Starting phenix.real_space_refine on Fri Feb 16 07:45:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ztq_11424/02_2024/6ztq_11424_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ztq_11424/02_2024/6ztq_11424.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ztq_11424/02_2024/6ztq_11424_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ztq_11424/02_2024/6ztq_11424_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ztq_11424/02_2024/6ztq_11424_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ztq_11424/02_2024/6ztq_11424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ztq_11424/02_2024/6ztq_11424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ztq_11424/02_2024/6ztq_11424_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ztq_11424/02_2024/6ztq_11424_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 36 5.49 5 S 493 5.16 5 C 43354 2.51 5 N 11105 2.21 5 O 12056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 42": "OD1" <-> "OD2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 94": "OD1" <-> "OD2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D ASP 223": "OD1" <-> "OD2" Residue "D PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 429": "OD1" <-> "OD2" Residue "E ARG 10": "NH1" <-> "NH2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 187": "NH1" <-> "NH2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 19": "OD1" <-> "OD2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ASP 41": "OD1" <-> "OD2" Residue "F ASP 87": "OD1" <-> "OD2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "F ASP 114": "OD1" <-> "OD2" Residue "F ARG 127": "NH1" <-> "NH2" Residue "F TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 338": "OD1" <-> "OD2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F ARG 378": "NH1" <-> "NH2" Residue "F ASP 390": "OD1" <-> "OD2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 135": "NH1" <-> "NH2" Residue "G ASP 171": "OD1" <-> "OD2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 249": "NH1" <-> "NH2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G ARG 268": "NH1" <-> "NH2" Residue "G GLU 281": "OE1" <-> "OE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G ARG 359": "NH1" <-> "NH2" Residue "G TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 441": "OE1" <-> "OE2" Residue "G ASP 528": "OD1" <-> "OD2" Residue "G ARG 534": "NH1" <-> "NH2" Residue "G ASP 540": "OD1" <-> "OD2" Residue "G TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 635": "OD1" <-> "OD2" Residue "H PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 9": "OE1" <-> "OE2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "I TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 62": "NH1" <-> "NH2" Residue "I GLU 76": "OE1" <-> "OE2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 118": "OD1" <-> "OD2" Residue "J TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 171": "NH1" <-> "NH2" Residue "K PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L ASP 83": "OD1" <-> "OD2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 208": "OD1" <-> "OD2" Residue "L PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 436": "NH1" <-> "NH2" Residue "L PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 535": "NH1" <-> "NH2" Residue "M GLU 114": "OE1" <-> "OE2" Residue "M TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 281": "OD1" <-> "OD2" Residue "M PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "O ARG 2": "NH1" <-> "NH2" Residue "O ARG 67": "NH1" <-> "NH2" Residue "O TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 145": "NH1" <-> "NH2" Residue "O TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 237": "OD1" <-> "OD2" Residue "O TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 13": "NH1" <-> "NH2" Residue "P PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 186": "NH1" <-> "NH2" Residue "P PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 320": "NH1" <-> "NH2" Residue "P ARG 322": "NH1" <-> "NH2" Residue "Q PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 30": "OD1" <-> "OD2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 25": "NH1" <-> "NH2" Residue "S ARG 55": "NH1" <-> "NH2" Residue "S ASP 84": "OD1" <-> "OD2" Residue "T ASP 9": "OD1" <-> "OD2" Residue "T ASP 13": "OD1" <-> "OD2" Residue "T ASP 56": "OD1" <-> "OD2" Residue "T ASP 64": "OD1" <-> "OD2" Residue "T ASP 66": "OD1" <-> "OD2" Residue "U ASP 26": "OD1" <-> "OD2" Residue "U ASP 39": "OD1" <-> "OD2" Residue "U PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 84": "OE1" <-> "OE2" Residue "W ARG 32": "NH1" <-> "NH2" Residue "W ARG 33": "NH1" <-> "NH2" Residue "W TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 79": "NH1" <-> "NH2" Residue "W ARG 107": "NH1" <-> "NH2" Residue "W ASP 119": "OD1" <-> "OD2" Residue "W PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ASP 120": "OD1" <-> "OD2" Residue "X ASP 133": "OD1" <-> "OD2" Residue "X TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "Y PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 12": "OE1" <-> "OE2" Residue "Y TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 48": "OD1" <-> "OD2" Residue "Y ARG 105": "NH1" <-> "NH2" Residue "Y TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 22": "NH1" <-> "NH2" Residue "Z ARG 26": "NH1" <-> "NH2" Residue "Z ARG 57": "NH1" <-> "NH2" Residue "Z ARG 67": "NH1" <-> "NH2" Residue "Z ARG 81": "NH1" <-> "NH2" Residue "Z ARG 114": "NH1" <-> "NH2" Residue "a ARG 37": "NH1" <-> "NH2" Residue "a ARG 40": "NH1" <-> "NH2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "a TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 45": "NH1" <-> "NH2" Residue "d ASP 45": "OD1" <-> "OD2" Residue "d ARG 55": "NH1" <-> "NH2" Residue "d PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 120": "NH1" <-> "NH2" Residue "e PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e ARG 100": "NH1" <-> "NH2" Residue "e ARG 104": "NH1" <-> "NH2" Residue "f ASP 30": "OD1" <-> "OD2" Residue "g GLU 31": "OE1" <-> "OE2" Residue "g ARG 57": "NH1" <-> "NH2" Residue "g ARG 89": "NH1" <-> "NH2" Residue "g ARG 93": "NH1" <-> "NH2" Residue "g GLU 99": "OE1" <-> "OE2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 115": "NH1" <-> "NH2" Residue "i ARG 10": "NH1" <-> "NH2" Residue "i ARG 30": "NH1" <-> "NH2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 43": "OD1" <-> "OD2" Residue "j ASP 55": "OD1" <-> "OD2" Residue "j GLU 63": "OE1" <-> "OE2" Residue "k TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 44": "NH1" <-> "NH2" Residue "k ARG 52": "NH1" <-> "NH2" Residue "k GLU 54": "OE1" <-> "OE2" Residue "k TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 18": "OE1" <-> "OE2" Residue "l ASP 58": "OD1" <-> "OD2" Residue "l ARG 85": "NH1" <-> "NH2" Residue "l GLU 148": "OE1" <-> "OE2" Residue "m ASP 18": "OD1" <-> "OD2" Residue "m ARG 29": "NH1" <-> "NH2" Residue "m ARG 30": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 80": "NH1" <-> "NH2" Residue "m GLU 112": "OE1" <-> "OE2" Residue "m ASP 121": "OD1" <-> "OD2" Residue "n ARG 33": "NH1" <-> "NH2" Residue "n TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 146": "OD1" <-> "OD2" Residue "n ARG 157": "NH1" <-> "NH2" Residue "n ARG 158": "NH1" <-> "NH2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o ARG 7": "NH1" <-> "NH2" Residue "o ARG 33": "NH1" <-> "NH2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "o ARG 110": "NH1" <-> "NH2" Residue "p GLU 11": "OE1" <-> "OE2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 65": "NH1" <-> "NH2" Residue "p ARG 68": "NH1" <-> "NH2" Residue "p ARG 92": "NH1" <-> "NH2" Residue "p TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 60": "NH1" <-> "NH2" Residue "q TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 5": "NH1" <-> "NH2" Residue "r ARG 26": "NH1" <-> "NH2" Residue "r TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 90": "OE1" <-> "OE2" Residue "r ARG 102": "NH1" <-> "NH2" Residue "s ASP 28": "OD1" <-> "OD2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 67073 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 933 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "C" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 15, 'TRANS': 191} Chain: "D" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3464 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 26, 'TRANS': 403} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1648 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 21, 'TRANS': 190} Chain: "F" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3300 Classifications: {'peptide': 428} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 406} Chain: "G" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5296 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 31, 'TRANS': 656} Chain: "H" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2540 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1431 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 9, 'TRANS': 168} Chain: "J" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1300 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 3, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4800 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3632 Classifications: {'peptide': 459} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2696 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 323} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2607 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 16, 'TRANS': 303} Chain: "P" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2748 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain: "Q" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1015 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "R" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 738 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "S" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 611 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "U" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 692 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Chain: "V" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 105} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1396 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 11, 'TRANS': 159} Chain: "Y" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1037 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "Z" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1167 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "a" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 556 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "b" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 628 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "c" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 398 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "d" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 996 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 12, 'TRANS': 107} Chain: "e" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 877 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "f" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 456 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "g" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 850 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "h" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1162 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain: "i" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 787 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 12, 'TRANS': 81} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 537 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 6, 'TRANS': 55} Chain: "k" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 609 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 4, 'TRANS': 70} Chain: "l" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1294 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 18, 'TRANS': 135} Chain: "m" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1050 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 11, 'TRANS': 114} Chain: "n" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1534 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "o" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 957 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "p" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1433 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 10, 'TRANS': 158} Chain: "q" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "r" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 11, 'TRANS': 88} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 344 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 86 Unusual residues: {'PC1': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "D" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {'3PE': 1, 'HQH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "L" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 123 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "M" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "N" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 124 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 76 Planarities with less than four sites: {'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "U" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "Z" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "d" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 130 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 70 Chain: "h" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Chain: "i" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "l" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "q" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1688 SG CYS B 129 96.278 92.137 202.384 1.00 14.93 S ATOM 1191 SG CYS B 65 90.249 94.392 204.110 1.00 16.54 S ATOM 1185 SG CYS B 64 90.496 88.947 200.953 1.00 16.43 S ATOM 1918 SG CYS B 159 93.604 89.231 206.684 1.00 14.73 S ATOM 8167 SG CYS E 103 113.391 42.305 256.313 1.00 46.62 S ATOM 8201 SG CYS E 108 112.105 38.942 257.722 1.00 47.48 S ATOM 8485 SG CYS E 144 116.760 39.473 253.174 1.00 45.13 S ATOM 8508 SG CYS E 148 115.494 36.642 253.944 1.00 48.52 S ATOM 11718 SG CYS F 362 118.869 49.687 233.266 1.00 27.29 S ATOM 11738 SG CYS F 365 116.295 49.129 238.368 1.00 28.79 S ATOM 12060 SG CYS F 405 120.600 44.639 237.173 1.00 31.50 S ATOM 11699 SG CYS F 359 122.559 50.746 238.456 1.00 30.68 S ATOM 13138 SG CYS G 114 115.566 68.302 224.565 1.00 19.59 S ATOM 13077 SG CYS G 105 109.621 70.772 226.560 1.00 17.64 S ATOM 13098 SG CYS G 108 115.554 73.241 228.025 1.00 18.94 S ATOM 13470 SG CYS G 156 123.964 62.234 229.326 1.00 23.37 S ATOM 13447 SG CYS G 153 121.030 64.339 234.768 1.00 22.48 S ATOM 13494 SG CYS G 159 127.328 65.213 233.446 1.00 25.24 S ATOM 13823 SG CYS G 203 122.659 68.263 229.835 1.00 22.08 S ATOM 12584 SG CYS G 41 124.678 55.872 225.968 1.00 23.88 S ATOM 12670 SG CYS G 52 120.519 55.791 225.415 1.00 24.11 S ATOM 12695 SG CYS G 55 122.510 51.688 222.320 1.00 24.45 S ATOM 12796 SG CYS G 69 125.508 52.453 223.580 1.00 25.57 S ATOM 21120 SG CYS I 121 97.018 83.599 212.985 1.00 13.76 S ATOM 21094 SG CYS I 118 97.008 90.155 213.827 1.00 13.62 S ATOM 21141 SG CYS I 124 98.464 85.682 218.386 1.00 14.37 S ATOM 20868 SG CYS I 89 102.472 86.861 213.170 1.00 13.87 S ATOM 21170 SG CYS I 128 101.314 82.340 225.767 1.00 15.72 S ATOM 20840 SG CYS I 85 104.911 85.076 220.786 1.00 14.74 S ATOM 20798 SG CYS I 79 106.056 86.653 226.858 1.00 17.30 S ATOM 20817 SG CYS I 82 106.572 80.451 224.314 1.00 16.68 S ATOM 41595 SG CYS R 59 102.861 77.472 240.681 1.00 22.92 S ATOM 41771 SG CYS R 84 105.900 78.051 238.411 1.00 21.89 S ATOM 41793 SG CYS R 87 103.936 80.663 239.746 1.00 20.46 S Time building chain proxies: 27.26, per 1000 atoms: 0.41 Number of scatterers: 67073 At special positions: 0 Unit cell: (186.9, 184.8, 288.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 493 16.00 P 36 15.00 O 12056 8.00 N 11105 7.00 C 43354 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS X 35 " - pdb=" SG CYS X 65 " distance=2.03 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.02 Simple disulfide: pdb=" SG CYS X 77 " - pdb=" SG CYS X 109 " distance=2.03 Simple disulfide: pdb=" SG CYS X 87 " - pdb=" SG CYS X 99 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 96 " - pdb=" SG CYS Y 116 " distance=2.03 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.03 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.03 Simple disulfide: pdb=" SG CYS o 68 " - pdb=" SG CYS o 79 " distance=2.04 Simple disulfide: pdb=" SG CYS p 76 " - pdb=" SG CYS p 83 " distance=2.03 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.89 Conformation dependent library (CDL) restraints added in 8.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb=" SF4 B 201 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 159 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 64 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 65 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb=" SF4 G 802 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb=" SF4 I 201 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 121 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 118 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 89 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 124 " pdb=" SF4 I 202 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 82 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 128 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 79 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 85 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 313 helices and 33 sheets defined 49.0% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.32 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 Processing helix chain 'A' and resid 56 through 80 Proline residue: A 74 - end of helix removed outlier: 5.710A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 107 Processing helix chain 'B' and resid 36 through 53 Processing helix chain 'B' and resid 64 through 73 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 128 through 131 No H-bonds generated for 'chain 'B' and resid 128 through 131' Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 163 through 179 removed outlier: 3.603A pdb=" N ARG B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'C' and resid 17 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.746A pdb=" N VAL C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.525A pdb=" N THR C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 4.114A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE C 138 " --> pdb=" O TRP C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'D' and resid 8 through 14 removed outlier: 4.219A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 93 Processing helix chain 'D' and resid 100 through 106 removed outlier: 3.601A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 Processing helix chain 'D' and resid 165 through 184 removed outlier: 4.213A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 229 removed outlier: 4.179A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 257 through 261 Processing helix chain 'D' and resid 269 through 272 No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 295 through 316 removed outlier: 4.138A pdb=" N ARG D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 339 No H-bonds generated for 'chain 'D' and resid 337 through 339' Processing helix chain 'D' and resid 342 through 353 Processing helix chain 'D' and resid 396 through 405 removed outlier: 4.467A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 Processing helix chain 'D' and resid 425 through 428 No H-bonds generated for 'chain 'D' and resid 425 through 428' Processing helix chain 'E' and resid 25 through 36 removed outlier: 3.660A pdb=" N LYS E 29 " --> pdb=" O PRO E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 3.587A pdb=" N ALA E 46 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix removed outlier: 3.679A pdb=" N ASN E 58 " --> pdb=" O GLN E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 removed outlier: 3.693A pdb=" N ALA E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 86 Processing helix chain 'E' and resid 106 through 111 removed outlier: 4.718A pdb=" N ARG E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 122 Processing helix chain 'E' and resid 167 through 177 removed outlier: 4.615A pdb=" N ILE E 172 " --> pdb=" O ASP E 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 39 removed outlier: 6.926A pdb=" N ARG F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG F 39 " --> pdb=" O GLY F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 51 Processing helix chain 'F' and resid 53 through 63 Processing helix chain 'F' and resid 79 through 82 removed outlier: 3.864A pdb=" N MET F 82 " --> pdb=" O TRP F 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 79 through 82' Processing helix chain 'F' and resid 106 through 111 Processing helix chain 'F' and resid 115 through 128 Processing helix chain 'F' and resid 143 through 159 Processing helix chain 'F' and resid 184 through 187 Processing helix chain 'F' and resid 189 through 197 removed outlier: 3.646A pdb=" N ILE F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 225 through 229 Processing helix chain 'F' and resid 231 through 237 Processing helix chain 'F' and resid 239 through 244 Processing helix chain 'F' and resid 276 through 282 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 343 through 356 Processing helix chain 'F' and resid 363 through 381 removed outlier: 3.913A pdb=" N VAL F 369 " --> pdb=" O CYS F 365 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 400 removed outlier: 4.357A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU F 400 " --> pdb=" O LYS F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 421 Proline residue: F 414 - end of helix Processing helix chain 'F' and resid 423 through 435 Processing helix chain 'G' and resid 26 through 33 removed outlier: 3.626A pdb=" N VAL G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 158 through 165 removed outlier: 3.820A pdb=" N PHE G 162 " --> pdb=" O ARG G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 197 through 202 Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 266 through 269 No H-bonds generated for 'chain 'G' and resid 266 through 269' Processing helix chain 'G' and resid 271 through 275 removed outlier: 3.640A pdb=" N LYS G 275 " --> pdb=" O ASP G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 309 removed outlier: 3.877A pdb=" N ASN G 309 " --> pdb=" O GLY G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 338 removed outlier: 3.790A pdb=" N VAL G 338 " --> pdb=" O LEU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 362 Processing helix chain 'G' and resid 389 through 401 Processing helix chain 'G' and resid 427 through 434 Processing helix chain 'G' and resid 438 through 443 removed outlier: 3.989A pdb=" N VAL G 442 " --> pdb=" O SER G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 480 Processing helix chain 'G' and resid 497 through 505 removed outlier: 4.273A pdb=" N VAL G 500 " --> pdb=" O ALA G 497 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ALA G 501 " --> pdb=" O SER G 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 534 through 536 No H-bonds generated for 'chain 'G' and resid 534 through 536' Processing helix chain 'G' and resid 566 through 568 No H-bonds generated for 'chain 'G' and resid 566 through 568' Processing helix chain 'G' and resid 596 through 606 Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 642 through 649 Processing helix chain 'G' and resid 668 through 670 No H-bonds generated for 'chain 'G' and resid 668 through 670' Processing helix chain 'G' and resid 682 through 691 Processing helix chain 'H' and resid 3 through 32 Proline residue: H 12 - end of helix removed outlier: 3.610A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 68 through 84 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 122 removed outlier: 4.418A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TRP H 121 " --> pdb=" O LEU H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 156 removed outlier: 4.876A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 168 Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 180 through 194 removed outlier: 4.358A pdb=" N THR H 193 " --> pdb=" O THR H 189 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN H 194 " --> pdb=" O LEU H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 241 removed outlier: 3.957A pdb=" N ILE H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 276 Processing helix chain 'H' and resid 284 through 291 Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 16 through 25 Processing helix chain 'I' and resid 30 through 44 removed outlier: 3.635A pdb=" N ARG I 34 " --> pdb=" O THR I 30 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY I 35 " --> pdb=" O GLU I 31 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE I 44 " --> pdb=" O LEU I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 88 No H-bonds generated for 'chain 'I' and resid 85 through 88' Processing helix chain 'I' and resid 123 through 127 Processing helix chain 'I' and resid 146 through 149 Processing helix chain 'I' and resid 153 through 174 removed outlier: 6.051A pdb=" N ALA I 165 " --> pdb=" O ASP I 161 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLU I 166 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA I 169 " --> pdb=" O ALA I 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 21 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 50 through 70 removed outlier: 3.727A pdb=" N VAL J 65 " --> pdb=" O GLY J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 109 removed outlier: 3.982A pdb=" N TYR J 108 " --> pdb=" O CYS J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 145 removed outlier: 4.278A pdb=" N MET J 144 " --> pdb=" O GLY J 140 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR J 145 " --> pdb=" O VAL J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 170 removed outlier: 3.596A pdb=" N PHE J 164 " --> pdb=" O PHE J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 20 Processing helix chain 'K' and resid 27 through 51 Processing helix chain 'K' and resid 58 through 84 removed outlier: 3.641A pdb=" N THR K 62 " --> pdb=" O PRO K 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 23 removed outlier: 3.759A pdb=" N PHE L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix removed outlier: 3.605A pdb=" N MET L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 57 removed outlier: 4.221A pdb=" N LEU L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 84 through 106 removed outlier: 3.588A pdb=" N VAL L 92 " --> pdb=" O LEU L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 133 Processing helix chain 'L' and resid 138 through 155 Processing helix chain 'L' and resid 164 through 191 removed outlier: 4.316A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 removed outlier: 4.640A pdb=" N PHE L 203 " --> pdb=" O GLN L 199 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 223 Processing helix chain 'L' and resid 227 through 229 No H-bonds generated for 'chain 'L' and resid 227 through 229' Processing helix chain 'L' and resid 232 through 235 No H-bonds generated for 'chain 'L' and resid 232 through 235' Processing helix chain 'L' and resid 241 through 250 removed outlier: 4.154A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 267 Proline residue: L 265 - end of helix Processing helix chain 'L' and resid 271 through 292 removed outlier: 3.738A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 317 Processing helix chain 'L' and resid 322 through 349 removed outlier: 4.380A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 380 Processing helix chain 'L' and resid 389 through 401 removed outlier: 5.211A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 429 Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.887A pdb=" N ASN L 452 " --> pdb=" O PRO L 448 " (cutoff:3.500A) Proline residue: L 453 - end of helix removed outlier: 6.428A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N PHE L 466 " --> pdb=" O ILE L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 506 Processing helix chain 'L' and resid 529 through 546 removed outlier: 4.938A pdb=" N ARG L 535 " --> pdb=" O SER L 531 " (cutoff:3.500A) Proline residue: L 538 - end of helix Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 578 Processing helix chain 'L' and resid 584 through 605 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.353A pdb=" N LEU M 12 " --> pdb=" O SER M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 24 through 42 removed outlier: 3.986A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 81 Proline residue: M 64 - end of helix removed outlier: 3.806A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix removed outlier: 3.926A pdb=" N GLN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 110 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.633A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 142 through 170 removed outlier: 3.981A pdb=" N THR M 153 " --> pdb=" O PHE M 149 " (cutoff:3.500A) Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 176 through 181 Processing helix chain 'M' and resid 190 through 200 removed outlier: 3.768A pdb=" N LEU M 195 " --> pdb=" O SER M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 206 No H-bonds generated for 'chain 'M' and resid 203 through 206' Processing helix chain 'M' and resid 214 through 220 removed outlier: 3.774A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 233 Processing helix chain 'M' and resid 237 through 249 removed outlier: 3.872A pdb=" N GLY M 242 " --> pdb=" O LEU M 238 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE M 248 " --> pdb=" O ILE M 244 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 255 No H-bonds generated for 'chain 'M' and resid 253 through 255' Processing helix chain 'M' and resid 259 through 276 Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.646A pdb=" N ALA M 287 " --> pdb=" O LYS M 283 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.661A pdb=" N ASN M 333 " --> pdb=" O LEU M 329 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 355 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 390 through 414 removed outlier: 3.872A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE M 394 " --> pdb=" O PHE M 391 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY M 397 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER M 407 " --> pdb=" O GLY M 404 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 449 removed outlier: 3.911A pdb=" N MET M 437 " --> pdb=" O GLU M 433 " (cutoff:3.500A) Proline residue: M 443 - end of helix Processing helix chain 'N' and resid 3 through 21 Proline residue: N 17 - end of helix Processing helix chain 'N' and resid 26 through 44 removed outlier: 3.754A pdb=" N ILE N 41 " --> pdb=" O LEU N 37 " (cutoff:3.500A) Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 removed outlier: 3.901A pdb=" N THR N 65 " --> pdb=" O VAL N 61 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA N 66 " --> pdb=" O THR N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 115 through 120 Processing helix chain 'N' and resid 128 through 132 Processing helix chain 'N' and resid 135 through 148 removed outlier: 3.677A pdb=" N LEU N 142 " --> pdb=" O PRO N 138 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 153 through 169 removed outlier: 3.572A pdb=" N ALA N 158 " --> pdb=" O ILE N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 193 removed outlier: 3.756A pdb=" N ALA N 180 " --> pdb=" O ARG N 176 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 221 Proline residue: N 214 - end of helix Processing helix chain 'N' and resid 227 through 230 No H-bonds generated for 'chain 'N' and resid 227 through 230' Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.842A pdb=" N LEU N 241 " --> pdb=" O PRO N 238 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR N 242 " --> pdb=" O ALA N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 273 Proline residue: N 262 - end of helix removed outlier: 3.639A pdb=" N ILE N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS N 272 " --> pdb=" O GLU N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 301 removed outlier: 3.954A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU N 288 " --> pdb=" O MET N 284 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE N 292 " --> pdb=" O LEU N 288 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR N 293 " --> pdb=" O ASN N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 316 removed outlier: 3.553A pdb=" N MET N 313 " --> pdb=" O ASN N 310 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET N 314 " --> pdb=" O SER N 311 " (cutoff:3.500A) Processing helix chain 'N' and resid 325 through 332 Processing helix chain 'N' and resid 337 through 342 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 5 through 10 Processing helix chain 'O' and resid 36 through 46 removed outlier: 3.846A pdb=" N GLU O 41 " --> pdb=" O LYS O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 92 through 118 Processing helix chain 'O' and resid 132 through 140 Processing helix chain 'O' and resid 146 through 159 Processing helix chain 'O' and resid 176 through 184 Processing helix chain 'O' and resid 191 through 193 No H-bonds generated for 'chain 'O' and resid 191 through 193' Processing helix chain 'O' and resid 197 through 215 removed outlier: 4.440A pdb=" N LEU O 211 " --> pdb=" O LYS O 207 " (cutoff:3.500A) Proline residue: O 212 - end of helix Processing helix chain 'O' and resid 225 through 228 No H-bonds generated for 'chain 'O' and resid 225 through 228' Processing helix chain 'O' and resid 231 through 240 removed outlier: 4.265A pdb=" N TYR O 240 " --> pdb=" O GLU O 236 " (cutoff:3.500A) Processing helix chain 'O' and resid 253 through 264 Processing helix chain 'O' and resid 266 through 273 removed outlier: 5.062A pdb=" N TYR O 272 " --> pdb=" O GLU O 268 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N THR O 273 " --> pdb=" O VAL O 269 " (cutoff:3.500A) Processing helix chain 'O' and resid 286 through 297 Processing helix chain 'O' and resid 317 through 319 No H-bonds generated for 'chain 'O' and resid 317 through 319' Processing helix chain 'P' and resid 3 through 5 No H-bonds generated for 'chain 'P' and resid 3 through 5' Processing helix chain 'P' and resid 31 through 39 Processing helix chain 'P' and resid 53 through 60 removed outlier: 3.747A pdb=" N MET P 57 " --> pdb=" O TYR P 54 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N HIS P 58 " --> pdb=" O ASP P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 87 removed outlier: 5.448A pdb=" N HIS P 87 " --> pdb=" O LYS P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 110 No H-bonds generated for 'chain 'P' and resid 107 through 110' Processing helix chain 'P' and resid 112 through 124 Processing helix chain 'P' and resid 144 through 159 removed outlier: 3.590A pdb=" N ARG P 157 " --> pdb=" O GLU P 153 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 186 removed outlier: 3.801A pdb=" N TYR P 185 " --> pdb=" O HIS P 181 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 197 Processing helix chain 'P' and resid 207 through 217 Processing helix chain 'P' and resid 238 through 248 Processing helix chain 'P' and resid 260 through 271 Processing helix chain 'P' and resid 281 through 288 Processing helix chain 'P' and resid 310 through 321 removed outlier: 6.037A pdb=" N ILE P 315 " --> pdb=" O GLU P 311 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLU P 316 " --> pdb=" O LEU P 312 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL P 317 " --> pdb=" O LYS P 313 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N HIS P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 23 No H-bonds generated for 'chain 'Q' and resid 20 through 23' Processing helix chain 'Q' and resid 28 through 31 No H-bonds generated for 'chain 'Q' and resid 28 through 31' Processing helix chain 'Q' and resid 90 through 99 Processing helix chain 'Q' and resid 120 through 122 No H-bonds generated for 'chain 'Q' and resid 120 through 122' Processing helix chain 'R' and resid 23 through 28 removed outlier: 4.018A pdb=" N ARG R 27 " --> pdb=" O ARG R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 Processing helix chain 'S' and resid 27 through 29 No H-bonds generated for 'chain 'S' and resid 27 through 29' Processing helix chain 'S' and resid 32 through 46 removed outlier: 6.099A pdb=" N VAL S 41 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLU S 42 " --> pdb=" O GLN S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 94 Processing helix chain 'T' and resid 8 through 22 removed outlier: 3.798A pdb=" N LYS T 12 " --> pdb=" O LEU T 8 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP T 13 " --> pdb=" O ASP T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 29 No H-bonds generated for 'chain 'T' and resid 27 through 29' Processing helix chain 'T' and resid 44 through 57 Processing helix chain 'T' and resid 64 through 69 Processing helix chain 'T' and resid 73 through 81 removed outlier: 3.674A pdb=" N ALA T 81 " --> pdb=" O VAL T 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 21 removed outlier: 3.999A pdb=" N LEU U 21 " --> pdb=" O TYR U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 40 No H-bonds generated for 'chain 'U' and resid 37 through 40' Processing helix chain 'U' and resid 44 through 58 Processing helix chain 'U' and resid 64 through 67 No H-bonds generated for 'chain 'U' and resid 64 through 67' Processing helix chain 'U' and resid 73 through 84 Processing helix chain 'V' and resid 22 through 36 removed outlier: 3.608A pdb=" N LYS V 35 " --> pdb=" O LEU V 31 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 Processing helix chain 'V' and resid 64 through 70 Processing helix chain 'V' and resid 76 through 96 Processing helix chain 'W' and resid 28 through 51 removed outlier: 3.970A pdb=" N ARG W 33 " --> pdb=" O GLU W 29 " (cutoff:3.500A) Proline residue: W 46 - end of helix removed outlier: 3.605A pdb=" N HIS W 50 " --> pdb=" O PRO W 46 " (cutoff:3.500A) Processing helix chain 'W' and resid 58 through 72 removed outlier: 4.732A pdb=" N ASN W 72 " --> pdb=" O MET W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 96 Processing helix chain 'W' and resid 102 through 106 Processing helix chain 'W' and resid 120 through 125 Processing helix chain 'X' and resid 22 through 26 Processing helix chain 'X' and resid 28 through 31 No H-bonds generated for 'chain 'X' and resid 28 through 31' Processing helix chain 'X' and resid 37 through 48 Processing helix chain 'X' and resid 57 through 75 Processing helix chain 'X' and resid 79 through 88 Processing helix chain 'X' and resid 96 through 98 No H-bonds generated for 'chain 'X' and resid 96 through 98' Processing helix chain 'X' and resid 102 through 112 Processing helix chain 'X' and resid 140 through 142 No H-bonds generated for 'chain 'X' and resid 140 through 142' Processing helix chain 'Y' and resid 4 through 11 removed outlier: 4.190A pdb=" N TYR Y 10 " --> pdb=" O PHE Y 6 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N HIS Y 11 " --> pdb=" O PHE Y 7 " (cutoff:3.500A) Processing helix chain 'Y' and resid 19 through 43 Processing helix chain 'Y' and resid 50 through 80 Processing helix chain 'Y' and resid 88 through 105 Processing helix chain 'Y' and resid 109 through 132 Processing helix chain 'Z' and resid 32 through 96 removed outlier: 3.566A pdb=" N ARG Z 58 " --> pdb=" O GLN Z 54 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE Z 61 " --> pdb=" O ARG Z 57 " (cutoff:3.500A) Proline residue: Z 72 - end of helix removed outlier: 4.013A pdb=" N ILE Z 95 " --> pdb=" O GLU Z 91 " (cutoff:3.500A) Processing helix chain 'Z' and resid 129 through 135 Processing helix chain 'a' and resid 2 through 31 Proline residue: a 7 - end of helix removed outlier: 3.711A pdb=" N VAL a 17 " --> pdb=" O VAL a 14 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE a 18 " --> pdb=" O CYS a 15 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 4.479A pdb=" N SER a 22 " --> pdb=" O PRO a 19 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN a 31 " --> pdb=" O LYS a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'b' and resid 5 through 13 removed outlier: 3.731A pdb=" N ALA b 13 " --> pdb=" O LYS b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 31 Processing helix chain 'b' and resid 37 through 47 removed outlier: 3.724A pdb=" N ALA b 41 " --> pdb=" O THR b 38 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER b 42 " --> pdb=" O LYS b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 79 No H-bonds generated for 'chain 'b' and resid 77 through 79' Processing helix chain 'c' and resid 14 through 45 Processing helix chain 'd' and resid 2 through 4 No H-bonds generated for 'chain 'd' and resid 2 through 4' Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 48 Processing helix chain 'd' and resid 58 through 96 removed outlier: 4.345A pdb=" N PHE d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 33 through 42 Processing helix chain 'e' and resid 48 through 54 removed outlier: 4.095A pdb=" N LYS e 52 " --> pdb=" O THR e 49 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU e 54 " --> pdb=" O ALA e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 66 Processing helix chain 'e' and resid 70 through 88 Processing helix chain 'e' and resid 95 through 98 No H-bonds generated for 'chain 'e' and resid 95 through 98' Processing helix chain 'f' and resid 10 through 32 removed outlier: 4.706A pdb=" N VAL f 15 " --> pdb=" O HIS f 12 " (cutoff:3.500A) Proline residue: f 16 - end of helix Processing helix chain 'g' and resid 49 through 64 removed outlier: 3.750A pdb=" N ALA g 58 " --> pdb=" O TRP g 54 " (cutoff:3.500A) Processing helix chain 'g' and resid 67 through 76 removed outlier: 4.173A pdb=" N THR g 72 " --> pdb=" O LEU g 68 " (cutoff:3.500A) Processing helix chain 'g' and resid 85 through 100 Processing helix chain 'g' and resid 113 through 115 No H-bonds generated for 'chain 'g' and resid 113 through 115' Processing helix chain 'h' and resid 17 through 46 removed outlier: 4.926A pdb=" N LEU h 22 " --> pdb=" O ASP h 18 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR h 32 " --> pdb=" O TYR h 28 " (cutoff:3.500A) Proline residue: h 35 - end of helix Processing helix chain 'h' and resid 63 through 66 Processing helix chain 'h' and resid 70 through 79 Processing helix chain 'h' and resid 83 through 116 Processing helix chain 'i' and resid 5 through 24 removed outlier: 3.585A pdb=" N LEU i 9 " --> pdb=" O PRO i 5 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 73 Processing helix chain 'i' and resid 75 through 87 Processing helix chain 'j' and resid 19 through 42 Processing helix chain 'k' and resid 34 through 44 Processing helix chain 'k' and resid 53 through 58 removed outlier: 4.323A pdb=" N TRP k 56 " --> pdb=" O ASN k 53 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG k 57 " --> pdb=" O GLU k 54 " (cutoff:3.500A) Processing helix chain 'k' and resid 68 through 72 Processing helix chain 'k' and resid 76 through 92 Processing helix chain 'l' and resid 16 through 26 Processing helix chain 'l' and resid 97 through 120 Processing helix chain 'l' and resid 139 through 141 No H-bonds generated for 'chain 'l' and resid 139 through 141' Processing helix chain 'm' and resid 27 through 50 removed outlier: 3.979A pdb=" N ALA m 31 " --> pdb=" O GLU m 27 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 72 Processing helix chain 'm' and resid 86 through 116 Proline residue: m 96 - end of helix Processing helix chain 'n' and resid 11 through 29 Processing helix chain 'n' and resid 33 through 48 Processing helix chain 'n' and resid 59 through 71 Processing helix chain 'n' and resid 92 through 96 removed outlier: 3.856A pdb=" N CYS n 95 " --> pdb=" O ARG n 92 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 105 removed outlier: 3.501A pdb=" N TYR n 105 " --> pdb=" O CYS n 102 " (cutoff:3.500A) Processing helix chain 'n' and resid 111 through 142 Proline residue: n 115 - end of helix removed outlier: 3.733A pdb=" N GLU n 122 " --> pdb=" O SER n 119 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP n 132 " --> pdb=" O MET n 129 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP n 133 " --> pdb=" O GLU n 130 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG n 134 " --> pdb=" O SER n 131 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU n 142 " --> pdb=" O LEU n 139 " (cutoff:3.500A) Processing helix chain 'o' and resid 5 through 8 No H-bonds generated for 'chain 'o' and resid 5 through 8' Processing helix chain 'o' and resid 42 through 47 Processing helix chain 'o' and resid 59 through 71 Processing helix chain 'o' and resid 81 through 111 removed outlier: 3.536A pdb=" N LYS o 111 " --> pdb=" O LEU o 107 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 58 removed outlier: 5.249A pdb=" N TRP p 42 " --> pdb=" O LEU p 38 " (cutoff:3.500A) Proline residue: p 43 - end of helix removed outlier: 3.853A pdb=" N ASN p 58 " --> pdb=" O GLN p 54 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 75 No H-bonds generated for 'chain 'p' and resid 73 through 75' Processing helix chain 'p' and resid 81 through 116 Processing helix chain 'p' and resid 125 through 142 removed outlier: 3.873A pdb=" N VAL p 134 " --> pdb=" O GLN p 130 " (cutoff:3.500A) Processing helix chain 'p' and resid 151 through 169 Processing helix chain 'q' and resid 3 through 14 Processing helix chain 'q' and resid 20 through 30 removed outlier: 3.636A pdb=" N VAL q 26 " --> pdb=" O GLY q 22 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG q 29 " --> pdb=" O ARG q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 79 through 81 No H-bonds generated for 'chain 'q' and resid 79 through 81' Processing helix chain 'q' and resid 84 through 90 removed outlier: 3.576A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 7 through 15 Processing helix chain 's' and resid 36 through 39 Processing helix chain 's' and resid 44 through 55 removed outlier: 4.077A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE s 55 " --> pdb=" O ASP s 51 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.624A pdb=" N TYR B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL B 98 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 154 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 49 through 51 removed outlier: 8.558A pdb=" N ILE C 50 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG C 106 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL C 93 " --> pdb=" O THR C 79 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP C 77 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU C 97 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU C 75 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.531A pdb=" N ARG C 182 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 47 through 50 removed outlier: 3.916A pdb=" N LYS D 75 " --> pdb=" O GLU D 67 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 362 through 368 Processing sheet with id= F, first strand: chain 'E' and resid 154 through 156 removed outlier: 6.831A pdb=" N ILE E 140 " --> pdb=" O VAL E 102 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 219 through 224 removed outlier: 3.910A pdb=" N THR F 221 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL F 94 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 267 through 271 removed outlier: 3.539A pdb=" N ALA F 296 " --> pdb=" O MET F 337 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 8 through 13 Processing sheet with id= J, first strand: chain 'G' and resid 56 through 58 removed outlier: 3.541A pdb=" N VAL G 57 " --> pdb=" O VAL G 66 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= L, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= M, first strand: chain 'G' and resid 223 through 228 removed outlier: 3.588A pdb=" N ARG G 249 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG G 243 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL G 247 " --> pdb=" O ARG G 243 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 283 through 285 Processing sheet with id= O, first strand: chain 'G' and resid 317 through 319 Processing sheet with id= P, first strand: chain 'G' and resid 405 through 409 Processing sheet with id= Q, first strand: chain 'G' and resid 544 through 547 removed outlier: 6.982A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= S, first strand: chain 'I' and resid 67 through 69 Processing sheet with id= T, first strand: chain 'I' and resid 94 through 96 Processing sheet with id= U, first strand: chain 'I' and resid 98 through 100 removed outlier: 3.524A pdb=" N ARG I 107 " --> pdb=" O GLU I 99 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 61 through 63 Processing sheet with id= W, first strand: chain 'L' and resid 66 through 70 removed outlier: 3.623A pdb=" N TRP L 66 " --> pdb=" O MET L 78 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU L 76 " --> pdb=" O TRP L 68 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'O' and resid 122 through 125 removed outlier: 6.681A pdb=" N ALA O 168 " --> pdb=" O THR O 26 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ASP O 28 " --> pdb=" O ALA O 168 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE O 170 " --> pdb=" O ASP O 28 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'P' and resid 21 through 23 removed outlier: 6.898A pdb=" N VAL P 90 " --> pdb=" O THR P 22 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'P' and resid 45 through 49 removed outlier: 3.543A pdb=" N LEU P 71 " --> pdb=" O ILE P 47 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'P' and resid 130 through 134 removed outlier: 6.065A pdb=" N ILE P 164 " --> pdb=" O HIS P 131 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER P 133 " --> pdb=" O ILE P 164 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE P 166 " --> pdb=" O SER P 133 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'P' and resid 191 through 193 Processing sheet with id= AC, first strand: chain 'Q' and resid 102 through 105 removed outlier: 3.729A pdb=" N LEU Q 84 " --> pdb=" O MET Q 57 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Q' and resid 64 through 66 removed outlier: 3.500A pdb=" N TRP Q 65 " --> pdb=" O SER Q 74 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'R' and resid 50 through 52 removed outlier: 3.586A pdb=" N LYS R 92 " --> pdb=" O ASN R 50 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'R' and resid 56 through 59 removed outlier: 3.604A pdb=" N ILE R 57 " --> pdb=" O ILE R 73 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'S' and resid 51 through 57 removed outlier: 3.735A pdb=" N ILE S 18 " --> pdb=" O PRO S 51 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU S 22 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS S 21 " --> pdb=" O LYS S 63 " (cutoff:3.500A) 2661 hydrogen bonds defined for protein. 7449 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: 18.33 Time building geometry restraints manager: 22.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 27772 1.40 - 1.63: 40045 1.63 - 1.85: 865 1.85 - 2.08: 0 2.08 - 2.30: 80 Bond restraints: 68762 Sorted by residual: bond pdb=" C4 ATP O 401 " pdb=" C5 ATP O 401 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.34e+01 bond pdb=" C24 HQH D 501 " pdb=" C25 HQH D 501 " ideal model delta sigma weight residual 1.533 1.397 0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C12 HQH D 501 " pdb=" C19 HQH D 501 " ideal model delta sigma weight residual 1.539 1.409 0.130 2.00e-02 2.50e+03 4.23e+01 bond pdb=" C24 HQH D 501 " pdb=" N5 HQH D 501 " ideal model delta sigma weight residual 1.498 1.370 0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" CB7 CDL N 401 " pdb=" OB8 CDL N 401 " ideal model delta sigma weight residual 1.334 1.403 -0.069 1.10e-02 8.26e+03 3.92e+01 ... (remaining 68757 not shown) Histogram of bond angle deviations from ideal: 72.64 - 85.57: 76 85.57 - 98.51: 50 98.51 - 111.45: 30621 111.45 - 124.38: 60342 124.38 - 137.32: 2023 Bond angle restraints: 93112 Sorted by residual: angle pdb=" PB ATP O 401 " pdb=" O3B ATP O 401 " pdb=" PG ATP O 401 " ideal model delta sigma weight residual 139.87 119.34 20.53 1.00e+00 1.00e+00 4.21e+02 angle pdb=" PA ATP O 401 " pdb=" O3A ATP O 401 " pdb=" PB ATP O 401 " ideal model delta sigma weight residual 136.83 118.03 18.80 1.00e+00 1.00e+00 3.54e+02 angle pdb=" C14 HQH D 501 " pdb=" C9 HQH D 501 " pdb=" C7 HQH D 501 " ideal model delta sigma weight residual 68.23 113.11 -44.88 3.00e+00 1.11e-01 2.24e+02 angle pdb=" C18 HQH D 501 " pdb=" C11 HQH D 501 " pdb=" C22 HQH D 501 " ideal model delta sigma weight residual 74.52 118.61 -44.09 3.00e+00 1.11e-01 2.16e+02 angle pdb=" C13 HQH D 501 " pdb=" C20 HQH D 501 " pdb=" C17 HQH D 501 " ideal model delta sigma weight residual 85.92 129.04 -43.12 3.00e+00 1.11e-01 2.07e+02 ... (remaining 93107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 40385 35.16 - 70.31: 1177 70.31 - 105.47: 59 105.47 - 140.62: 6 140.62 - 175.78: 4 Dihedral angle restraints: 41631 sinusoidal: 17753 harmonic: 23878 Sorted by residual: dihedral pdb=" CB CYS X 87 " pdb=" SG CYS X 87 " pdb=" SG CYS X 99 " pdb=" CB CYS X 99 " ideal model delta sinusoidal sigma weight residual 93.00 177.71 -84.71 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CB CYS p 76 " pdb=" SG CYS p 76 " pdb=" SG CYS p 83 " pdb=" CB CYS p 83 " ideal model delta sinusoidal sigma weight residual -86.00 -165.95 79.95 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CB CYS p 112 " pdb=" SG CYS p 112 " pdb=" SG CYS p 124 " pdb=" CB CYS p 124 " ideal model delta sinusoidal sigma weight residual 93.00 169.65 -76.65 1 1.00e+01 1.00e-02 7.38e+01 ... (remaining 41628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.260: 10127 4.260 - 8.521: 0 8.521 - 12.781: 0 12.781 - 17.041: 0 17.041 - 21.302: 24 Chirality restraints: 10151 Sorted by residual: chirality pdb="FE2 SF4 B 201 " pdb=" S1 SF4 B 201 " pdb=" S3 SF4 B 201 " pdb=" S4 SF4 B 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.75 21.30 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE3 SF4 B 201 " pdb=" S1 SF4 B 201 " pdb=" S2 SF4 B 201 " pdb=" S4 SF4 B 201 " both_signs ideal model delta sigma weight residual False -10.55 10.74 -21.30 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE3 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.65 -21.21 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10148 not shown) Planarity restraints: 11655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N SAC i 1 " 0.186 2.00e-02 2.50e+03 1.15e-01 1.65e+02 pdb=" CA SAC i 1 " -0.139 2.00e-02 2.50e+03 pdb=" C1A SAC i 1 " 0.034 2.00e-02 2.50e+03 pdb=" C2A SAC i 1 " -0.102 2.00e-02 2.50e+03 pdb=" OAC SAC i 1 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 HQH D 501 " -0.031 2.00e-02 2.50e+03 5.68e-02 3.23e+01 pdb=" C15 HQH D 501 " 0.030 2.00e-02 2.50e+03 pdb=" C18 HQH D 501 " 0.075 2.00e-02 2.50e+03 pdb=" C21 HQH D 501 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 135 " 0.032 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR B 135 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR B 135 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 135 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 135 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 135 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 135 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 135 " 0.004 2.00e-02 2.50e+03 ... (remaining 11652 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.14: 48 2.14 - 2.83: 20729 2.83 - 3.52: 94728 3.52 - 4.21: 162810 4.21 - 4.90: 292399 Nonbonded interactions: 570714 Sorted by model distance: nonbonded pdb=" OXT AME q 1 " pdb=" CA GLU q 2 " model vdw 1.445 2.776 nonbonded pdb=" OH TYR A 37 " pdb=" OE1 GLN D 54 " model vdw 1.977 2.440 nonbonded pdb=" OG SER C 43 " pdb=" O LEU C 45 " model vdw 2.010 2.440 nonbonded pdb=" O LEU A 73 " pdb=" OH TYR H 160 " model vdw 2.013 2.440 nonbonded pdb=" OG SER D 341 " pdb=" OG SER D 344 " model vdw 2.020 2.440 ... (remaining 570709 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 'T' selection = (chain 'U' and (resid 7 through 82 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 21.160 Check model and map are aligned: 0.770 Set scattering table: 0.470 Process input model: 146.770 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:9.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.011 0.136 68762 Z= 0.693 Angle : 1.080 44.876 93112 Z= 0.527 Chirality : 1.031 21.302 10151 Planarity : 0.006 0.115 11655 Dihedral : 16.333 175.778 26193 Min Nonbonded Distance : 1.445 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.90 % Favored : 92.06 % Rotamer: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.08), residues: 8075 helix: -1.43 (0.07), residues: 4216 sheet: -2.89 (0.22), residues: 400 loop : -2.99 (0.10), residues: 3459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 371 HIS 0.011 0.002 HIS S 21 PHE 0.033 0.002 PHE H 310 TYR 0.066 0.002 TYR B 135 ARG 0.011 0.001 ARG I 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1649 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1644 time to evaluate : 5.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 292 ASP cc_start: 0.8215 (p0) cc_final: 0.7967 (p0) REVERT: G 272 ASP cc_start: 0.7604 (t0) cc_final: 0.7288 (t0) REVERT: G 405 LYS cc_start: 0.7702 (ptpt) cc_final: 0.7434 (mmmm) REVERT: H 57 MET cc_start: 0.8041 (mtt) cc_final: 0.7782 (mtm) REVERT: L 23 MET cc_start: 0.7345 (mtm) cc_final: 0.7043 (mtm) REVERT: L 399 ILE cc_start: 0.8710 (tt) cc_final: 0.8492 (mp) REVERT: M 166 LEU cc_start: 0.8336 (tp) cc_final: 0.8115 (mt) REVERT: M 177 MET cc_start: 0.7500 (mtm) cc_final: 0.7261 (mtm) REVERT: M 350 MET cc_start: 0.7007 (mtt) cc_final: 0.6807 (mtt) REVERT: M 454 ILE cc_start: 0.8900 (tp) cc_final: 0.8673 (tt) REVERT: N 61 VAL cc_start: 0.9077 (t) cc_final: 0.8869 (m) REVERT: N 159 ILE cc_start: 0.8502 (mt) cc_final: 0.8203 (tp) REVERT: T 29 LYS cc_start: 0.7461 (mtpt) cc_final: 0.6934 (mtmm) REVERT: U 20 LYS cc_start: 0.8472 (mttt) cc_final: 0.8119 (mtmm) REVERT: Z 133 SER cc_start: 0.8418 (p) cc_final: 0.8193 (t) REVERT: h 8 LEU cc_start: 0.8326 (mt) cc_final: 0.8096 (mt) REVERT: i 15 ARG cc_start: 0.8488 (ttm110) cc_final: 0.8000 (ttm-80) REVERT: j 13 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7315 (pt0) REVERT: j 44 SER cc_start: 0.8559 (p) cc_final: 0.8300 (t) REVERT: m 4 LYS cc_start: 0.7440 (mttm) cc_final: 0.7053 (mmtt) outliers start: 5 outliers final: 7 residues processed: 1648 average time/residue: 1.5276 time to fit residues: 3249.4809 Evaluate side-chains 1034 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1027 time to evaluate : 5.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain h residue 127 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 674 optimal weight: 2.9990 chunk 605 optimal weight: 0.8980 chunk 336 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 408 optimal weight: 0.8980 chunk 323 optimal weight: 1.9990 chunk 626 optimal weight: 0.7980 chunk 242 optimal weight: 0.9990 chunk 380 optimal weight: 0.9990 chunk 466 optimal weight: 3.9990 chunk 725 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS C 21 GLN C 69 ASN C 145 HIS ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS E 58 ASN E 99 HIS F 83 ASN ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 ASN F 200 GLN F 257 ASN ** F 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN F 324 GLN G 237 ASN G 459 GLN ** G 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 629 ASN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN L 2 ASN L 72 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 269 ASN L 320 ASN L 452 ASN ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN M 44 GLN M 92 GLN M 139 GLN ** M 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 421 ASN N 49 ASN N 223 ASN N 235 ASN N 274 ASN O 50 HIS O 153 ASN P 136 ASN R 13 HIS R 94 HIS ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 72 GLN ** S 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 91 GLN T 35 HIS W 72 ASN ** X 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 150 ASN c 35 HIS c 36 ASN e 24 GLN e 28 ASN f 9 HIS g 25 GLN h 63 HIS h 108 GLN k 53 ASN n 107 HIS o 75 ASN p 27 ASN p 139 GLN q 69 ASN q 87 HIS q 116 ASN r 24 GLN ** s 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.279 68762 Z= 0.567 Angle : 1.600 51.052 93112 Z= 1.025 Chirality : 0.306 6.666 10151 Planarity : 0.005 0.075 11655 Dihedral : 12.597 173.801 10028 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.82 % Favored : 94.15 % Rotamer: Outliers : 2.81 % Allowed : 14.92 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -1.65 (0.09), residues: 8075 helix: -0.04 (0.08), residues: 4187 sheet: -2.15 (0.23), residues: 420 loop : -2.29 (0.10), residues: 3468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 144 HIS 0.007 0.001 HIS R 94 PHE 0.024 0.001 PHE H 211 TYR 0.026 0.001 TYR Y 24 ARG 0.009 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1391 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1189 time to evaluate : 5.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7384 (t70) cc_final: 0.7062 (m-30) REVERT: C 73 LYS cc_start: 0.8275 (ptpp) cc_final: 0.7999 (ptmt) REVERT: C 118 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.6985 (p0) REVERT: C 144 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.7866 (m110) REVERT: D 170 MET cc_start: 0.8241 (mmm) cc_final: 0.7879 (mmm) REVERT: D 249 ASP cc_start: 0.7502 (m-30) cc_final: 0.7301 (m-30) REVERT: D 292 ASP cc_start: 0.8369 (p0) cc_final: 0.8102 (p0) REVERT: E 10 ARG cc_start: 0.7653 (mtm-85) cc_final: 0.7305 (mmt90) REVERT: E 171 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6745 (mt-10) REVERT: E 174 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.6990 (m-30) REVERT: F 109 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7183 (mm-30) REVERT: F 112 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.6347 (ptm-80) REVERT: G 95 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7283 (tp30) REVERT: G 208 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7804 (pp) REVERT: G 272 ASP cc_start: 0.7643 (t0) cc_final: 0.7416 (t0) REVERT: G 351 THR cc_start: 0.7301 (t) cc_final: 0.6960 (t) REVERT: G 373 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: H 262 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8421 (mt-10) REVERT: I 99 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7612 (tt0) REVERT: M 35 SER cc_start: 0.9211 (t) cc_final: 0.8938 (p) REVERT: M 166 LEU cc_start: 0.8409 (tp) cc_final: 0.8066 (mt) REVERT: M 334 TYR cc_start: 0.8863 (t80) cc_final: 0.8620 (t80) REVERT: M 454 ILE cc_start: 0.8902 (tp) cc_final: 0.8664 (tt) REVERT: N 21 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7335 (mmt) REVERT: N 89 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.6546 (pm20) REVERT: N 225 MET cc_start: 0.7716 (mtt) cc_final: 0.7465 (mtt) REVERT: Q 31 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8364 (mmpt) REVERT: S 70 PHE cc_start: 0.4548 (m-10) cc_final: 0.3811 (m-80) REVERT: U 6 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8039 (pp) REVERT: U 20 LYS cc_start: 0.8471 (mttt) cc_final: 0.8257 (mtmm) REVERT: Y 38 SER cc_start: 0.8784 (m) cc_final: 0.8423 (m) REVERT: b 29 ILE cc_start: 0.9163 (mt) cc_final: 0.8926 (mm) REVERT: g 115 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7711 (ptmm) REVERT: h 67 TYR cc_start: 0.9064 (m-80) cc_final: 0.8764 (m-10) REVERT: h 109 GLU cc_start: 0.7777 (tp30) cc_final: 0.7556 (tt0) REVERT: h 131 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7792 (pt0) REVERT: i 112 THR cc_start: 0.7668 (p) cc_final: 0.7189 (m) REVERT: l 31 GLU cc_start: 0.8536 (mp0) cc_final: 0.8188 (mp0) REVERT: l 125 GLN cc_start: 0.8153 (mm110) cc_final: 0.7884 (mm110) REVERT: m 4 LYS cc_start: 0.7395 (mttm) cc_final: 0.7020 (mmtt) REVERT: q 78 ASP cc_start: 0.7897 (p0) cc_final: 0.7675 (p0) REVERT: q 81 MET cc_start: 0.8634 (mtp) cc_final: 0.8394 (mtp) REVERT: q 94 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8805 (p) REVERT: r 5 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6832 (ttm110) REVERT: r 69 MET cc_start: 0.7406 (tmm) cc_final: 0.7176 (tmt) outliers start: 202 outliers final: 50 residues processed: 1294 average time/residue: 1.4322 time to fit residues: 2438.5232 Evaluate side-chains 1053 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 988 time to evaluate : 5.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 666 LEU Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 317 VAL Chi-restraints excluded: chain P residue 335 LYS Chi-restraints excluded: chain Q residue 31 LYS Chi-restraints excluded: chain Q residue 80 SER Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 33 ASN Chi-restraints excluded: chain U residue 38 LYS Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 125 SER Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain X residue 158 LYS Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 48 THR Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain g residue 115 LYS Chi-restraints excluded: chain h residue 34 ILE Chi-restraints excluded: chain h residue 131 GLU Chi-restraints excluded: chain i residue 33 VAL Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 123 SER Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 94 THR Chi-restraints excluded: chain r residue 5 ARG Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain s residue 66 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 403 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 603 optimal weight: 1.9990 chunk 494 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 726 optimal weight: 9.9990 chunk 785 optimal weight: 1.9990 chunk 647 optimal weight: 3.9990 chunk 720 optimal weight: 10.0000 chunk 247 optimal weight: 6.9990 chunk 583 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN D 5 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN E 16 ASN E 58 ASN F 200 GLN ** F 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 GLN ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 682 GLN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN I 67 HIS I 158 ASN I 159 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 2 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 570 HIS M 175 ASN M 213 HIS M 304 GLN M 374 ASN M 421 ASN N 49 ASN N 222 ASN N 228 ASN O 97 GLN O 107 GLN O 294 ASN R 94 HIS S 30 GLN S 79 ASN S 91 GLN V 52 ASN X 72 GLN ** X 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 ASN e 81 GLN f 4 GLN g 43 HIS l 55 HIS l 77 HIS n 13 GLN n 25 HIS n 32 HIS o 75 ASN p 27 ASN q 116 ASN r 20 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.247 68762 Z= 0.594 Angle : 1.616 50.837 93112 Z= 1.031 Chirality : 0.310 6.395 10151 Planarity : 0.005 0.068 11655 Dihedral : 12.049 170.202 10020 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.24 % Favored : 93.73 % Rotamer: Outliers : 4.36 % Allowed : 16.90 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -1.05 (0.09), residues: 8075 helix: 0.35 (0.08), residues: 4215 sheet: -1.39 (0.25), residues: 391 loop : -1.94 (0.10), residues: 3469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP X 85 HIS 0.008 0.001 HIS o 60 PHE 0.026 0.002 PHE M 151 TYR 0.031 0.002 TYR Y 24 ARG 0.006 0.001 ARG G 515 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1456 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 1143 time to evaluate : 5.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7487 (t70) cc_final: 0.7156 (m-30) REVERT: B 45 ASP cc_start: 0.7772 (m-30) cc_final: 0.7484 (m-30) REVERT: C 97 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8443 (pt) REVERT: D 170 MET cc_start: 0.8441 (mmm) cc_final: 0.8189 (mmm) REVERT: D 295 ASP cc_start: 0.8332 (m-30) cc_final: 0.8132 (m-30) REVERT: D 318 MET cc_start: 0.8078 (tpp) cc_final: 0.7303 (tpp) REVERT: E 10 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.7377 (mmt90) REVERT: F 77 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8076 (tp) REVERT: F 84 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.6329 (pptt) REVERT: F 158 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7082 (tp30) REVERT: F 435 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6811 (tt0) REVERT: G 181 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8483 (ttm) REVERT: G 272 ASP cc_start: 0.7799 (t0) cc_final: 0.7553 (t0) REVERT: H 62 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.6183 (ptm160) REVERT: H 181 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7545 (mmt) REVERT: H 262 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8573 (mt-10) REVERT: I 84 LEU cc_start: 0.9023 (pp) cc_final: 0.8778 (pt) REVERT: J 166 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8712 (pt) REVERT: L 15 LEU cc_start: 0.8867 (mm) cc_final: 0.8546 (mt) REVERT: M 166 LEU cc_start: 0.8686 (tp) cc_final: 0.8188 (mt) REVERT: M 334 TYR cc_start: 0.8983 (t80) cc_final: 0.8762 (t80) REVERT: M 454 ILE cc_start: 0.8929 (tp) cc_final: 0.8649 (tt) REVERT: N 314 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7853 (mmm) REVERT: P 127 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6878 (pt0) REVERT: P 207 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8798 (p) REVERT: P 244 TYR cc_start: 0.9137 (t80) cc_final: 0.8413 (t80) REVERT: P 330 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: Q 63 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7233 (tp30) REVERT: U 6 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8241 (pp) REVERT: U 20 LYS cc_start: 0.8531 (mttt) cc_final: 0.8296 (mtmm) REVERT: U 37 MET cc_start: 0.5354 (OUTLIER) cc_final: 0.4619 (mmm) REVERT: W 43 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7616 (mmp-170) REVERT: X 90 TYR cc_start: 0.8720 (t80) cc_final: 0.8507 (t80) REVERT: Y 8 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7431 (mm-30) REVERT: Y 38 SER cc_start: 0.8930 (m) cc_final: 0.8556 (m) REVERT: b 9 LYS cc_start: 0.7823 (ttpt) cc_final: 0.7143 (mptt) REVERT: d 19 ARG cc_start: 0.8395 (mmm-85) cc_final: 0.8185 (mtm-85) REVERT: d 47 MET cc_start: 0.7917 (mtp) cc_final: 0.7514 (mtp) REVERT: e 18 MET cc_start: 0.8658 (mmm) cc_final: 0.8433 (mmm) REVERT: e 72 MET cc_start: 0.8395 (mtt) cc_final: 0.8059 (mtt) REVERT: f 4 GLN cc_start: 0.5479 (mt0) cc_final: 0.5192 (mm-40) REVERT: g 115 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7743 (ptmm) REVERT: h 67 TYR cc_start: 0.9029 (m-10) cc_final: 0.8752 (m-10) REVERT: h 109 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: l 125 GLN cc_start: 0.8209 (mm110) cc_final: 0.7958 (mm110) REVERT: m 4 LYS cc_start: 0.7429 (mttm) cc_final: 0.7044 (mmtt) REVERT: o 42 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: o 75 ASN cc_start: 0.7554 (t0) cc_final: 0.7352 (t0) REVERT: o 102 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6949 (tm-30) REVERT: p 11 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6947 (tm-30) outliers start: 313 outliers final: 107 residues processed: 1325 average time/residue: 1.3951 time to fit residues: 2443.3161 Evaluate side-chains 1142 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1012 time to evaluate : 5.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 181 MET Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 614 ASP Chi-restraints excluded: chain G residue 629 ASN Chi-restraints excluded: chain G residue 666 LEU Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 378 LEU Chi-restraints excluded: chain L residue 565 SER Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 344 MET Chi-restraints excluded: chain M residue 351 VAL Chi-restraints excluded: chain M residue 372 SER Chi-restraints excluded: chain M residue 411 ILE Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain N residue 2 ASN Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 283 THR Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 317 VAL Chi-restraints excluded: chain P residue 330 GLU Chi-restraints excluded: chain P residue 335 LYS Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain Q residue 80 SER Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain T residue 64 ASP Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain U residue 38 LYS Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 43 ARG Chi-restraints excluded: chain W residue 75 VAL Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain X residue 158 LYS Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 48 THR Chi-restraints excluded: chain b residue 67 SER Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain g residue 115 LYS Chi-restraints excluded: chain h residue 109 GLU Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain i residue 33 VAL Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain m residue 125 ASN Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain n residue 153 LEU Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 42 GLN Chi-restraints excluded: chain o residue 53 GLN Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain p residue 11 GLU Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain p residue 116 GLU Chi-restraints excluded: chain q residue 94 THR Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain s residue 54 LYS Chi-restraints excluded: chain s residue 66 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 718 optimal weight: 8.9990 chunk 546 optimal weight: 6.9990 chunk 377 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 346 optimal weight: 0.5980 chunk 488 optimal weight: 0.0970 chunk 729 optimal weight: 1.9990 chunk 772 optimal weight: 8.9990 chunk 381 optimal weight: 5.9990 chunk 691 optimal weight: 3.9990 chunk 208 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** F 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 GLN ** G 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 109 HIS L 113 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 579 ASN M 88 ASN M 415 GLN M 421 ASN N 63 GLN N 87 GLN O 309 ASN Q 121 ASN R 94 HIS V 109 ASN W 60 GLN W 72 ASN ** X 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 ASN g 84 GLN g 117 GLN l 77 HIS n 13 GLN ** o 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 27 ASN q 116 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 68762 Z= 0.534 Angle : 1.580 50.545 93112 Z= 1.017 Chirality : 0.310 6.367 10151 Planarity : 0.005 0.067 11655 Dihedral : 11.583 170.927 10020 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.41 % Favored : 94.56 % Rotamer: Outliers : 3.92 % Allowed : 18.88 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -0.63 (0.09), residues: 8075 helix: 0.68 (0.08), residues: 4204 sheet: -1.16 (0.25), residues: 407 loop : -1.71 (0.10), residues: 3464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 371 HIS 0.006 0.001 HIS o 3 PHE 0.020 0.001 PHE H 211 TYR 0.026 0.001 TYR Y 24 ARG 0.004 0.000 ARG L 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1378 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1097 time to evaluate : 5.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7504 (t70) cc_final: 0.7176 (m-30) REVERT: C 73 LYS cc_start: 0.8335 (ptpp) cc_final: 0.8020 (ptmt) REVERT: D 170 MET cc_start: 0.8428 (mmm) cc_final: 0.8133 (mmm) REVERT: D 318 MET cc_start: 0.8236 (tpp) cc_final: 0.7789 (tpp) REVERT: E 10 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7287 (mmt90) REVERT: F 84 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.6269 (pptt) REVERT: G 7 ASN cc_start: 0.7086 (p0) cc_final: 0.6861 (p0) REVERT: G 107 ILE cc_start: 0.8030 (mt) cc_final: 0.7821 (mt) REVERT: G 249 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8767 (ptt180) REVERT: G 373 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: G 405 LYS cc_start: 0.7612 (mmmt) cc_final: 0.7185 (mttp) REVERT: G 654 GLN cc_start: 0.6772 (mm-40) cc_final: 0.6216 (mt0) REVERT: H 262 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8542 (mt-10) REVERT: I 84 LEU cc_start: 0.8866 (pp) cc_final: 0.8648 (pt) REVERT: I 172 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8502 (tp40) REVERT: L 15 LEU cc_start: 0.8904 (mm) cc_final: 0.8541 (mt) REVERT: M 166 LEU cc_start: 0.8647 (tp) cc_final: 0.8177 (mt) REVERT: M 334 TYR cc_start: 0.8992 (t80) cc_final: 0.8754 (t80) REVERT: M 335 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7631 (mt-10) REVERT: M 454 ILE cc_start: 0.8891 (tp) cc_final: 0.8640 (tt) REVERT: N 117 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7710 (mt-10) REVERT: N 313 MET cc_start: 0.8670 (mmt) cc_final: 0.8365 (mmt) REVERT: N 314 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7739 (mtm) REVERT: P 127 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6691 (pt0) REVERT: S 39 ARG cc_start: 0.7615 (mmm-85) cc_final: 0.7410 (mtt-85) REVERT: T 29 LYS cc_start: 0.7922 (ptmt) cc_final: 0.7526 (ptpp) REVERT: U 20 LYS cc_start: 0.8524 (mttt) cc_final: 0.8281 (mtmm) REVERT: W 43 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7640 (mmp-170) REVERT: X 15 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.6163 (mp0) REVERT: Y 38 SER cc_start: 0.8849 (m) cc_final: 0.8478 (m) REVERT: Y 114 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7296 (ttt) REVERT: Y 141 LYS cc_start: 0.7759 (ptmt) cc_final: 0.7503 (pptt) REVERT: a 54 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8353 (mp) REVERT: b 9 LYS cc_start: 0.7777 (ttpt) cc_final: 0.7124 (mptt) REVERT: b 51 ASN cc_start: 0.8127 (m-40) cc_final: 0.7915 (m-40) REVERT: d 47 MET cc_start: 0.7829 (mtp) cc_final: 0.7462 (mtp) REVERT: e 68 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.6699 (mpt-90) REVERT: e 72 MET cc_start: 0.8364 (mtt) cc_final: 0.8073 (mtt) REVERT: g 115 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7727 (ptmm) REVERT: h 67 TYR cc_start: 0.8965 (m-10) cc_final: 0.8678 (m-10) REVERT: h 109 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: j 60 THR cc_start: 0.8447 (p) cc_final: 0.8159 (t) REVERT: l 125 GLN cc_start: 0.8215 (mm110) cc_final: 0.7979 (mm110) REVERT: n 56 MET cc_start: 0.6080 (mmp) cc_final: 0.5861 (mmm) REVERT: o 102 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6879 (tm-30) REVERT: p 11 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6950 (tm-30) REVERT: p 54 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7466 (mp10) REVERT: q 32 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.7084 (m-30) outliers start: 281 outliers final: 100 residues processed: 1264 average time/residue: 1.3963 time to fit residues: 2351.0578 Evaluate side-chains 1139 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1021 time to evaluate : 5.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 275 TYR Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain E residue 89 MET Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain G residue 272 ASP Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 604 SER Chi-restraints excluded: chain G residue 614 ASP Chi-restraints excluded: chain G residue 629 ASN Chi-restraints excluded: chain G residue 666 LEU Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 240 ILE Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 172 GLN Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 308 SER Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain N residue 2 ASN Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 283 THR Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 317 VAL Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 80 SER Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain S residue 17 GLU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain U residue 52 MET Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 43 ARG Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain X residue 15 GLU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain X residue 158 LYS Chi-restraints excluded: chain Y residue 114 MET Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 48 THR Chi-restraints excluded: chain b residue 67 SER Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 20 VAL Chi-restraints excluded: chain g residue 35 VAL Chi-restraints excluded: chain g residue 115 LYS Chi-restraints excluded: chain h residue 109 GLU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 33 VAL Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain n residue 153 LEU Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 53 GLN Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain p residue 11 GLU Chi-restraints excluded: chain p residue 54 GLN Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 32 ASP Chi-restraints excluded: chain q residue 94 THR Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 100 MET Chi-restraints excluded: chain s residue 66 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 643 optimal weight: 7.9990 chunk 438 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 575 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 chunk 659 optimal weight: 6.9990 chunk 533 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 394 optimal weight: 1.9990 chunk 693 optimal weight: 0.0870 chunk 194 optimal weight: 0.0670 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** F 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 ASN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 403 ASN ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 579 ASN M 82 ASN M 88 ASN M 430 HIS N 87 GLN R 94 HIS S 72 GLN ** X 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 89 ASN e 81 GLN f 4 GLN g 84 GLN g 117 GLN m 78 ASN n 13 GLN ** o 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 55 HIS q 116 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.249 68762 Z= 0.529 Angle : 1.575 50.664 93112 Z= 1.015 Chirality : 0.308 6.331 10151 Planarity : 0.004 0.065 11655 Dihedral : 11.258 173.771 10020 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.35 % Favored : 94.63 % Rotamer: Outliers : 3.83 % Allowed : 20.03 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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 (0.09), residues: 8075 helix: 0.88 (0.08), residues: 4193 sheet: -1.01 (0.26), residues: 416 loop : -1.54 (0.10), residues: 3466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 144 HIS 0.012 0.001 HIS D 79 PHE 0.023 0.001 PHE H 211 TYR 0.025 0.001 TYR Y 24 ARG 0.006 0.000 ARG i 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1384 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1109 time to evaluate : 6.013 Fit side-chains revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7530 (t70) cc_final: 0.7249 (m-30) REVERT: C 73 LYS cc_start: 0.8198 (ptpp) cc_final: 0.7957 (ptmt) REVERT: C 97 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8544 (pt) REVERT: C 118 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7556 (p0) REVERT: D 170 MET cc_start: 0.8453 (mmm) cc_final: 0.8085 (mmm) REVERT: E 18 ASP cc_start: 0.6843 (OUTLIER) cc_final: 0.6637 (t0) REVERT: F 84 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.6291 (pptt) REVERT: F 258 ILE cc_start: 0.8215 (mt) cc_final: 0.7974 (mp) REVERT: F 307 ILE cc_start: 0.8069 (mm) cc_final: 0.7632 (mt) REVERT: G 202 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8206 (mm) REVERT: G 249 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8754 (ptt180) REVERT: G 272 ASP cc_start: 0.7848 (t0) cc_final: 0.7549 (t0) REVERT: G 405 LYS cc_start: 0.7640 (mmmt) cc_final: 0.7087 (mttp) REVERT: G 654 GLN cc_start: 0.6739 (mm-40) cc_final: 0.6535 (mt0) REVERT: H 62 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.5816 (ptm160) REVERT: H 89 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8812 (mp) REVERT: I 172 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8503 (tp40) REVERT: L 15 LEU cc_start: 0.8789 (mm) cc_final: 0.8450 (mt) REVERT: L 539 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7520 (tmm) REVERT: M 41 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8120 (mt) REVERT: M 334 TYR cc_start: 0.8990 (t80) cc_final: 0.8743 (t80) REVERT: M 335 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7597 (mt-10) REVERT: M 454 ILE cc_start: 0.8892 (tp) cc_final: 0.8656 (tt) REVERT: N 314 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7760 (mtm) REVERT: P 127 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6578 (pt0) REVERT: P 207 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8754 (p) REVERT: Q 63 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7032 (tp30) REVERT: T 29 LYS cc_start: 0.7823 (ptmt) cc_final: 0.7581 (ptpp) REVERT: U 20 LYS cc_start: 0.8518 (mttt) cc_final: 0.8274 (mtmm) REVERT: V 56 ASP cc_start: 0.8437 (m-30) cc_final: 0.8224 (m-30) REVERT: W 43 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7672 (mmp-170) REVERT: X 15 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.6121 (mp0) REVERT: Y 38 SER cc_start: 0.8826 (m) cc_final: 0.8473 (m) REVERT: Y 141 LYS cc_start: 0.7715 (ptmt) cc_final: 0.7469 (pptt) REVERT: a 54 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8380 (mp) REVERT: b 9 LYS cc_start: 0.7769 (ttpt) cc_final: 0.7344 (tppt) REVERT: e 68 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.6677 (mpt-90) REVERT: e 72 MET cc_start: 0.8345 (mtt) cc_final: 0.8094 (mtt) REVERT: e 75 MET cc_start: 0.7891 (mmt) cc_final: 0.7629 (mmt) REVERT: g 109 ASN cc_start: 0.7660 (OUTLIER) cc_final: 0.7396 (p0) REVERT: g 115 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7669 (ptmm) REVERT: h 67 TYR cc_start: 0.8976 (m-10) cc_final: 0.8671 (m-10) REVERT: i 89 MET cc_start: 0.8004 (mtp) cc_final: 0.7766 (mtm) REVERT: j 60 THR cc_start: 0.8412 (p) cc_final: 0.8151 (t) REVERT: n 56 MET cc_start: 0.6095 (mmp) cc_final: 0.5884 (mmm) REVERT: o 102 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6865 (tm-30) REVERT: p 11 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7026 (tm-30) REVERT: p 54 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7453 (mp10) REVERT: q 41 GLU cc_start: 0.7693 (tp30) cc_final: 0.7316 (tp30) outliers start: 275 outliers final: 115 residues processed: 1281 average time/residue: 1.4092 time to fit residues: 2390.2955 Evaluate side-chains 1173 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1034 time to evaluate : 5.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 275 TYR Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 89 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain G residue 357 ASP Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 572 THR Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 604 SER Chi-restraints excluded: chain G residue 629 ASN Chi-restraints excluded: chain G residue 666 LEU Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 172 GLN Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 98 MET Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 378 LEU Chi-restraints excluded: chain L residue 539 MET Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 308 SER Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 283 THR Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 317 VAL Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain Q residue 80 SER Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain S residue 17 GLU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 64 ASP Chi-restraints excluded: chain U residue 33 ASN Chi-restraints excluded: chain U residue 52 MET Chi-restraints excluded: chain W residue 43 ARG Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain X residue 15 GLU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain X residue 156 ASP Chi-restraints excluded: chain X residue 158 LYS Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 48 THR Chi-restraints excluded: chain b residue 67 SER Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 20 VAL Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 109 ASN Chi-restraints excluded: chain g residue 115 LYS Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 16 GLU Chi-restraints excluded: chain i residue 33 VAL Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 123 SER Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain n residue 153 LEU Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 53 GLN Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain p residue 11 GLU Chi-restraints excluded: chain p residue 54 GLN Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 94 THR Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 100 MET Chi-restraints excluded: chain s residue 66 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 259 optimal weight: 1.9990 chunk 695 optimal weight: 0.0870 chunk 152 optimal weight: 2.9990 chunk 453 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 773 optimal weight: 5.9990 chunk 641 optimal weight: 7.9990 chunk 357 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 255 optimal weight: 1.9990 chunk 405 optimal weight: 1.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 HIS ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 7 ASN G 51 ASN ** G 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 ASN ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 579 ASN M 82 ASN M 88 ASN N 87 GLN R 94 HIS S 72 GLN S 91 GLN ** X 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 ASN e 28 ASN e 81 GLN g 84 GLN g 117 GLN h 108 GLN n 13 GLN ** o 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 116 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 68762 Z= 0.550 Angle : 1.585 50.542 93112 Z= 1.019 Chirality : 0.310 6.354 10151 Planarity : 0.005 0.062 11655 Dihedral : 11.169 177.672 10020 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.44 % Favored : 94.54 % Rotamer: Outliers : 3.87 % Allowed : 20.93 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.09), residues: 8075 helix: 0.90 (0.08), residues: 4199 sheet: -0.95 (0.26), residues: 425 loop : -1.42 (0.11), residues: 3451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 371 HIS 0.007 0.001 HIS G 101 PHE 0.024 0.001 PHE H 211 TYR 0.027 0.001 TYR Y 24 ARG 0.012 0.000 ARG L 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 1082 time to evaluate : 5.926 Fit side-chains revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7609 (t70) cc_final: 0.7277 (m-30) REVERT: C 73 LYS cc_start: 0.8322 (ptpp) cc_final: 0.8074 (ptmt) REVERT: C 97 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8545 (pt) REVERT: C 118 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7576 (p0) REVERT: D 170 MET cc_start: 0.8509 (mmm) cc_final: 0.8098 (mmm) REVERT: E 10 ARG cc_start: 0.7420 (mtt-85) cc_final: 0.7053 (mmt90) REVERT: E 18 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6774 (t0) REVERT: E 106 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7854 (m) REVERT: F 73 PHE cc_start: 0.6833 (t80) cc_final: 0.6074 (m-80) REVERT: F 84 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.6327 (pptt) REVERT: F 101 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6790 (tt0) REVERT: F 307 ILE cc_start: 0.8099 (mm) cc_final: 0.7604 (mt) REVERT: F 435 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6886 (tt0) REVERT: G 249 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8795 (ptt180) REVERT: G 272 ASP cc_start: 0.7852 (t0) cc_final: 0.7541 (t0) REVERT: G 654 GLN cc_start: 0.6860 (mm-40) cc_final: 0.6627 (mt0) REVERT: H 89 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8814 (mp) REVERT: H 265 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7812 (tp) REVERT: H 302 MET cc_start: 0.8673 (mtp) cc_final: 0.8388 (mtp) REVERT: L 15 LEU cc_start: 0.8815 (mm) cc_final: 0.8455 (mt) REVERT: L 359 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.6858 (mtt) REVERT: M 41 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8216 (mt) REVERT: M 334 TYR cc_start: 0.9033 (t80) cc_final: 0.8760 (t80) REVERT: M 335 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7715 (mt-10) REVERT: M 454 ILE cc_start: 0.8922 (tp) cc_final: 0.8670 (tt) REVERT: N 314 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7854 (mtm) REVERT: O 144 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8147 (mp) REVERT: P 127 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6606 (pt0) REVERT: P 207 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8797 (p) REVERT: P 330 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: Q 63 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7036 (tp30) REVERT: R 21 LYS cc_start: 0.8617 (mppt) cc_final: 0.8343 (mtmt) REVERT: T 29 LYS cc_start: 0.7901 (ptmt) cc_final: 0.7580 (ptpp) REVERT: T 52 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7182 (mtt) REVERT: T 80 ILE cc_start: 0.7148 (mm) cc_final: 0.6721 (mm) REVERT: U 20 LYS cc_start: 0.8552 (mttt) cc_final: 0.8303 (mtmm) REVERT: V 56 ASP cc_start: 0.8465 (m-30) cc_final: 0.8218 (m-30) REVERT: W 43 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7685 (mmp-170) REVERT: X 15 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6292 (mp0) REVERT: Y 38 SER cc_start: 0.8854 (m) cc_final: 0.8491 (m) REVERT: Y 82 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7787 (ptm160) REVERT: Y 141 LYS cc_start: 0.7828 (ptmt) cc_final: 0.7599 (pptt) REVERT: a 54 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8407 (mp) REVERT: b 9 LYS cc_start: 0.7779 (ttpt) cc_final: 0.7162 (mptt) REVERT: e 68 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.6721 (mpt-90) REVERT: g 115 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7702 (ptmm) REVERT: h 67 TYR cc_start: 0.9012 (m-10) cc_final: 0.8713 (m-10) REVERT: j 60 THR cc_start: 0.8478 (p) cc_final: 0.8222 (t) REVERT: n 56 MET cc_start: 0.6196 (mmp) cc_final: 0.5972 (mmm) REVERT: o 45 MET cc_start: 0.8231 (tpp) cc_final: 0.7902 (ttt) REVERT: o 102 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6858 (tm-30) REVERT: p 11 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: q 54 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7569 (mt0) outliers start: 278 outliers final: 131 residues processed: 1256 average time/residue: 1.4030 time to fit residues: 2356.3515 Evaluate side-chains 1184 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1025 time to evaluate : 5.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 275 TYR Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 357 ASP Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 572 THR Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 614 ASP Chi-restraints excluded: chain G residue 629 ASN Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain G residue 666 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain L residue 359 MET Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 565 SER Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 308 SER Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain N residue 2 ASN Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 209 THR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 283 THR Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 317 VAL Chi-restraints excluded: chain P residue 330 GLU Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain Q residue 80 SER Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 64 ASP Chi-restraints excluded: chain T residue 82 ASP Chi-restraints excluded: chain U residue 33 ASN Chi-restraints excluded: chain W residue 43 ARG Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain X residue 15 GLU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain X residue 156 ASP Chi-restraints excluded: chain X residue 158 LYS Chi-restraints excluded: chain Y residue 82 ARG Chi-restraints excluded: chain Z residue 71 MET Chi-restraints excluded: chain Z residue 102 ASN Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 67 SER Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain f residue 20 VAL Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 115 LYS Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 16 GLU Chi-restraints excluded: chain i residue 33 VAL Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 79 ASP Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain n residue 153 LEU Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 53 GLN Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain p residue 11 GLU Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 54 GLN Chi-restraints excluded: chain q residue 94 THR Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 100 MET Chi-restraints excluded: chain s residue 66 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 745 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 440 optimal weight: 6.9990 chunk 564 optimal weight: 1.9990 chunk 437 optimal weight: 0.9990 chunk 650 optimal weight: 6.9990 chunk 431 optimal weight: 3.9990 chunk 770 optimal weight: 7.9990 chunk 481 optimal weight: 0.7980 chunk 469 optimal weight: 0.7980 chunk 355 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 HIS ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 7 ASN G 51 ASN ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 579 ASN M 82 ASN M 88 ASN M 139 GLN N 87 GLN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 HIS S 72 GLN ** X 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 ASN d 61 GLN e 28 ASN e 81 GLN f 12 HIS n 13 GLN ** o 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 119 ASN p 121 GLN q 116 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 68762 Z= 0.540 Angle : 1.582 50.565 93112 Z= 1.018 Chirality : 0.309 6.341 10151 Planarity : 0.004 0.064 11655 Dihedral : 11.018 179.995 10020 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.47 % Favored : 94.50 % Rotamer: Outliers : 3.85 % Allowed : 21.63 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -0.15 (0.10), residues: 8075 helix: 0.97 (0.08), residues: 4191 sheet: -0.73 (0.26), residues: 403 loop : -1.36 (0.11), residues: 3481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 371 HIS 0.005 0.001 HIS D 347 PHE 0.020 0.001 PHE H 211 TYR 0.025 0.001 TYR Y 24 ARG 0.010 0.000 ARG X 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1361 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1085 time to evaluate : 6.319 Fit side-chains revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7575 (t70) cc_final: 0.7244 (m-30) REVERT: A 79 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8422 (pt) REVERT: C 73 LYS cc_start: 0.8284 (ptpp) cc_final: 0.8053 (ptmt) REVERT: C 97 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8548 (pt) REVERT: D 170 MET cc_start: 0.8508 (mmm) cc_final: 0.8115 (mmm) REVERT: E 10 ARG cc_start: 0.7425 (mtt-85) cc_final: 0.7199 (mmt90) REVERT: F 21 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.8004 (mt) REVERT: F 73 PHE cc_start: 0.6840 (t80) cc_final: 0.6086 (m-80) REVERT: F 84 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.6331 (pptt) REVERT: F 101 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6811 (tt0) REVERT: F 307 ILE cc_start: 0.8090 (mm) cc_final: 0.7598 (mt) REVERT: F 435 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6877 (tt0) REVERT: G 202 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8126 (mm) REVERT: G 249 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8766 (ptt180) REVERT: G 272 ASP cc_start: 0.7810 (t0) cc_final: 0.7553 (t0) REVERT: G 405 LYS cc_start: 0.7580 (mmmt) cc_final: 0.7061 (mttp) REVERT: G 654 GLN cc_start: 0.6929 (mm-40) cc_final: 0.6530 (mt0) REVERT: H 89 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8809 (mp) REVERT: H 265 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7828 (tp) REVERT: H 302 MET cc_start: 0.8703 (mtp) cc_final: 0.8421 (mtp) REVERT: L 15 LEU cc_start: 0.8790 (mm) cc_final: 0.8576 (mt) REVERT: L 136 ASN cc_start: 0.8049 (m110) cc_final: 0.7793 (m-40) REVERT: L 359 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.6797 (mtt) REVERT: L 482 MET cc_start: 0.8161 (ptt) cc_final: 0.7939 (ptt) REVERT: M 41 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8254 (mt) REVERT: M 263 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8814 (mm) REVERT: M 334 TYR cc_start: 0.9075 (t80) cc_final: 0.8767 (t80) REVERT: M 335 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7687 (mt-10) REVERT: M 454 ILE cc_start: 0.8929 (tp) cc_final: 0.8686 (tt) REVERT: N 313 MET cc_start: 0.8626 (mmt) cc_final: 0.8252 (mmt) REVERT: N 314 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7818 (mtm) REVERT: O 144 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8135 (mp) REVERT: P 127 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6683 (pt0) REVERT: P 207 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8795 (p) REVERT: Q 63 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7021 (tp30) REVERT: R 21 LYS cc_start: 0.8603 (mppt) cc_final: 0.8341 (mtmt) REVERT: T 29 LYS cc_start: 0.7861 (ptmt) cc_final: 0.7571 (ptpp) REVERT: U 20 LYS cc_start: 0.8528 (mttt) cc_final: 0.8327 (mtpt) REVERT: V 56 ASP cc_start: 0.8456 (m-30) cc_final: 0.8195 (m-30) REVERT: W 43 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7679 (mmp-170) REVERT: X 15 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6300 (mp0) REVERT: Y 8 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7103 (mt-10) REVERT: Y 38 SER cc_start: 0.8831 (m) cc_final: 0.8476 (m) REVERT: Y 82 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7731 (ptm160) REVERT: Y 141 LYS cc_start: 0.7866 (ptmt) cc_final: 0.7627 (pptt) REVERT: a 54 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8443 (mp) REVERT: e 68 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.6718 (mpt-90) REVERT: f 41 MET cc_start: 0.7445 (mmm) cc_final: 0.7090 (mmm) REVERT: h 67 TYR cc_start: 0.9024 (m-10) cc_final: 0.8817 (m-10) REVERT: j 60 THR cc_start: 0.8520 (p) cc_final: 0.8247 (t) REVERT: q 32 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.6870 (t0) REVERT: q 54 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7563 (mt0) outliers start: 276 outliers final: 134 residues processed: 1255 average time/residue: 1.3953 time to fit residues: 2313.9122 Evaluate side-chains 1196 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1037 time to evaluate : 5.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 275 TYR Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 431 GLN Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 357 ASP Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 572 THR Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 604 SER Chi-restraints excluded: chain G residue 614 ASP Chi-restraints excluded: chain G residue 629 ASN Chi-restraints excluded: chain G residue 640 ASN Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 211 PHE Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 98 MET Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 359 MET Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 378 LEU Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 565 SER Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 308 SER Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain N residue 2 ASN Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 283 THR Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 282 ASP Chi-restraints excluded: chain P residue 317 VAL Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain Q residue 80 SER Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 64 ASP Chi-restraints excluded: chain U residue 33 ASN Chi-restraints excluded: chain U residue 56 ASP Chi-restraints excluded: chain W residue 43 ARG Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain X residue 15 GLU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain X residue 156 ASP Chi-restraints excluded: chain X residue 158 LYS Chi-restraints excluded: chain Y residue 82 ARG Chi-restraints excluded: chain Z residue 71 MET Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 67 SER Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain f residue 20 VAL Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 16 GLU Chi-restraints excluded: chain i residue 33 VAL Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 51 PHE Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 79 ASP Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain n residue 153 LEU Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 53 GLN Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 32 ASP Chi-restraints excluded: chain q residue 54 GLN Chi-restraints excluded: chain q residue 94 THR Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 100 MET Chi-restraints excluded: chain s residue 66 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 476 optimal weight: 3.9990 chunk 307 optimal weight: 4.9990 chunk 459 optimal weight: 8.9990 chunk 231 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 489 optimal weight: 1.9990 chunk 524 optimal weight: 2.9990 chunk 380 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 605 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 HIS ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 7 ASN G 51 ASN ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 365 ASN ** G 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 446 ASN ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 579 ASN L 580 GLN M 82 ASN M 88 ASN N 87 GLN O 36 ASN P 112 ASN P 234 ASN R 94 HIS S 72 GLN S 79 ASN S 92 ASN ** X 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 ASN e 28 ASN e 81 GLN n 13 GLN ** o 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 116 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 68762 Z= 0.538 Angle : 1.583 50.586 93112 Z= 1.018 Chirality : 0.309 6.350 10151 Planarity : 0.004 0.063 11655 Dihedral : 10.883 178.481 10020 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.34 % Favored : 94.64 % Rotamer: Outliers : 3.41 % Allowed : 22.24 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.10), residues: 8075 helix: 1.00 (0.08), residues: 4209 sheet: -0.70 (0.26), residues: 404 loop : -1.30 (0.11), residues: 3462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 371 HIS 0.009 0.001 HIS G 101 PHE 0.021 0.001 PHE o 24 TYR 0.024 0.001 TYR Y 24 ARG 0.005 0.000 ARG a 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1345 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1100 time to evaluate : 5.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7600 (t70) cc_final: 0.7257 (m-30) REVERT: A 79 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8428 (pt) REVERT: C 73 LYS cc_start: 0.8283 (ptpp) cc_final: 0.8056 (ptmt) REVERT: C 97 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8541 (pt) REVERT: D 170 MET cc_start: 0.8527 (mmm) cc_final: 0.8137 (mmm) REVERT: E 10 ARG cc_start: 0.7459 (mtt-85) cc_final: 0.7214 (mmt90) REVERT: F 21 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.8020 (mt) REVERT: F 73 PHE cc_start: 0.6785 (t80) cc_final: 0.6060 (m-80) REVERT: F 84 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6321 (pptt) REVERT: F 101 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6810 (tt0) REVERT: F 307 ILE cc_start: 0.8085 (mm) cc_final: 0.7599 (mt) REVERT: G 19 MET cc_start: 0.7494 (mmm) cc_final: 0.7287 (mmt) REVERT: G 74 MET cc_start: 0.7527 (mtp) cc_final: 0.7187 (ptp) REVERT: G 202 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8074 (mm) REVERT: G 249 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8757 (ptt180) REVERT: G 272 ASP cc_start: 0.7781 (t0) cc_final: 0.7544 (t0) REVERT: H 89 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8756 (mp) REVERT: H 265 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7833 (tp) REVERT: H 302 MET cc_start: 0.8717 (mtp) cc_final: 0.8458 (mtp) REVERT: I 172 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: L 359 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.6773 (mtt) REVERT: L 562 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8466 (mm) REVERT: M 41 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8212 (mt) REVERT: M 263 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8791 (mm) REVERT: M 286 ILE cc_start: 0.8539 (mm) cc_final: 0.8091 (mm) REVERT: M 334 TYR cc_start: 0.9019 (t80) cc_final: 0.8755 (t80) REVERT: M 454 ILE cc_start: 0.8986 (tp) cc_final: 0.8698 (tt) REVERT: N 313 MET cc_start: 0.8639 (mmt) cc_final: 0.8260 (mmt) REVERT: N 314 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7811 (mtm) REVERT: P 127 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6670 (pt0) REVERT: P 207 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8791 (p) REVERT: P 330 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: Q 63 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.6997 (tp30) REVERT: R 21 LYS cc_start: 0.8571 (mppt) cc_final: 0.8315 (mtmt) REVERT: R 46 GLN cc_start: 0.8031 (mt0) cc_final: 0.7811 (mt0) REVERT: T 29 LYS cc_start: 0.7861 (ptmt) cc_final: 0.7579 (ptpp) REVERT: U 20 LYS cc_start: 0.8611 (mttt) cc_final: 0.8321 (mtpt) REVERT: U 29 LYS cc_start: 0.6822 (mmtt) cc_final: 0.6264 (tmtt) REVERT: U 61 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: V 56 ASP cc_start: 0.8467 (m-30) cc_final: 0.8195 (m-30) REVERT: W 43 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7667 (mmp-170) REVERT: X 15 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6359 (mp0) REVERT: Y 8 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7064 (mt-10) REVERT: Y 38 SER cc_start: 0.8814 (m) cc_final: 0.8451 (m) REVERT: Y 82 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7794 (ptm160) REVERT: Y 141 LYS cc_start: 0.7892 (ptmt) cc_final: 0.7659 (pptt) REVERT: Z 113 THR cc_start: 0.8164 (p) cc_final: 0.7946 (t) REVERT: Z 133 SER cc_start: 0.8645 (p) cc_final: 0.8411 (t) REVERT: a 54 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8415 (mp) REVERT: b 9 LYS cc_start: 0.7706 (ttpt) cc_final: 0.7194 (mptt) REVERT: e 68 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.6727 (mpt-90) REVERT: f 44 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.6798 (tm-30) REVERT: h 67 TYR cc_start: 0.9027 (m-10) cc_final: 0.8761 (m-80) REVERT: j 60 THR cc_start: 0.8537 (p) cc_final: 0.8259 (t) REVERT: q 32 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6885 (t0) REVERT: q 54 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7599 (mt0) REVERT: r 5 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6647 (ttm110) outliers start: 245 outliers final: 135 residues processed: 1250 average time/residue: 1.4216 time to fit residues: 2350.9540 Evaluate side-chains 1213 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1049 time to evaluate : 5.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 275 TYR Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 431 GLN Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 357 ASP Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 528 ASP Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 572 THR Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 604 SER Chi-restraints excluded: chain G residue 614 ASP Chi-restraints excluded: chain G residue 629 ASN Chi-restraints excluded: chain G residue 640 ASN Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 211 PHE Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 172 GLN Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 98 MET Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain L residue 359 MET Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 378 LEU Chi-restraints excluded: chain L residue 492 ILE Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 562 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain N residue 2 ASN Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 209 THR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 283 THR Chi-restraints excluded: chain O residue 312 VAL Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 317 VAL Chi-restraints excluded: chain P residue 330 GLU Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain Q residue 80 SER Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain S residue 17 GLU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 64 ASP Chi-restraints excluded: chain U residue 33 ASN Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain W residue 43 ARG Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain X residue 15 GLU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain X residue 158 LYS Chi-restraints excluded: chain Y residue 82 ARG Chi-restraints excluded: chain Y residue 116 CYS Chi-restraints excluded: chain Z residue 102 ASN Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 67 SER Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain d residue 95 LYS Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain f residue 20 VAL Chi-restraints excluded: chain f residue 30 ASP Chi-restraints excluded: chain f residue 44 GLN Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 16 GLU Chi-restraints excluded: chain i residue 33 VAL Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain j residue 51 PHE Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain n residue 153 LEU Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 53 GLN Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 32 ASP Chi-restraints excluded: chain q residue 54 GLN Chi-restraints excluded: chain q residue 94 THR Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 5 ARG Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain s residue 66 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 700 optimal weight: 1.9990 chunk 737 optimal weight: 5.9990 chunk 673 optimal weight: 3.9990 chunk 717 optimal weight: 0.0170 chunk 431 optimal weight: 0.0370 chunk 312 optimal weight: 6.9990 chunk 563 optimal weight: 8.9990 chunk 220 optimal weight: 0.9980 chunk 648 optimal weight: 0.9980 chunk 678 optimal weight: 9.9990 chunk 715 optimal weight: 0.0470 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 HIS ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 7 ASN G 51 ASN ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 475 GLN ** G 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 605 ASN M 82 ASN M 88 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 366 ASN N 87 GLN P 36 ASN P 112 ASN P 184 ASN Q 46 GLN R 94 HIS S 72 GLN S 92 ASN ** X 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 ASN e 28 ASN e 81 GLN h 69 HIS n 13 GLN o 53 GLN q 116 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 68762 Z= 0.525 Angle : 1.575 50.579 93112 Z= 1.014 Chirality : 0.308 6.383 10151 Planarity : 0.004 0.063 11655 Dihedral : 10.547 179.722 10020 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.11 % Favored : 94.86 % Rotamer: Outliers : 2.26 % Allowed : 23.65 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: 0.11 (0.10), residues: 8075 helix: 1.15 (0.08), residues: 4186 sheet: -0.49 (0.26), residues: 406 loop : -1.20 (0.11), residues: 3483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 144 HIS 0.006 0.001 HIS F 29 PHE 0.022 0.001 PHE H 211 TYR 0.022 0.001 TYR L 422 ARG 0.004 0.000 ARG c 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1317 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1155 time to evaluate : 5.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7641 (t70) cc_final: 0.7260 (m-30) REVERT: B 112 LYS cc_start: 0.8557 (tptt) cc_final: 0.8334 (tptp) REVERT: C 73 LYS cc_start: 0.8128 (ptpp) cc_final: 0.7926 (ptmt) REVERT: D 170 MET cc_start: 0.8554 (mmm) cc_final: 0.8242 (mmm) REVERT: F 73 PHE cc_start: 0.6714 (t80) cc_final: 0.6003 (m-80) REVERT: F 84 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.6254 (pptt) REVERT: F 307 ILE cc_start: 0.8072 (mm) cc_final: 0.7596 (mt) REVERT: G 74 MET cc_start: 0.7373 (mtp) cc_final: 0.7055 (ptp) REVERT: G 202 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7841 (mm) REVERT: G 249 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8718 (ptt180) REVERT: G 453 LEU cc_start: 0.8925 (tt) cc_final: 0.8611 (tp) REVERT: H 89 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8664 (mp) REVERT: H 302 MET cc_start: 0.8706 (mtp) cc_final: 0.8481 (mtp) REVERT: I 172 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: L 418 MET cc_start: 0.7756 (mtm) cc_final: 0.7525 (mtm) REVERT: M 41 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8158 (mt) REVERT: M 169 ASN cc_start: 0.7774 (m110) cc_final: 0.7569 (m-40) REVERT: M 286 ILE cc_start: 0.8506 (mm) cc_final: 0.8104 (mm) REVERT: M 334 TYR cc_start: 0.9079 (t80) cc_final: 0.8738 (t80) REVERT: M 454 ILE cc_start: 0.8965 (tp) cc_final: 0.8694 (tt) REVERT: N 314 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7750 (mtm) REVERT: P 127 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6527 (pt0) REVERT: R 21 LYS cc_start: 0.8490 (mppt) cc_final: 0.8237 (mtmt) REVERT: R 46 GLN cc_start: 0.8011 (mt0) cc_final: 0.7738 (mt0) REVERT: T 29 LYS cc_start: 0.7814 (ptmt) cc_final: 0.7578 (ptpp) REVERT: U 20 LYS cc_start: 0.8612 (mttt) cc_final: 0.8358 (mtmm) REVERT: U 28 GLU cc_start: 0.5418 (mm-30) cc_final: 0.5178 (mm-30) REVERT: U 29 LYS cc_start: 0.6845 (mmtt) cc_final: 0.6348 (tmtt) REVERT: U 61 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7470 (tt0) REVERT: W 43 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7640 (mmp-170) REVERT: Y 8 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7050 (mt-10) REVERT: Y 38 SER cc_start: 0.8759 (m) cc_final: 0.8407 (m) REVERT: Y 141 LYS cc_start: 0.7991 (ptmt) cc_final: 0.7783 (pptt) REVERT: Z 133 SER cc_start: 0.8555 (p) cc_final: 0.8348 (t) REVERT: a 54 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8364 (mp) REVERT: c 38 ASP cc_start: 0.7964 (m-30) cc_final: 0.7665 (m-30) REVERT: e 68 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.6744 (mpt-90) REVERT: e 72 MET cc_start: 0.8462 (mtt) cc_final: 0.8157 (mtt) REVERT: f 44 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.6776 (tm-30) REVERT: g 29 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6985 (mt-10) REVERT: j 16 GLN cc_start: 0.7156 (pm20) cc_final: 0.6397 (pp30) REVERT: j 60 THR cc_start: 0.8549 (p) cc_final: 0.8266 (t) REVERT: l 31 GLU cc_start: 0.8662 (mp0) cc_final: 0.8449 (mp0) REVERT: o 45 MET cc_start: 0.7838 (tpp) cc_final: 0.7264 (tpp) REVERT: q 54 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7526 (mt0) REVERT: r 32 LYS cc_start: 0.7555 (ptpp) cc_final: 0.7323 (ptmm) outliers start: 162 outliers final: 85 residues processed: 1261 average time/residue: 1.3944 time to fit residues: 2343.5895 Evaluate side-chains 1152 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1052 time to evaluate : 5.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 275 TYR Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 431 GLN Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain G residue 272 ASP Chi-restraints excluded: chain G residue 357 ASP Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 572 THR Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 604 SER Chi-restraints excluded: chain G residue 640 ASN Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 211 PHE Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 172 GLN Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain J residue 98 MET Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain N residue 2 ASN Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain O residue 209 THR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 317 VAL Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain S residue 17 GLU Chi-restraints excluded: chain T residue 64 ASP Chi-restraints excluded: chain U residue 33 ASN Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 43 ARG Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 158 LYS Chi-restraints excluded: chain Y residue 116 CYS Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 67 SER Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain f residue 20 VAL Chi-restraints excluded: chain f residue 30 ASP Chi-restraints excluded: chain f residue 44 GLN Chi-restraints excluded: chain g residue 29 GLU Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 33 VAL Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 51 PHE Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 123 SER Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 153 LEU Chi-restraints excluded: chain q residue 32 ASP Chi-restraints excluded: chain q residue 54 GLN Chi-restraints excluded: chain q residue 94 THR Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain s residue 66 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 471 optimal weight: 2.9990 chunk 758 optimal weight: 5.9990 chunk 463 optimal weight: 4.9990 chunk 359 optimal weight: 7.9990 chunk 527 optimal weight: 9.9990 chunk 796 optimal weight: 1.9990 chunk 732 optimal weight: 10.0000 chunk 633 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 489 optimal weight: 2.9990 chunk 388 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 HIS ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 ASN F 96 ASN ** F 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 HIS ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 ASN G 237 ASN ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 365 ASN ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 581 GLN G 629 ASN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 505 ASN ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 ASN M 88 ASN N 49 ASN N 87 GLN O 19 HIS Q 46 GLN R 94 HIS ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN b 51 ASN e 28 ASN e 81 GLN l 77 HIS m 85 ASN n 13 GLN o 53 GLN q 116 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.244 68762 Z= 0.574 Angle : 1.607 50.617 93112 Z= 1.027 Chirality : 0.310 6.403 10151 Planarity : 0.005 0.065 11655 Dihedral : 10.787 174.325 10018 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.56 % Favored : 94.41 % Rotamer: Outliers : 2.29 % Allowed : 24.11 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -0.02 (0.10), residues: 8075 helix: 1.01 (0.08), residues: 4199 sheet: -0.53 (0.26), residues: 404 loop : -1.22 (0.11), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 371 HIS 0.009 0.001 HIS r 46 PHE 0.023 0.002 PHE M 151 TYR 0.020 0.002 TYR M 406 ARG 0.011 0.001 ARG i 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16150 Ramachandran restraints generated. 8075 Oldfield, 0 Emsley, 8075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1242 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1078 time to evaluate : 5.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7593 (t70) cc_final: 0.7221 (m-30) REVERT: C 73 LYS cc_start: 0.8403 (ptpp) cc_final: 0.8160 (ptmt) REVERT: D 170 MET cc_start: 0.8594 (mmm) cc_final: 0.8300 (mmm) REVERT: F 73 PHE cc_start: 0.6809 (t80) cc_final: 0.6078 (m-80) REVERT: F 84 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.6303 (pptt) REVERT: F 307 ILE cc_start: 0.8145 (mm) cc_final: 0.7663 (mt) REVERT: G 74 MET cc_start: 0.7581 (mtp) cc_final: 0.7252 (ptp) REVERT: G 249 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8762 (ptt180) REVERT: G 254 MET cc_start: 0.7944 (tmm) cc_final: 0.7391 (tmt) REVERT: G 272 ASP cc_start: 0.7793 (t0) cc_final: 0.7309 (t0) REVERT: G 367 THR cc_start: 0.7200 (p) cc_final: 0.6965 (p) REVERT: H 89 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8739 (mp) REVERT: H 302 MET cc_start: 0.8712 (mtp) cc_final: 0.8446 (mtp) REVERT: I 172 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: M 41 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8308 (mt) REVERT: M 454 ILE cc_start: 0.9024 (tp) cc_final: 0.8778 (tt) REVERT: N 314 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7968 (mtm) REVERT: P 127 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6734 (pt0) REVERT: R 46 GLN cc_start: 0.8120 (mt0) cc_final: 0.7874 (mt0) REVERT: T 29 LYS cc_start: 0.7835 (ptmt) cc_final: 0.7571 (ptpp) REVERT: U 20 LYS cc_start: 0.8655 (mttt) cc_final: 0.8440 (mtpt) REVERT: U 28 GLU cc_start: 0.5521 (mm-30) cc_final: 0.5314 (mm-30) REVERT: U 29 LYS cc_start: 0.6957 (mmtt) cc_final: 0.6415 (tmtt) REVERT: U 30 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7258 (pt) REVERT: V 56 ASP cc_start: 0.8338 (m-30) cc_final: 0.8097 (m-30) REVERT: W 43 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7579 (mmp-170) REVERT: Y 8 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7025 (mt-10) REVERT: Y 38 SER cc_start: 0.8860 (m) cc_final: 0.8493 (m) REVERT: Y 141 LYS cc_start: 0.8020 (ptmt) cc_final: 0.7809 (pptt) REVERT: a 54 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8439 (mp) REVERT: c 38 ASP cc_start: 0.8040 (m-30) cc_final: 0.7837 (m-30) REVERT: e 68 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.6709 (mpt-90) REVERT: f 41 MET cc_start: 0.7509 (mmm) cc_final: 0.7226 (mmm) REVERT: f 44 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.6946 (tm-30) REVERT: g 29 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6991 (mt-10) REVERT: q 54 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7683 (mt0) REVERT: r 32 LYS cc_start: 0.7667 (ptpp) cc_final: 0.7432 (ptmm) outliers start: 164 outliers final: 96 residues processed: 1188 average time/residue: 1.4501 time to fit residues: 2277.5565 Evaluate side-chains 1146 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1036 time to evaluate : 5.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 431 GLN Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 357 ASP Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 572 THR Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 640 ASN Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 211 PHE Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 172 GLN Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 98 MET Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain N residue 2 ASN Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain O residue 209 THR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain O residue 312 VAL Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 317 VAL Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain T residue 64 ASP Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 33 ASN Chi-restraints excluded: chain W residue 43 ARG Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 158 LYS Chi-restraints excluded: chain Z residue 102 ASN Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 67 SER Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain f residue 20 VAL Chi-restraints excluded: chain f residue 30 ASP Chi-restraints excluded: chain f residue 44 GLN Chi-restraints excluded: chain g residue 29 GLU Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain i residue 33 VAL Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 79 ASP Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain n residue 153 LEU Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain q residue 54 GLN Chi-restraints excluded: chain q residue 94 THR Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain s residue 66 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 503 optimal weight: 4.9990 chunk 675 optimal weight: 0.9980 chunk 194 optimal weight: 0.0770 chunk 584 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 634 optimal weight: 0.7980 chunk 265 optimal weight: 7.9990 chunk 651 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 HIS ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 HIS G 51 ASN ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 365 ASN ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 ASN M 88 ASN N 87 GLN R 94 HIS S 72 GLN S 92 ASN W 93 GLN b 51 ASN e 81 GLN l 77 HIS m 85 ASN n 13 GLN n 61 GLN o 53 GLN p 27 ASN q 116 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.121678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.105051 restraints weight = 86142.235| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.26 r_work: 0.3135 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.248 68762 Z= 0.533 Angle : 1.585 50.547 93112 Z= 1.018 Chirality : 0.309 6.347 10151 Planarity : 0.004 0.063 11655 Dihedral : 10.566 177.359 10018 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.13 % Favored : 94.85 % Rotamer: Outliers : 1.94 % Allowed : 24.69 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: 0.09 (0.10), residues: 8075 helix: 1.13 (0.08), residues: 4161 sheet: -0.59 (0.26), residues: 411 loop : -1.16 (0.11), residues: 3503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP M 307 HIS 0.006 0.001 HIS o 3 PHE 0.023 0.001 PHE o 24 TYR 0.020 0.001 TYR L 422 ARG 0.012 0.000 ARG i 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31142.54 seconds wall clock time: 538 minutes 51.81 seconds (32331.81 seconds total)