Starting phenix.real_space_refine on Wed Feb 21 11:32:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a94_11684/02_2024/7a94_11684.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a94_11684/02_2024/7a94_11684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a94_11684/02_2024/7a94_11684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a94_11684/02_2024/7a94_11684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a94_11684/02_2024/7a94_11684.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a94_11684/02_2024/7a94_11684.pdb" } resolution = 3.9 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= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 143 5.16 5 C 19433 2.51 5 N 5046 2.21 5 O 5840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A ASP 1146": "OD1" <-> "OD2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 737": "OD1" <-> "OD2" Residue "C TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 936": "OD1" <-> "OD2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "C ASP 1146": "OD1" <-> "OD2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 295": "OD1" <-> "OD2" Residue "D GLU 312": "OE1" <-> "OE2" Residue "D PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D ASP 335": "OD1" <-> "OD2" Residue "D PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ASP 367": "OD1" <-> "OD2" Residue "D ASP 368": "OD1" <-> "OD2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D GLU 433": "OE1" <-> "OE2" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 509": "OD1" <-> "OD2" Residue "D TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "D PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 589": "OE1" <-> "OE2" Residue "D ASP 609": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30463 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8456 Classifications: {'peptide': 1080} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1025} Chain breaks: 5 Chain: "B" Number of atoms: 8445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8445 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 54, 'TRANS': 1024} Chain breaks: 5 Chain: "C" Number of atoms: 8438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8438 Classifications: {'peptide': 1078} Link IDs: {'PTRANS': 54, 'TRANS': 1023} Chain breaks: 5 Chain: "D" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.27, per 1000 atoms: 0.53 Number of scatterers: 30463 At special positions: 0 Unit cell: (147.686, 160.622, 247.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 143 16.00 O 5840 8.00 N 5046 7.00 C 19433 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 717 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B1134 " " NAG C1301 " - " ASN C 165 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " Time building additional restraints: 11.59 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 901 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 378 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 374 " 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7172 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 56 sheets defined 32.2% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 340 through 344 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.955A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.173A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.212A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 4.127A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.737A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.880A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 4.612A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.560A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.269A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.692A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 992 through 1033 removed outlier: 3.711A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.760A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.597A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.381A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.051A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.515A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.432A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.298A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.582A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.520A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 removed outlier: 4.470A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.673A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.352A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.712A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B1009 " --> pdb=" O GLN B1005 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG B1014 " --> pdb=" O GLN B1010 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 Processing helix chain 'C' and resid 147 through 150 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.532A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.649A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 624 Proline residue: C 621 - end of helix removed outlier: 4.099A pdb=" N ILE C 624 " --> pdb=" O PRO C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.550A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.645A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.204A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.702A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 4.277A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.713A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 938 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.113A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.568A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C1004 " --> pdb=" O ARG C1000 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN C1023 " --> pdb=" O ARG C1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.886A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 81 removed outlier: 3.530A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.696A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 Proline residue: D 178 - end of helix removed outlier: 4.064A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.648A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 223 Processing helix chain 'D' and resid 225 through 249 removed outlier: 3.592A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 304 through 319 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.909A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.564A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 414 removed outlier: 3.786A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 412 " --> pdb=" O MET D 408 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.670A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.133A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 4.403A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.628A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.667A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.904A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 600 removed outlier: 4.367A pdb=" N LYS D 600 " --> pdb=" O LYS D 596 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 9.206A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 10.104A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.857A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.274A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 5.951A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.193A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.539A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.527A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.133A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.133A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.943A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.170A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.752A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.636A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.613A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.921A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC6, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.726A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.174A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS B 146 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.144A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 13.241A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 13.756A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 11.521A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 11.976A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS B 146 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AD1, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AD2, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.383A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.315A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL B 395 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER B 514 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA B 397 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL B 512 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER B 399 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL B 510 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL B 401 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR B 508 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.714A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.240A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.786A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.420A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.513A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE4, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.724A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.950A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.775A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.385A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.568A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 609 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 357 removed outlier: 6.732A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 357 removed outlier: 5.082A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.113A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.724A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.752A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.598A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AG1, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.397A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'D' and resid 347 through 352 removed outlier: 5.395A pdb=" N ALA D 348 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU D 359 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASP D 350 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG D 357 " --> pdb=" O ASP D 350 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY D 352 " --> pdb=" O ASP D 355 " (cutoff:3.500A) 1245 hydrogen bonds defined for protein. 3378 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: 14.48 Time building geometry restraints manager: 12.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9782 1.34 - 1.47: 7854 1.47 - 1.59: 13360 1.59 - 1.72: 0 1.72 - 1.84: 194 Bond restraints: 31190 Sorted by residual: bond pdb=" N VAL C 615 " pdb=" CA VAL C 615 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.08e-02 8.57e+03 1.30e+01 bond pdb=" N ASN A 343 " pdb=" CA ASN A 343 " ideal model delta sigma weight residual 1.458 1.489 -0.031 9.00e-03 1.23e+04 1.20e+01 bond pdb=" N HIS D 345 " pdb=" CA HIS D 345 " ideal model delta sigma weight residual 1.455 1.487 -0.032 9.60e-03 1.09e+04 1.14e+01 bond pdb=" N VAL B1133 " pdb=" CA VAL B1133 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.01e+01 bond pdb=" N VAL C1133 " pdb=" CA VAL C1133 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.18e-02 7.18e+03 9.65e+00 ... (remaining 31185 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.09: 749 106.09 - 113.09: 16698 113.09 - 120.10: 11120 120.10 - 127.10: 13542 127.10 - 134.10: 330 Bond angle restraints: 42439 Sorted by residual: angle pdb=" CA HIS D 345 " pdb=" C HIS D 345 " pdb=" N PRO D 346 " ideal model delta sigma weight residual 117.95 121.94 -3.99 7.70e-01 1.69e+00 2.69e+01 angle pdb=" C ASN A 282 " pdb=" CA ASN A 282 " pdb=" CB ASN A 282 " ideal model delta sigma weight residual 111.13 117.45 -6.32 1.61e+00 3.86e-01 1.54e+01 angle pdb=" N PRO B 589 " pdb=" CA PRO B 589 " pdb=" C PRO B 589 " ideal model delta sigma weight residual 112.47 104.39 8.08 2.06e+00 2.36e-01 1.54e+01 angle pdb=" CA HIS D 345 " pdb=" C HIS D 345 " pdb=" O HIS D 345 " ideal model delta sigma weight residual 120.34 116.77 3.57 9.20e-01 1.18e+00 1.51e+01 angle pdb=" C GLN C 613 " pdb=" N ASP C 614 " pdb=" CA ASP C 614 " ideal model delta sigma weight residual 123.03 117.90 5.13 1.34e+00 5.57e-01 1.46e+01 ... (remaining 42434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17445 17.92 - 35.84: 1095 35.84 - 53.76: 206 53.76 - 71.68: 66 71.68 - 89.60: 37 Dihedral angle restraints: 18849 sinusoidal: 7700 harmonic: 11149 Sorted by residual: dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -141.74 55.74 1 1.00e+01 1.00e-02 4.20e+01 dihedral pdb=" CA GLU A 96 " pdb=" C GLU A 96 " pdb=" N LYS A 97 " pdb=" CA LYS A 97 " ideal model delta harmonic sigma weight residual 180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA PRO A 589 " pdb=" C PRO A 589 " pdb=" N CYS A 590 " pdb=" CA CYS A 590 " ideal model delta harmonic sigma weight residual -180.00 -151.03 -28.97 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 18846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4319 0.089 - 0.179: 464 0.179 - 0.268: 19 0.268 - 0.358: 5 0.358 - 0.447: 3 Chirality restraints: 4810 Sorted by residual: chirality pdb=" CA CYS B 590 " pdb=" N CYS B 590 " pdb=" C CYS B 590 " pdb=" CB CYS B 590 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CA ASN A 282 " pdb=" N ASN A 282 " pdb=" C ASN A 282 " pdb=" CB ASN A 282 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.64e+00 ... (remaining 4807 not shown) Planarity restraints: 5491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1302 " -0.335 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG B1302 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B1302 " -0.177 2.00e-02 2.50e+03 pdb=" N2 NAG B1302 " 0.500 2.00e-02 2.50e+03 pdb=" O7 NAG B1302 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1303 " -0.322 2.00e-02 2.50e+03 2.79e-01 9.76e+02 pdb=" C7 NAG A1303 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A1303 " -0.131 2.00e-02 2.50e+03 pdb=" N2 NAG A1303 " 0.500 2.00e-02 2.50e+03 pdb=" O7 NAG A1303 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1302 " 0.283 2.00e-02 2.50e+03 2.44e-01 7.42e+02 pdb=" C7 NAG A1302 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG A1302 " 0.164 2.00e-02 2.50e+03 pdb=" N2 NAG A1302 " -0.427 2.00e-02 2.50e+03 pdb=" O7 NAG A1302 " 0.049 2.00e-02 2.50e+03 ... (remaining 5488 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 422 2.65 - 3.21: 29968 3.21 - 3.77: 45794 3.77 - 4.34: 63884 4.34 - 4.90: 103237 Nonbonded interactions: 243305 Sorted by model distance: nonbonded pdb=" O TRP A 353 " pdb=" NH1 ARG A 466 " model vdw 2.085 2.520 nonbonded pdb=" OD1 ASN D 90 " pdb=" OG1 THR D 92 " model vdw 2.091 2.440 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.126 2.440 nonbonded pdb=" OD1 ASP D 382 " pdb=" OH TYR D 385 " model vdw 2.153 2.440 nonbonded pdb=" OD1 ASN A 777 " pdb=" NH1 ARG A1019 " model vdw 2.214 2.520 ... (remaining 243300 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 826 or resid 855 through 1146 or resid 1301 thr \ ough 1306)) selection = (chain 'B' and (resid 14 through 624 or resid 633 through 826 or resid 855 throu \ gh 1146 or resid 1301 through 1306)) selection = (chain 'C' and (resid 14 through 624 or resid 633 through 1146 or resid 1301 thr \ ough 1306)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 29.140 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 88.220 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.150 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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 : 0.007 0.054 31190 Z= 0.440 Angle : 0.869 9.928 42439 Z= 0.502 Chirality : 0.055 0.447 4810 Planarity : 0.011 0.285 5468 Dihedral : 13.402 89.597 11542 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.87 % Allowed : 4.57 % Favored : 94.57 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.12), residues: 3785 helix: -1.71 (0.14), residues: 988 sheet: 0.49 (0.18), residues: 725 loop : -1.58 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 886 HIS 0.011 0.002 HIS B1101 PHE 0.045 0.003 PHE A 486 TYR 0.035 0.005 TYR D 207 ARG 0.096 0.011 ARG D 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 3.549 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 110 LEU cc_start: 0.8374 (mt) cc_final: 0.7916 (mt) REVERT: A 215 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8305 (t0) REVERT: A 231 ILE cc_start: 0.7678 (mm) cc_final: 0.7453 (mm) REVERT: A 387 LEU cc_start: 0.9283 (mt) cc_final: 0.9082 (mt) REVERT: A 508 TYR cc_start: 0.8873 (m-80) cc_final: 0.8218 (m-80) REVERT: A 740 MET cc_start: 0.8848 (ttm) cc_final: 0.8551 (ttt) REVERT: A 1017 GLU cc_start: 0.8405 (pp20) cc_final: 0.8086 (tm-30) REVERT: B 79 PHE cc_start: 0.8054 (t80) cc_final: 0.7721 (t80) REVERT: B 133 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7306 (m-80) REVERT: B 633 TRP cc_start: 0.8378 (OUTLIER) cc_final: 0.8138 (m-90) REVERT: B 869 MET cc_start: 0.9058 (mtt) cc_final: 0.8856 (mtm) REVERT: B 1050 MET cc_start: 0.8687 (ptp) cc_final: 0.8432 (ptp) REVERT: C 273 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7458 (tpp80) REVERT: C 489 TYR cc_start: 0.8439 (m-80) cc_final: 0.8075 (m-80) REVERT: C 505 TYR cc_start: 0.9588 (m-80) cc_final: 0.9081 (t80) REVERT: D 62 MET cc_start: 0.8777 (ttp) cc_final: 0.8478 (ttp) REVERT: D 270 MET cc_start: 0.3121 (ptm) cc_final: 0.2441 (tmm) REVERT: D 408 MET cc_start: 0.9204 (mpp) cc_final: 0.8509 (tpt) REVERT: D 455 MET cc_start: 0.7416 (tpt) cc_final: 0.5702 (tpt) REVERT: D 480 MET cc_start: 0.7059 (mmp) cc_final: 0.6405 (ptt) REVERT: D 516 TYR cc_start: 0.9274 (t80) cc_final: 0.8964 (t80) outliers start: 29 outliers final: 8 residues processed: 192 average time/residue: 0.3743 time to fit residues: 123.9313 Evaluate side-chains 109 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 3.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 385 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 0.6980 chunk 288 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 297 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 181 optimal weight: 0.5980 chunk 221 optimal weight: 8.9990 chunk 345 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN A1023 ASN B 137 ASN B 544 ASN B 764 ASN B 955 ASN B1002 GLN C 87 ASN C 125 ASN C 271 GLN C 544 ASN C 641 ASN D 58 ASN D 330 ASN D 442 GLN D 522 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31190 Z= 0.199 Angle : 0.640 9.363 42439 Z= 0.340 Chirality : 0.045 0.223 4810 Planarity : 0.004 0.048 5468 Dihedral : 6.658 59.886 4614 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.06 % Favored : 96.88 % Rotamer: Outliers : 1.13 % Allowed : 6.89 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % 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: -0.77 (0.13), residues: 3785 helix: -0.05 (0.16), residues: 1005 sheet: 0.44 (0.18), residues: 756 loop : -1.12 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 633 HIS 0.006 0.001 HIS D 505 PHE 0.024 0.002 PHE B 133 TYR 0.017 0.001 TYR A1067 ARG 0.008 0.001 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 114 time to evaluate : 3.714 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 106 PHE cc_start: 0.8515 (m-80) cc_final: 0.8220 (m-80) REVERT: A 215 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8317 (t0) REVERT: A 231 ILE cc_start: 0.7507 (mm) cc_final: 0.7279 (mm) REVERT: A 508 TYR cc_start: 0.8739 (m-80) cc_final: 0.8109 (m-80) REVERT: A 740 MET cc_start: 0.8874 (ttm) cc_final: 0.8637 (ttt) REVERT: A 1017 GLU cc_start: 0.8373 (pp20) cc_final: 0.8161 (tm-30) REVERT: B 79 PHE cc_start: 0.7714 (t80) cc_final: 0.7202 (t80) REVERT: B 133 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7158 (m-80) REVERT: B 633 TRP cc_start: 0.8198 (OUTLIER) cc_final: 0.7762 (m-90) REVERT: B 1050 MET cc_start: 0.8551 (ptp) cc_final: 0.8238 (ptp) REVERT: C 118 LEU cc_start: 0.9492 (tp) cc_final: 0.9187 (mt) REVERT: C 135 PHE cc_start: 0.8178 (m-80) cc_final: 0.7975 (m-80) REVERT: C 238 PHE cc_start: 0.8308 (p90) cc_final: 0.7921 (p90) REVERT: C 273 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7264 (tpp80) REVERT: C 392 PHE cc_start: 0.9133 (m-80) cc_final: 0.8747 (m-10) REVERT: C 489 TYR cc_start: 0.8214 (m-80) cc_final: 0.7932 (m-80) REVERT: C 505 TYR cc_start: 0.9590 (m-80) cc_final: 0.9078 (t80) REVERT: D 249 MET cc_start: 0.6721 (mmm) cc_final: 0.6504 (tpt) REVERT: D 270 MET cc_start: 0.2455 (ptm) cc_final: 0.2254 (tmm) REVERT: D 323 MET cc_start: 0.7847 (ttp) cc_final: 0.7453 (tmm) REVERT: D 408 MET cc_start: 0.9222 (mpp) cc_final: 0.8580 (tpt) REVERT: D 455 MET cc_start: 0.7280 (tpt) cc_final: 0.5875 (tpt) REVERT: D 480 MET cc_start: 0.6883 (mmp) cc_final: 0.6389 (ptt) outliers start: 38 outliers final: 20 residues processed: 142 average time/residue: 0.3878 time to fit residues: 95.8158 Evaluate side-chains 120 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 3.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 156 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 1.9990 chunk 107 optimal weight: 0.0040 chunk 287 optimal weight: 0.9980 chunk 234 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 345 optimal weight: 0.9990 chunk 373 optimal weight: 20.0000 chunk 307 optimal weight: 2.9990 chunk 342 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 277 optimal weight: 0.9980 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A1002 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 895 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN D 524 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31190 Z= 0.218 Angle : 0.580 12.645 42439 Z= 0.304 Chirality : 0.043 0.197 4810 Planarity : 0.004 0.045 5468 Dihedral : 6.043 56.286 4610 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.49 % Allowed : 7.88 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % 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: -0.45 (0.13), residues: 3785 helix: 0.55 (0.17), residues: 1002 sheet: 0.46 (0.18), residues: 763 loop : -1.03 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 633 HIS 0.005 0.001 HIS D 505 PHE 0.023 0.001 PHE C 338 TYR 0.036 0.001 TYR C 365 ARG 0.005 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 102 time to evaluate : 3.718 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 106 PHE cc_start: 0.8423 (m-80) cc_final: 0.8121 (m-80) REVERT: A 1017 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8113 (tm-30) REVERT: B 633 TRP cc_start: 0.8158 (OUTLIER) cc_final: 0.7700 (m-90) REVERT: C 238 PHE cc_start: 0.8331 (p90) cc_final: 0.7961 (p90) REVERT: C 489 TYR cc_start: 0.8246 (m-80) cc_final: 0.7977 (m-80) REVERT: C 505 TYR cc_start: 0.9606 (m-80) cc_final: 0.9102 (t80) REVERT: D 62 MET cc_start: 0.8947 (ttp) cc_final: 0.8707 (ptt) REVERT: D 270 MET cc_start: 0.2843 (ptm) cc_final: 0.2258 (tmm) REVERT: D 455 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6586 (tpt) REVERT: D 480 MET cc_start: 0.6834 (mmp) cc_final: 0.6441 (ptt) REVERT: D 516 TYR cc_start: 0.9275 (t80) cc_final: 0.8692 (m-80) outliers start: 50 outliers final: 25 residues processed: 139 average time/residue: 0.4053 time to fit residues: 99.9681 Evaluate side-chains 122 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 4.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 455 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 8.9990 chunk 259 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 346 optimal weight: 30.0000 chunk 367 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 328 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B1005 GLN B1083 HIS C 146 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 31190 Z= 0.353 Angle : 0.629 10.221 42439 Z= 0.327 Chirality : 0.044 0.195 4810 Planarity : 0.004 0.048 5468 Dihedral : 5.919 56.943 4605 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.67 % Allowed : 8.62 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.13), residues: 3785 helix: 0.72 (0.17), residues: 994 sheet: 0.20 (0.17), residues: 789 loop : -1.08 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 633 HIS 0.010 0.001 HIS C 146 PHE 0.016 0.002 PHE B 92 TYR 0.025 0.002 TYR A1067 ARG 0.003 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 94 time to evaluate : 3.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.8419 (m-80) cc_final: 0.8208 (m-80) REVERT: A 338 PHE cc_start: 0.8327 (t80) cc_final: 0.8045 (m-80) REVERT: A 387 LEU cc_start: 0.9301 (mm) cc_final: 0.9070 (mm) REVERT: A 1017 GLU cc_start: 0.8481 (pp20) cc_final: 0.8189 (tm-30) REVERT: B 177 MET cc_start: 0.8341 (mmm) cc_final: 0.7291 (mpp) REVERT: B 633 TRP cc_start: 0.8226 (OUTLIER) cc_final: 0.7933 (m-90) REVERT: C 195 LYS cc_start: 0.8776 (mtmt) cc_final: 0.8412 (mtmt) REVERT: C 238 PHE cc_start: 0.8339 (p90) cc_final: 0.8003 (p90) REVERT: C 275 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8735 (m-10) REVERT: C 505 TYR cc_start: 0.9635 (m-80) cc_final: 0.9165 (t80) REVERT: C 633 TRP cc_start: 0.7346 (OUTLIER) cc_final: 0.6698 (p-90) REVERT: C 736 VAL cc_start: 0.9508 (OUTLIER) cc_final: 0.9183 (m) REVERT: D 62 MET cc_start: 0.9011 (ttp) cc_final: 0.8759 (ptt) REVERT: D 270 MET cc_start: 0.2591 (ptm) cc_final: 0.2022 (tmm) REVERT: D 455 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6069 (tpt) REVERT: D 462 MET cc_start: 0.8347 (mpp) cc_final: 0.7822 (ptp) REVERT: D 480 MET cc_start: 0.7012 (mmp) cc_final: 0.6509 (ptt) REVERT: D 516 TYR cc_start: 0.9267 (t80) cc_final: 0.8635 (m-80) outliers start: 56 outliers final: 28 residues processed: 141 average time/residue: 0.3651 time to fit residues: 92.7061 Evaluate side-chains 123 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 90 time to evaluate : 3.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 455 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 0.5980 chunk 208 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 273 optimal weight: 0.7980 chunk 151 optimal weight: 7.9990 chunk 313 optimal weight: 0.8980 chunk 253 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 187 optimal weight: 0.0060 chunk 329 optimal weight: 7.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 31190 Z= 0.155 Angle : 0.543 11.608 42439 Z= 0.281 Chirality : 0.042 0.195 4810 Planarity : 0.004 0.046 5468 Dihedral : 5.535 56.427 4601 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.31 % Allowed : 9.73 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % 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 (0.14), residues: 3785 helix: 1.00 (0.17), residues: 993 sheet: 0.32 (0.18), residues: 761 loop : -1.02 (0.14), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 633 HIS 0.004 0.001 HIS A1048 PHE 0.023 0.001 PHE B 133 TYR 0.016 0.001 TYR A1067 ARG 0.004 0.000 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 100 time to evaluate : 4.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.8421 (m-80) cc_final: 0.8177 (m-80) REVERT: A 338 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: A 387 LEU cc_start: 0.9172 (mm) cc_final: 0.8882 (mm) REVERT: A 1017 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8174 (tm-30) REVERT: B 105 ILE cc_start: 0.9152 (mm) cc_final: 0.8925 (mm) REVERT: B 177 MET cc_start: 0.8339 (mmm) cc_final: 0.7329 (mpp) REVERT: B 633 TRP cc_start: 0.8191 (OUTLIER) cc_final: 0.7659 (m-90) REVERT: B 1101 HIS cc_start: 0.6154 (OUTLIER) cc_final: 0.4668 (m90) REVERT: C 104 TRP cc_start: 0.8985 (m-90) cc_final: 0.8702 (m-90) REVERT: C 195 LYS cc_start: 0.8757 (mtmt) cc_final: 0.8472 (mtmt) REVERT: C 238 PHE cc_start: 0.8254 (p90) cc_final: 0.7934 (p90) REVERT: C 275 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8723 (m-10) REVERT: C 505 TYR cc_start: 0.9638 (m-80) cc_final: 0.9166 (t80) REVERT: C 633 TRP cc_start: 0.7218 (OUTLIER) cc_final: 0.6446 (p-90) REVERT: C 736 VAL cc_start: 0.9518 (OUTLIER) cc_final: 0.9194 (m) REVERT: C 936 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7228 (p0) REVERT: D 62 MET cc_start: 0.9024 (ttp) cc_final: 0.8765 (ptt) REVERT: D 123 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.6905 (ptt) REVERT: D 270 MET cc_start: 0.2550 (ptm) cc_final: 0.1933 (tpp) REVERT: D 455 MET cc_start: 0.7291 (tpt) cc_final: 0.6262 (tpt) REVERT: D 480 MET cc_start: 0.7032 (mmp) cc_final: 0.6574 (ptt) REVERT: D 516 TYR cc_start: 0.9218 (t80) cc_final: 0.8594 (m-80) outliers start: 44 outliers final: 27 residues processed: 135 average time/residue: 0.3627 time to fit residues: 87.3418 Evaluate side-chains 131 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 95 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 1.9990 chunk 330 optimal weight: 0.0770 chunk 72 optimal weight: 2.9990 chunk 215 optimal weight: 20.0000 chunk 90 optimal weight: 0.0370 chunk 367 optimal weight: 7.9990 chunk 305 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN C 487 ASN D 34 HIS D 305 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 31190 Z= 0.310 Angle : 0.592 11.376 42439 Z= 0.306 Chirality : 0.043 0.203 4810 Planarity : 0.004 0.046 5468 Dihedral : 5.511 58.874 4601 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.76 % Allowed : 9.94 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % 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: -0.35 (0.13), residues: 3785 helix: 1.06 (0.17), residues: 988 sheet: 0.20 (0.18), residues: 797 loop : -1.09 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 633 HIS 0.005 0.001 HIS B1064 PHE 0.019 0.002 PHE B 133 TYR 0.022 0.001 TYR A1067 ARG 0.003 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 94 time to evaluate : 3.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.5867 (mm) REVERT: A 106 PHE cc_start: 0.8421 (m-80) cc_final: 0.8110 (m-10) REVERT: A 177 MET cc_start: 0.4880 (mtt) cc_final: 0.2945 (mpp) REVERT: A 215 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8279 (t0) REVERT: A 387 LEU cc_start: 0.9252 (mm) cc_final: 0.8942 (mm) REVERT: A 441 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8912 (pp) REVERT: A 508 TYR cc_start: 0.8707 (m-80) cc_final: 0.8195 (m-80) REVERT: A 1017 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8235 (tm-30) REVERT: B 633 TRP cc_start: 0.8215 (OUTLIER) cc_final: 0.7895 (m-90) REVERT: B 1101 HIS cc_start: 0.6573 (OUTLIER) cc_final: 0.5263 (m90) REVERT: C 195 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8446 (mtmt) REVERT: C 238 PHE cc_start: 0.8278 (p90) cc_final: 0.8017 (p90) REVERT: C 275 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8719 (m-10) REVERT: C 505 TYR cc_start: 0.9640 (m-80) cc_final: 0.9178 (t80) REVERT: C 633 TRP cc_start: 0.7329 (OUTLIER) cc_final: 0.7050 (p90) REVERT: C 736 VAL cc_start: 0.9527 (OUTLIER) cc_final: 0.9218 (m) REVERT: D 62 MET cc_start: 0.9039 (ttp) cc_final: 0.8794 (ptt) REVERT: D 123 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.6990 (ptt) REVERT: D 249 MET cc_start: 0.5980 (tpt) cc_final: 0.5584 (mmt) REVERT: D 270 MET cc_start: 0.2579 (ptm) cc_final: 0.1953 (tpp) REVERT: D 455 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6626 (tpt) REVERT: D 480 MET cc_start: 0.7016 (mmp) cc_final: 0.6565 (ptt) REVERT: D 516 TYR cc_start: 0.9252 (t80) cc_final: 0.8662 (m-80) outliers start: 59 outliers final: 40 residues processed: 141 average time/residue: 0.3574 time to fit residues: 89.2777 Evaluate side-chains 142 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 91 time to evaluate : 3.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 268 optimal weight: 6.9990 chunk 208 optimal weight: 0.8980 chunk 309 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 366 optimal weight: 0.0370 chunk 229 optimal weight: 4.9990 chunk 223 optimal weight: 9.9990 chunk 169 optimal weight: 0.0570 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31190 Z= 0.166 Angle : 0.524 10.376 42439 Z= 0.270 Chirality : 0.042 0.197 4810 Planarity : 0.004 0.045 5468 Dihedral : 5.226 59.310 4601 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.82 % Allowed : 10.33 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % 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: -0.20 (0.14), residues: 3785 helix: 1.25 (0.17), residues: 993 sheet: 0.28 (0.18), residues: 787 loop : -1.02 (0.14), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 633 HIS 0.004 0.001 HIS A1048 PHE 0.018 0.001 PHE B 133 TYR 0.018 0.001 TYR B1067 ARG 0.003 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 96 time to evaluate : 3.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.5929 (mm) REVERT: A 118 LEU cc_start: 0.9413 (tt) cc_final: 0.9193 (tt) REVERT: A 177 MET cc_start: 0.4912 (mtt) cc_final: 0.4642 (mtt) REVERT: A 215 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8280 (t0) REVERT: A 387 LEU cc_start: 0.9193 (mm) cc_final: 0.8673 (mm) REVERT: A 441 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8887 (pp) REVERT: A 979 ASP cc_start: 0.8775 (m-30) cc_final: 0.8383 (p0) REVERT: A 1017 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8260 (tm-30) REVERT: A 1084 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8375 (p0) REVERT: B 633 TRP cc_start: 0.8179 (OUTLIER) cc_final: 0.7642 (m-90) REVERT: B 1101 HIS cc_start: 0.6311 (OUTLIER) cc_final: 0.5135 (m90) REVERT: C 195 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8446 (mtmt) REVERT: C 238 PHE cc_start: 0.8236 (p90) cc_final: 0.7971 (p90) REVERT: C 275 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8640 (m-10) REVERT: C 505 TYR cc_start: 0.9648 (m-80) cc_final: 0.9207 (t80) REVERT: C 633 TRP cc_start: 0.7285 (OUTLIER) cc_final: 0.6376 (p-90) REVERT: C 736 VAL cc_start: 0.9538 (OUTLIER) cc_final: 0.9184 (m) REVERT: D 62 MET cc_start: 0.9062 (ttp) cc_final: 0.8793 (ptt) REVERT: D 123 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7016 (ptt) REVERT: D 249 MET cc_start: 0.6070 (tpt) cc_final: 0.5685 (mmt) REVERT: D 270 MET cc_start: 0.2529 (ptm) cc_final: 0.1916 (tpp) REVERT: D 455 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6636 (tpt) REVERT: D 480 MET cc_start: 0.7056 (mmp) cc_final: 0.6711 (ptt) REVERT: D 516 TYR cc_start: 0.9262 (t80) cc_final: 0.8674 (m-80) outliers start: 61 outliers final: 36 residues processed: 147 average time/residue: 0.3557 time to fit residues: 93.5341 Evaluate side-chains 138 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 90 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 249 optimal weight: 7.9990 chunk 181 optimal weight: 0.5980 chunk 34 optimal weight: 9.9990 chunk 287 optimal weight: 0.9980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A1048 HIS A1088 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 751 ASN C 196 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 31190 Z= 0.348 Angle : 0.602 11.302 42439 Z= 0.311 Chirality : 0.043 0.210 4810 Planarity : 0.004 0.045 5468 Dihedral : 5.369 57.402 4601 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.94 % Allowed : 10.44 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % 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: -0.31 (0.14), residues: 3785 helix: 1.20 (0.17), residues: 987 sheet: 0.18 (0.18), residues: 775 loop : -1.09 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 633 HIS 0.005 0.001 HIS B1064 PHE 0.029 0.002 PHE A 106 TYR 0.019 0.001 TYR A 904 ARG 0.007 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 93 time to evaluate : 3.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6020 (mm) REVERT: A 106 PHE cc_start: 0.8819 (m-10) cc_final: 0.8190 (m-80) REVERT: A 177 MET cc_start: 0.5150 (mtt) cc_final: 0.3318 (mtt) REVERT: A 215 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8191 (t0) REVERT: A 387 LEU cc_start: 0.9254 (mm) cc_final: 0.8736 (mm) REVERT: A 441 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8850 (pp) REVERT: A 508 TYR cc_start: 0.8650 (m-80) cc_final: 0.8032 (m-10) REVERT: A 823 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8380 (m-10) REVERT: A 1017 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8280 (tm-30) REVERT: B 1101 HIS cc_start: 0.6639 (OUTLIER) cc_final: 0.5470 (m90) REVERT: C 195 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8371 (mtmt) REVERT: C 238 PHE cc_start: 0.8278 (p90) cc_final: 0.8013 (p90) REVERT: C 275 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8708 (m-10) REVERT: C 505 TYR cc_start: 0.9652 (m-80) cc_final: 0.9227 (t80) REVERT: C 633 TRP cc_start: 0.7456 (OUTLIER) cc_final: 0.6468 (p-90) REVERT: C 736 VAL cc_start: 0.9541 (OUTLIER) cc_final: 0.9256 (m) REVERT: D 62 MET cc_start: 0.9091 (ttp) cc_final: 0.8818 (ptt) REVERT: D 123 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7191 (ptt) REVERT: D 249 MET cc_start: 0.6120 (tpt) cc_final: 0.5728 (mmt) REVERT: D 270 MET cc_start: 0.2590 (ptm) cc_final: 0.1952 (tpp) REVERT: D 376 MET cc_start: 0.9088 (tpt) cc_final: 0.8289 (ptm) REVERT: D 455 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6277 (tpt) REVERT: D 462 MET cc_start: 0.8360 (pmm) cc_final: 0.7993 (pmm) REVERT: D 480 MET cc_start: 0.7119 (mmp) cc_final: 0.6711 (ptt) REVERT: D 516 TYR cc_start: 0.9279 (t80) cc_final: 0.8673 (m-80) outliers start: 65 outliers final: 48 residues processed: 145 average time/residue: 0.3761 time to fit residues: 97.2155 Evaluate side-chains 150 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 91 time to evaluate : 3.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 30.0000 chunk 350 optimal weight: 10.0000 chunk 320 optimal weight: 0.1980 chunk 341 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 268 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 308 optimal weight: 0.6980 chunk 322 optimal weight: 9.9990 chunk 340 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 644 GLN C 196 ASN D 522 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 31190 Z= 0.316 Angle : 0.591 10.767 42439 Z= 0.304 Chirality : 0.043 0.215 4810 Planarity : 0.004 0.045 5468 Dihedral : 5.371 58.340 4599 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.85 % Allowed : 10.71 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % 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: -0.35 (0.14), residues: 3785 helix: 1.21 (0.17), residues: 978 sheet: 0.13 (0.18), residues: 781 loop : -1.12 (0.14), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 633 HIS 0.005 0.001 HIS D 378 PHE 0.022 0.002 PHE B 133 TYR 0.020 0.001 TYR A1067 ARG 0.004 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 90 time to evaluate : 3.579 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 24 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6090 (mm) REVERT: A 106 PHE cc_start: 0.8848 (m-10) cc_final: 0.8136 (m-80) REVERT: A 177 MET cc_start: 0.5170 (mtt) cc_final: 0.3249 (mtt) REVERT: A 215 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8145 (t0) REVERT: A 387 LEU cc_start: 0.9240 (mm) cc_final: 0.8905 (mm) REVERT: A 441 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8847 (pp) REVERT: A 508 TYR cc_start: 0.8679 (m-80) cc_final: 0.8032 (m-10) REVERT: A 823 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8409 (m-10) REVERT: A 1017 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8261 (tm-30) REVERT: B 1101 HIS cc_start: 0.6964 (OUTLIER) cc_final: 0.5862 (m90) REVERT: C 195 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8362 (mtmt) REVERT: C 238 PHE cc_start: 0.8288 (p90) cc_final: 0.8022 (p90) REVERT: C 275 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8598 (m-10) REVERT: C 505 TYR cc_start: 0.9637 (m-80) cc_final: 0.9203 (t80) REVERT: C 633 TRP cc_start: 0.7450 (OUTLIER) cc_final: 0.6400 (p-90) REVERT: C 736 VAL cc_start: 0.9562 (OUTLIER) cc_final: 0.9293 (m) REVERT: D 62 MET cc_start: 0.9150 (ttp) cc_final: 0.8887 (ptt) REVERT: D 123 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7242 (ptt) REVERT: D 249 MET cc_start: 0.6308 (tpt) cc_final: 0.5928 (mmt) REVERT: D 270 MET cc_start: 0.2591 (ptm) cc_final: 0.1965 (tpp) REVERT: D 376 MET cc_start: 0.9200 (tpt) cc_final: 0.8433 (ptm) REVERT: D 462 MET cc_start: 0.8316 (pmm) cc_final: 0.7922 (pmm) REVERT: D 516 TYR cc_start: 0.9254 (t80) cc_final: 0.8642 (m-80) outliers start: 62 outliers final: 45 residues processed: 139 average time/residue: 0.3642 time to fit residues: 89.7532 Evaluate side-chains 144 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 89 time to evaluate : 3.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 3.9990 chunk 360 optimal weight: 20.0000 chunk 220 optimal weight: 4.9990 chunk 171 optimal weight: 0.0670 chunk 250 optimal weight: 0.0870 chunk 378 optimal weight: 10.0000 chunk 348 optimal weight: 0.0980 chunk 301 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A1064 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN D 522 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 31190 Z= 0.132 Angle : 0.527 11.279 42439 Z= 0.269 Chirality : 0.042 0.194 4810 Planarity : 0.004 0.046 5468 Dihedral : 4.995 59.049 4599 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.34 % Allowed : 11.34 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % 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: -0.10 (0.14), residues: 3785 helix: 1.44 (0.17), residues: 985 sheet: 0.27 (0.18), residues: 765 loop : -0.97 (0.14), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 459 HIS 0.022 0.001 HIS A1083 PHE 0.022 0.001 PHE D 400 TYR 0.017 0.001 TYR B1067 ARG 0.003 0.000 ARG B1039 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 94 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6016 (mm) REVERT: A 106 PHE cc_start: 0.8742 (m-10) cc_final: 0.8033 (m-80) REVERT: A 177 MET cc_start: 0.4814 (mtt) cc_final: 0.2897 (mtt) REVERT: A 215 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8170 (t0) REVERT: A 387 LEU cc_start: 0.9125 (mm) cc_final: 0.8554 (mm) REVERT: A 441 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8825 (pp) REVERT: A 508 TYR cc_start: 0.8622 (m-80) cc_final: 0.7907 (m-10) REVERT: A 823 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8486 (m-10) REVERT: A 1017 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8325 (tm-30) REVERT: C 195 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8462 (mtmt) REVERT: C 238 PHE cc_start: 0.8216 (p90) cc_final: 0.7927 (p90) REVERT: C 275 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8635 (m-10) REVERT: C 505 TYR cc_start: 0.9625 (m-80) cc_final: 0.9185 (t80) REVERT: C 633 TRP cc_start: 0.7171 (OUTLIER) cc_final: 0.6969 (p90) REVERT: D 62 MET cc_start: 0.9179 (ttp) cc_final: 0.8913 (ptt) REVERT: D 123 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7328 (ptt) REVERT: D 249 MET cc_start: 0.6380 (tpt) cc_final: 0.6002 (mmt) REVERT: D 270 MET cc_start: 0.2460 (ptm) cc_final: 0.1821 (tpp) REVERT: D 376 MET cc_start: 0.9169 (tpt) cc_final: 0.8394 (ptm) REVERT: D 462 MET cc_start: 0.8287 (pmm) cc_final: 0.7957 (pmm) REVERT: D 480 MET cc_start: 0.6725 (mmm) cc_final: 0.5849 (ptt) REVERT: D 516 TYR cc_start: 0.9223 (t80) cc_final: 0.8600 (m-80) outliers start: 45 outliers final: 27 residues processed: 132 average time/residue: 0.4138 time to fit residues: 96.8738 Evaluate side-chains 127 residues out of total 3351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 92 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 0.9990 chunk 321 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 277 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 301 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 310 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1083 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 607 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.086138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.052169 restraints weight = 143543.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.053651 restraints weight = 88006.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.053755 restraints weight = 51804.424| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31190 Z= 0.184 Angle : 0.530 11.236 42439 Z= 0.270 Chirality : 0.042 0.193 4810 Planarity : 0.004 0.044 5468 Dihedral : 4.905 59.534 4597 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.10 % Allowed : 11.55 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3785 helix: 1.51 (0.17), residues: 983 sheet: 0.28 (0.18), residues: 770 loop : -0.96 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 633 HIS 0.013 0.001 HIS A1083 PHE 0.022 0.001 PHE D 400 TYR 0.019 0.001 TYR A 904 ARG 0.003 0.000 ARG B1039 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4865.29 seconds wall clock time: 91 minutes 38.61 seconds (5498.61 seconds total)