLU cc_start: 0.7042 (tp30) cc_final: 0.6772 (tp30) REVERT: A 320 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7720 (ttmt) REVERT: A 323 ASP cc_start: 0.7154 (t0) cc_final: 0.6896 (t70) REVERT: A 324 ASP cc_start: 0.7357 (m-30) cc_final: 0.7156 (m-30) REVERT: A 333 LYS cc_start: 0.7914 (tttp) cc_final: 0.7710 (tttp) REVERT: C 43 TYR cc_start: 0.8683 (t80) cc_final: 0.8289 (t80) REVERT: C 304 GLU cc_start: 0.6958 (mp0) cc_final: 0.6571 (mp0) REVERT: C 311 SER cc_start: 0.7550 (OUTLIER) cc_final: 0.7321 (p) REVERT: C 320 LYS cc_start: 0.8062 (ttmt) cc_final: 0.7710 (ttmt) REVERT: C 323 ASP cc_start: 0.7298 (t0) cc_final: 0.7083 (t0) REVERT: D 170 GLN cc_start: 0.7551 (pt0) cc_final: 0.7333 (pt0) REVERT: D 307 THR cc_start: 0.7966 (m) cc_final: 0.7742 (p) REVERT: D 320 LYS cc_start: 0.8300 (ttmt) cc_final: 0.7828 (ttmt) REVERT: D 441 ILE cc_start: 0.6732 (mt) cc_final: 0.6513 (mp) REVERT: E 47 ILE cc_start: 0.8131 (tt) cc_final: 0.7906 (mt) REVERT: E 52 VAL cc_start: 0.8320 (m) cc_final: 0.8068 (p) REVERT: E 316 GLU cc_start: 0.7125 (tp30) cc_final: 0.6850 (tp30) REVERT: E 318 MET cc_start: 0.8192 (mtp) cc_final: 0.7950 (mtp) REVERT: E 441 ILE cc_start: 0.6555 (mt) cc_final: 0.6303 (mp) REVERT: F 175 LEU cc_start: 0.8594 (tp) cc_final: 0.8355 (tt) REVERT: F 320 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7859 (ttmt) REVERT: G 37 GLU cc_start: 0.7251 (pm20) cc_final: 0.6972 (pm20) REVERT: G 47 ILE cc_start: 0.8111 (tt) cc_final: 0.7875 (mt) REVERT: G 181 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7858 (mppt) REVERT: G 241 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.6792 (mtmm) REVERT: G 309 CYS cc_start: 0.7167 (t) cc_final: 0.6925 (t) REVERT: G 311 SER cc_start: 0.7390 (m) cc_final: 0.6998 (t) REVERT: H 47 ILE cc_start: 0.8359 (tt) cc_final: 0.8137 (mt) REVERT: H 181 LYS cc_start: 0.8031 (mmmt) cc_final: 0.7810 (mmmm) REVERT: H 310 SER cc_start: 0.8395 (t) cc_final: 0.8190 (p) REVERT: H 311 SER cc_start: 0.7563 (OUTLIER) cc_final: 0.7332 (p) REVERT: H 320 LYS cc_start: 0.8353 (ttmt) cc_final: 0.7887 (ttmt) REVERT: H 324 ASP cc_start: 0.7190 (m-30) cc_final: 0.6978 (m-30) REVERT: I 316 GLU cc_start: 0.7096 (tm-30) cc_final: 0.6824 (tm-30) REVERT: I 333 LYS cc_start: 0.7831 (tttp) cc_final: 0.7615 (tttt) REVERT: I 441 ILE cc_start: 0.6786 (mt) cc_final: 0.6493 (mp) REVERT: J 36 VAL cc_start: 0.8227 (p) cc_final: 0.7910 (t) REVERT: J 37 GLU cc_start: 0.7279 (pm20) cc_final: 0.6925 (pm20) REVERT: J 47 ILE cc_start: 0.8361 (tt) cc_final: 0.8015 (mt) REVERT: J 320 LYS cc_start: 0.8280 (ttmt) cc_final: 0.7664 (ttmt) REVERT: J 435 TYR cc_start: 0.6684 (t80) cc_final: 0.6459 (t80) REVERT: J 441 ILE cc_start: 0.6478 (mt) cc_final: 0.6219 (mp) REVERT: J 460 TYR cc_start: 0.5832 (m-80) cc_final: 0.5590 (m-80) REVERT: K 316 GLU cc_start: 0.7121 (tp30) cc_final: 0.6712 (tp30) REVERT: K 430 TYR cc_start: 0.5362 (p90) cc_final: 0.5061 (p90) REVERT: K 441 ILE cc_start: 0.6737 (mt) cc_final: 0.6451 (mp) REVERT: L 178 ASN cc_start: 0.8071 (m-40) cc_final: 0.7777 (m110) REVERT: L 316 GLU cc_start: 0.7079 (tp30) cc_final: 0.6822 (tp30) REVERT: L 320 LYS cc_start: 0.7732 (ttmt) cc_final: 0.7517 (tppp) REVERT: L 441 ILE cc_start: 0.6559 (mt) cc_final: 0.6344 (mp) REVERT: M 170 GLN cc_start: 0.7468 (pt0) cc_final: 0.7237 (pt0) REVERT: M 176 ASN cc_start: 0.7686 (t0) cc_final: 0.7475 (OUTLIER) REVERT: M 304 GLU cc_start: 0.7113 (mp0) cc_final: 0.6822 (mp0) REVERT: M 320 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7983 (ttmm) REVERT: M 441 ILE cc_start: 0.6579 (mt) cc_final: 0.6270 (mp) REVERT: N 162 GLU cc_start: 0.7116 (mp0) cc_final: 0.6908 (mp0) REVERT: N 254 TYR cc_start: 0.5965 (t80) cc_final: 0.5762 (t80) REVERT: N 285 ASP cc_start: 0.7289 (m-30) cc_final: 0.7071 (m-30) REVERT: N 316 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6861 (tp30) REVERT: N 333 LYS cc_start: 0.7792 (tttp) cc_final: 0.7511 (ttpp) REVERT: O 87 ASN cc_start: 0.8094 (t0) cc_final: 0.7513 (t0) REVERT: O 219 TYR cc_start: 0.6150 (p90) cc_final: 0.5819 (p90) REVERT: O 320 LYS cc_start: 0.8166 (ttmt) cc_final: 0.7716 (ttmt) REVERT: O 324 ASP cc_start: 0.7365 (m-30) cc_final: 0.7116 (m-30) REVERT: P 87 ASN cc_start: 0.8381 (t0) cc_final: 0.8137 (t160) REVERT: P 479 CYS cc_start: 0.6778 (m) cc_final: 0.6131 (p) REVERT: Q 162 GLU cc_start: 0.6874 (mp0) cc_final: 0.6632 (mp0) REVERT: Q 170 GLN cc_start: 0.7642 (pt0) cc_final: 0.7233 (pt0) REVERT: Q 173 ASP cc_start: 0.8103 (p0) cc_final: 0.7884 (p0) REVERT: Q 174 GLU cc_start: 0.7177 (pt0) cc_final: 0.6913 (pt0) REVERT: Q 183 ILE cc_start: 0.8405 (mt) cc_final: 0.8182 (mm) REVERT: Q 189 ARG cc_start: 0.8494 (mmm160) cc_final: 0.8147 (mtp180) REVERT: Q 304 GLU cc_start: 0.7027 (mp0) cc_final: 0.6788 (mp0) REVERT: Q 320 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7665 (ttpp) REVERT: R 307 THR cc_start: 0.8104 (m) cc_final: 0.7826 (p) REVERT: R 316 GLU cc_start: 0.7192 (tp30) cc_final: 0.6881 (tp30) REVERT: S 304 GLU cc_start: 0.6834 (mp0) cc_final: 0.6486 (mp0) REVERT: S 307 THR cc_start: 0.8048 (m) cc_final: 0.7776 (p) REVERT: T 47 ILE cc_start: 0.8325 (tt) cc_final: 0.8036 (mt) REVERT: T 68 ARG cc_start: 0.7709 (ptm-80) cc_final: 0.7477 (ptt180) REVERT: T 179 ASP cc_start: 0.6643 (t0) cc_final: 0.6439 (t0) REVERT: T 316 GLU cc_start: 0.7237 (tp30) cc_final: 0.6762 (tp30) REVERT: T 320 LYS cc_start: 0.8370 (ttmt) cc_final: 0.7787 (ttmt) REVERT: U 68 ARG cc_start: 0.7823 (ptm-80) cc_final: 0.7531 (ptt90) REVERT: U 286 SER cc_start: 0.7910 (p) cc_final: 0.7691 (p) REVERT: U 320 LYS cc_start: 0.8362 (ttmt) cc_final: 0.7775 (ttmm) REVERT: U 324 ASP cc_start: 0.7484 (m-30) cc_final: 0.7282 (m-30) REVERT: V 47 ILE cc_start: 0.8246 (tt) cc_final: 0.7972 (mt) REVERT: V 61 ASP cc_start: 0.7351 (t0) cc_final: 0.7021 (t0) REVERT: V 144 GLN cc_start: 0.7057 (mt0) cc_final: 0.6855 (mt0) REVERT: V 162 GLU cc_start: 0.6787 (mp0) cc_final: 0.6384 (mp0) REVERT: V 170 GLN cc_start: 0.7635 (pt0) cc_final: 0.7236 (pt0) REVERT: V 174 GLU cc_start: 0.7138 (pt0) cc_final: 0.6928 (pt0) REVERT: V 185 ARG cc_start: 0.7644 (ttm-80) cc_final: 0.7395 (ttt180) REVERT: V 286 SER cc_start: 0.7990 (p) cc_final: 0.7754 (p) REVERT: V 320 LYS cc_start: 0.8349 (ttmt) cc_final: 0.7865 (ttmt) outliers start: 94 outliers final: 42 residues processed: 1722 average time/residue: 3.5602 time to fit residues: 7891.6701 Evaluate side-chains 1660 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1616 time to evaluate : 7.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 241 LYS Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain H residue 311 SER Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 214 ARG Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 311 SER Chi-restraints excluded: chain K residue 450 ASN Chi-restraints excluded: chain L residue 311 SER Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 311 SER Chi-restraints excluded: chain N residue 324 ASP Chi-restraints excluded: chain N residue 450 ASN Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain P residue 310 SER Chi-restraints excluded: chain Q residue 184 SER Chi-restraints excluded: chain Q residue 308 LEU Chi-restraints excluded: chain R residue 310 SER Chi-restraints excluded: chain S residue 308 LEU Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain T residue 184 SER Chi-restraints excluded: chain T residue 308 LEU Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 308 LEU Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain V residue 308 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 476 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 714 optimal weight: 7.9990 chunk 584 optimal weight: 7.9990 chunk 236 optimal weight: 1.9990 chunk 859 optimal weight: 0.7980 chunk 928 optimal weight: 3.9990 chunk 765 optimal weight: 1.9990 chunk 852 optimal weight: 0.0010 chunk 293 optimal weight: 2.9990 chunk 689 optimal weight: 1.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 144 GLN ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 ASN F 256 ASN ** F 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 GLN H 178 ASN H 253 GLN ** H 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN I 256 ASN ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN J 144 GLN J 256 ASN ** J 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 GLN K 170 GLN K 253 GLN K 256 ASN ** K 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 GLN ** M 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 176 ASN N 256 ASN ** N 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 ASN ** O 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 303 GLN ** P 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN Q 144 GLN ** Q 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 253 GLN ** R 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 53 ASN ** S 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 58 GLN T 144 GLN T 253 GLN ** T 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 253 GLN V 303 GLN ** V 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 75705 Z= 0.321 Angle : 0.614 11.085 102795 Z= 0.322 Chirality : 0.078 1.465 11130 Planarity : 0.004 0.077 13503 Dihedral : 5.426 20.425 10416 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.43 % Allowed : 12.53 % Favored : 86.04 % 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: -0.06 (0.08), residues: 9492 helix: 0.82 (0.13), residues: 1575 sheet: 0.69 (0.07), residues: 3717 loop : -1.03 (0.08), residues: 4200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 306 HIS 0.009 0.002 HIS C 167 PHE 0.020 0.002 PHE S 293 TYR 0.023 0.002 TYR H 92 ARG 0.006 0.001 ARG H 153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Evaluate side-chains 1762 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1649 time to evaluate : 7.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.6853 (mmt180) REVERT: A 230 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6263 (mp0) REVERT: A 304 GLU cc_start: 0.6856 (mp0) cc_final: 0.6424 (mp0) REVERT: A 316 GLU cc_start: 0.7259 (tp30) cc_final: 0.7008 (tp30) REVERT: A 320 LYS cc_start: 0.8332 (ttmt) cc_final: 0.7788 (ttmt) REVERT: A 323 ASP cc_start: 0.7193 (t0) cc_final: 0.6924 (t70) REVERT: C 47 ILE cc_start: 0.8300 (tt) cc_final: 0.8070 (mt) REVERT: C 230 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6513 (mp0) REVERT: C 304 GLU cc_start: 0.6929 (mp0) cc_final: 0.6519 (mp0) REVERT: C 320 LYS cc_start: 0.8055 (ttmt) cc_final: 0.7692 (ttmt) REVERT: C 323 ASP cc_start: 0.7274 (t0) cc_final: 0.7008 (t0) REVERT: D 307 THR cc_start: 0.8010 (m) cc_final: 0.7784 (p) REVERT: D 320 LYS cc_start: 0.8220 (ttmt) cc_final: 0.8009 (ttmt) REVERT: D 435 TYR cc_start: 0.6907 (t80) cc_final: 0.6707 (t80) REVERT: D 441 ILE cc_start: 0.6780 (mt) cc_final: 0.6543 (mp) REVERT: E 230 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6358 (mp0) REVERT: E 268 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7577 (mptp) REVERT: E 316 GLU cc_start: 0.7298 (tp30) cc_final: 0.7017 (tp30) REVERT: E 441 ILE cc_start: 0.6632 (mt) cc_final: 0.6334 (mp) REVERT: F 47 ILE cc_start: 0.8397 (tt) cc_final: 0.8182 (mt) REVERT: F 175 LEU cc_start: 0.8724 (tp) cc_final: 0.8503 (tt) REVERT: F 230 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.6126 (mp0) REVERT: F 320 LYS cc_start: 0.8253 (ttmt) cc_final: 0.7922 (ttmt) REVERT: G 37 GLU cc_start: 0.7320 (pm20) cc_final: 0.7043 (pm20) REVERT: G 181 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7883 (mppt) REVERT: G 230 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6262 (mp0) REVERT: G 311 SER cc_start: 0.7698 (m) cc_final: 0.7429 (t) REVERT: H 181 LYS cc_start: 0.8025 (mmmt) cc_final: 0.7794 (mmmm) REVERT: H 323 ASP cc_start: 0.7445 (t0) cc_final: 0.7188 (m-30) REVERT: I 333 LYS cc_start: 0.7832 (tttp) cc_final: 0.7588 (tttt) REVERT: I 435 TYR cc_start: 0.7073 (t80) cc_final: 0.6830 (t80) REVERT: I 441 ILE cc_start: 0.6909 (mt) cc_final: 0.6568 (mp) REVERT: J 36 VAL cc_start: 0.8224 (p) cc_final: 0.7945 (t) REVERT: J 37 GLU cc_start: 0.7296 (pm20) cc_final: 0.6914 (pm20) REVERT: J 47 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8092 (mt) REVERT: J 320 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7696 (ttmm) REVERT: J 441 ILE cc_start: 0.6627 (mt) cc_final: 0.6337 (mp) REVERT: J 460 TYR cc_start: 0.5884 (m-80) cc_final: 0.5659 (m-80) REVERT: K 47 ILE cc_start: 0.8269 (tt) cc_final: 0.8062 (mt) REVERT: K 316 GLU cc_start: 0.7212 (tp30) cc_final: 0.6708 (tp30) REVERT: K 320 LYS cc_start: 0.7781 (ttmt) cc_final: 0.7539 (ttmm) REVERT: K 430 TYR cc_start: 0.5715 (p90) cc_final: 0.5359 (p90) REVERT: K 441 ILE cc_start: 0.6750 (mt) cc_final: 0.6455 (mp) REVERT: L 162 GLU cc_start: 0.6909 (mp0) cc_final: 0.6642 (mp0) REVERT: L 170 GLN cc_start: 0.7534 (pt0) cc_final: 0.7328 (tt0) REVERT: L 178 ASN cc_start: 0.8166 (m-40) cc_final: 0.7892 (m110) REVERT: L 316 GLU cc_start: 0.7249 (tp30) cc_final: 0.6983 (tp30) REVERT: L 320 LYS cc_start: 0.7786 (ttmt) cc_final: 0.7576 (tppp) REVERT: L 441 ILE cc_start: 0.6583 (mt) cc_final: 0.6314 (mp) REVERT: M 176 ASN cc_start: 0.7744 (t0) cc_final: 0.7534 (t0) REVERT: M 304 GLU cc_start: 0.7122 (mp0) cc_final: 0.6788 (mp0) REVERT: M 441 ILE cc_start: 0.6617 (mt) cc_final: 0.6373 (mp) REVERT: N 87 ASN cc_start: 0.8215 (t0) cc_final: 0.7879 (t0) REVERT: N 162 GLU cc_start: 0.7164 (mp0) cc_final: 0.6809 (mp0) REVERT: N 179 ASP cc_start: 0.6875 (t0) cc_final: 0.6650 (t0) REVERT: N 311 SER cc_start: 0.7582 (OUTLIER) cc_final: 0.7364 (p) REVERT: N 316 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6914 (tp30) REVERT: N 333 LYS cc_start: 0.7779 (tttp) cc_final: 0.7504 (ttpp) REVERT: O 64 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7945 (t) REVERT: O 87 ASN cc_start: 0.8139 (t0) cc_final: 0.7667 (t0) REVERT: O 219 TYR cc_start: 0.6272 (p90) cc_final: 0.5890 (p90) REVERT: O 320 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7825 (ttmt) REVERT: O 324 ASP cc_start: 0.7383 (m-30) cc_final: 0.7160 (m-30) REVERT: P 162 GLU cc_start: 0.7133 (mp0) cc_final: 0.6773 (mp0) REVERT: P 170 GLN cc_start: 0.7611 (pt0) cc_final: 0.7252 (pt0) REVERT: P 173 ASP cc_start: 0.7981 (p0) cc_final: 0.7713 (p0) REVERT: P 316 GLU cc_start: 0.7401 (tp30) cc_final: 0.6897 (tp30) REVERT: P 479 CYS cc_start: 0.6894 (m) cc_final: 0.6135 (p) REVERT: Q 162 GLU cc_start: 0.6948 (mp0) cc_final: 0.6415 (mp0) REVERT: Q 170 GLN cc_start: 0.7671 (pt0) cc_final: 0.7235 (pt0) REVERT: Q 173 ASP cc_start: 0.8028 (p0) cc_final: 0.7790 (p0) REVERT: Q 174 GLU cc_start: 0.7321 (pt0) cc_final: 0.7064 (pt0) REVERT: Q 183 ILE cc_start: 0.8414 (mt) cc_final: 0.8174 (mm) REVERT: Q 189 ARG cc_start: 0.8514 (mmm160) cc_final: 0.8268 (mmp-170) REVERT: Q 304 GLU cc_start: 0.7004 (mp0) cc_final: 0.6637 (mp0) REVERT: Q 320 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7825 (ttmt) REVERT: R 68 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7388 (ptt-90) REVERT: R 185 ARG cc_start: 0.7369 (ttt90) cc_final: 0.7133 (ttt90) REVERT: R 307 THR cc_start: 0.8184 (m) cc_final: 0.7916 (p) REVERT: R 316 GLU cc_start: 0.7354 (tp30) cc_final: 0.7075 (tp30) REVERT: R 320 LYS cc_start: 0.8182 (ttpp) cc_final: 0.7951 (ttpp) REVERT: S 304 GLU cc_start: 0.6910 (mp0) cc_final: 0.6425 (mp0) REVERT: T 47 ILE cc_start: 0.8367 (tt) cc_final: 0.8078 (mt) REVERT: T 160 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8190 (mt) REVERT: T 316 GLU cc_start: 0.7407 (tp30) cc_final: 0.6903 (tp30) REVERT: T 320 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7928 (ttmt) REVERT: U 68 ARG cc_start: 0.7847 (ptm-80) cc_final: 0.7603 (ptt90) REVERT: U 173 ASP cc_start: 0.7977 (p0) cc_final: 0.7752 (p0) REVERT: U 316 GLU cc_start: 0.7258 (tp30) cc_final: 0.7017 (tp30) REVERT: U 320 LYS cc_start: 0.8464 (ttmt) cc_final: 0.7838 (ttmm) REVERT: U 332 GLU cc_start: 0.7058 (tp30) cc_final: 0.6743 (tp30) REVERT: V 66 LYS cc_start: 0.7850 (tppp) cc_final: 0.7647 (mtpp) REVERT: V 162 GLU cc_start: 0.6854 (mp0) cc_final: 0.6428 (mp0) REVERT: V 170 GLN cc_start: 0.7698 (pt0) cc_final: 0.7332 (pt0) REVERT: V 174 GLU cc_start: 0.7190 (pt0) cc_final: 0.6977 (pt0) REVERT: V 178 ASN cc_start: 0.8071 (m-40) cc_final: 0.7844 (m110) REVERT: V 286 SER cc_start: 0.8043 (p) cc_final: 0.7831 (p) REVERT: V 311 SER cc_start: 0.7785 (OUTLIER) cc_final: 0.7550 (p) REVERT: V 316 GLU cc_start: 0.7197 (tp30) cc_final: 0.6925 (tp30) REVERT: V 320 LYS cc_start: 0.8322 (ttmt) cc_final: 0.8020 (ttmt) outliers start: 113 outliers final: 61 residues processed: 1714 average time/residue: 3.5502 time to fit residues: 7828.8485 Evaluate side-chains 1676 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1602 time to evaluate : 7.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 230 GLU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain H residue 308 LEU Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 310 SER Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 311 SER Chi-restraints excluded: chain K residue 324 ASP Chi-restraints excluded: chain K residue 439 THR Chi-restraints excluded: chain L residue 311 SER Chi-restraints excluded: chain L residue 439 THR Chi-restraints excluded: chain M residue 257 THR Chi-restraints excluded: chain M residue 308 LEU Chi-restraints excluded: chain M residue 311 SER Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain M residue 439 THR Chi-restraints excluded: chain N residue 311 SER Chi-restraints excluded: chain N residue 324 ASP Chi-restraints excluded: chain N residue 439 THR Chi-restraints excluded: chain N residue 450 ASN Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 450 ASN Chi-restraints excluded: chain P residue 303 GLN Chi-restraints excluded: chain P residue 310 SER Chi-restraints excluded: chain P residue 439 THR Chi-restraints excluded: chain P residue 450 ASN Chi-restraints excluded: chain Q residue 184 SER Chi-restraints excluded: chain Q residue 308 LEU Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 303 GLN Chi-restraints excluded: chain R residue 310 SER Chi-restraints excluded: chain S residue 114 GLU Chi-restraints excluded: chain S residue 214 ARG Chi-restraints excluded: chain S residue 226 LYS Chi-restraints excluded: chain S residue 308 LEU Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 184 SER Chi-restraints excluded: chain T residue 308 LEU Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 308 LEU Chi-restraints excluded: chain U residue 311 SER Chi-restraints excluded: chain V residue 83 ASP Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain V residue 308 LEU Chi-restraints excluded: chain V residue 311 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 849 optimal weight: 7.9990 chunk 646 optimal weight: 1.9990 chunk 446 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 410 optimal weight: 1.9990 chunk 577 optimal weight: 5.9990 chunk 862 optimal weight: 1.9990 chunk 913 optimal weight: 0.9990 chunk 450 optimal weight: 1.9990 chunk 817 optimal weight: 0.9990 chunk 246 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN F 178 ASN ** F 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 ASN ** G 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 GLN H 178 ASN ** H 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 GLN I 256 ASN ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 GLN J 256 ASN J 330 GLN ** J 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN K 253 GLN ** K 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 303 GLN ** M 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 ASN ** N 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN P 87 ASN ** P 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN Q 87 ASN Q 256 ASN ** Q 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 53 ASN ** T 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 144 GLN ** T 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 87 ASN ** U 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 176 ASN V 253 GLN ** V 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 75705 Z= 0.271 Angle : 0.590 10.994 102795 Z= 0.307 Chirality : 0.077 1.466 11130 Planarity : 0.003 0.073 13503 Dihedral : 5.108 19.731 10416 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.82 % Allowed : 13.65 % Favored : 84.53 % 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: -0.05 (0.08), residues: 9492 helix: 1.01 (0.13), residues: 1575 sheet: 0.55 (0.07), residues: 3717 loop : -0.94 (0.09), residues: 4200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 62 HIS 0.007 0.001 HIS C 167 PHE 0.019 0.002 PHE L 128 TYR 0.026 0.002 TYR L 229 ARG 0.011 0.000 ARG G 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Evaluate side-chains 1814 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1670 time to evaluate : 8.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.6914 (mmt180) REVERT: A 230 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6200 (mp0) REVERT: A 316 GLU cc_start: 0.7310 (tp30) cc_final: 0.7058 (tp30) REVERT: A 320 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7967 (ttmt) REVERT: A 323 ASP cc_start: 0.7192 (t0) cc_final: 0.6893 (t70) REVERT: C 47 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8055 (mt) REVERT: C 304 GLU cc_start: 0.6997 (mp0) cc_final: 0.6377 (mp0) REVERT: C 320 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7736 (ttmt) REVERT: D 68 ARG cc_start: 0.7701 (ptm-80) cc_final: 0.7497 (ptt-90) REVERT: D 307 THR cc_start: 0.8062 (m) cc_final: 0.7833 (p) REVERT: D 441 ILE cc_start: 0.6773 (mt) cc_final: 0.6529 (mp) REVERT: E 230 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: E 316 GLU cc_start: 0.7392 (tp30) cc_final: 0.7112 (tp30) REVERT: E 333 LYS cc_start: 0.7899 (tttt) cc_final: 0.7689 (tttt) REVERT: E 441 ILE cc_start: 0.6648 (mt) cc_final: 0.6341 (mp) REVERT: F 47 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8179 (mt) REVERT: F 175 LEU cc_start: 0.8784 (tp) cc_final: 0.8578 (tt) REVERT: F 230 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6117 (mp0) REVERT: F 320 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7913 (ttmt) REVERT: F 435 TYR cc_start: 0.7250 (t80) cc_final: 0.6990 (t80) REVERT: G 37 GLU cc_start: 0.7269 (pm20) cc_final: 0.6983 (pm20) REVERT: G 181 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7883 (mppt) REVERT: H 181 LYS cc_start: 0.7999 (mmmt) cc_final: 0.7756 (mmmm) REVERT: H 323 ASP cc_start: 0.7408 (t0) cc_final: 0.7202 (m-30) REVERT: I 316 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6925 (tm-30) REVERT: I 333 LYS cc_start: 0.7939 (tttp) cc_final: 0.7706 (tttt) REVERT: I 435 TYR cc_start: 0.6937 (t80) cc_final: 0.6723 (t80) REVERT: I 441 ILE cc_start: 0.6915 (mt) cc_final: 0.6563 (mp) REVERT: J 37 GLU cc_start: 0.7232 (pm20) cc_final: 0.6876 (pm20) REVERT: J 47 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8112 (mt) REVERT: J 316 GLU cc_start: 0.7403 (tp30) cc_final: 0.6787 (tp30) REVERT: J 441 ILE cc_start: 0.6689 (mt) cc_final: 0.6386 (mp) REVERT: J 460 TYR cc_start: 0.5926 (m-80) cc_final: 0.5659 (m-80) REVERT: K 68 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7582 (ptt-90) REVERT: K 170 GLN cc_start: 0.7741 (pt0) cc_final: 0.7450 (tt0) REVERT: K 173 ASP cc_start: 0.7839 (p0) cc_final: 0.7582 (p0) REVERT: K 316 GLU cc_start: 0.7272 (tp30) cc_final: 0.6809 (tp30) REVERT: K 320 LYS cc_start: 0.7790 (ttmt) cc_final: 0.7523 (ttmm) REVERT: K 396 ASP cc_start: 0.6038 (t0) cc_final: 0.5763 (p0) REVERT: K 430 TYR cc_start: 0.5816 (p90) cc_final: 0.5462 (p90) REVERT: K 441 ILE cc_start: 0.6752 (mt) cc_final: 0.6451 (mp) REVERT: L 162 GLU cc_start: 0.6931 (mp0) cc_final: 0.6689 (mp0) REVERT: L 178 ASN cc_start: 0.8211 (m-40) cc_final: 0.7947 (m110) REVERT: L 181 LYS cc_start: 0.8101 (mmmm) cc_final: 0.7833 (mmmm) REVERT: L 320 LYS cc_start: 0.7817 (ttmt) cc_final: 0.7253 (tppp) REVERT: L 441 ILE cc_start: 0.6643 (mt) cc_final: 0.6359 (mp) REVERT: M 162 GLU cc_start: 0.7092 (mp0) cc_final: 0.6869 (mp0) REVERT: M 176 ASN cc_start: 0.7758 (t0) cc_final: 0.7546 (t0) REVERT: M 304 GLU cc_start: 0.7123 (mp0) cc_final: 0.6774 (mp0) REVERT: M 320 LYS cc_start: 0.8340 (ttmm) cc_final: 0.8138 (ttmm) REVERT: M 441 ILE cc_start: 0.6581 (mt) cc_final: 0.6341 (mp) REVERT: N 87 ASN cc_start: 0.8146 (t0) cc_final: 0.7791 (t0) REVERT: N 162 GLU cc_start: 0.7176 (mp0) cc_final: 0.6831 (mp0) REVERT: N 265 ASP cc_start: 0.7157 (p0) cc_final: 0.6943 (p0) REVERT: N 316 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6975 (tp30) REVERT: N 333 LYS cc_start: 0.7786 (tttp) cc_final: 0.7536 (ttpp) REVERT: O 47 ILE cc_start: 0.8275 (tt) cc_final: 0.7853 (mt) REVERT: O 61 ASP cc_start: 0.7236 (t0) cc_final: 0.6997 (t0) REVERT: O 64 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7924 (t) REVERT: O 87 ASN cc_start: 0.8109 (t0) cc_final: 0.7653 (t0) REVERT: O 181 LYS cc_start: 0.8091 (mmmm) cc_final: 0.7866 (mmmm) REVERT: O 265 ASP cc_start: 0.7057 (p0) cc_final: 0.6595 (p0) REVERT: O 320 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7828 (ttmt) REVERT: O 324 ASP cc_start: 0.7379 (m-30) cc_final: 0.7132 (m-30) REVERT: P 162 GLU cc_start: 0.7146 (mp0) cc_final: 0.6772 (mp0) REVERT: P 311 SER cc_start: 0.8020 (t) cc_final: 0.7809 (p) REVERT: P 316 GLU cc_start: 0.7459 (tp30) cc_final: 0.6883 (tp30) REVERT: P 479 CYS cc_start: 0.6939 (m) cc_final: 0.6190 (p) REVERT: Q 47 ILE cc_start: 0.8302 (tt) cc_final: 0.7956 (mt) REVERT: Q 87 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8405 (t0) REVERT: Q 162 GLU cc_start: 0.6982 (mp0) cc_final: 0.6473 (mp0) REVERT: Q 170 GLN cc_start: 0.7700 (pt0) cc_final: 0.7306 (pt0) REVERT: Q 173 ASP cc_start: 0.7972 (p0) cc_final: 0.7723 (p0) REVERT: Q 174 GLU cc_start: 0.7376 (pt0) cc_final: 0.7115 (pt0) REVERT: Q 189 ARG cc_start: 0.8517 (mmm160) cc_final: 0.8264 (mmp-170) REVERT: Q 304 GLU cc_start: 0.6937 (mp0) cc_final: 0.6584 (mp0) REVERT: Q 320 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7809 (ttmt) REVERT: R 185 ARG cc_start: 0.7387 (ttt90) cc_final: 0.7158 (ttt90) REVERT: R 307 THR cc_start: 0.8207 (m) cc_final: 0.8000 (p) REVERT: R 316 GLU cc_start: 0.7468 (tp30) cc_final: 0.7200 (tp30) REVERT: S 88 ASP cc_start: 0.7114 (m-30) cc_final: 0.6905 (m-30) REVERT: S 304 GLU cc_start: 0.6866 (mp0) cc_final: 0.6477 (mp0) REVERT: T 37 GLU cc_start: 0.7141 (pm20) cc_final: 0.6768 (pm20) REVERT: T 47 ILE cc_start: 0.8371 (tt) cc_final: 0.8092 (mt) REVERT: T 160 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8196 (mt) REVERT: T 316 GLU cc_start: 0.7483 (tp30) cc_final: 0.6952 (tp30) REVERT: T 320 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7875 (ttmm) REVERT: U 68 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7596 (ptt90) REVERT: U 173 ASP cc_start: 0.7846 (p0) cc_final: 0.7612 (p0) REVERT: U 316 GLU cc_start: 0.7343 (tp30) cc_final: 0.7046 (tp30) REVERT: U 320 LYS cc_start: 0.8356 (ttmt) cc_final: 0.7926 (ttmm) REVERT: V 162 GLU cc_start: 0.6896 (mp0) cc_final: 0.6500 (mp0) REVERT: V 170 GLN cc_start: 0.7654 (pt0) cc_final: 0.7413 (pt0) REVERT: V 178 ASN cc_start: 0.8135 (m-40) cc_final: 0.7895 (m110) REVERT: V 286 SER cc_start: 0.8029 (p) cc_final: 0.7794 (p) REVERT: V 316 GLU cc_start: 0.7302 (tp30) cc_final: 0.7047 (tp30) REVERT: V 433 GLU cc_start: 0.6763 (tp30) cc_final: 0.5977 (mp0) outliers start: 144 outliers final: 71 residues processed: 1746 average time/residue: 3.6421 time to fit residues: 8267.5509 Evaluate side-chains 1702 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1619 time to evaluate : 7.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 158 LYS Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 309 CYS Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 439 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 310 SER Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 439 THR Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain K residue 68 ARG Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 439 THR Chi-restraints excluded: chain K residue 450 ASN Chi-restraints excluded: chain L residue 309 CYS Chi-restraints excluded: chain L residue 311 SER Chi-restraints excluded: chain L residue 439 THR Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 308 LEU Chi-restraints excluded: chain M residue 311 SER Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain M residue 439 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 67 LYS Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 324 ASP Chi-restraints excluded: chain N residue 325 VAL Chi-restraints excluded: chain N residue 439 THR Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 160 LEU Chi-restraints excluded: chain P residue 439 THR Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 184 SER Chi-restraints excluded: chain Q residue 308 LEU Chi-restraints excluded: chain Q residue 325 VAL Chi-restraints excluded: chain R residue 217 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 310 SER Chi-restraints excluded: chain R residue 439 THR Chi-restraints excluded: chain S residue 308 LEU Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 184 SER Chi-restraints excluded: chain T residue 265 ASP Chi-restraints excluded: chain T residue 308 LEU Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain T residue 439 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 68 ARG Chi-restraints excluded: chain U residue 311 SER Chi-restraints excluded: chain U residue 325 VAL Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain V residue 439 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 760 optimal weight: 9.9990 chunk 518 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 680 optimal weight: 1.9990 chunk 376 optimal weight: 1.9990 chunk 779 optimal weight: 1.9990 chunk 631 optimal weight: 0.0270 chunk 1 optimal weight: 1.9990 chunk 466 optimal weight: 1.9990 chunk 819 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 overall best weight: 0.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 87 ASN ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 ASN ** F 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 GLN H 178 ASN ** H 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN J 58 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 256 ASN ** J 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 GLN K 256 ASN ** K 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 303 GLN ** M 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 GLN ** N 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 ASN ** N 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 314 GLN ** O 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN ** P 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN Q 144 GLN ** Q 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 256 ASN ** R 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 87 ASN T 253 GLN ** T 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 75705 Z= 0.253 Angle : 0.575 10.908 102795 Z= 0.299 Chirality : 0.077 1.455 11130 Planarity : 0.003 0.039 13503 Dihedral : 4.897 19.628 10416 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.38 % Allowed : 14.98 % Favored : 83.64 % 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: -0.21 (0.08), residues: 9492 helix: 0.75 (0.13), residues: 1701 sheet: 0.44 (0.08), residues: 3612 loop : -0.99 (0.09), residues: 4179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 306 HIS 0.007 0.001 HIS H 167 PHE 0.021 0.002 PHE C 128 TYR 0.026 0.001 TYR I 219 ARG 0.006 0.000 ARG G 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Evaluate side-chains 1731 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1622 time to evaluate : 8.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.6932 (mmt180) REVERT: A 230 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6170 (mp0) REVERT: A 316 GLU cc_start: 0.7355 (tp30) cc_final: 0.7110 (tp30) REVERT: A 320 LYS cc_start: 0.8246 (ttmt) cc_final: 0.7954 (ttmt) REVERT: C 47 ILE cc_start: 0.8293 (tt) cc_final: 0.8051 (mt) REVERT: C 304 GLU cc_start: 0.6906 (mp0) cc_final: 0.6395 (mp0) REVERT: C 320 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7747 (ttmt) REVERT: D 307 THR cc_start: 0.8110 (m) cc_final: 0.7906 (p) REVERT: D 435 TYR cc_start: 0.6992 (t80) cc_final: 0.6743 (t80) REVERT: D 441 ILE cc_start: 0.6799 (mt) cc_final: 0.6555 (mp) REVERT: E 173 ASP cc_start: 0.7764 (p0) cc_final: 0.7524 (p0) REVERT: E 230 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6636 (mp0) REVERT: E 316 GLU cc_start: 0.7441 (tp30) cc_final: 0.7164 (tp30) REVERT: E 333 LYS cc_start: 0.7922 (tttt) cc_final: 0.7716 (tttt) REVERT: E 441 ILE cc_start: 0.6681 (mt) cc_final: 0.6367 (mp) REVERT: F 47 ILE cc_start: 0.8404 (tt) cc_final: 0.8178 (mt) REVERT: F 175 LEU cc_start: 0.8836 (tp) cc_final: 0.8634 (tt) REVERT: F 230 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.6131 (mp0) REVERT: F 320 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7916 (ttmt) REVERT: G 181 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7851 (mppt) REVERT: H 181 LYS cc_start: 0.8000 (mmmt) cc_final: 0.7753 (mmmm) REVERT: H 323 ASP cc_start: 0.7386 (t0) cc_final: 0.7182 (m-30) REVERT: I 316 GLU cc_start: 0.7288 (tm-30) cc_final: 0.6954 (tm-30) REVERT: I 333 LYS cc_start: 0.7945 (tttp) cc_final: 0.7688 (tttt) REVERT: I 435 TYR cc_start: 0.6989 (t80) cc_final: 0.6721 (t80) REVERT: I 441 ILE cc_start: 0.6952 (mt) cc_final: 0.6602 (mp) REVERT: J 37 GLU cc_start: 0.7236 (pm20) cc_final: 0.6949 (pm20) REVERT: J 47 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8117 (mt) REVERT: J 230 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.6177 (mp0) REVERT: J 441 ILE cc_start: 0.6706 (mt) cc_final: 0.6387 (mp) REVERT: K 170 GLN cc_start: 0.7689 (pt0) cc_final: 0.7442 (tt0) REVERT: K 173 ASP cc_start: 0.7774 (p0) cc_final: 0.7516 (p0) REVERT: K 316 GLU cc_start: 0.7339 (tp30) cc_final: 0.6836 (tp30) REVERT: K 320 LYS cc_start: 0.7796 (ttmt) cc_final: 0.7559 (ttmm) REVERT: K 396 ASP cc_start: 0.6075 (t0) cc_final: 0.5719 (p0) REVERT: K 430 TYR cc_start: 0.5862 (p90) cc_final: 0.5502 (p90) REVERT: K 441 ILE cc_start: 0.6772 (mt) cc_final: 0.6477 (mp) REVERT: L 68 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7398 (ptt90) REVERT: L 162 GLU cc_start: 0.6963 (mp0) cc_final: 0.6720 (mp0) REVERT: L 178 ASN cc_start: 0.8231 (m-40) cc_final: 0.7993 (m110) REVERT: L 181 LYS cc_start: 0.8119 (mmmm) cc_final: 0.7894 (mmmm) REVERT: L 441 ILE cc_start: 0.6657 (mt) cc_final: 0.6372 (mp) REVERT: M 162 GLU cc_start: 0.7112 (mp0) cc_final: 0.6876 (mp0) REVERT: M 176 ASN cc_start: 0.7816 (t0) cc_final: 0.7601 (t0) REVERT: M 304 GLU cc_start: 0.7132 (mp0) cc_final: 0.6674 (mp0) REVERT: M 311 SER cc_start: 0.7452 (OUTLIER) cc_final: 0.7212 (p) REVERT: M 441 ILE cc_start: 0.6559 (mt) cc_final: 0.6299 (mp) REVERT: N 87 ASN cc_start: 0.8099 (t0) cc_final: 0.7718 (t0) REVERT: N 162 GLU cc_start: 0.7132 (mp0) cc_final: 0.6769 (mp0) REVERT: N 257 THR cc_start: 0.7364 (OUTLIER) cc_final: 0.7147 (m) REVERT: N 316 GLU cc_start: 0.7289 (tm-30) cc_final: 0.6996 (tp30) REVERT: O 47 ILE cc_start: 0.8284 (tt) cc_final: 0.8078 (mt) REVERT: O 61 ASP cc_start: 0.7263 (t0) cc_final: 0.6893 (t0) REVERT: O 64 THR cc_start: 0.8141 (OUTLIER) cc_final: 0.7918 (t) REVERT: O 87 ASN cc_start: 0.8090 (t0) cc_final: 0.7637 (t0) REVERT: O 181 LYS cc_start: 0.8041 (mmmm) cc_final: 0.7827 (mmmm) REVERT: O 265 ASP cc_start: 0.7035 (p0) cc_final: 0.6550 (p0) REVERT: O 320 LYS cc_start: 0.8266 (ttmt) cc_final: 0.7802 (ttmt) REVERT: O 324 ASP cc_start: 0.7353 (m-30) cc_final: 0.7120 (m-30) REVERT: P 162 GLU cc_start: 0.7091 (mp0) cc_final: 0.6720 (mp0) REVERT: P 185 ARG cc_start: 0.7869 (ttm-80) cc_final: 0.7631 (ttt180) REVERT: P 311 SER cc_start: 0.8092 (t) cc_final: 0.7890 (p) REVERT: P 316 GLU cc_start: 0.7508 (tp30) cc_final: 0.6950 (tp30) REVERT: P 479 CYS cc_start: 0.6938 (m) cc_final: 0.6191 (p) REVERT: Q 47 ILE cc_start: 0.8299 (tt) cc_final: 0.8003 (mt) REVERT: Q 162 GLU cc_start: 0.6992 (mp0) cc_final: 0.6475 (mp0) REVERT: Q 170 GLN cc_start: 0.7670 (pt0) cc_final: 0.7283 (pt0) REVERT: Q 173 ASP cc_start: 0.7929 (p0) cc_final: 0.7685 (p0) REVERT: Q 174 GLU cc_start: 0.7388 (pt0) cc_final: 0.7142 (pt0) REVERT: Q 189 ARG cc_start: 0.8512 (mmm160) cc_final: 0.8197 (mmt180) REVERT: Q 304 GLU cc_start: 0.6905 (mp0) cc_final: 0.6578 (mp0) REVERT: Q 320 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7846 (ttmt) REVERT: R 316 GLU cc_start: 0.7436 (tp30) cc_final: 0.7174 (tp30) REVERT: S 88 ASP cc_start: 0.7121 (m-30) cc_final: 0.6895 (m-30) REVERT: S 181 LYS cc_start: 0.8394 (mmmm) cc_final: 0.8138 (mmmm) REVERT: S 304 GLU cc_start: 0.6836 (mp0) cc_final: 0.6420 (mp0) REVERT: T 37 GLU cc_start: 0.7159 (pm20) cc_final: 0.6787 (pm20) REVERT: T 47 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8070 (mt) REVERT: T 160 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8210 (mt) REVERT: T 316 GLU cc_start: 0.7504 (tp30) cc_final: 0.6972 (tp30) REVERT: T 320 LYS cc_start: 0.8289 (ttmt) cc_final: 0.7898 (ttmm) REVERT: U 68 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7583 (ptt90) REVERT: U 173 ASP cc_start: 0.7779 (p0) cc_final: 0.7538 (p0) REVERT: U 316 GLU cc_start: 0.7351 (tp30) cc_final: 0.7036 (tp30) REVERT: U 320 LYS cc_start: 0.8355 (ttmt) cc_final: 0.7843 (ttmm) REVERT: V 162 GLU cc_start: 0.6798 (mp0) cc_final: 0.6401 (mp0) REVERT: V 170 GLN cc_start: 0.7617 (pt0) cc_final: 0.7377 (pt0) REVERT: V 173 ASP cc_start: 0.7773 (p0) cc_final: 0.7551 (p0) REVERT: V 178 ASN cc_start: 0.8169 (m-40) cc_final: 0.7942 (m110) REVERT: V 286 SER cc_start: 0.8008 (p) cc_final: 0.7785 (p) REVERT: V 316 GLU cc_start: 0.7311 (tp30) cc_final: 0.7071 (tp30) outliers start: 109 outliers final: 71 residues processed: 1688 average time/residue: 3.5953 time to fit residues: 7787.9603 Evaluate side-chains 1669 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1585 time to evaluate : 7.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 309 CYS Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 439 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 310 SER Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 439 THR Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 230 GLU Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 439 THR Chi-restraints excluded: chain K residue 450 ASN Chi-restraints excluded: chain L residue 68 ARG Chi-restraints excluded: chain L residue 309 CYS Chi-restraints excluded: chain L residue 439 THR Chi-restraints excluded: chain M residue 308 LEU Chi-restraints excluded: chain M residue 311 SER Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain M residue 439 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 67 LYS Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 257 THR Chi-restraints excluded: chain N residue 325 VAL Chi-restraints excluded: chain N residue 439 THR Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 256 ASN Chi-restraints excluded: chain O residue 450 ASN Chi-restraints excluded: chain P residue 439 THR Chi-restraints excluded: chain P residue 450 ASN Chi-restraints excluded: chain Q residue 184 SER Chi-restraints excluded: chain Q residue 308 LEU Chi-restraints excluded: chain Q residue 325 VAL Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 439 THR Chi-restraints excluded: chain S residue 37 GLU Chi-restraints excluded: chain S residue 308 LEU Chi-restraints excluded: chain T residue 47 ILE Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 184 SER Chi-restraints excluded: chain T residue 308 LEU Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain T residue 439 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 68 ARG Chi-restraints excluded: chain U residue 325 VAL Chi-restraints excluded: chain U residue 439 THR Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain V residue 325 VAL Chi-restraints excluded: chain V residue 439 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 307 optimal weight: 0.0170 chunk 822 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 536 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 914 optimal weight: 1.9990 chunk 759 optimal weight: 8.9990 chunk 423 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 302 optimal weight: 3.9990 chunk 480 optimal weight: 4.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 ASN ** F 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 GLN H 178 ASN ** H 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 256 ASN ** J 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 GLN K 256 ASN ** K 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 303 GLN N 86 GLN N 87 ASN N 256 ASN ** O 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN ** Q 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 ASN R 256 ASN ** R 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 144 GLN ** T 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 87 ASN ** U 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 75705 Z= 0.295 Angle : 0.584 10.904 102795 Z= 0.303 Chirality : 0.077 1.459 11130 Planarity : 0.004 0.065 13503 Dihedral : 4.821 19.538 10416 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.72 % Allowed : 15.07 % Favored : 83.21 % 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: -0.33 (0.08), residues: 9492 helix: 0.78 (0.13), residues: 1701 sheet: 0.23 (0.08), residues: 3612 loop : -0.99 (0.09), residues: 4179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 62 HIS 0.009 0.002 HIS H 167 PHE 0.023 0.002 PHE S 128 TYR 0.023 0.002 TYR G 219 ARG 0.019 0.001 ARG P 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Evaluate side-chains 1738 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1602 time to evaluate : 8.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.6942 (mmt180) REVERT: A 316 GLU cc_start: 0.7405 (tp30) cc_final: 0.7180 (tp30) REVERT: A 320 LYS cc_start: 0.8261 (ttmt) cc_final: 0.7977 (ttmt) REVERT: C 304 GLU cc_start: 0.6882 (mp0) cc_final: 0.6388 (mp0) REVERT: C 320 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7764 (ttmt) REVERT: C 323 ASP cc_start: 0.7295 (t0) cc_final: 0.6991 (m-30) REVERT: D 307 THR cc_start: 0.8144 (m) cc_final: 0.7940 (p) REVERT: D 435 TYR cc_start: 0.6925 (t80) cc_final: 0.6632 (t80) REVERT: D 441 ILE cc_start: 0.6877 (mt) cc_final: 0.6652 (mp) REVERT: E 230 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: E 241 LYS cc_start: 0.7108 (ttmt) cc_final: 0.6895 (ttpt) REVERT: E 316 GLU cc_start: 0.7464 (tp30) cc_final: 0.7110 (tp30) REVERT: E 320 LYS cc_start: 0.7917 (ttmt) cc_final: 0.7459 (ttmt) REVERT: E 441 ILE cc_start: 0.6651 (mt) cc_final: 0.6327 (mp) REVERT: F 175 LEU cc_start: 0.8906 (tp) cc_final: 0.8695 (tt) REVERT: F 230 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.6115 (mp0) REVERT: F 320 LYS cc_start: 0.8260 (ttmt) cc_final: 0.7895 (ttmt) REVERT: F 332 GLU cc_start: 0.6886 (tp30) cc_final: 0.6515 (tp30) REVERT: G 178 ASN cc_start: 0.8182 (m110) cc_final: 0.7963 (m110) REVERT: G 181 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7861 (mppt) REVERT: G 230 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6295 (mp0) REVERT: H 181 LYS cc_start: 0.7987 (mmmt) cc_final: 0.7765 (mmmm) REVERT: H 219 TYR cc_start: 0.6225 (p90) cc_final: 0.5829 (p90) REVERT: H 323 ASP cc_start: 0.7359 (t0) cc_final: 0.7132 (m-30) REVERT: I 333 LYS cc_start: 0.7986 (tttp) cc_final: 0.7739 (tttt) REVERT: J 36 VAL cc_start: 0.8050 (p) cc_final: 0.7833 (m) REVERT: J 37 GLU cc_start: 0.7194 (pm20) cc_final: 0.6896 (pm20) REVERT: J 47 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8066 (mt) REVERT: J 325 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.8162 (t) REVERT: J 441 ILE cc_start: 0.6692 (mt) cc_final: 0.6339 (mp) REVERT: K 57 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8200 (t) REVERT: K 68 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7602 (ptt-90) REVERT: K 170 GLN cc_start: 0.7662 (pt0) cc_final: 0.7423 (tt0) REVERT: K 173 ASP cc_start: 0.7733 (p0) cc_final: 0.7496 (p0) REVERT: K 316 GLU cc_start: 0.7365 (tp30) cc_final: 0.6905 (tp30) REVERT: K 320 LYS cc_start: 0.7830 (ttmt) cc_final: 0.7586 (ttmm) REVERT: K 396 ASP cc_start: 0.6128 (t0) cc_final: 0.5747 (p0) REVERT: K 441 ILE cc_start: 0.6727 (mt) cc_final: 0.6442 (mp) REVERT: L 68 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7388 (ptt90) REVERT: L 162 GLU cc_start: 0.6875 (mp0) cc_final: 0.6622 (mp0) REVERT: L 178 ASN cc_start: 0.8281 (m-40) cc_final: 0.8037 (m110) REVERT: L 320 LYS cc_start: 0.7595 (tppp) cc_final: 0.7314 (ttpp) REVERT: L 441 ILE cc_start: 0.6676 (mt) cc_final: 0.6408 (mp) REVERT: L 477 TYR cc_start: 0.4320 (m-80) cc_final: 0.4118 (m-80) REVERT: M 149 LEU cc_start: 0.7931 (mt) cc_final: 0.7710 (mp) REVERT: M 162 GLU cc_start: 0.7152 (mp0) cc_final: 0.6913 (mp0) REVERT: M 176 ASN cc_start: 0.7843 (t0) cc_final: 0.7628 (t0) REVERT: M 304 GLU cc_start: 0.7140 (mp0) cc_final: 0.6720 (mp0) REVERT: M 311 SER cc_start: 0.7656 (OUTLIER) cc_final: 0.7400 (p) REVERT: M 323 ASP cc_start: 0.7270 (t0) cc_final: 0.7040 (m-30) REVERT: M 441 ILE cc_start: 0.6557 (mt) cc_final: 0.6204 (mp) REVERT: N 87 ASN cc_start: 0.7982 (t0) cc_final: 0.7695 (t0) REVERT: N 162 GLU cc_start: 0.7156 (mp0) cc_final: 0.6781 (mp0) REVERT: N 316 GLU cc_start: 0.7260 (tm-30) cc_final: 0.6942 (tp30) REVERT: O 61 ASP cc_start: 0.7264 (t0) cc_final: 0.6989 (t0) REVERT: O 87 ASN cc_start: 0.8078 (t0) cc_final: 0.7630 (t0) REVERT: O 181 LYS cc_start: 0.8059 (mmmm) cc_final: 0.7847 (mmmm) REVERT: O 265 ASP cc_start: 0.7058 (p0) cc_final: 0.6567 (p0) REVERT: O 320 LYS cc_start: 0.8264 (ttmt) cc_final: 0.7779 (ttmt) REVERT: O 324 ASP cc_start: 0.7356 (m-30) cc_final: 0.7096 (m-30) REVERT: P 162 GLU cc_start: 0.7091 (mp0) cc_final: 0.6697 (mp0) REVERT: P 304 GLU cc_start: 0.7174 (mp0) cc_final: 0.6672 (mp0) REVERT: P 311 SER cc_start: 0.8111 (t) cc_final: 0.7904 (p) REVERT: P 316 GLU cc_start: 0.7530 (tp30) cc_final: 0.6964 (tp30) REVERT: P 323 ASP cc_start: 0.7279 (t0) cc_final: 0.7035 (m-30) REVERT: P 479 CYS cc_start: 0.6953 (m) cc_final: 0.6184 (p) REVERT: Q 47 ILE cc_start: 0.8288 (tt) cc_final: 0.8010 (mt) REVERT: Q 162 GLU cc_start: 0.7012 (mp0) cc_final: 0.6505 (mp0) REVERT: Q 170 GLN cc_start: 0.7655 (pt0) cc_final: 0.7402 (pt0) REVERT: Q 173 ASP cc_start: 0.7908 (p0) cc_final: 0.7679 (p0) REVERT: Q 189 ARG cc_start: 0.8514 (mmm160) cc_final: 0.8231 (mtp180) REVERT: Q 304 GLU cc_start: 0.6902 (mp0) cc_final: 0.6556 (mp0) REVERT: Q 320 LYS cc_start: 0.8178 (ttmt) cc_final: 0.7862 (ttmt) REVERT: R 170 GLN cc_start: 0.7715 (pt0) cc_final: 0.7458 (tt0) REVERT: R 316 GLU cc_start: 0.7477 (tp30) cc_final: 0.7226 (tp30) REVERT: T 37 GLU cc_start: 0.7200 (pm20) cc_final: 0.6815 (pm20) REVERT: T 47 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8083 (mt) REVERT: T 160 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8242 (mt) REVERT: T 262 ARG cc_start: 0.7208 (mtm180) cc_final: 0.7004 (mtm-85) REVERT: T 316 GLU cc_start: 0.7545 (tp30) cc_final: 0.7045 (tp30) REVERT: T 320 LYS cc_start: 0.8288 (ttmt) cc_final: 0.8086 (ttmm) REVERT: U 173 ASP cc_start: 0.7745 (p0) cc_final: 0.7509 (p0) REVERT: U 316 GLU cc_start: 0.7376 (tp30) cc_final: 0.7068 (tp30) REVERT: U 320 LYS cc_start: 0.8356 (ttmt) cc_final: 0.7964 (ttmt) REVERT: V 162 GLU cc_start: 0.6835 (mp0) cc_final: 0.6446 (mp0) REVERT: V 170 GLN cc_start: 0.7590 (pt0) cc_final: 0.7343 (pt0) REVERT: V 178 ASN cc_start: 0.8206 (m-40) cc_final: 0.7974 (m110) REVERT: V 286 SER cc_start: 0.8007 (p) cc_final: 0.7781 (p) REVERT: V 316 GLU cc_start: 0.7277 (tp30) cc_final: 0.7032 (tp30) outliers start: 136 outliers final: 85 residues processed: 1676 average time/residue: 3.7114 time to fit residues: 8096.2858 Evaluate side-chains 1699 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1602 time to evaluate : 7.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 158 LYS Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 230 GLU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 309 CYS Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 439 THR Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 310 SER Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 439 THR Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 68 ARG Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 309 CYS Chi-restraints excluded: chain K residue 399 ILE Chi-restraints excluded: chain K residue 439 THR Chi-restraints excluded: chain K residue 450 ASN Chi-restraints excluded: chain L residue 68 ARG Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 309 CYS Chi-restraints excluded: chain L residue 439 THR Chi-restraints excluded: chain M residue 308 LEU Chi-restraints excluded: chain M residue 309 CYS Chi-restraints excluded: chain M residue 311 SER Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain M residue 439 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 67 LYS Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 325 VAL Chi-restraints excluded: chain N residue 439 THR Chi-restraints excluded: chain O residue 160 LEU Chi-restraints excluded: chain O residue 256 ASN Chi-restraints excluded: chain O residue 439 THR Chi-restraints excluded: chain O residue 450 ASN Chi-restraints excluded: chain P residue 139 GLU Chi-restraints excluded: chain P residue 170 GLN Chi-restraints excluded: chain P residue 439 THR Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 184 SER Chi-restraints excluded: chain Q residue 325 VAL Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 217 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 439 THR Chi-restraints excluded: chain S residue 308 LEU Chi-restraints excluded: chain T residue 47 ILE Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 184 SER Chi-restraints excluded: chain T residue 226 LYS Chi-restraints excluded: chain T residue 265 ASP Chi-restraints excluded: chain T residue 308 LEU Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain T residue 439 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 311 SER Chi-restraints excluded: chain U residue 325 VAL Chi-restraints excluded: chain U residue 439 THR Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain V residue 325 VAL Chi-restraints excluded: chain V residue 439 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 881 optimal weight: 0.8980 chunk 103 optimal weight: 0.2980 chunk 520 optimal weight: 2.9990 chunk 667 optimal weight: 3.9990 chunk 517 optimal weight: 0.9980 chunk 769 optimal weight: 0.9990 chunk 510 optimal weight: 0.9990 chunk 910 optimal weight: 0.9980 chunk 570 optimal weight: 4.9990 chunk 555 optimal weight: 0.5980 chunk 420 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN E 86 GLN ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 GLN H 178 ASN ** H 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 ASN ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 GLN K 144 GLN K 256 ASN ** K 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 303 GLN M 144 GLN N 256 ASN ** O 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 171 GLN ** P 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN Q 144 GLN ** Q 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 303 GLN ** T 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 253 GLN ** U 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 75705 Z= 0.211 Angle : 0.561 10.891 102795 Z= 0.290 Chirality : 0.076 1.454 11130 Planarity : 0.003 0.053 13503 Dihedral : 4.651 19.187 10416 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.44 % Allowed : 15.50 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.27 (0.08), residues: 9492 helix: 0.93 (0.13), residues: 1701 sheet: 0.20 (0.08), residues: 3675 loop : -0.93 (0.09), residues: 4116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 306 HIS 0.006 0.001 HIS I 167 PHE 0.022 0.001 PHE C 140 TYR 0.025 0.001 TYR I 219 ARG 0.009 0.000 ARG G 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Evaluate side-chains 1740 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1626 time to evaluate : 8.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 GLN cc_start: 0.7548 (pt0) cc_final: 0.7194 (tt0) REVERT: A 189 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.6926 (mmt180) REVERT: A 316 GLU cc_start: 0.7411 (tp30) cc_final: 0.7196 (tp30) REVERT: A 320 LYS cc_start: 0.8253 (ttmt) cc_final: 0.7983 (ttmt) REVERT: C 304 GLU cc_start: 0.6863 (mp0) cc_final: 0.6358 (mp0) REVERT: C 320 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7751 (ttmt) REVERT: C 323 ASP cc_start: 0.7291 (t0) cc_final: 0.6991 (m-30) REVERT: D 307 THR cc_start: 0.8144 (m) cc_final: 0.7939 (p) REVERT: D 330 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7587 (mm-40) REVERT: D 435 TYR cc_start: 0.6938 (t80) cc_final: 0.6660 (t80) REVERT: D 441 ILE cc_start: 0.6953 (mt) cc_final: 0.6719 (mp) REVERT: E 170 GLN cc_start: 0.7658 (pt0) cc_final: 0.7361 (pt0) REVERT: E 173 ASP cc_start: 0.7638 (p0) cc_final: 0.7431 (p0) REVERT: E 230 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: E 316 GLU cc_start: 0.7472 (tp30) cc_final: 0.7107 (tp30) REVERT: E 320 LYS cc_start: 0.7835 (ttmt) cc_final: 0.7479 (ttmt) REVERT: E 441 ILE cc_start: 0.6675 (mt) cc_final: 0.6359 (mp) REVERT: F 230 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.6073 (mp0) REVERT: F 320 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7835 (ttmt) REVERT: F 332 GLU cc_start: 0.6892 (tp30) cc_final: 0.6484 (tp30) REVERT: G 178 ASN cc_start: 0.8210 (m110) cc_final: 0.8000 (m110) REVERT: G 181 LYS cc_start: 0.8151 (mmmt) cc_final: 0.7861 (mppt) REVERT: H 181 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7756 (mmmm) REVERT: H 219 TYR cc_start: 0.6216 (p90) cc_final: 0.5792 (p90) REVERT: H 235 GLN cc_start: 0.6973 (OUTLIER) cc_final: 0.6052 (tm-30) REVERT: H 323 ASP cc_start: 0.7352 (t0) cc_final: 0.7115 (m-30) REVERT: I 333 LYS cc_start: 0.7983 (tttp) cc_final: 0.7747 (tttt) REVERT: J 37 GLU cc_start: 0.7216 (pm20) cc_final: 0.6865 (pm20) REVERT: J 47 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8063 (mt) REVERT: J 304 GLU cc_start: 0.6918 (mp0) cc_final: 0.6401 (mp0) REVERT: J 316 GLU cc_start: 0.7422 (tp30) cc_final: 0.6827 (tp30) REVERT: J 325 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.8121 (t) REVERT: J 441 ILE cc_start: 0.6698 (mt) cc_final: 0.6313 (mp) REVERT: K 170 GLN cc_start: 0.7631 (pt0) cc_final: 0.7386 (tt0) REVERT: K 173 ASP cc_start: 0.7702 (p0) cc_final: 0.7471 (p0) REVERT: K 316 GLU cc_start: 0.7366 (tp30) cc_final: 0.6911 (tp30) REVERT: K 320 LYS cc_start: 0.7831 (ttmt) cc_final: 0.7587 (ttmm) REVERT: K 396 ASP cc_start: 0.6165 (t0) cc_final: 0.5758 (p0) REVERT: K 441 ILE cc_start: 0.6719 (mt) cc_final: 0.6429 (mp) REVERT: L 68 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7427 (ptt90) REVERT: L 162 GLU cc_start: 0.6875 (mp0) cc_final: 0.6626 (mp0) REVERT: L 178 ASN cc_start: 0.8289 (m-40) cc_final: 0.8059 (m110) REVERT: L 441 ILE cc_start: 0.6721 (mt) cc_final: 0.6458 (mp) REVERT: L 477 TYR cc_start: 0.4333 (m-80) cc_final: 0.4128 (m-80) REVERT: M 67 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7868 (mtpp) REVERT: M 162 GLU cc_start: 0.7142 (mp0) cc_final: 0.6904 (mp0) REVERT: M 176 ASN cc_start: 0.7847 (t0) cc_final: 0.7634 (t0) REVERT: M 304 GLU cc_start: 0.7128 (mp0) cc_final: 0.6705 (mp0) REVERT: M 323 ASP cc_start: 0.7255 (t0) cc_final: 0.7030 (m-30) REVERT: M 441 ILE cc_start: 0.6568 (mt) cc_final: 0.6216 (mp) REVERT: N 162 GLU cc_start: 0.7155 (mp0) cc_final: 0.6782 (mp0) REVERT: N 316 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6940 (tp30) REVERT: O 61 ASP cc_start: 0.7254 (t0) cc_final: 0.7018 (t0) REVERT: O 87 ASN cc_start: 0.8040 (t0) cc_final: 0.7518 (t0) REVERT: O 265 ASP cc_start: 0.7045 (p0) cc_final: 0.6560 (p0) REVERT: O 320 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7717 (ttmt) REVERT: O 324 ASP cc_start: 0.7350 (m-30) cc_final: 0.7085 (m-30) REVERT: P 162 GLU cc_start: 0.7016 (mp0) cc_final: 0.6608 (mp0) REVERT: P 304 GLU cc_start: 0.7151 (mp0) cc_final: 0.6646 (mp0) REVERT: P 311 SER cc_start: 0.8058 (t) cc_final: 0.7845 (p) REVERT: P 316 GLU cc_start: 0.7533 (tp30) cc_final: 0.6965 (tp30) REVERT: P 479 CYS cc_start: 0.6959 (m) cc_final: 0.6189 (p) REVERT: Q 47 ILE cc_start: 0.8212 (tt) cc_final: 0.7952 (mt) REVERT: Q 162 GLU cc_start: 0.7009 (mp0) cc_final: 0.6499 (mp0) REVERT: Q 170 GLN cc_start: 0.7623 (pt0) cc_final: 0.7371 (pt0) REVERT: Q 173 ASP cc_start: 0.7870 (p0) cc_final: 0.7629 (p0) REVERT: Q 189 ARG cc_start: 0.8511 (mmm160) cc_final: 0.8218 (mtp180) REVERT: Q 304 GLU cc_start: 0.6890 (mp0) cc_final: 0.6561 (mp0) REVERT: Q 320 LYS cc_start: 0.8161 (ttmt) cc_final: 0.7842 (ttmt) REVERT: R 68 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7336 (ptt-90) REVERT: R 170 GLN cc_start: 0.7674 (pt0) cc_final: 0.7385 (tt0) REVERT: R 316 GLU cc_start: 0.7468 (tp30) cc_final: 0.7228 (tp30) REVERT: S 181 LYS cc_start: 0.8394 (mmmm) cc_final: 0.8135 (mmmm) REVERT: T 37 GLU cc_start: 0.7184 (pm20) cc_final: 0.6805 (pm20) REVERT: T 47 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8071 (mt) REVERT: T 160 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8228 (mt) REVERT: T 316 GLU cc_start: 0.7542 (tp30) cc_final: 0.7038 (tp30) REVERT: T 320 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7865 (ttmm) REVERT: U 173 ASP cc_start: 0.7696 (p0) cc_final: 0.7436 (p0) REVERT: U 316 GLU cc_start: 0.7369 (tp30) cc_final: 0.7063 (tp30) REVERT: U 320 LYS cc_start: 0.8328 (ttmt) cc_final: 0.8000 (ttmt) REVERT: V 178 ASN cc_start: 0.8203 (m-40) cc_final: 0.7977 (m110) REVERT: V 189 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7867 (mmt180) REVERT: V 316 GLU cc_start: 0.7286 (tp30) cc_final: 0.7028 (tp30) outliers start: 114 outliers final: 79 residues processed: 1686 average time/residue: 3.5493 time to fit residues: 7685.3956 Evaluate side-chains 1677 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1587 time to evaluate : 7.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 158 LYS Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 309 CYS Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain H residue 178 ASN Chi-restraints excluded: chain H residue 235 GLN Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 439 THR Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 439 THR Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 286 SER Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 311 SER Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 309 CYS Chi-restraints excluded: chain K residue 439 THR Chi-restraints excluded: chain K residue 450 ASN Chi-restraints excluded: chain L residue 68 ARG Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 290 SER Chi-restraints excluded: chain L residue 309 CYS Chi-restraints excluded: chain L residue 439 THR Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 308 LEU Chi-restraints excluded: chain M residue 309 CYS Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain M residue 439 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 67 LYS Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 325 VAL Chi-restraints excluded: chain N residue 439 THR Chi-restraints excluded: chain O residue 256 ASN Chi-restraints excluded: chain O residue 439 THR Chi-restraints excluded: chain P residue 139 GLU Chi-restraints excluded: chain P residue 170 GLN Chi-restraints excluded: chain P residue 439 THR Chi-restraints excluded: chain Q residue 184 SER Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 217 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 439 THR Chi-restraints excluded: chain S residue 37 GLU Chi-restraints excluded: chain S residue 308 LEU Chi-restraints excluded: chain T residue 47 ILE Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 184 SER Chi-restraints excluded: chain T residue 265 ASP Chi-restraints excluded: chain T residue 308 LEU Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain T residue 439 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 325 VAL Chi-restraints excluded: chain U residue 439 THR Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain V residue 189 ARG Chi-restraints excluded: chain V residue 325 VAL Chi-restraints excluded: chain V residue 439 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 563 optimal weight: 3.9990 chunk 363 optimal weight: 1.9990 chunk 543 optimal weight: 0.8980 chunk 274 optimal weight: 0.4980 chunk 178 optimal weight: 5.9990 chunk 176 optimal weight: 0.5980 chunk 579 optimal weight: 6.9990 chunk 620 optimal weight: 7.9990 chunk 450 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 715 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN C 53 ASN ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 GLN H 178 ASN ** H 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 ASN ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 256 ASN K 58 GLN K 144 GLN K 256 ASN ** K 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 303 GLN N 53 ASN N 87 ASN N 256 ASN O 176 ASN ** O 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN ** Q 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 144 GLN T 253 GLN ** T 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 256 ASN ** U 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 75705 Z= 0.302 Angle : 0.586 10.914 102795 Z= 0.303 Chirality : 0.077 1.456 11130 Planarity : 0.003 0.055 13503 Dihedral : 4.655 19.195 10416 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.47 % Allowed : 16.02 % Favored : 82.52 % 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: -0.40 (0.08), residues: 9492 helix: 0.89 (0.13), residues: 1701 sheet: 0.00 (0.08), residues: 3675 loop : -0.94 (0.09), residues: 4116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP U 306 HIS 0.007 0.002 HIS H 167 PHE 0.023 0.002 PHE C 140 TYR 0.029 0.002 TYR D 219 ARG 0.011 0.001 ARG G 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Evaluate side-chains 1705 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1589 time to evaluate : 8.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7592 (t0) cc_final: 0.7174 (t0) REVERT: A 170 GLN cc_start: 0.7577 (pt0) cc_final: 0.7038 (tt0) REVERT: A 173 ASP cc_start: 0.7732 (p0) cc_final: 0.7508 (p0) REVERT: A 189 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.6947 (mmp-170) REVERT: A 230 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6081 (mp0) REVERT: A 316 GLU cc_start: 0.7442 (tp30) cc_final: 0.7218 (tp30) REVERT: A 320 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7991 (ttmt) REVERT: C 230 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6290 (mp0) REVERT: C 304 GLU cc_start: 0.6859 (mp0) cc_final: 0.6363 (mp0) REVERT: C 320 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7773 (ttmt) REVERT: C 323 ASP cc_start: 0.7286 (t0) cc_final: 0.7000 (m-30) REVERT: D 307 THR cc_start: 0.8180 (m) cc_final: 0.7954 (p) REVERT: D 435 TYR cc_start: 0.6856 (t80) cc_final: 0.6553 (t80) REVERT: D 441 ILE cc_start: 0.6961 (mt) cc_final: 0.6727 (mp) REVERT: E 170 GLN cc_start: 0.7685 (pt0) cc_final: 0.7456 (pt0) REVERT: E 230 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: E 316 GLU cc_start: 0.7487 (tp30) cc_final: 0.7216 (tp30) REVERT: E 320 LYS cc_start: 0.7858 (ttmt) cc_final: 0.7588 (ttmt) REVERT: E 441 ILE cc_start: 0.6642 (mt) cc_final: 0.6305 (mp) REVERT: F 230 GLU cc_start: 0.6338 (OUTLIER) cc_final: 0.6048 (mp0) REVERT: F 320 LYS cc_start: 0.8194 (ttmt) cc_final: 0.7833 (ttmt) REVERT: F 332 GLU cc_start: 0.6909 (tp30) cc_final: 0.6498 (tp30) REVERT: G 178 ASN cc_start: 0.8246 (m110) cc_final: 0.8024 (m110) REVERT: G 181 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7866 (mppt) REVERT: H 235 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6190 (tm-30) REVERT: H 323 ASP cc_start: 0.7338 (t0) cc_final: 0.7108 (m-30) REVERT: I 286 SER cc_start: 0.7956 (p) cc_final: 0.7732 (t) REVERT: I 333 LYS cc_start: 0.7991 (tttp) cc_final: 0.7753 (tttt) REVERT: J 37 GLU cc_start: 0.7175 (pm20) cc_final: 0.6890 (pm20) REVERT: J 47 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8084 (mt) REVERT: J 304 GLU cc_start: 0.6912 (mp0) cc_final: 0.6389 (mp0) REVERT: J 316 GLU cc_start: 0.7442 (tp30) cc_final: 0.6826 (tp30) REVERT: J 441 ILE cc_start: 0.6756 (mt) cc_final: 0.6377 (mp) REVERT: K 57 VAL cc_start: 0.8385 (OUTLIER) cc_final: 0.8171 (t) REVERT: K 68 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7557 (ptt-90) REVERT: K 170 GLN cc_start: 0.7628 (pt0) cc_final: 0.7417 (tt0) REVERT: K 316 GLU cc_start: 0.7392 (tp30) cc_final: 0.6964 (tp30) REVERT: K 320 LYS cc_start: 0.7827 (ttmt) cc_final: 0.7595 (ttmm) REVERT: K 396 ASP cc_start: 0.6277 (t0) cc_final: 0.5839 (p0) REVERT: K 441 ILE cc_start: 0.6715 (mt) cc_final: 0.6444 (mp) REVERT: L 68 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7431 (ptt90) REVERT: L 162 GLU cc_start: 0.6894 (mp0) cc_final: 0.6654 (mp0) REVERT: L 441 ILE cc_start: 0.6727 (mt) cc_final: 0.6459 (mp) REVERT: M 162 GLU cc_start: 0.7172 (mp0) cc_final: 0.6933 (mp0) REVERT: M 176 ASN cc_start: 0.7864 (t0) cc_final: 0.7655 (t0) REVERT: M 304 GLU cc_start: 0.7119 (mp0) cc_final: 0.6741 (mp0) REVERT: M 323 ASP cc_start: 0.7258 (t0) cc_final: 0.7033 (m-30) REVERT: N 162 GLU cc_start: 0.7176 (mp0) cc_final: 0.6799 (mp0) REVERT: N 316 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6972 (tp30) REVERT: O 61 ASP cc_start: 0.7268 (t0) cc_final: 0.7024 (t0) REVERT: O 87 ASN cc_start: 0.8053 (t0) cc_final: 0.7540 (t0) REVERT: O 265 ASP cc_start: 0.7045 (p0) cc_final: 0.6573 (p0) REVERT: O 320 LYS cc_start: 0.8267 (ttmt) cc_final: 0.7746 (ttmt) REVERT: O 324 ASP cc_start: 0.7337 (m-30) cc_final: 0.7073 (m-30) REVERT: P 162 GLU cc_start: 0.7036 (mp0) cc_final: 0.6636 (mp0) REVERT: P 304 GLU cc_start: 0.7147 (mp0) cc_final: 0.6635 (mp0) REVERT: P 311 SER cc_start: 0.8086 (t) cc_final: 0.7865 (p) REVERT: P 316 GLU cc_start: 0.7550 (tp30) cc_final: 0.6985 (tp30) REVERT: P 479 CYS cc_start: 0.6971 (m) cc_final: 0.6192 (p) REVERT: Q 47 ILE cc_start: 0.8282 (tt) cc_final: 0.8028 (mt) REVERT: Q 162 GLU cc_start: 0.7032 (mp0) cc_final: 0.6531 (mp0) REVERT: Q 170 GLN cc_start: 0.7669 (pt0) cc_final: 0.7319 (tt0) REVERT: Q 173 ASP cc_start: 0.7873 (p0) cc_final: 0.7622 (p0) REVERT: Q 189 ARG cc_start: 0.8522 (mmm160) cc_final: 0.8231 (mtp180) REVERT: Q 304 GLU cc_start: 0.6895 (mp0) cc_final: 0.6544 (mp0) REVERT: Q 320 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7873 (ttmt) REVERT: R 170 GLN cc_start: 0.7668 (pt0) cc_final: 0.7434 (tt0) REVERT: R 290 SER cc_start: 0.7807 (OUTLIER) cc_final: 0.7532 (p) REVERT: R 312 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6930 (mm-30) REVERT: T 37 GLU cc_start: 0.7211 (pm20) cc_final: 0.6823 (pm20) REVERT: T 316 GLU cc_start: 0.7573 (tp30) cc_final: 0.7073 (tp30) REVERT: T 320 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7981 (ttmm) REVERT: U 173 ASP cc_start: 0.7664 (p0) cc_final: 0.7399 (p0) REVERT: U 316 GLU cc_start: 0.7388 (tp30) cc_final: 0.7084 (tp30) REVERT: U 320 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7707 (ttmt) REVERT: V 162 GLU cc_start: 0.6874 (mp0) cc_final: 0.6498 (mp0) REVERT: V 178 ASN cc_start: 0.8213 (m-40) cc_final: 0.7983 (m110) REVERT: V 316 GLU cc_start: 0.7342 (tp30) cc_final: 0.7096 (tp30) outliers start: 116 outliers final: 81 residues processed: 1658 average time/residue: 3.6760 time to fit residues: 7867.3013 Evaluate side-chains 1673 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1581 time to evaluate : 7.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 170 GLN Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 158 LYS Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 309 CYS Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain H residue 235 GLN Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 439 THR Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 439 THR Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 286 SER Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 311 SER Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 68 ARG Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 309 CYS Chi-restraints excluded: chain K residue 439 THR Chi-restraints excluded: chain L residue 68 ARG Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 290 SER Chi-restraints excluded: chain L residue 309 CYS Chi-restraints excluded: chain L residue 439 THR Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 308 LEU Chi-restraints excluded: chain M residue 309 CYS Chi-restraints excluded: chain M residue 311 SER Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain M residue 439 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 256 ASN Chi-restraints excluded: chain N residue 325 VAL Chi-restraints excluded: chain O residue 160 LEU Chi-restraints excluded: chain O residue 256 ASN Chi-restraints excluded: chain O residue 439 THR Chi-restraints excluded: chain O residue 450 ASN Chi-restraints excluded: chain P residue 139 GLU Chi-restraints excluded: chain P residue 213 LEU Chi-restraints excluded: chain Q residue 184 SER Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 217 ARG Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 439 THR Chi-restraints excluded: chain S residue 308 LEU Chi-restraints excluded: chain S residue 439 THR Chi-restraints excluded: chain T residue 184 SER Chi-restraints excluded: chain T residue 265 ASP Chi-restraints excluded: chain T residue 290 SER Chi-restraints excluded: chain T residue 308 LEU Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain T residue 439 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 325 VAL Chi-restraints excluded: chain U residue 439 THR Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain V residue 325 VAL Chi-restraints excluded: chain V residue 439 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 828 optimal weight: 0.9990 chunk 872 optimal weight: 0.9980 chunk 796 optimal weight: 5.9990 chunk 848 optimal weight: 5.9990 chunk 510 optimal weight: 1.9990 chunk 369 optimal weight: 2.9990 chunk 666 optimal weight: 5.9990 chunk 260 optimal weight: 0.0170 chunk 766 optimal weight: 0.9980 chunk 802 optimal weight: 0.8980 chunk 845 optimal weight: 5.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** C 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN E 87 ASN ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 ASN H 144 GLN ** H 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 ASN ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 GLN K 256 ASN ** K 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 303 GLN N 53 ASN N 256 ASN ** O 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN Q 144 GLN ** T 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 144 GLN ** T 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 256 ASN ** U 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 75705 Z= 0.214 Angle : 0.566 10.899 102795 Z= 0.291 Chirality : 0.077 1.455 11130 Planarity : 0.003 0.054 13503 Dihedral : 4.544 25.853 10416 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.35 % Allowed : 16.60 % Favored : 82.05 % 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: -0.38 (0.08), residues: 9492 helix: 0.98 (0.13), residues: 1701 sheet: -0.05 (0.08), residues: 3696 loop : -0.87 (0.09), residues: 4095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 62 HIS 0.006 0.001 HIS I 167 PHE 0.024 0.001 PHE C 140 TYR 0.031 0.001 TYR I 219 ARG 0.007 0.000 ARG G 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Evaluate side-chains 1701 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1594 time to evaluate : 8.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLN cc_start: 0.8007 (tp40) cc_final: 0.7801 (tp40) REVERT: A 61 ASP cc_start: 0.7576 (t0) cc_final: 0.7154 (t0) REVERT: A 189 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.6929 (mmp-170) REVERT: A 230 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6084 (mp0) REVERT: A 316 GLU cc_start: 0.7443 (tp30) cc_final: 0.7206 (tp30) REVERT: A 320 LYS cc_start: 0.8261 (ttmt) cc_final: 0.7990 (ttmt) REVERT: C 304 GLU cc_start: 0.6855 (mp0) cc_final: 0.6353 (mp0) REVERT: C 320 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7771 (ttmt) REVERT: C 323 ASP cc_start: 0.7279 (t0) cc_final: 0.7000 (m-30) REVERT: D 307 THR cc_start: 0.8171 (m) cc_final: 0.7941 (p) REVERT: D 435 TYR cc_start: 0.6863 (t80) cc_final: 0.6615 (t80) REVERT: D 441 ILE cc_start: 0.6978 (mt) cc_final: 0.6746 (mp) REVERT: E 170 GLN cc_start: 0.7657 (pt0) cc_final: 0.7369 (pt0) REVERT: E 173 ASP cc_start: 0.7557 (p0) cc_final: 0.7343 (p0) REVERT: E 316 GLU cc_start: 0.7484 (tp30) cc_final: 0.7205 (tp30) REVERT: E 320 LYS cc_start: 0.7839 (ttmt) cc_final: 0.7620 (ttmt) REVERT: E 441 ILE cc_start: 0.6649 (mt) cc_final: 0.6310 (mp) REVERT: F 230 GLU cc_start: 0.6294 (OUTLIER) cc_final: 0.6008 (mp0) REVERT: F 320 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7820 (ttmt) REVERT: F 332 GLU cc_start: 0.6899 (tp30) cc_final: 0.6468 (tp30) REVERT: G 58 GLN cc_start: 0.8441 (tp40) cc_final: 0.7986 (tp40) REVERT: G 178 ASN cc_start: 0.8243 (m110) cc_final: 0.8027 (m110) REVERT: G 181 LYS cc_start: 0.8161 (mmmt) cc_final: 0.7860 (mppt) REVERT: H 235 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6132 (tm-30) REVERT: H 323 ASP cc_start: 0.7351 (t0) cc_final: 0.7097 (m-30) REVERT: I 333 LYS cc_start: 0.7982 (tttp) cc_final: 0.7760 (tttt) REVERT: J 37 GLU cc_start: 0.7191 (pm20) cc_final: 0.6838 (pm20) REVERT: J 47 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8067 (mt) REVERT: J 304 GLU cc_start: 0.6900 (mp0) cc_final: 0.6411 (mp0) REVERT: J 316 GLU cc_start: 0.7437 (tp30) cc_final: 0.6817 (tp30) REVERT: J 325 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.8108 (t) REVERT: J 441 ILE cc_start: 0.6768 (mt) cc_final: 0.6418 (mp) REVERT: K 170 GLN cc_start: 0.7607 (pt0) cc_final: 0.7371 (tt0) REVERT: K 174 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7156 (mt-10) REVERT: K 316 GLU cc_start: 0.7387 (tp30) cc_final: 0.6968 (tp30) REVERT: K 320 LYS cc_start: 0.7825 (ttmt) cc_final: 0.7599 (ttmm) REVERT: K 396 ASP cc_start: 0.6284 (t0) cc_final: 0.5836 (p0) REVERT: K 441 ILE cc_start: 0.6724 (mt) cc_final: 0.6440 (mp) REVERT: L 68 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7411 (ptt90) REVERT: L 162 GLU cc_start: 0.6888 (mp0) cc_final: 0.6656 (mp0) REVERT: L 173 ASP cc_start: 0.7805 (p0) cc_final: 0.7561 (p0) REVERT: L 441 ILE cc_start: 0.6715 (mt) cc_final: 0.6455 (mp) REVERT: M 162 GLU cc_start: 0.7160 (mp0) cc_final: 0.6921 (mp0) REVERT: M 176 ASN cc_start: 0.7887 (t0) cc_final: 0.7678 (t0) REVERT: M 304 GLU cc_start: 0.7106 (mp0) cc_final: 0.6715 (mp0) REVERT: M 323 ASP cc_start: 0.7246 (t0) cc_final: 0.7027 (m-30) REVERT: N 162 GLU cc_start: 0.7166 (mp0) cc_final: 0.6792 (mp0) REVERT: N 316 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6965 (tp30) REVERT: O 61 ASP cc_start: 0.7236 (t0) cc_final: 0.7028 (t0) REVERT: O 87 ASN cc_start: 0.8017 (t0) cc_final: 0.7515 (t0) REVERT: O 265 ASP cc_start: 0.7025 (p0) cc_final: 0.6550 (p0) REVERT: O 320 LYS cc_start: 0.8263 (ttmt) cc_final: 0.7699 (ttmt) REVERT: O 324 ASP cc_start: 0.7324 (m-30) cc_final: 0.7054 (m-30) REVERT: O 325 VAL cc_start: 0.8388 (t) cc_final: 0.8150 (m) REVERT: P 53 ASN cc_start: 0.7858 (m110) cc_final: 0.7651 (m-40) REVERT: P 162 GLU cc_start: 0.7033 (mp0) cc_final: 0.6631 (mp0) REVERT: P 304 GLU cc_start: 0.7127 (mp0) cc_final: 0.6621 (mp0) REVERT: P 311 SER cc_start: 0.8068 (t) cc_final: 0.7845 (p) REVERT: P 316 GLU cc_start: 0.7552 (tp30) cc_final: 0.6984 (tp30) REVERT: P 479 CYS cc_start: 0.6978 (m) cc_final: 0.6200 (p) REVERT: Q 47 ILE cc_start: 0.8205 (tt) cc_final: 0.7961 (mt) REVERT: Q 53 ASN cc_start: 0.7795 (m-40) cc_final: 0.7579 (m-40) REVERT: Q 162 GLU cc_start: 0.7020 (mp0) cc_final: 0.6519 (mp0) REVERT: Q 170 GLN cc_start: 0.7637 (pt0) cc_final: 0.7292 (tt0) REVERT: Q 173 ASP cc_start: 0.7840 (p0) cc_final: 0.7602 (p0) REVERT: Q 189 ARG cc_start: 0.8516 (mmm160) cc_final: 0.8222 (mtp180) REVERT: Q 304 GLU cc_start: 0.6890 (mp0) cc_final: 0.6468 (mp0) REVERT: Q 320 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7861 (ttmt) REVERT: R 290 SER cc_start: 0.7793 (OUTLIER) cc_final: 0.7526 (p) REVERT: R 312 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6917 (mm-30) REVERT: T 37 GLU cc_start: 0.7194 (pm20) cc_final: 0.6783 (pm20) REVERT: T 316 GLU cc_start: 0.7569 (tp30) cc_final: 0.7063 (tp30) REVERT: T 320 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7983 (ttmm) REVERT: U 173 ASP cc_start: 0.7646 (p0) cc_final: 0.7341 (p0) REVERT: U 316 GLU cc_start: 0.7396 (tp30) cc_final: 0.7084 (tp30) REVERT: U 320 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7904 (ttmm) REVERT: V 162 GLU cc_start: 0.6867 (mp0) cc_final: 0.6490 (mp0) REVERT: V 178 ASN cc_start: 0.8249 (m-40) cc_final: 0.8011 (m110) REVERT: V 316 GLU cc_start: 0.7341 (tp30) cc_final: 0.7093 (tp30) outliers start: 107 outliers final: 82 residues processed: 1661 average time/residue: 3.6112 time to fit residues: 7697.1761 Evaluate side-chains 1663 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1573 time to evaluate : 7.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 158 LYS Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 309 CYS Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain H residue 235 GLN Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 439 THR Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 439 THR Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 286 SER Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 311 SER Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 309 CYS Chi-restraints excluded: chain K residue 439 THR Chi-restraints excluded: chain K residue 450 ASN Chi-restraints excluded: chain L residue 68 ARG Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 290 SER Chi-restraints excluded: chain L residue 309 CYS Chi-restraints excluded: chain L residue 439 THR Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 308 LEU Chi-restraints excluded: chain M residue 309 CYS Chi-restraints excluded: chain M residue 311 SER Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 325 VAL Chi-restraints excluded: chain N residue 439 THR Chi-restraints excluded: chain O residue 160 LEU Chi-restraints excluded: chain O residue 256 ASN Chi-restraints excluded: chain O residue 439 THR Chi-restraints excluded: chain P residue 170 GLN Chi-restraints excluded: chain P residue 439 THR Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 184 SER Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 217 ARG Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 303 GLN Chi-restraints excluded: chain R residue 439 THR Chi-restraints excluded: chain S residue 308 LEU Chi-restraints excluded: chain S residue 439 THR Chi-restraints excluded: chain T residue 184 SER Chi-restraints excluded: chain T residue 265 ASP Chi-restraints excluded: chain T residue 290 SER Chi-restraints excluded: chain T residue 308 LEU Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain T residue 439 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 290 SER Chi-restraints excluded: chain U residue 325 VAL Chi-restraints excluded: chain U residue 439 THR Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain V residue 325 VAL Chi-restraints excluded: chain V residue 439 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 557 optimal weight: 0.7980 chunk 897 optimal weight: 0.0770 chunk 547 optimal weight: 2.9990 chunk 425 optimal weight: 2.9990 chunk 623 optimal weight: 0.6980 chunk 941 optimal weight: 2.9990 chunk 866 optimal weight: 1.9990 chunk 749 optimal weight: 3.9990 chunk 77 optimal weight: 0.0870 chunk 579 optimal weight: 6.9990 chunk 459 optimal weight: 0.8980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** C 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 144 GLN ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 256 ASN K 144 GLN K 256 ASN ** K 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 303 GLN M 144 GLN N 53 ASN N 256 ASN ** O 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 GLN Q 87 ASN Q 144 GLN Q 256 ASN ** S 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 144 GLN ** U 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 303 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 75705 Z= 0.177 Angle : 0.556 10.871 102795 Z= 0.284 Chirality : 0.076 1.450 11130 Planarity : 0.003 0.108 13503 Dihedral : 4.411 18.708 10416 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.16 % Allowed : 17.05 % Favored : 81.79 % 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: -0.30 (0.09), residues: 9492 helix: 1.06 (0.13), residues: 1701 sheet: -0.01 (0.08), residues: 3696 loop : -0.83 (0.09), residues: 4095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 62 HIS 0.006 0.001 HIS T 167 PHE 0.024 0.001 PHE C 140 TYR 0.028 0.001 TYR F 219 ARG 0.014 0.000 ARG S 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18984 Ramachandran restraints generated. 9492 Oldfield, 0 Emsley, 9492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Evaluate side-chains 1677 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1585 time to evaluate : 8.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLN cc_start: 0.8011 (tp40) cc_final: 0.7793 (tp40) REVERT: A 61 ASP cc_start: 0.7537 (t0) cc_final: 0.7199 (t0) REVERT: A 230 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6075 (mp0) REVERT: A 316 GLU cc_start: 0.7441 (tp30) cc_final: 0.7200 (tp30) REVERT: A 320 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7987 (ttmt) REVERT: C 304 GLU cc_start: 0.6844 (mp0) cc_final: 0.6333 (mp0) REVERT: C 320 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7497 (ttmt) REVERT: C 323 ASP cc_start: 0.7275 (t0) cc_final: 0.6993 (m-30) REVERT: D 307 THR cc_start: 0.8147 (m) cc_final: 0.7923 (p) REVERT: D 435 TYR cc_start: 0.6882 (t80) cc_final: 0.6640 (t80) REVERT: D 441 ILE cc_start: 0.6887 (mt) cc_final: 0.6660 (mp) REVERT: E 316 GLU cc_start: 0.7493 (tp30) cc_final: 0.7202 (tp30) REVERT: E 320 LYS cc_start: 0.7831 (ttmt) cc_final: 0.7610 (ttmt) REVERT: E 441 ILE cc_start: 0.6651 (mt) cc_final: 0.6326 (mp) REVERT: F 230 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.6009 (mp0) REVERT: F 320 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7815 (ttmt) REVERT: F 332 GLU cc_start: 0.6917 (tp30) cc_final: 0.6490 (tp30) REVERT: G 178 ASN cc_start: 0.8237 (m110) cc_final: 0.8020 (m110) REVERT: G 181 LYS cc_start: 0.8156 (mmmt) cc_final: 0.7855 (mppt) REVERT: G 268 LYS cc_start: 0.7944 (mmtp) cc_final: 0.7634 (mttm) REVERT: H 235 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.6118 (tm-30) REVERT: H 323 ASP cc_start: 0.7352 (t0) cc_final: 0.7091 (m-30) REVERT: I 333 LYS cc_start: 0.8015 (tttp) cc_final: 0.7778 (tttt) REVERT: J 37 GLU cc_start: 0.7177 (pm20) cc_final: 0.6830 (pm20) REVERT: J 47 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8112 (mt) REVERT: J 304 GLU cc_start: 0.6888 (mp0) cc_final: 0.6423 (mp0) REVERT: J 316 GLU cc_start: 0.7433 (tp30) cc_final: 0.6815 (tp30) REVERT: J 325 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.8076 (t) REVERT: J 441 ILE cc_start: 0.6784 (mt) cc_final: 0.6401 (mp) REVERT: K 57 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8138 (t) REVERT: K 170 GLN cc_start: 0.7573 (pt0) cc_final: 0.7338 (tt0) REVERT: K 174 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7163 (mt-10) REVERT: K 316 GLU cc_start: 0.7391 (tp30) cc_final: 0.6964 (tp30) REVERT: K 320 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7594 (ttmm) REVERT: K 342 ASP cc_start: 0.6802 (t0) cc_final: 0.6577 (t0) REVERT: K 396 ASP cc_start: 0.6292 (t0) cc_final: 0.5836 (p0) REVERT: K 441 ILE cc_start: 0.6769 (mt) cc_final: 0.6491 (mp) REVERT: L 68 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7400 (ptt90) REVERT: L 162 GLU cc_start: 0.6889 (mp0) cc_final: 0.6642 (mp0) REVERT: L 173 ASP cc_start: 0.7764 (p0) cc_final: 0.7519 (p0) REVERT: L 441 ILE cc_start: 0.6711 (mt) cc_final: 0.6452 (mp) REVERT: M 78 VAL cc_start: 0.8549 (m) cc_final: 0.8261 (p) REVERT: M 162 GLU cc_start: 0.7156 (mp0) cc_final: 0.6916 (mp0) REVERT: M 176 ASN cc_start: 0.7888 (t0) cc_final: 0.7676 (t0) REVERT: M 304 GLU cc_start: 0.7107 (mp0) cc_final: 0.6693 (mp0) REVERT: M 323 ASP cc_start: 0.7249 (t0) cc_final: 0.7043 (m-30) REVERT: M 441 ILE cc_start: 0.6607 (mt) cc_final: 0.6251 (mp) REVERT: N 162 GLU cc_start: 0.7163 (mp0) cc_final: 0.6792 (mp0) REVERT: N 316 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6959 (tp30) REVERT: O 61 ASP cc_start: 0.7202 (t0) cc_final: 0.6918 (t0) REVERT: O 87 ASN cc_start: 0.7983 (t0) cc_final: 0.7496 (t0) REVERT: O 265 ASP cc_start: 0.6886 (p0) cc_final: 0.6573 (p0) REVERT: O 320 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7686 (ttmt) REVERT: O 324 ASP cc_start: 0.7308 (m-30) cc_final: 0.7035 (m-30) REVERT: O 325 VAL cc_start: 0.8383 (t) cc_final: 0.8160 (m) REVERT: P 162 GLU cc_start: 0.7021 (mp0) cc_final: 0.6677 (mp0) REVERT: P 304 GLU cc_start: 0.7117 (mp0) cc_final: 0.6610 (mp0) REVERT: P 310 SER cc_start: 0.8435 (t) cc_final: 0.8229 (p) REVERT: P 311 SER cc_start: 0.8028 (t) cc_final: 0.7767 (p) REVERT: P 316 GLU cc_start: 0.7539 (tp30) cc_final: 0.6978 (tp30) REVERT: P 479 CYS cc_start: 0.6989 (m) cc_final: 0.6204 (p) REVERT: Q 47 ILE cc_start: 0.8198 (tt) cc_final: 0.7921 (mt) REVERT: Q 53 ASN cc_start: 0.7746 (m-40) cc_final: 0.7521 (m-40) REVERT: Q 162 GLU cc_start: 0.7017 (mp0) cc_final: 0.6518 (mp0) REVERT: Q 170 GLN cc_start: 0.7618 (pt0) cc_final: 0.7274 (tt0) REVERT: Q 173 ASP cc_start: 0.7820 (p0) cc_final: 0.7585 (p0) REVERT: Q 189 ARG cc_start: 0.8512 (mmm160) cc_final: 0.8210 (mtp180) REVERT: Q 304 GLU cc_start: 0.6853 (mp0) cc_final: 0.6436 (mp0) REVERT: Q 311 SER cc_start: 0.7633 (t) cc_final: 0.7416 (p) REVERT: Q 320 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7856 (ttmt) REVERT: T 37 GLU cc_start: 0.7193 (pm20) cc_final: 0.6771 (pm20) REVERT: T 316 GLU cc_start: 0.7562 (tp30) cc_final: 0.7056 (tp30) REVERT: T 320 LYS cc_start: 0.8267 (ttmt) cc_final: 0.8035 (ttmm) REVERT: U 173 ASP cc_start: 0.7621 (p0) cc_final: 0.7312 (p0) REVERT: U 316 GLU cc_start: 0.7395 (tp30) cc_final: 0.7055 (tp30) REVERT: U 320 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7888 (ttmt) REVERT: V 162 GLU cc_start: 0.6857 (mp0) cc_final: 0.6521 (mp0) REVERT: V 178 ASN cc_start: 0.8238 (m-40) cc_final: 0.7998 (m110) REVERT: V 316 GLU cc_start: 0.7338 (tp30) cc_final: 0.7087 (tp30) outliers start: 92 outliers final: 78 residues processed: 1643 average time/residue: 3.6391 time to fit residues: 7679.7757 Evaluate side-chains 1664 residues out of total 7917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1579 time to evaluate : 7.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 158 LYS Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 309 CYS Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain H residue 235 GLN Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 439 THR Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 439 THR Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 286 SER Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 311 SER Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 309 CYS Chi-restraints excluded: chain K residue 439 THR Chi-restraints excluded: chain K residue 450 ASN Chi-restraints excluded: chain L residue 68 ARG Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 290 SER Chi-restraints excluded: chain L residue 309 CYS Chi-restraints excluded: chain L residue 439 THR Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 308 LEU Chi-restraints excluded: chain M residue 309 CYS Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain M residue 439 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 325 VAL Chi-restraints excluded: chain N residue 439 THR Chi-restraints excluded: chain O residue 160 LEU Chi-restraints excluded: chain O residue 256 ASN Chi-restraints excluded: chain O residue 439 THR Chi-restraints excluded: chain P residue 170 GLN Chi-restraints excluded: chain P residue 439 THR Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 217 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 303 GLN Chi-restraints excluded: chain R residue 439 THR Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 308 LEU Chi-restraints excluded: chain S residue 439 THR Chi-restraints excluded: chain T residue 184 SER Chi-restraints excluded: chain T residue 265 ASP Chi-restraints excluded: chain T residue 290 SER Chi-restraints excluded: chain T residue 308 LEU Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain T residue 439 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 290 SER Chi-restraints excluded: chain U residue 325 VAL Chi-restraints excluded: chain U residue 439 THR Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain V residue 325 VAL Chi-restraints excluded: chain V residue 439 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 595 optimal weight: 1.9990 chunk 798 optimal weight: 5.9990 chunk 229 optimal weight: 0.9990 chunk 691 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 chunk 750 optimal weight: 4.9990 chunk 314 optimal weight: 10.0000 chunk 771 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN C 86 GLN C 256 ASN ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 ASN ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 GLN G 86 GLN ** H 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 256 ASN K 58 GLN K 144 GLN K 256 ASN ** K 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 ASN L 303 GLN N 53 ASN O 86 GLN O 144 GLN ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN Q 144 GLN ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 144 GLN U 314 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.184824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.146553 restraints weight = 265561.126| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.81 r_work: 0.3882 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 75705 Z= 0.339 Angle : 0.590 10.945 102795 Z= 0.305 Chirality : 0.077 1.456 11130 Planarity : 0.004 0.082 13503 Dihedral : 4.497 18.944 10416 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.26 % Allowed : 17.08 % Favored : 81.66 % 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: -0.49 (0.09), residues: 9492 helix: 0.97 (0.13), residues: 1701 sheet: -0.23 (0.08), residues: 3696 loop : -0.86 (0.09), residues: 4095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 306 HIS 0.007 0.002 HIS H 167 PHE 0.025 0.002 PHE C 140 TYR 0.032 0.002 TYR I 219 ARG 0.017 0.001 ARG S 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 93469.58 seconds wall clock time: 1588 minutes 7.34 seconds (95287.34 seconds total)