Starting phenix.real_space_refine on Sun Jul 21 18:36:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9c_37364/07_2024/8w9c_37364_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9c_37364/07_2024/8w9c_37364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9c_37364/07_2024/8w9c_37364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9c_37364/07_2024/8w9c_37364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9c_37364/07_2024/8w9c_37364_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9c_37364/07_2024/8w9c_37364_neut.cif" } resolution = 3.3 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= 0.009 sd= 0.092 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 K 2 8.98 5 Zn 7 6.06 5 S 86 5.16 5 C 9769 2.51 5 N 2557 2.21 5 O 2857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 698": "OD1" <-> "OD2" Residue "A ASP 707": "OD1" <-> "OD2" Residue "A PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A ASP 772": "OD1" <-> "OD2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A GLU 781": "OE1" <-> "OE2" Residue "A PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 804": "OE1" <-> "OE2" Residue "A GLU 805": "OE1" <-> "OE2" Residue "A GLU 813": "OE1" <-> "OE2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 818": "OD1" <-> "OD2" Residue "A PHE 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 822": "OE1" <-> "OE2" Residue "A GLU 832": "OE1" <-> "OE2" Residue "A GLU 843": "OE1" <-> "OE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A PHE 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 872": "OD1" <-> "OD2" Residue "A GLU 878": "OE1" <-> "OE2" Residue "A ASP 881": "OD1" <-> "OD2" Residue "A GLU 920": "OE1" <-> "OE2" Residue "A PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 981": "OD1" <-> "OD2" Residue "A ASP 987": "OD1" <-> "OD2" Residue "A ASP 993": "OD1" <-> "OD2" Residue "A PHE 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1008": "OE1" <-> "OE2" Residue "A ASP 1012": "OD1" <-> "OD2" Residue "A PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A TYR 1034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1156": "OE1" <-> "OE2" Residue "A GLU 1166": "OE1" <-> "OE2" Residue "A PHE 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1185": "OD1" <-> "OD2" Residue "A PHE 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1220": "OE1" <-> "OE2" Residue "A PHE 1224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1264": "OE1" <-> "OE2" Residue "A PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1298": "OE1" <-> "OE2" Residue "A PHE 1301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1304": "OE1" <-> "OE2" Residue "A TYR 1316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1320": "OD1" <-> "OD2" Residue "A ASP 1321": "OD1" <-> "OD2" Residue "A ASP 1330": "OD1" <-> "OD2" Residue "A GLU 1331": "OE1" <-> "OE2" Residue "A ASP 1332": "OD1" <-> "OD2" Residue "A TYR 1336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 292": "OD1" <-> "OD2" Residue "E ASP 300": "OD1" <-> "OD2" Residue "E PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 323": "OE1" <-> "OE2" Residue "E PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 359": "OE1" <-> "OE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 377": "OD1" <-> "OD2" Residue "E TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 424": "NH1" <-> "NH2" Residue "E ARG 454": "NH1" <-> "NH2" Residue "E PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 496": "NH1" <-> "NH2" Residue "E TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 571": "OE1" <-> "OE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 84": "OD1" <-> "OD2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 108": "OD1" <-> "OD2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 279": "OD1" <-> "OD2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 367": "OE1" <-> "OE2" Residue "B TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 370": "OD1" <-> "OD2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "C ASP 235": "OD1" <-> "OD2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 251": "OD1" <-> "OD2" Residue "C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 360": "OE1" <-> "OE2" Residue "C ASP 361": "OD1" <-> "OD2" Residue "C PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 381": "NH1" <-> "NH2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "D ASP 235": "OD1" <-> "OD2" Residue "D ASP 242": "OD1" <-> "OD2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "D TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "D ASP 316": "OD1" <-> "OD2" Residue "D TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 340": "OE1" <-> "OE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D ASP 383": "OD1" <-> "OD2" Residue "D ASP 384": "OD1" <-> "OD2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "F PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 260": "OE1" <-> "OE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 288": "OD1" <-> "OD2" Residue "F ASP 292": "OD1" <-> "OD2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 344": "OD1" <-> "OD2" Residue "F PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 553": "OD1" <-> "OD2" Residue "F TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 575": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 15278 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 5066 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2884 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 333} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3057 Classifications: {'peptide': 385} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 366} Chain: "C" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1483 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain: "D" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1497 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 176} Chain: "F" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1282 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5538 SG CYS E 263 34.086 49.663 104.185 1.00 60.61 S ATOM 5555 SG CYS E 266 36.357 51.085 101.911 1.00 47.09 S ATOM 5708 SG CYS E 286 33.258 52.780 101.241 1.00 40.71 S ATOM 5619 SG CYS E 275 23.463 42.608 109.874 1.00 85.76 S ATOM 5640 SG CYS E 278 26.235 40.933 108.153 1.00 87.11 S ATOM 5843 SG CYS E 303 24.485 42.041 105.361 1.00 82.80 S ATOM 5866 SG CYS E 306 23.157 39.356 107.231 1.00 84.14 S ATOM 6956 SG CYS E 440 69.578 57.886 88.096 1.00 28.90 S ATOM 6982 SG CYS E 443 71.299 57.467 84.950 1.00 29.47 S ATOM 7170 SG CYS E 466 71.957 61.090 86.940 1.00 40.27 S ATOM 6795 SG CYS E 420 81.860 67.677 89.782 1.00 31.10 S ATOM 7051 SG CYS E 451 78.596 68.932 90.092 1.00 25.88 S ATOM 14235 SG CYS F 286 58.783 28.464 28.916 1.00 88.61 S ATOM 14146 SG CYS F 275 59.837 18.553 40.471 1.00 96.34 S ATOM 14393 SG CYS F 306 58.885 20.509 43.480 1.00 89.64 S Time building chain proxies: 8.59, per 1000 atoms: 0.56 Number of scatterers: 15278 At special positions: 0 Unit cell: (138.933, 116.316, 161.55, 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) Zn 7 29.99 K 2 19.00 S 86 16.00 O 2857 8.00 N 2557 7.00 C 9769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.52 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1000 " pdb="ZN ZN B1000 " - pdb=" ND1 HIS B 188 " pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb=" ND1 HIS E 283 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 263 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 266 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 286 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 303 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 275 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 306 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 278 " pdb=" ZN E1002 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 443 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 440 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 466 " pdb=" ZN E1003 " pdb="ZN ZN E1003 " - pdb=" ND1 HIS E 448 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 420 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 451 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" ND1 HIS F 283 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 286 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 306 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 275 " Number of angles added : 9 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3572 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 10 sheets defined 55.0% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 665 through 677 Processing helix chain 'A' and resid 679 through 694 Processing helix chain 'A' and resid 698 through 708 removed outlier: 3.882A pdb=" N PHE A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 724 Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.519A pdb=" N GLU A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 839 removed outlier: 3.857A pdb=" N CYS A 830 " --> pdb=" O ARG A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 849 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 872 through 886 Processing helix chain 'A' and resid 886 through 923 removed outlier: 4.032A pdb=" N THR A 890 " --> pdb=" O HIS A 886 " (cutoff:3.500A) Proline residue: A 892 - end of helix removed outlier: 4.454A pdb=" N VAL A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 928 Processing helix chain 'A' and resid 931 through 935 removed outlier: 3.908A pdb=" N PHE A 935 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 964 removed outlier: 4.277A pdb=" N ILE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 999 removed outlier: 3.917A pdb=" N ASP A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1021 Processing helix chain 'A' and resid 1025 through 1038 Processing helix chain 'A' and resid 1065 through 1070 removed outlier: 3.505A pdb=" N HIS A1070 " --> pdb=" O LEU A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1081 removed outlier: 3.852A pdb=" N TYR A1074 " --> pdb=" O HIS A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1127 removed outlier: 3.644A pdb=" N GLN A1127 " --> pdb=" O GLU A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1174 removed outlier: 4.982A pdb=" N GLU A1166 " --> pdb=" O LYS A1162 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ARG A1167 " --> pdb=" O GLN A1163 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A1174 " --> pdb=" O LYS A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1184 removed outlier: 3.533A pdb=" N LYS A1182 " --> pdb=" O VAL A1178 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A1184 " --> pdb=" O PHE A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 3.882A pdb=" N MET A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1217 removed outlier: 3.557A pdb=" N GLN A1206 " --> pdb=" O ASP A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1232 removed outlier: 3.552A pdb=" N TYR A1232 " --> pdb=" O LEU A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1242 removed outlier: 3.834A pdb=" N LEU A1239 " --> pdb=" O ALA A1236 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR A1241 " --> pdb=" O LYS A1238 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A1242 " --> pdb=" O LEU A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1259 removed outlier: 3.928A pdb=" N MET A1257 " --> pdb=" O ALA A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1275 removed outlier: 3.563A pdb=" N ALA A1275 " --> pdb=" O LYS A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1292 Processing helix chain 'A' and resid 1329 through 1341 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 303 through 312 Processing helix chain 'E' and resid 315 through 330 removed outlier: 3.643A pdb=" N LEU E 319 " --> pdb=" O SER E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.544A pdb=" N ILE E 343 " --> pdb=" O LEU E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.564A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 389 Processing helix chain 'E' and resid 430 through 434 removed outlier: 3.665A pdb=" N SER E 434 " --> pdb=" O PRO E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 579 Processing helix chain 'B' and resid 28 through 32 removed outlier: 4.102A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 55 removed outlier: 3.913A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.780A pdb=" N LYS B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.876A pdb=" N CYS B 75 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 92 through 97 removed outlier: 4.352A pdb=" N GLU B 95 " --> pdb=" O ASP B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 removed outlier: 3.791A pdb=" N LYS B 103 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 137 removed outlier: 3.725A pdb=" N GLY B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.576A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 196 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 243 through 262 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 287 through 302 removed outlier: 4.727A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE B 301 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 removed outlier: 3.651A pdb=" N VAL B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'C' and resid 225 through 240 Processing helix chain 'C' and resid 253 through 266 Processing helix chain 'C' and resid 271 through 297 removed outlier: 3.771A pdb=" N GLN C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 316 removed outlier: 3.557A pdb=" N TYR C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP C 316 " --> pdb=" O LYS C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 325 removed outlier: 3.700A pdb=" N ARG C 324 " --> pdb=" O VAL C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 345 removed outlier: 4.047A pdb=" N LEU C 331 " --> pdb=" O GLY C 327 " (cutoff:3.500A) Proline residue: C 339 - end of helix removed outlier: 3.795A pdb=" N THR C 345 " --> pdb=" O LEU C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 374 removed outlier: 4.126A pdb=" N CYS C 352 " --> pdb=" O ASP C 348 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ASP C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU C 372 " --> pdb=" O MET C 368 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR C 373 " --> pdb=" O HIS C 369 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 399 removed outlier: 3.537A pdb=" N LEU C 399 " --> pdb=" O GLU C 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 241 removed outlier: 3.548A pdb=" N LYS D 229 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 266 Processing helix chain 'D' and resid 267 through 269 No H-bonds generated for 'chain 'D' and resid 267 through 269' Processing helix chain 'D' and resid 271 through 297 removed outlier: 5.748A pdb=" N GLY D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASN D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 316 Processing helix chain 'D' and resid 321 through 325 removed outlier: 3.962A pdb=" N ILE D 325 " --> pdb=" O PRO D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 344 Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 348 through 369 Processing helix chain 'D' and resid 391 through 399 removed outlier: 4.087A pdb=" N LEU D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 287 No H-bonds generated for 'chain 'F' and resid 285 through 287' Processing helix chain 'F' and resid 303 through 313 Processing helix chain 'F' and resid 315 through 330 Processing helix chain 'F' and resid 333 through 335 No H-bonds generated for 'chain 'F' and resid 333 through 335' Processing helix chain 'F' and resid 336 through 344 removed outlier: 3.961A pdb=" N ASN F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE F 343 " --> pdb=" O LEU F 339 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 576 Processing sheet with id=AA1, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AA2, first strand: chain 'A' and resid 975 through 978 Processing sheet with id=AA3, first strand: chain 'E' and resid 177 through 179 removed outlier: 6.081A pdb=" N GLU E 177 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA B 22 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS B 209 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 273 through 274 Processing sheet with id=AA5, first strand: chain 'E' and resid 437 through 439 Processing sheet with id=AA6, first strand: chain 'E' and resid 505 through 506 removed outlier: 5.833A pdb=" N GLN E 521 " --> pdb=" O ILE E 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AA8, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AA9, first strand: chain 'F' and resid 260 through 263 removed outlier: 6.954A pdb=" N GLU F 260 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N HIS F 283 " --> pdb=" O GLU F 260 " (cutoff:3.500A) removed outlier: 11.188A pdb=" N PHE F 262 " --> pdb=" O HIS F 283 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 364 through 366 700 hydrogen bonds defined for protein. 2022 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: 4.13 Time building geometry restraints manager: 6.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 2546 1.26 - 1.40: 3878 1.40 - 1.53: 8709 1.53 - 1.67: 354 1.67 - 1.81: 128 Bond restraints: 15615 Sorted by residual: bond pdb=" CE1 HIS E 469 " pdb=" NE2 HIS E 469 " ideal model delta sigma weight residual 1.321 1.215 0.106 1.00e-02 1.00e+04 1.12e+02 bond pdb=" C PRO E 471 " pdb=" O PRO E 471 " ideal model delta sigma weight residual 1.233 1.121 0.112 1.18e-02 7.18e+03 9.08e+01 bond pdb=" CG HIS E 469 " pdb=" ND1 HIS E 469 " ideal model delta sigma weight residual 1.378 1.302 0.076 1.10e-02 8.26e+03 4.72e+01 bond pdb=" N ASN E 517 " pdb=" CA ASN E 517 " ideal model delta sigma weight residual 1.457 1.544 -0.087 1.29e-02 6.01e+03 4.50e+01 bond pdb=" CA GLY E 518 " pdb=" C GLY E 518 " ideal model delta sigma weight residual 1.514 1.435 0.079 1.41e-02 5.03e+03 3.17e+01 ... (remaining 15610 not shown) Histogram of bond angle deviations from ideal: 91.69 - 100.77: 25 100.77 - 109.84: 1840 109.84 - 118.92: 10846 118.92 - 128.00: 8239 128.00 - 137.08: 125 Bond angle restraints: 21075 Sorted by residual: angle pdb=" C HIS E 469 " pdb=" N SER E 470 " pdb=" CA SER E 470 " ideal model delta sigma weight residual 120.49 137.08 -16.59 1.42e+00 4.96e-01 1.36e+02 angle pdb=" N PRO E 471 " pdb=" CA PRO E 471 " pdb=" C PRO E 471 " ideal model delta sigma weight residual 111.41 125.55 -14.14 1.50e+00 4.44e-01 8.88e+01 angle pdb=" N GLY E 518 " pdb=" CA GLY E 518 " pdb=" C GLY E 518 " ideal model delta sigma weight residual 113.18 91.69 21.49 2.37e+00 1.78e-01 8.22e+01 angle pdb=" CA ASN E 517 " pdb=" CB ASN E 517 " pdb=" CG ASN E 517 " ideal model delta sigma weight residual 112.60 104.68 7.92 1.00e+00 1.00e+00 6.27e+01 angle pdb=" CA THR E 472 " pdb=" C THR E 472 " pdb=" O THR E 472 " ideal model delta sigma weight residual 120.55 111.40 9.15 1.21e+00 6.83e-01 5.71e+01 ... (remaining 21070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 7944 17.87 - 35.74: 1104 35.74 - 53.62: 314 53.62 - 71.49: 70 71.49 - 89.36: 17 Dihedral angle restraints: 9449 sinusoidal: 3930 harmonic: 5519 Sorted by residual: dihedral pdb=" C ASN E 517 " pdb=" N ASN E 517 " pdb=" CA ASN E 517 " pdb=" CB ASN E 517 " ideal model delta harmonic sigma weight residual -122.60 -160.57 37.97 0 2.50e+00 1.60e-01 2.31e+02 dihedral pdb=" N ASN E 517 " pdb=" C ASN E 517 " pdb=" CA ASN E 517 " pdb=" CB ASN E 517 " ideal model delta harmonic sigma weight residual 122.80 160.71 -37.91 0 2.50e+00 1.60e-01 2.30e+02 dihedral pdb=" N THR E 472 " pdb=" C THR E 472 " pdb=" CA THR E 472 " pdb=" CB THR E 472 " ideal model delta harmonic sigma weight residual 123.40 141.04 -17.64 0 2.50e+00 1.60e-01 4.98e+01 ... (remaining 9446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.320: 2273 0.320 - 0.641: 2 0.641 - 0.961: 1 0.961 - 1.281: 0 1.281 - 1.601: 1 Chirality restraints: 2277 Sorted by residual: chirality pdb=" CA ASN E 517 " pdb=" N ASN E 517 " pdb=" C ASN E 517 " pdb=" CB ASN E 517 " both_signs ideal model delta sigma weight residual False 2.51 0.91 1.60 2.00e-01 2.50e+01 6.41e+01 chirality pdb=" CA THR E 472 " pdb=" N THR E 472 " pdb=" C THR E 472 " pdb=" CB THR E 472 " both_signs ideal model delta sigma weight residual False 2.53 1.79 0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" CA PRO E 471 " pdb=" N PRO E 471 " pdb=" C PRO E 471 " pdb=" CB PRO E 471 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.56e+00 ... (remaining 2274 not shown) Planarity restraints: 2694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 469 " -0.053 2.00e-02 2.50e+03 4.65e-02 3.24e+01 pdb=" CG HIS E 469 " 0.083 2.00e-02 2.50e+03 pdb=" ND1 HIS E 469 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS E 469 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 HIS E 469 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS E 469 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 470 " -0.021 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C SER E 470 " 0.071 2.00e-02 2.50e+03 pdb=" O SER E 470 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO E 471 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 471 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C PRO E 471 " -0.065 2.00e-02 2.50e+03 pdb=" O PRO E 471 " 0.025 2.00e-02 2.50e+03 pdb=" N THR E 472 " 0.021 2.00e-02 2.50e+03 ... (remaining 2691 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.60: 186 2.60 - 3.23: 15432 3.23 - 3.87: 29121 3.87 - 4.50: 39218 4.50 - 5.14: 63639 Nonbonded interactions: 147596 Sorted by model distance: nonbonded pdb=" N GLY E 518 " pdb=" N ASN E 519 " model vdw 1.965 2.560 nonbonded pdb=" OD2 ASP B 274 " pdb="ZN ZN B1000 " model vdw 1.981 2.230 nonbonded pdb=" OD1 ASP B 186 " pdb="ZN ZN B1000 " model vdw 2.038 2.230 nonbonded pdb=" O THR E 472 " pdb=" OG1 THR E 472 " model vdw 2.061 2.440 nonbonded pdb=" O LEU E 171 " pdb=" OG1 THR E 172 " model vdw 2.086 2.440 ... (remaining 147591 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 'C' selection = (chain 'D' and resid 219 through 401) } 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 42.030 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 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 : 0.005 0.112 15615 Z= 0.304 Angle : 0.789 21.493 21075 Z= 0.467 Chirality : 0.058 1.601 2277 Planarity : 0.005 0.072 2694 Dihedral : 18.159 89.361 5877 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.14 % Favored : 93.64 % Rotamer: Outliers : 7.42 % Allowed : 19.10 % Favored : 73.48 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.16), residues: 1840 helix: -1.40 (0.14), residues: 924 sheet: -2.00 (0.55), residues: 86 loop : -2.84 (0.18), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 492 HIS 0.035 0.001 HIS E 469 PHE 0.027 0.002 PHE C 374 TYR 0.018 0.001 TYR E 356 ARG 0.011 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 304 time to evaluate : 1.782 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: A 679 LYS cc_start: 0.6075 (mmtt) cc_final: 0.5817 (pttp) REVERT: A 1256 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6960 (tt) REVERT: A 1337 TYR cc_start: -0.2315 (OUTLIER) cc_final: -0.3761 (t80) REVERT: E 107 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5672 (tptp) REVERT: E 262 PHE cc_start: 0.5551 (m-80) cc_final: 0.4830 (m-80) REVERT: E 287 LEU cc_start: 0.6995 (mt) cc_final: 0.6721 (mt) REVERT: E 345 SER cc_start: 0.8436 (m) cc_final: 0.7519 (t) REVERT: E 490 LYS cc_start: 0.7578 (pttp) cc_final: 0.6779 (mmtm) REVERT: E 565 LYS cc_start: 0.7619 (ttpt) cc_final: 0.7201 (ttpt) REVERT: B 72 GLN cc_start: 0.7593 (tt0) cc_final: 0.7248 (mm-40) REVERT: B 114 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: B 248 ARG cc_start: 0.6650 (ttt180) cc_final: 0.6390 (ttt90) REVERT: D 223 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7514 (tm-30) REVERT: D 228 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6334 (mp) REVERT: D 315 LYS cc_start: 0.7158 (pttt) cc_final: 0.6800 (tppt) REVERT: D 350 GLN cc_start: 0.6929 (OUTLIER) cc_final: 0.6526 (tt0) REVERT: D 356 ILE cc_start: 0.7956 (pp) cc_final: 0.7512 (pp) REVERT: F 285 LEU cc_start: 0.7224 (mt) cc_final: 0.6426 (tt) REVERT: F 560 MET cc_start: 0.7887 (tpt) cc_final: 0.7604 (tpt) outliers start: 127 outliers final: 83 residues processed: 417 average time/residue: 0.3052 time to fit residues: 181.9325 Evaluate side-chains 320 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 231 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 907 ARG Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1235 LYS Chi-restraints excluded: chain A residue 1241 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1262 THR Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1299 ASN Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 371 GLN Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 454 ARG Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 350 GLN Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 74 optimal weight: 0.0980 chunk 144 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 GLN ** A 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 ASN A1075 GLN A1216 ASN A1247 GLN E 331 ASN E 352 GLN E 376 ASN E 402 ASN E 433 ASN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 541 GLN E 580 ASN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS B 235 ASN B 317 ASN B 364 ASN C 305 GLN C 358 GLN D 350 GLN D 358 GLN D 375 ASN D 380 ASN F 259 ASN F 355 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15615 Z= 0.218 Angle : 0.641 11.237 21075 Z= 0.337 Chirality : 0.043 0.237 2277 Planarity : 0.005 0.092 2694 Dihedral : 9.859 65.495 2184 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.63 % Favored : 93.26 % Rotamer: Outliers : 6.54 % Allowed : 21.73 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.18), residues: 1840 helix: -0.14 (0.16), residues: 957 sheet: -1.63 (0.56), residues: 80 loop : -2.30 (0.19), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 492 HIS 0.005 0.001 HIS B 150 PHE 0.026 0.002 PHE E 387 TYR 0.015 0.001 TYR C 326 ARG 0.005 0.001 ARG A 799 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 257 time to evaluate : 1.958 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: A 912 TRP cc_start: 0.5421 (OUTLIER) cc_final: 0.5051 (t-100) REVERT: A 1256 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6791 (tt) REVERT: A 1307 LYS cc_start: 0.7817 (tmmt) cc_final: 0.7543 (ttmt) REVERT: A 1316 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.7455 (t80) REVERT: A 1337 TYR cc_start: -0.2893 (OUTLIER) cc_final: -0.3968 (t80) REVERT: E 107 LYS cc_start: 0.6174 (OUTLIER) cc_final: 0.5816 (tptp) REVERT: E 345 SER cc_start: 0.8043 (m) cc_final: 0.7763 (t) REVERT: E 490 LYS cc_start: 0.7539 (pttp) cc_final: 0.6786 (mmtm) REVERT: E 570 GLN cc_start: 0.7482 (pt0) cc_final: 0.6883 (pt0) REVERT: B 72 GLN cc_start: 0.7561 (tt0) cc_final: 0.7328 (mm-40) REVERT: B 114 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7046 (m-30) REVERT: B 116 LEU cc_start: 0.8144 (tp) cc_final: 0.7917 (tt) REVERT: C 358 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.6693 (mt0) REVERT: D 228 LEU cc_start: 0.6721 (mm) cc_final: 0.6411 (mp) REVERT: D 247 ARG cc_start: 0.7285 (ptp90) cc_final: 0.7004 (ptp90) REVERT: D 315 LYS cc_start: 0.7086 (pttt) cc_final: 0.6751 (tppt) REVERT: F 285 LEU cc_start: 0.7170 (mt) cc_final: 0.6836 (pt) REVERT: F 301 TRP cc_start: 0.7200 (t60) cc_final: 0.6988 (t60) REVERT: F 309 LYS cc_start: 0.7618 (mmmt) cc_final: 0.7384 (mttt) outliers start: 112 outliers final: 65 residues processed: 346 average time/residue: 0.2850 time to fit residues: 145.1270 Evaluate side-chains 301 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 229 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 907 ARG Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1299 ASN Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1316 TYR Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 410 ASN Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 358 GLN Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 371 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 180 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 HIS A 961 ASN ** A1283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 ASN E 521 GLN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN D 393 GLN ** F 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15615 Z= 0.184 Angle : 0.594 9.327 21075 Z= 0.314 Chirality : 0.041 0.225 2277 Planarity : 0.004 0.056 2694 Dihedral : 8.328 59.771 2113 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.76 % Favored : 94.13 % Rotamer: Outliers : 5.72 % Allowed : 23.54 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -0.89 (0.19), residues: 1840 helix: 0.64 (0.17), residues: 942 sheet: -1.40 (0.56), residues: 80 loop : -2.03 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 236 HIS 0.004 0.001 HIS B 150 PHE 0.028 0.001 PHE E 387 TYR 0.019 0.001 TYR A1240 ARG 0.008 0.000 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 241 time to evaluate : 2.009 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: A 912 TRP cc_start: 0.5385 (OUTLIER) cc_final: 0.4971 (t-100) REVERT: A 1235 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6463 (pttm) REVERT: A 1287 ARG cc_start: 0.6704 (tmt170) cc_final: 0.6493 (tmt170) REVERT: A 1316 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7488 (t80) REVERT: A 1331 GLU cc_start: 0.2683 (OUTLIER) cc_final: 0.1843 (tm-30) REVERT: A 1337 TYR cc_start: -0.2758 (OUTLIER) cc_final: -0.3686 (t80) REVERT: E 107 LYS cc_start: 0.6071 (OUTLIER) cc_final: 0.5721 (tptp) REVERT: E 115 LEU cc_start: 0.5915 (OUTLIER) cc_final: 0.5362 (mp) REVERT: E 342 ASN cc_start: 0.6663 (OUTLIER) cc_final: 0.6233 (m110) REVERT: E 490 LYS cc_start: 0.7390 (pttp) cc_final: 0.6685 (mmtm) REVERT: E 514 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.6882 (t80) REVERT: E 570 GLN cc_start: 0.7402 (pt0) cc_final: 0.7109 (pt0) REVERT: B 72 GLN cc_start: 0.7526 (tt0) cc_final: 0.7289 (mm-40) REVERT: B 114 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6848 (m-30) REVERT: F 285 LEU cc_start: 0.7070 (mt) cc_final: 0.6790 (pt) REVERT: F 309 LYS cc_start: 0.7514 (mmmt) cc_final: 0.7278 (mttt) outliers start: 98 outliers final: 64 residues processed: 319 average time/residue: 0.2704 time to fit residues: 128.5818 Evaluate side-chains 293 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 219 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 907 ARG Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1235 LYS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1316 TYR Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain A residue 1331 GLU Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 342 ASN Chi-restraints excluded: chain E residue 371 GLN Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 514 TYR Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 288 TYR Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 278 CYS Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 371 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 159 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN B 317 ASN C 350 GLN ** C 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 15615 Z= 0.245 Angle : 0.627 10.195 21075 Z= 0.330 Chirality : 0.043 0.230 2277 Planarity : 0.004 0.068 2694 Dihedral : 7.950 57.929 2093 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.85 % Favored : 93.04 % Rotamer: Outliers : 6.54 % Allowed : 23.71 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.19), residues: 1840 helix: 0.71 (0.17), residues: 949 sheet: -1.19 (0.56), residues: 84 loop : -1.96 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 492 HIS 0.006 0.001 HIS B 150 PHE 0.037 0.002 PHE E 387 TYR 0.028 0.002 TYR A1240 ARG 0.007 0.000 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 237 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 912 TRP cc_start: 0.5556 (OUTLIER) cc_final: 0.5071 (t-100) REVERT: A 926 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7631 (mtmt) REVERT: A 1235 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6766 (pttt) REVERT: A 1300 MET cc_start: 0.5114 (ttt) cc_final: 0.4759 (ttt) REVERT: A 1316 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7394 (t80) REVERT: A 1331 GLU cc_start: 0.2607 (OUTLIER) cc_final: 0.1917 (tm-30) REVERT: A 1337 TYR cc_start: -0.2880 (OUTLIER) cc_final: -0.3667 (t80) REVERT: E 107 LYS cc_start: 0.5790 (OUTLIER) cc_final: 0.5450 (tptp) REVERT: E 115 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5377 (mp) REVERT: E 342 ASN cc_start: 0.6660 (OUTLIER) cc_final: 0.6219 (m110) REVERT: E 387 PHE cc_start: 0.3131 (OUTLIER) cc_final: 0.2906 (p90) REVERT: E 490 LYS cc_start: 0.7406 (pttp) cc_final: 0.6674 (mmtm) REVERT: B 72 GLN cc_start: 0.7496 (tt0) cc_final: 0.7268 (mm-40) REVERT: B 352 LYS cc_start: 0.7440 (mtpt) cc_final: 0.7162 (mtpp) REVERT: D 223 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7548 (tm-30) REVERT: F 285 LEU cc_start: 0.7139 (mt) cc_final: 0.6852 (pt) outliers start: 112 outliers final: 84 residues processed: 329 average time/residue: 0.2521 time to fit residues: 125.2945 Evaluate side-chains 318 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 224 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 907 ARG Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LYS Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1134 SER Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1235 LYS Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1316 TYR Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain A residue 1331 GLU Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 342 ASN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 371 GLN Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 410 ASN Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 278 CYS Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 371 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 151 optimal weight: 0.3980 chunk 122 optimal weight: 0.0060 chunk 0 optimal weight: 4.9990 chunk 90 optimal weight: 0.4980 chunk 159 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1221 HIS ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN C 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15615 Z= 0.159 Angle : 0.578 11.011 21075 Z= 0.304 Chirality : 0.041 0.218 2277 Planarity : 0.004 0.056 2694 Dihedral : 7.294 59.191 2089 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.49 % Favored : 94.40 % Rotamer: Outliers : 5.43 % Allowed : 24.88 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 (0.19), residues: 1840 helix: 1.11 (0.17), residues: 939 sheet: -0.96 (0.56), residues: 84 loop : -1.69 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 492 HIS 0.004 0.001 HIS B 150 PHE 0.032 0.001 PHE E 387 TYR 0.020 0.001 TYR A1240 ARG 0.007 0.000 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 250 time to evaluate : 1.799 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: A 690 ASN cc_start: 0.7240 (OUTLIER) cc_final: 0.5887 (t0) REVERT: A 912 TRP cc_start: 0.5481 (OUTLIER) cc_final: 0.5124 (t-100) REVERT: A 926 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7512 (mtmt) REVERT: A 986 TYR cc_start: 0.6712 (m-80) cc_final: 0.6420 (m-80) REVERT: A 1331 GLU cc_start: 0.2607 (OUTLIER) cc_final: 0.2295 (tm-30) REVERT: E 115 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5275 (mp) REVERT: E 342 ASN cc_start: 0.6487 (OUTLIER) cc_final: 0.6127 (m110) REVERT: E 490 LYS cc_start: 0.7286 (pttp) cc_final: 0.6649 (mmtm) REVERT: E 514 TYR cc_start: 0.7691 (OUTLIER) cc_final: 0.6894 (t80) REVERT: E 556 TYR cc_start: 0.7340 (m-80) cc_final: 0.6870 (m-80) REVERT: B 53 MET cc_start: 0.8122 (mmm) cc_final: 0.7725 (mmp) REVERT: B 72 GLN cc_start: 0.7444 (tt0) cc_final: 0.7205 (mm-40) REVERT: B 114 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6702 (m-30) REVERT: B 352 LYS cc_start: 0.7100 (mtpt) cc_final: 0.6824 (mtpp) REVERT: C 394 TYR cc_start: 0.7521 (t80) cc_final: 0.7247 (t80) REVERT: D 223 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7461 (tm-30) REVERT: D 290 ASP cc_start: 0.6647 (OUTLIER) cc_final: 0.6389 (p0) REVERT: F 285 LEU cc_start: 0.7019 (mt) cc_final: 0.6797 (pt) REVERT: F 309 LYS cc_start: 0.7835 (mmmt) cc_final: 0.7616 (mttt) REVERT: F 350 GLN cc_start: 0.7095 (mt0) cc_final: 0.6833 (mt0) outliers start: 93 outliers final: 51 residues processed: 325 average time/residue: 0.2577 time to fit residues: 125.6533 Evaluate side-chains 286 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 226 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 907 ARG Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LYS Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain A residue 1331 GLU Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 342 ASN Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 420 CYS Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 514 TYR Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 288 TYR Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 371 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 4.9990 chunk 160 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 104 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 178 optimal weight: 0.0870 chunk 147 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN ** A1283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15615 Z= 0.158 Angle : 0.563 9.245 21075 Z= 0.297 Chirality : 0.040 0.218 2277 Planarity : 0.004 0.050 2694 Dihedral : 6.814 56.173 2074 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.33 % Favored : 94.57 % Rotamer: Outliers : 4.61 % Allowed : 25.70 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -0.03 (0.20), residues: 1840 helix: 1.30 (0.17), residues: 940 sheet: -0.73 (0.56), residues: 84 loop : -1.57 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 428 HIS 0.004 0.001 HIS B 150 PHE 0.037 0.001 PHE E 387 TYR 0.015 0.001 TYR A1232 ARG 0.005 0.000 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 240 time to evaluate : 1.870 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: A 690 ASN cc_start: 0.7384 (OUTLIER) cc_final: 0.6092 (t0) REVERT: A 912 TRP cc_start: 0.5464 (OUTLIER) cc_final: 0.5071 (t-100) REVERT: A 926 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7382 (mtmt) REVERT: A 986 TYR cc_start: 0.6673 (m-80) cc_final: 0.6373 (m-80) REVERT: A 1325 LYS cc_start: 0.0864 (OUTLIER) cc_final: 0.0357 (tptt) REVERT: E 342 ASN cc_start: 0.6684 (OUTLIER) cc_final: 0.6331 (m110) REVERT: E 389 THR cc_start: 0.4957 (OUTLIER) cc_final: 0.4750 (t) REVERT: E 454 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7154 (ptm160) REVERT: E 490 LYS cc_start: 0.7340 (pttp) cc_final: 0.6637 (mmtm) REVERT: E 556 TYR cc_start: 0.7337 (m-80) cc_final: 0.6870 (m-80) REVERT: B 19 ARG cc_start: 0.6300 (OUTLIER) cc_final: 0.5812 (mtp180) REVERT: B 114 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.6628 (m-30) REVERT: B 352 LYS cc_start: 0.7142 (mtpt) cc_final: 0.6885 (mtpp) REVERT: C 315 LYS cc_start: 0.7760 (tppt) cc_final: 0.7448 (ttmm) REVERT: C 381 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6987 (tpp-160) REVERT: C 394 TYR cc_start: 0.7574 (t80) cc_final: 0.7322 (t80) REVERT: D 290 ASP cc_start: 0.6524 (OUTLIER) cc_final: 0.6189 (p0) REVERT: F 285 LEU cc_start: 0.6970 (mt) cc_final: 0.6746 (pt) outliers start: 79 outliers final: 50 residues processed: 304 average time/residue: 0.2755 time to fit residues: 127.0620 Evaluate side-chains 276 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 215 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LYS Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 342 ASN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 410 ASN Chi-restraints excluded: chain E residue 420 CYS Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 454 ARG Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 288 TYR Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 371 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 108 optimal weight: 0.0000 chunk 81 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN ** A1283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 15615 Z= 0.246 Angle : 0.637 8.937 21075 Z= 0.333 Chirality : 0.043 0.203 2277 Planarity : 0.004 0.053 2694 Dihedral : 6.770 57.015 2059 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.25 % Favored : 93.64 % Rotamer: Outliers : 5.61 % Allowed : 25.58 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -0.18 (0.19), residues: 1840 helix: 1.14 (0.17), residues: 945 sheet: -0.66 (0.57), residues: 84 loop : -1.62 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 236 HIS 0.006 0.001 HIS B 150 PHE 0.034 0.002 PHE E 387 TYR 0.041 0.002 TYR A1016 ARG 0.004 0.000 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 220 time to evaluate : 1.772 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: A 690 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.5488 (t0) REVERT: A 912 TRP cc_start: 0.5662 (OUTLIER) cc_final: 0.5161 (t-100) REVERT: A 926 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7543 (mtmt) REVERT: A 986 TYR cc_start: 0.6736 (m-80) cc_final: 0.6441 (m-80) REVERT: A 1009 ARG cc_start: 0.7615 (tpt-90) cc_final: 0.7286 (ttt90) REVERT: A 1033 LEU cc_start: 0.2319 (OUTLIER) cc_final: 0.2090 (tp) REVERT: A 1136 PHE cc_start: 0.7419 (m-80) cc_final: 0.7180 (m-80) REVERT: A 1300 MET cc_start: 0.5575 (OUTLIER) cc_final: 0.5194 (mmm) REVERT: A 1316 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7503 (t80) REVERT: A 1325 LYS cc_start: 0.0712 (OUTLIER) cc_final: 0.0418 (tptt) REVERT: E 342 ASN cc_start: 0.6891 (OUTLIER) cc_final: 0.6506 (m110) REVERT: E 389 THR cc_start: 0.4938 (OUTLIER) cc_final: 0.4730 (t) REVERT: E 454 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7150 (ptm160) REVERT: E 490 LYS cc_start: 0.7311 (pttp) cc_final: 0.6547 (mmtm) REVERT: E 507 GLU cc_start: 0.6980 (tt0) cc_final: 0.6611 (pm20) REVERT: E 514 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.7156 (t80) REVERT: B 62 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.6008 (mt-10) REVERT: B 114 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6864 (m-30) REVERT: B 128 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7155 (mtm) REVERT: C 241 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7467 (pptt) REVERT: C 296 MET cc_start: 0.6621 (ptp) cc_final: 0.6376 (ptp) REVERT: D 290 ASP cc_start: 0.6640 (OUTLIER) cc_final: 0.6391 (p0) outliers start: 96 outliers final: 64 residues processed: 296 average time/residue: 0.2521 time to fit residues: 113.6201 Evaluate side-chains 290 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 210 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LYS Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1134 SER Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 1316 TYR Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 342 ASN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 371 GLN Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 410 ASN Chi-restraints excluded: chain E residue 420 CYS Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 454 ARG Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 514 TYR Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 288 TYR Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 371 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN ** A1283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 15615 Z= 0.297 Angle : 0.683 13.758 21075 Z= 0.354 Chirality : 0.044 0.204 2277 Planarity : 0.005 0.054 2694 Dihedral : 7.040 62.221 2059 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.74 % Favored : 93.15 % Rotamer: Outliers : 5.55 % Allowed : 26.05 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.19), residues: 1840 helix: 0.99 (0.17), residues: 949 sheet: -0.67 (0.57), residues: 84 loop : -1.68 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 492 HIS 0.005 0.001 HIS B 150 PHE 0.039 0.002 PHE E 567 TYR 0.021 0.002 TYR A1016 ARG 0.005 0.000 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 218 time to evaluate : 1.910 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: A 690 ASN cc_start: 0.7692 (OUTLIER) cc_final: 0.6296 (t0) REVERT: A 863 TYR cc_start: 0.5886 (p90) cc_final: 0.5617 (p90) REVERT: A 912 TRP cc_start: 0.5746 (OUTLIER) cc_final: 0.5187 (t-100) REVERT: A 926 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7507 (mtmt) REVERT: A 986 TYR cc_start: 0.6740 (m-80) cc_final: 0.6374 (m-80) REVERT: A 1136 PHE cc_start: 0.7432 (m-80) cc_final: 0.7205 (m-80) REVERT: A 1316 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7379 (t80) REVERT: E 342 ASN cc_start: 0.7158 (OUTLIER) cc_final: 0.6634 (m110) REVERT: E 454 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7279 (ptm160) REVERT: E 490 LYS cc_start: 0.7271 (pttp) cc_final: 0.6591 (mmtm) REVERT: E 507 GLU cc_start: 0.7019 (tt0) cc_final: 0.6666 (pm20) REVERT: E 514 TYR cc_start: 0.7800 (OUTLIER) cc_final: 0.7434 (t80) REVERT: B 62 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.6018 (mt-10) REVERT: B 114 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.7063 (m-30) REVERT: C 241 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7511 (pptt) REVERT: D 228 LEU cc_start: 0.6858 (mm) cc_final: 0.6558 (mp) REVERT: D 290 ASP cc_start: 0.6749 (OUTLIER) cc_final: 0.6337 (p0) REVERT: F 331 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.7914 (t0) REVERT: F 365 LYS cc_start: 0.5294 (mmmt) cc_final: 0.4455 (ptpt) outliers start: 95 outliers final: 69 residues processed: 297 average time/residue: 0.2648 time to fit residues: 119.0922 Evaluate side-chains 286 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 205 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LYS Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1134 SER Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1316 TYR Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 342 ASN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 371 GLN Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 410 ASN Chi-restraints excluded: chain E residue 420 CYS Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 454 ARG Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 514 TYR Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 371 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 129 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 108 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN ** A1283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 ASN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15615 Z= 0.183 Angle : 0.611 12.546 21075 Z= 0.319 Chirality : 0.042 0.211 2277 Planarity : 0.004 0.051 2694 Dihedral : 6.662 64.212 2057 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.29 % Rotamer: Outliers : 4.09 % Allowed : 27.63 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -0.08 (0.20), residues: 1840 helix: 1.14 (0.17), residues: 961 sheet: -0.45 (0.58), residues: 82 loop : -1.54 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 492 HIS 0.004 0.001 HIS B 150 PHE 0.046 0.002 PHE E 567 TYR 0.027 0.001 TYR A1016 ARG 0.005 0.000 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 220 time to evaluate : 1.921 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: A 690 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.5623 (t0) REVERT: A 912 TRP cc_start: 0.5601 (OUTLIER) cc_final: 0.5141 (t-100) REVERT: A 926 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7145 (mtmt) REVERT: A 986 TYR cc_start: 0.6739 (m-80) cc_final: 0.6413 (m-80) REVERT: A 1136 PHE cc_start: 0.7393 (m-80) cc_final: 0.7176 (m-80) REVERT: E 342 ASN cc_start: 0.7115 (OUTLIER) cc_final: 0.6660 (m110) REVERT: E 454 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7078 (ptm160) REVERT: E 490 LYS cc_start: 0.7244 (pttp) cc_final: 0.6536 (mmtm) REVERT: E 514 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.7297 (t80) REVERT: B 62 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.6100 (mt-10) REVERT: B 114 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6827 (m-30) REVERT: C 241 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7462 (pptt) REVERT: C 368 MET cc_start: 0.5578 (mpp) cc_final: 0.5030 (mmt) REVERT: D 290 ASP cc_start: 0.6589 (OUTLIER) cc_final: 0.6288 (p0) REVERT: F 285 LEU cc_start: 0.7232 (mt) cc_final: 0.6931 (pt) REVERT: F 365 LYS cc_start: 0.4941 (mmmt) cc_final: 0.4407 (ptpp) outliers start: 70 outliers final: 52 residues processed: 276 average time/residue: 0.2522 time to fit residues: 106.1670 Evaluate side-chains 272 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 210 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LYS Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 342 ASN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 420 CYS Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 454 ARG Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 514 TYR Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN F 350 GLN ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15615 Z= 0.203 Angle : 0.632 12.327 21075 Z= 0.328 Chirality : 0.042 0.213 2277 Planarity : 0.004 0.061 2694 Dihedral : 6.553 66.473 2053 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.14 % Favored : 93.80 % Rotamer: Outliers : 4.03 % Allowed : 28.04 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -0.04 (0.20), residues: 1840 helix: 1.13 (0.17), residues: 965 sheet: -0.44 (0.57), residues: 82 loop : -1.47 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 236 HIS 0.004 0.001 HIS B 150 PHE 0.030 0.002 PHE A1026 TYR 0.017 0.001 TYR F 372 ARG 0.010 0.000 ARG A1009 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 217 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 690 ASN cc_start: 0.7561 (OUTLIER) cc_final: 0.5566 (t0) REVERT: A 912 TRP cc_start: 0.5685 (OUTLIER) cc_final: 0.5200 (t-100) REVERT: A 926 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7051 (mtmt) REVERT: A 986 TYR cc_start: 0.6756 (m-80) cc_final: 0.6433 (m-80) REVERT: E 342 ASN cc_start: 0.7063 (OUTLIER) cc_final: 0.6595 (m110) REVERT: E 454 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7030 (ptm160) REVERT: E 490 LYS cc_start: 0.7211 (pttp) cc_final: 0.6508 (mmtm) REVERT: E 507 GLU cc_start: 0.6989 (tt0) cc_final: 0.6591 (pm20) REVERT: E 514 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.7171 (t80) REVERT: B 62 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.6069 (mt-10) REVERT: B 114 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6901 (m-30) REVERT: C 368 MET cc_start: 0.5577 (mpp) cc_final: 0.5114 (mmt) REVERT: D 290 ASP cc_start: 0.6585 (OUTLIER) cc_final: 0.6249 (p0) REVERT: F 285 LEU cc_start: 0.7221 (mt) cc_final: 0.6927 (pt) REVERT: F 365 LYS cc_start: 0.4859 (mmmt) cc_final: 0.4503 (ptpp) outliers start: 69 outliers final: 56 residues processed: 272 average time/residue: 0.2564 time to fit residues: 106.2964 Evaluate side-chains 276 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 211 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LYS Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 342 ASN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 410 ASN Chi-restraints excluded: chain E residue 420 CYS Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 454 ARG Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 514 TYR Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9980 chunk 44 optimal weight: 0.0470 chunk 134 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 146 optimal weight: 0.0020 chunk 61 optimal weight: 4.9990 chunk 150 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 128 optimal weight: 0.0670 overall best weight: 0.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.221731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.181191 restraints weight = 17936.507| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 2.46 r_work: 0.4024 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15615 Z= 0.160 Angle : 0.609 12.198 21075 Z= 0.314 Chirality : 0.041 0.203 2277 Planarity : 0.004 0.051 2694 Dihedral : 6.114 65.985 2053 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.54 % Favored : 94.40 % Rotamer: Outliers : 3.10 % Allowed : 29.38 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 (0.20), residues: 1840 helix: 1.42 (0.17), residues: 954 sheet: -0.21 (0.58), residues: 82 loop : -1.30 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 428 HIS 0.003 0.001 HIS B 150 PHE 0.027 0.001 PHE E 387 TYR 0.021 0.001 TYR A1016 ARG 0.006 0.000 ARG A1009 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3613.80 seconds wall clock time: 65 minutes 30.72 seconds (3930.72 seconds total)