Starting phenix.real_space_refine on Wed Mar 13 06:04:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ak5_11810/03_2024/7ak5_11810_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ak5_11810/03_2024/7ak5_11810.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ak5_11810/03_2024/7ak5_11810_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ak5_11810/03_2024/7ak5_11810_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ak5_11810/03_2024/7ak5_11810_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ak5_11810/03_2024/7ak5_11810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ak5_11810/03_2024/7ak5_11810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ak5_11810/03_2024/7ak5_11810_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ak5_11810/03_2024/7ak5_11810_updated.pdb" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 27 5.49 5 S 490 5.16 5 C 42586 2.51 5 N 10962 2.21 5 O 11801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B ARG 179": "NH1" <-> "NH2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 118": "OD1" <-> "OD2" Residue "C ASP 147": "OD1" <-> "OD2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D ASP 35": "OD1" <-> "OD2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 133": "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 241": "OD1" <-> "OD2" Residue "D TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 290": "NH1" <-> "NH2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "E ARG 10": "NH1" <-> "NH2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E ASP 163": "OD1" <-> "OD2" Residue "E ASP 174": "OD1" <-> "OD2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 107": "OD1" <-> "OD2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "F TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 204": "NH1" <-> "NH2" Residue "F ARG 339": "NH1" <-> "NH2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "F ARG 378": "NH1" <-> "NH2" Residue "F GLU 394": "OE1" <-> "OE2" Residue "G GLU 132": "OE1" <-> "OE2" Residue "G ARG 135": "NH1" <-> "NH2" 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 ARG 285": "NH1" <-> "NH2" Residue "G GLU 287": "OE1" <-> "OE2" Residue "G GLU 326": "OE1" <-> "OE2" Residue "G ASP 339": "OD1" <-> "OD2" Residue "G ASP 341": "OD1" <-> "OD2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G ASP 357": "OD1" <-> "OD2" Residue "G ARG 359": "NH1" <-> "NH2" Residue "G GLU 512": "OE1" <-> "OE2" Residue "G ARG 515": "NH1" <-> "NH2" Residue "G PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 528": "OD1" <-> "OD2" Residue "G GLU 577": "OE1" <-> "OE2" Residue "G TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 659": "OD1" <-> "OD2" Residue "H ASP 51": "OD1" <-> "OD2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 25": "NH1" <-> "NH2" Residue "I TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 62": "NH1" <-> "NH2" Residue "I GLU 86": "OE1" <-> "OE2" Residue "I GLU 154": "OE1" <-> "OE2" Residue "J GLU 99": "OE1" <-> "OE2" Residue "K ARG 23": "NH1" <-> "NH2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 436": "NH1" <-> "NH2" Residue "L ARG 535": "NH1" <-> "NH2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "M ASP 187": "OD1" <-> "OD2" Residue "M ASP 281": "OD1" <-> "OD2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 53": "OE1" <-> "OE2" Residue "O ASP 65": "OD1" <-> "OD2" Residue "O GLU 72": "OE1" <-> "OE2" Residue "O ASP 85": "OD1" <-> "OD2" Residue "O ARG 145": "NH1" <-> "NH2" Residue "O ASP 201": "OD1" <-> "OD2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P ARG 76": "NH1" <-> "NH2" Residue "P ASP 77": "OD1" <-> "OD2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 296": "OD1" <-> "OD2" Residue "P GLU 311": "OE1" <-> "OE2" Residue "P ARG 320": "NH1" <-> "NH2" Residue "P ARG 322": "NH1" <-> "NH2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "Q GLU 107": "OE1" <-> "OE2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 55": "NH1" <-> "NH2" Residue "T TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 23": "OD1" <-> "OD2" Residue "T ASP 26": "OD1" <-> "OD2" Residue "T ASP 78": "OD1" <-> "OD2" Residue "U ASP 2": "OD1" <-> "OD2" Residue "U TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 39": "OD1" <-> "OD2" Residue "U ASP 64": "OD1" <-> "OD2" Residue "U GLU 68": "OE1" <-> "OE2" Residue "U ASP 78": "OD1" <-> "OD2" Residue "V ARG 44": "NH1" <-> "NH2" Residue "W ARG 32": "NH1" <-> "NH2" Residue "W ARG 33": "NH1" <-> "NH2" Residue "W ARG 79": "NH1" <-> "NH2" Residue "W ARG 107": "NH1" <-> "NH2" Residue "W GLU 111": "OE1" <-> "OE2" Residue "X GLU 5": "OE1" <-> "OE2" Residue "X ARG 54": "NH1" <-> "NH2" Residue "X PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 112": "OD1" <-> "OD2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X GLU 138": "OE1" <-> "OE2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "X PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 5": "NH1" <-> "NH2" Residue "Z ARG 22": "NH1" <-> "NH2" Residue "Z ARG 26": "NH1" <-> "NH2" Residue "Z ARG 27": "NH1" <-> "NH2" Residue "Z ARG 48": "NH1" <-> "NH2" Residue "Z GLU 55": "OE1" <-> "OE2" Residue "Z GLU 62": "OE1" <-> "OE2" Residue "Z ARG 67": "NH1" <-> "NH2" Residue "Z ARG 81": "NH1" <-> "NH2" Residue "Z GLU 107": "OE1" <-> "OE2" Residue "a ARG 40": "NH1" <-> "NH2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "b ASP 64": "OD1" <-> "OD2" Residue "c ARG 5": "NH1" <-> "NH2" Residue "c ARG 45": "NH1" <-> "NH2" Residue "d ASP 87": "OD1" <-> "OD2" Residue "d GLU 105": "OE1" <-> "OE2" Residue "e ASP 4": "OD1" <-> "OD2" 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 GLU 31": "OE1" <-> "OE2" Residue "f GLU 46": "OE1" <-> "OE2" Residue "g ARG 57": "NH1" <-> "NH2" Residue "g ARG 89": "NH1" <-> "NH2" Residue "g ARG 93": "NH1" <-> "NH2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h GLU 62": "OE1" <-> "OE2" Residue "h ARG 115": "NH1" <-> "NH2" Residue "i GLU 7": "OE1" <-> "OE2" Residue "i ARG 10": "NH1" <-> "NH2" Residue "i ARG 65": "NH1" <-> "NH2" Residue "i ASP 107": "OD1" <-> "OD2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "i PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 55": "OD1" <-> "OD2" Residue "j GLU 62": "OE1" <-> "OE2" Residue "k GLU 35": "OE1" <-> "OE2" Residue "k ARG 44": "NH1" <-> "NH2" Residue "k ARG 52": "NH1" <-> "NH2" Residue "k PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 18": "OE1" <-> "OE2" Residue "l TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 39": "OD1" <-> "OD2" Residue "l ARG 85": "NH1" <-> "NH2" Residue "l GLU 150": "OE1" <-> "OE2" Residue "m ARG 29": "NH1" <-> "NH2" Residue "m ARG 30": "NH1" <-> "NH2" Residue "m GLU 34": "OE1" <-> "OE2" Residue "m TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 61": "OD1" <-> "OD2" Residue "m ARG 80": "NH1" <-> "NH2" Residue "n TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 27": "OE1" <-> "OE2" Residue "n ARG 33": "NH1" <-> "NH2" Residue "n PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 55": "OD1" <-> "OD2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n GLU 151": "OE1" <-> "OE2" Residue "n ARG 157": "NH1" <-> "NH2" Residue "n ARG 158": "NH1" <-> "NH2" Residue "n GLU 159": "OE1" <-> "OE2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o ARG 7": "NH1" <-> "NH2" Residue "o ASP 27": "OD1" <-> "OD2" Residue "o ARG 33": "NH1" <-> "NH2" Residue "o ASP 47": "OD1" <-> "OD2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "o ARG 110": "NH1" <-> "NH2" Residue "p ASP 5": "OD1" <-> "OD2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 164": "OE1" <-> "OE2" Residue "q GLU 2": "OE1" <-> "OE2" Residue "q ARG 60": "NH1" <-> "NH2" Residue "q PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 131": "NH1" <-> "NH2" Residue "r ARG 5": "NH1" <-> "NH2" Residue "r ARG 26": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 65895 Number of models: 1 Model: "" Number of chains: 64 Chain: "A" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 737 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 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: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 144} Chain: "C" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1712 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 15, 'TRANS': 190} Chain: "D" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3381 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 25, 'TRANS': 393} Chain breaks: 2 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: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1639 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 21, 'TRANS': 188} Chain: "F" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3301 Classifications: {'peptide': 428} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 406} Chain: "G" Number of atoms: 5287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5287 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 31, 'TRANS': 655} Chain: "H" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2465 Classifications: {'peptide': 308} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 285} Chain breaks: 1 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: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 168} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1277 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 167} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1, 'TYR:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 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: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2297 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 3 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: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 659 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "T" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 588 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "U" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 706 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} 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: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 9, 'TRANS': 129} 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: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} 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: "c" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 381 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "d" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 985 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 12, 'TRANS': 106} Chain: "e" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 870 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "f" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1153 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 11, 'TRANS': 125} Chain: "i" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 811 Classifications: {'peptide': 96} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 84} 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: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 542 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 56} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "k" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 630 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "l" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1312 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 18, 'TRANS': 137} Chain: "m" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1044 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 11, 'TRANS': 113} Chain: "n" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1527 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 15, 'TRANS': 160} Chain: "o" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 984 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 7, 'TRANS': 106} Chain: "p" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1424 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 10, 'TRANS': 157} Chain: "q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1192 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "r" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 776 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} 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: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 329 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 121 Unusual residues: {'3PE': 1, 'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "M" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} 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: "d" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "h" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 78 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 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: "q" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1486 SG CYS B 129 98.426 93.153 202.537 1.00 14.74 S ATOM 989 SG CYS B 65 92.636 94.984 204.974 1.00 17.55 S ATOM 983 SG CYS B 64 93.207 89.618 201.533 1.00 17.13 S ATOM 1716 SG CYS B 159 95.991 89.928 207.292 1.00 13.08 S ATOM 7873 SG CYS E 103 116.085 43.657 258.354 1.00 60.94 S ATOM 7907 SG CYS E 108 114.358 40.678 260.218 1.00 62.86 S ATOM 8191 SG CYS E 144 118.721 40.452 255.126 1.00 56.21 S ATOM 8214 SG CYS E 148 117.454 37.800 255.962 1.00 67.83 S ATOM 11406 SG CYS F 362 122.961 50.496 234.874 1.00 27.29 S ATOM 11426 SG CYS F 365 118.785 50.211 239.363 1.00 28.99 S ATOM 11748 SG CYS F 405 122.860 45.412 238.841 1.00 34.57 S ATOM 11387 SG CYS F 359 125.127 51.603 240.408 1.00 33.74 S ATOM 12836 SG CYS G 114 117.668 69.062 225.469 1.00 16.18 S ATOM 12775 SG CYS G 105 112.125 71.611 227.752 1.00 15.01 S ATOM 12796 SG CYS G 108 117.928 74.013 229.490 1.00 15.20 S ATOM 13168 SG CYS G 156 126.832 63.309 230.510 1.00 20.38 S ATOM 13145 SG CYS G 153 123.898 65.179 236.069 1.00 18.76 S ATOM 13192 SG CYS G 159 129.996 66.405 234.905 1.00 23.56 S ATOM 13521 SG CYS G 203 125.330 69.297 231.078 1.00 19.60 S ATOM 12282 SG CYS G 41 127.259 56.581 227.917 1.00 21.71 S ATOM 12368 SG CYS G 52 123.223 56.461 226.836 1.00 23.00 S ATOM 12393 SG CYS G 55 124.873 52.280 223.856 1.00 23.86 S ATOM 12494 SG CYS G 69 128.016 52.663 225.222 1.00 26.35 S ATOM 20711 SG CYS I 121 99.544 84.285 213.552 1.00 11.50 S ATOM 20685 SG CYS I 118 99.398 90.866 214.394 1.00 12.40 S ATOM 20732 SG CYS I 124 100.886 86.611 219.210 1.00 12.93 S ATOM 20459 SG CYS I 89 104.865 87.598 213.966 1.00 12.24 S ATOM 20761 SG CYS I 128 103.587 83.713 226.516 1.00 17.44 S ATOM 20431 SG CYS I 85 107.211 86.008 221.435 1.00 13.45 S ATOM 20389 SG CYS I 79 108.646 87.746 227.331 1.00 15.19 S ATOM 20408 SG CYS I 82 109.062 81.301 225.137 1.00 14.48 S ATOM 40712 SG CYS R 59 105.104 78.561 241.680 1.00 20.89 S ATOM 40888 SG CYS R 84 108.370 79.024 239.867 1.00 21.72 S ATOM 40910 SG CYS R 87 106.218 81.665 240.760 1.00 19.31 S Time building chain proxies: 25.94, per 1000 atoms: 0.39 Number of scatterers: 65895 At special positions: 0 Unit cell: (189, 194.4, 292.95, 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 490 16.00 P 27 15.00 O 11801 8.00 N 10962 7.00 C 42586 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.04 Simple disulfide: pdb=" SG CYS X 77 " - pdb=" SG CYS X 109 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 96 " - pdb=" SG CYS Y 116 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.45 Conformation dependent library (CDL) restraints added in 8.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb=" SF4 B 201 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 64 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 159 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 65 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 129 " pdb=" SF4 F 502 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " 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="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb=" SF4 I 203 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 118 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 89 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 121 " pdb="FE3 SF4 I 203 " - pdb=" SG CYS I 124 " pdb=" SF4 I 204 " pdb="FE4 SF4 I 204 " - pdb=" SG CYS I 82 " pdb="FE1 SF4 I 204 " - pdb=" SG CYS I 128 " pdb="FE2 SF4 I 204 " - pdb=" SG CYS I 85 " pdb="FE3 SF4 I 204 " - pdb=" SG CYS I 79 " 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 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15192 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 317 helices and 27 sheets defined 50.6% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.44 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 removed outlier: 3.843A pdb=" N PHE A 22 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 80 removed outlier: 3.785A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.554A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 removed outlier: 3.655A pdb=" N ILE A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 53 Processing helix chain 'B' and resid 67 through 73 Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 128 through 132 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 178 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'C' and resid 16 through 32 Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.505A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU C 131 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 4.332A 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: 4.281A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 93 removed outlier: 4.130A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.932A pdb=" N ALA D 117 " --> pdb=" O CYS D 113 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR D 118 " --> pdb=" O ASN D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 161 Processing helix chain 'D' and resid 165 through 185 removed outlier: 3.952A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 229 removed outlier: 3.942A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 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 277 through 280 Processing helix chain 'D' and resid 293 through 317 removed outlier: 3.635A pdb=" N LEU D 308 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 342 through 353 Processing helix chain 'D' and resid 394 through 405 removed outlier: 4.328A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 removed outlier: 4.150A pdb=" N VAL D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN D 421 " --> pdb=" O ILE D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 429 No H-bonds generated for 'chain 'D' and resid 426 through 429' Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.657A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.583A pdb=" N VAL E 47 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 86 removed outlier: 4.879A pdb=" N GLU E 82 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 110 Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 166 through 177 Processing helix chain 'F' and resid 33 through 39 Processing helix chain 'F' and resid 45 through 51 Processing helix chain 'F' and resid 53 through 62 Processing helix chain 'F' and resid 75 through 82 removed outlier: 4.396A pdb=" N MET F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 Processing helix chain 'F' and resid 115 through 129 Processing helix chain 'F' and resid 144 through 159 Processing helix chain 'F' and resid 185 through 187 No H-bonds generated for 'chain 'F' and resid 185 through 187' Processing helix chain 'F' and resid 189 through 197 removed outlier: 3.612A 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 237 Proline residue: F 232 - end of helix Processing helix chain 'F' and resid 242 through 245 Processing helix chain 'F' and resid 276 through 281 Processing helix chain 'F' and resid 309 through 312 No H-bonds generated for 'chain 'F' and resid 309 through 312' Processing helix chain 'F' and resid 319 through 322 No H-bonds generated for 'chain 'F' and resid 319 through 322' Processing helix chain 'F' and resid 343 through 357 removed outlier: 3.563A pdb=" N TYR F 354 " --> pdb=" O LEU F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 381 removed outlier: 4.343A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TRP F 371 " --> pdb=" O GLU F 367 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 400 removed outlier: 4.119A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (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 Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 198 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 265 through 269 Processing helix chain 'G' and resid 271 through 275 removed outlier: 3.545A pdb=" N LEU G 274 " --> pdb=" O TYR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 307 Processing helix chain 'G' and resid 312 through 314 No H-bonds generated for 'chain 'G' and resid 312 through 314' Processing helix chain 'G' and resid 325 through 335 Processing helix chain 'G' and resid 355 through 357 No H-bonds generated for 'chain 'G' and resid 355 through 357' Processing helix chain 'G' and resid 368 through 372 removed outlier: 3.975A pdb=" N VAL G 371 " --> pdb=" O ILE G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 389 through 401 Processing helix chain 'G' and resid 426 through 434 Processing helix chain 'G' and resid 440 through 445 removed outlier: 3.569A pdb=" N ASP G 445 " --> pdb=" O GLU G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 455 through 458 No H-bonds generated for 'chain 'G' and resid 455 through 458' Processing helix chain 'G' and resid 464 through 480 Processing helix chain 'G' and resid 499 through 505 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 607 Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 642 through 651 removed outlier: 4.456A pdb=" N LEU G 651 " --> pdb=" O GLU G 647 " (cutoff:3.500A) Processing helix chain 'G' and resid 668 through 671 No H-bonds generated for 'chain 'G' and resid 668 through 671' Processing helix chain 'G' and resid 676 through 680 Processing helix chain 'G' and resid 684 through 691 Processing helix chain 'H' and resid 3 through 31 Proline residue: H 12 - end of helix removed outlier: 3.905A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 68 through 86 removed outlier: 3.753A pdb=" N ALA H 74 " --> pdb=" O LEU H 70 " (cutoff:3.500A) Proline residue: H 75 - end of helix removed outlier: 4.372A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 122 removed outlier: 4.854A pdb=" N SER H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY H 120 " --> pdb=" O ILE H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 155 removed outlier: 3.561A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU H 150 " --> pdb=" O MET H 146 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU H 155 " --> pdb=" O LEU H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 168 No H-bonds generated for 'chain 'H' and resid 165 through 168' Processing helix chain 'H' and resid 179 through 192 removed outlier: 3.651A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE H 187 " --> pdb=" O MET H 183 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU H 190 " --> pdb=" O PHE H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 276 removed outlier: 3.714A pdb=" N LEU H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 310 removed outlier: 3.628A pdb=" N LEU H 289 " --> pdb=" O LEU H 285 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU H 294 " --> pdb=" O TRP H 290 " (cutoff:3.500A) Proline residue: H 295 - end of helix Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 16 through 27 Processing helix chain 'I' and resid 30 through 43 removed outlier: 3.760A pdb=" N ARG I 34 " --> pdb=" O THR I 30 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY I 35 " --> pdb=" O GLU I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 88 Processing helix chain 'I' and resid 123 through 127 Processing helix chain 'I' and resid 153 through 174 removed outlier: 5.559A pdb=" N ALA I 165 " --> pdb=" O ASP I 161 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU I 166 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA I 169 " --> pdb=" O ALA I 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 20 Processing helix chain 'J' and resid 27 through 45 Processing helix chain 'J' and resid 49 through 73 removed outlier: 3.557A pdb=" N LEU J 60 " --> pdb=" O PHE J 56 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY J 61 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU J 64 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL J 65 " --> pdb=" O GLY J 61 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL J 66 " --> pdb=" O GLY J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 109 removed outlier: 3.794A pdb=" N SER J 84 " --> pdb=" O THR J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 119 No H-bonds generated for 'chain 'J' and resid 117 through 119' Processing helix chain 'J' and resid 138 through 141 No H-bonds generated for 'chain 'J' and resid 138 through 141' Processing helix chain 'J' and resid 143 through 145 No H-bonds generated for 'chain 'J' and resid 143 through 145' Processing helix chain 'J' and resid 149 through 170 removed outlier: 3.604A pdb=" N ILE J 163 " --> pdb=" O LEU J 159 " (cutoff:3.500A) removed outlier: 4.072A 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 removed outlier: 3.941A pdb=" N CYS K 32 " --> pdb=" O SER K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 56 No H-bonds generated for 'chain 'K' and resid 54 through 56' Processing helix chain 'K' and resid 58 through 85 Processing helix chain 'L' and resid 3 through 23 removed outlier: 3.909A pdb=" N ILE L 11 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 27 through 29 No H-bonds generated for 'chain 'L' and resid 27 through 29' Processing helix chain 'L' and resid 32 through 57 removed outlier: 4.286A 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 107 removed outlier: 3.570A pdb=" N SER L 91 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER L 99 " --> pdb=" O PHE L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 133 removed outlier: 4.529A pdb=" N ASN L 115 " --> pdb=" O PRO L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 154 removed outlier: 3.582A pdb=" N PHE L 152 " --> pdb=" O GLY L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 193 removed outlier: 3.990A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 removed outlier: 4.051A pdb=" N PHE L 203 " --> pdb=" O GLN L 199 " (cutoff:3.500A) removed outlier: 4.427A 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 234 through 238 removed outlier: 3.628A pdb=" N GLU L 238 " --> pdb=" O SER L 235 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 246 Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 269 removed outlier: 5.673A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 273 through 278 Processing helix chain 'L' and resid 281 through 293 removed outlier: 3.578A pdb=" N PHE L 287 " --> pdb=" O LEU L 283 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS L 291 " --> pdb=" O PHE L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.760A pdb=" N ALA L 333 " --> pdb=" O ILE L 329 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE L 340 " --> pdb=" O LYS L 336 " (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 381 Processing helix chain 'L' and resid 389 through 401 removed outlier: 5.161A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN L 400 " --> pdb=" O ILE L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 408 through 431 removed outlier: 4.366A pdb=" N LEU L 413 " --> pdb=" O LEU L 409 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 469 Proline residue: L 453 - end of helix removed outlier: 5.914A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.418A 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 508 removed outlier: 3.729A pdb=" N THR L 508 " --> pdb=" O LEU L 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 547 removed outlier: 3.584A pdb=" N PHE L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix removed outlier: 5.268A pdb=" N HIS L 534 " --> pdb=" O SER L 531 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.512A pdb=" N LEU L 546 " --> pdb=" O ASN L 543 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS L 547 " --> pdb=" O LEU L 544 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 605 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.402A 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 23 through 42 removed outlier: 4.088A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N THR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 79 removed outlier: 3.679A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 110 Processing helix chain 'M' and resid 115 through 135 removed outlier: 5.204A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 5.064A 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 Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 178 through 181 No H-bonds generated for 'chain 'M' and resid 178 through 181' Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.225A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 222 Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 235 through 246 removed outlier: 4.494A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER M 240 " --> pdb=" O LEU M 236 " (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 273 removed outlier: 4.092A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 282 through 303 removed outlier: 4.106A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE M 303 " --> pdb=" O ALA M 299 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.610A pdb=" N ASN M 333 " --> pdb=" O LEU M 329 " (cutoff:3.500A) removed outlier: 3.728A 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 removed outlier: 4.093A pdb=" N PHE M 380 " --> pdb=" O MET M 376 " (cutoff:3.500A) Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.670A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE M 394 " --> pdb=" O PHE M 391 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER M 407 " --> pdb=" O GLY M 404 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 449 Proline residue: M 443 - end of helix Processing helix chain 'M' and resid 451 through 453 No H-bonds generated for 'chain 'M' and resid 451 through 453' Processing helix chain 'N' and resid 3 through 22 Proline residue: N 17 - end of helix Processing helix chain 'N' and resid 26 through 47 Proline residue: N 42 - end of helix removed outlier: 5.183A pdb=" N LYS N 47 " --> pdb=" O MET N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 113 through 121 removed outlier: 4.601A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 148 removed outlier: 3.618A pdb=" N ILE N 129 " --> pdb=" O HIS N 125 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.539A pdb=" N LEU N 142 " --> pdb=" O PRO N 138 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE N 145 " --> pdb=" O ILE N 141 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 151 through 169 Processing helix chain 'N' and resid 175 through 194 Processing helix chain 'N' and resid 198 through 222 Proline residue: N 214 - end of helix removed outlier: 4.091A pdb=" N ASN N 222 " --> pdb=" O ALA N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 236 removed outlier: 4.303A pdb=" N LEU N 232 " --> pdb=" O ASN N 228 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N TRP N 234 " --> pdb=" O ILE N 230 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 252 removed outlier: 5.130A pdb=" N THR N 242 " --> pdb=" O ALA N 239 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N SER N 245 " --> pdb=" O THR N 242 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 272 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 276 through 301 removed outlier: 4.213A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU N 288 " --> pdb=" O MET N 284 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN N 289 " --> pdb=" O MET N 285 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER N 299 " --> pdb=" O ARG N 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 311 through 316 Processing helix chain 'N' and resid 324 through 334 Processing helix chain 'N' and resid 340 through 343 No H-bonds generated for 'chain 'N' and resid 340 through 343' Processing helix chain 'O' and resid 5 through 10 Processing helix chain 'O' and resid 35 through 46 Processing helix chain 'O' and resid 58 through 62 Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 92 through 117 removed outlier: 3.796A pdb=" N TRP O 99 " --> pdb=" O ARG O 95 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS O 114 " --> pdb=" O ASP O 110 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 141 removed outlier: 4.197A pdb=" N ALA O 137 " --> pdb=" O PHE O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 162 Proline residue: O 161 - end of helix Processing helix chain 'O' and resid 176 through 186 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 196 through 215 removed outlier: 4.724A 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 231 through 240 Processing helix chain 'O' and resid 247 through 249 No H-bonds generated for 'chain 'O' and resid 247 through 249' Processing helix chain 'O' and resid 253 through 264 removed outlier: 3.857A pdb=" N LEU O 262 " --> pdb=" O TYR O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 286 through 298 Processing helix chain 'O' and resid 306 through 308 No H-bonds generated for 'chain 'O' and resid 306 through 308' Processing helix chain 'O' and resid 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' Processing helix chain 'P' and resid 31 through 41 removed outlier: 4.103A pdb=" N ASN P 36 " --> pdb=" O ARG P 32 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N MET P 41 " --> pdb=" O HIS P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 56 removed outlier: 3.614A pdb=" N ILE P 56 " --> pdb=" O VAL P 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 53 through 56' Processing helix chain 'P' and resid 82 through 85 No H-bonds generated for 'chain 'P' and resid 82 through 85' Processing helix chain 'P' and resid 106 through 124 removed outlier: 4.388A pdb=" N ILE P 113 " --> pdb=" O VAL P 109 " (cutoff:3.500A) Proline residue: P 114 - end of helix Processing helix chain 'P' and resid 144 through 157 removed outlier: 3.953A pdb=" N LYS P 154 " --> pdb=" O ALA P 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 183 Processing helix chain 'P' and resid 207 through 217 Processing helix chain 'P' and resid 238 through 248 Processing helix chain 'P' and resid 281 through 287 Processing helix chain 'P' and resid 310 through 321 removed outlier: 5.571A pdb=" N ILE P 315 " --> pdb=" O GLU P 311 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLU P 316 " --> pdb=" O LEU P 312 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.366A 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 27 through 31 Processing helix chain 'Q' and resid 89 through 99 Processing helix chain 'Q' and resid 118 through 122 removed outlier: 3.524A pdb=" N ASN Q 121 " --> pdb=" O TYR Q 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 28 removed outlier: 3.759A pdb=" N ARG R 27 " --> pdb=" O ARG R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 43 No H-bonds generated for 'chain 'R' and resid 40 through 43' Processing helix chain 'S' and resid 27 through 38 removed outlier: 4.759A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 46 Processing helix chain 'S' and resid 83 through 94 Processing helix chain 'T' and resid 11 through 19 removed outlier: 4.476A pdb=" N VAL T 18 " --> pdb=" O ARG T 14 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU T 19 " --> pdb=" O VAL T 15 " (cutoff:3.500A) Processing helix chain 'T' and resid 36 through 39 No H-bonds generated for 'chain 'T' and resid 36 through 39' Processing helix chain 'T' and resid 44 through 58 Processing helix chain 'T' and resid 64 through 69 Processing helix chain 'T' and resid 73 through 81 Processing helix chain 'U' and resid 8 through 21 Processing helix chain 'U' and resid 44 through 58 Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.492A pdb=" N LYS U 69 " --> pdb=" O ILE U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 84 Processing helix chain 'V' and resid 21 through 34 removed outlier: 3.615A pdb=" N ILE V 33 " --> pdb=" O LYS V 29 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 removed outlier: 4.218A pdb=" N GLN V 49 " --> pdb=" O LYS V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 71 removed outlier: 4.411A pdb=" N ALA V 69 " --> pdb=" O LYS V 65 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU V 70 " --> pdb=" O LYS V 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 93 Processing helix chain 'W' and resid 27 through 51 Proline residue: W 46 - end of helix removed outlier: 3.686A pdb=" N VAL W 49 " --> pdb=" O VAL W 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 58 through 72 removed outlier: 4.433A pdb=" N ASN W 72 " --> pdb=" O MET W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 96 removed outlier: 3.555A pdb=" N LEU W 84 " --> pdb=" O VAL W 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 102 through 108 removed outlier: 4.633A pdb=" N PHE W 108 " --> pdb=" O HIS W 104 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 126 removed outlier: 4.155A pdb=" N MET W 126 " --> pdb=" O SER W 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 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 removed outlier: 3.713A pdb=" N PHE X 42 " --> pdb=" O THR X 38 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TRP X 47 " --> pdb=" O MET X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 54 No H-bonds generated for 'chain 'X' and resid 52 through 54' Processing helix chain 'X' and resid 56 through 75 removed outlier: 4.025A pdb=" N LEU X 61 " --> pdb=" O LYS X 57 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE X 69 " --> pdb=" O CYS X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 79 through 90 removed outlier: 3.685A pdb=" N TYR X 90 " --> pdb=" O THR X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 113 Processing helix chain 'Y' and resid 9 through 11 No H-bonds generated for 'chain 'Y' and resid 9 through 11' Processing helix chain 'Y' and resid 19 through 43 Processing helix chain 'Y' and resid 50 through 81 Processing helix chain 'Y' and resid 88 through 106 Processing helix chain 'Y' and resid 109 through 132 Processing helix chain 'Z' and resid 31 through 96 removed outlier: 3.822A pdb=" N GLU Z 55 " --> pdb=" O ARG Z 51 " (cutoff:3.500A) Proline residue: Z 72 - end of helix removed outlier: 4.259A pdb=" N ILE Z 95 " --> pdb=" O GLU Z 91 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 123 No H-bonds generated for 'chain 'Z' and resid 120 through 123' Processing helix chain 'Z' and resid 129 through 136 Processing helix chain 'a' and resid 2 through 4 No H-bonds generated for 'chain 'a' and resid 2 through 4' Processing helix chain 'a' and resid 6 through 30 removed outlier: 3.968A pdb=" N ILE a 11 " --> pdb=" O PRO a 7 " (cutoff:3.500A) Proline residue: a 19 - end of helix Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'b' and resid 3 through 14 Processing helix chain 'b' and resid 16 through 34 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 39 through 47 Processing helix chain 'b' and resid 78 through 82 Processing helix chain 'c' and resid 8 through 10 No H-bonds generated for 'chain 'c' and resid 8 through 10' Processing helix chain 'c' and resid 14 through 46 Processing helix chain 'd' and resid 29 through 49 Processing helix chain 'd' and resid 58 through 96 removed outlier: 3.606A 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 43 Processing helix chain 'e' and resid 51 through 54 No H-bonds generated for 'chain 'e' and resid 51 through 54' Processing helix chain 'e' and resid 56 through 67 Processing helix chain 'e' and resid 69 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 6 through 9 No H-bonds generated for 'chain 'f' and resid 6 through 9' Processing helix chain 'f' and resid 15 through 31 Processing helix chain 'g' and resid 49 through 63 Processing helix chain 'g' and resid 67 through 76 Processing helix chain 'g' and resid 81 through 83 No H-bonds generated for 'chain 'g' and resid 81 through 83' Processing helix chain 'g' and resid 86 through 100 Processing helix chain 'h' and resid 16 through 46 removed outlier: 3.939A pdb=" N PHE h 21 " --> pdb=" O TYR h 17 " (cutoff:3.500A) removed outlier: 4.390A 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 70 through 79 Processing helix chain 'h' and resid 83 through 117 removed outlier: 3.782A pdb=" N GLU h 109 " --> pdb=" O LEU h 105 " (cutoff:3.500A) Processing helix chain 'h' and resid 130 through 132 No H-bonds generated for 'chain 'h' and resid 130 through 132' Processing helix chain 'i' and resid 5 through 25 removed outlier: 3.677A pdb=" N ARG i 20 " --> pdb=" O GLU i 16 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS i 23 " --> pdb=" O ARG i 19 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 88 removed outlier: 5.571A pdb=" N ILE i 76 " --> pdb=" O SER i 72 " (cutoff:3.500A) Proline residue: i 77 - end of helix Processing helix chain 'j' and resid 20 through 42 removed outlier: 3.815A pdb=" N GLY j 25 " --> pdb=" O GLN j 21 " (cutoff:3.500A) Processing helix chain 'j' and resid 44 through 48 Processing helix chain 'k' and resid 33 through 43 Processing helix chain 'k' and resid 51 through 56 removed outlier: 4.141A pdb=" N TRP k 56 " --> pdb=" O ARG k 52 " (cutoff:3.500A) Processing helix chain 'k' and resid 60 through 62 No H-bonds generated for 'chain 'k' and resid 60 through 62' Processing helix chain 'k' and resid 68 through 72 Processing helix chain 'k' and resid 76 through 93 Processing helix chain 'l' and resid 16 through 26 removed outlier: 4.010A pdb=" N ALA l 21 " --> pdb=" O GLU l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 80 through 82 No H-bonds generated for 'chain 'l' and resid 80 through 82' Processing helix chain 'l' and resid 97 through 120 removed outlier: 3.707A pdb=" N LYS l 102 " --> pdb=" O ASP l 98 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 50 removed outlier: 4.257A pdb=" N ALA m 31 " --> pdb=" O GLU m 27 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 72 Processing helix chain 'm' and resid 85 through 117 Proline residue: m 96 - end of helix Processing helix chain 'n' and resid 11 through 29 Processing helix chain 'n' and resid 33 through 50 removed outlier: 4.476A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 73 removed outlier: 3.600A pdb=" N GLU n 68 " --> pdb=" O ARG n 64 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 103 No H-bonds generated for 'chain 'n' and resid 101 through 103' Processing helix chain 'n' and resid 108 through 111 No H-bonds generated for 'chain 'n' and resid 108 through 111' Processing helix chain 'n' and resid 115 through 129 removed outlier: 3.738A pdb=" N LYS n 120 " --> pdb=" O ASP n 116 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG n 128 " --> pdb=" O TRP n 124 " (cutoff:3.500A) Processing helix chain 'n' and resid 133 through 140 removed outlier: 3.723A pdb=" N LEU n 139 " --> pdb=" O GLU n 135 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 8 Processing helix chain 'o' and resid 42 through 46 Processing helix chain 'o' and resid 59 through 70 Processing helix chain 'o' and resid 80 through 113 removed outlier: 3.517A pdb=" N ASP o 85 " --> pdb=" O HIS o 81 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 39 Processing helix chain 'p' and resid 41 through 58 Processing helix chain 'p' and resid 81 through 123 removed outlier: 3.957A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA p 111 " --> pdb=" O GLU p 107 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS p 112 " --> pdb=" O ARG p 108 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TYR p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLN p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) Processing helix chain 'p' and resid 125 through 142 Processing helix chain 'p' and resid 151 through 170 removed outlier: 4.162A pdb=" N GLU p 164 " --> pdb=" O GLN p 160 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 15 Processing helix chain 'q' and resid 19 through 29 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: 3.803A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 53 through 55 No H-bonds generated for 'chain 'r' and resid 53 through 55' Processing helix chain 's' and resid 42 through 53 removed outlier: 4.185A pdb=" N PHE s 45 " --> pdb=" O THR s 42 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU s 46 " --> pdb=" O TYR s 43 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 57 through 61 removed outlier: 6.778A pdb=" N VAL B 95 " --> pdb=" O MET B 58 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N PHE B 60 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE B 97 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL B 98 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.633A 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 74 through 82 removed outlier: 6.576A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLN C 39 " --> pdb=" O CYS C 51 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.581A pdb=" N ARG C 182 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 49 through 51 removed outlier: 4.349A pdb=" N ARG D 63 " --> pdb=" O HIS D 79 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N VAL D 73 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 361 through 369 removed outlier: 3.707A pdb=" N THR D 365 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG D 388 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 98 through 103 Processing sheet with id= G, first strand: chain 'E' and resid 153 through 155 Processing sheet with id= H, first strand: chain 'F' and resid 219 through 224 removed outlier: 6.313A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 266 through 271 Processing sheet with id= J, first strand: chain 'G' and resid 8 through 13 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 removed outlier: 3.589A pdb=" N GLN G 182 " --> pdb=" O THR G 175 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 223 through 228 removed outlier: 3.696A pdb=" N SER G 241 " --> pdb=" O ARG G 249 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG G 249 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG G 243 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 5.665A 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 343 through 345 removed outlier: 8.651A pdb=" N CYS G 344 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA G 317 " --> pdb=" O CYS G 344 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'G' and resid 490 through 493 removed outlier: 8.245A pdb=" N ASN G 491 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL G 451 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU G 493 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU G 453 " --> pdb=" O LEU G 493 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL G 376 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL G 452 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU G 378 " --> pdb=" O VAL G 452 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLY G 454 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL G 380 " --> pdb=" O GLY G 454 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP G 420 " --> pdb=" O LEU G 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= R, first strand: chain 'I' and resid 67 through 69 Processing sheet with id= S, first strand: chain 'I' and resid 94 through 100 removed outlier: 5.777A pdb=" N GLU I 99 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N THR I 108 " --> pdb=" O GLU I 99 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.686A pdb=" N MET L 78 " --> pdb=" O THR L 65 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 24 through 26 removed outlier: 6.780A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'O' and resid 168 through 172 removed outlier: 6.605A pdb=" N GLU O 219 " --> pdb=" O VAL O 169 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N TYR O 171 " --> pdb=" O GLU O 219 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU O 221 " --> pdb=" O TYR O 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'P' and resid 226 through 230 removed outlier: 3.554A pdb=" N VAL P 132 " --> pdb=" O ASN P 93 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 103 through 105 removed outlier: 6.536A pdb=" N VAL Q 35 " --> pdb=" O ASP Q 104 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= Z, first strand: chain 'S' and resid 51 through 56 Processing sheet with id= AA, first strand: chain 'q' and resid 60 through 63 removed outlier: 3.912A pdb=" N GLY q 40 " --> pdb=" O TYR q 48 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2706 hydrogen bonds defined for protein. 7596 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: 20.55 Time building geometry restraints manager: 23.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 27233 1.41 - 1.63: 39390 1.63 - 1.85: 842 1.85 - 2.08: 0 2.08 - 2.30: 80 Bond restraints: 67545 Sorted by residual: bond pdb=" C4 ATP O 401 " pdb=" C5 ATP O 401 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.14e+01 bond pdb=" C5 ATP O 401 " pdb=" C6 ATP O 401 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.15e+01 bond pdb=" CA7 CDL L 702 " pdb=" OA8 CDL L 702 " ideal model delta sigma weight residual 1.334 1.404 -0.070 1.10e-02 8.26e+03 4.07e+01 bond pdb=" CA7 CDL d 201 " pdb=" OA8 CDL d 201 " ideal model delta sigma weight residual 1.334 1.403 -0.069 1.10e-02 8.26e+03 3.96e+01 bond pdb=" CB7 CDL q 201 " pdb=" OB8 CDL q 201 " ideal model delta sigma weight residual 1.334 1.403 -0.069 1.10e-02 8.26e+03 3.91e+01 ... (remaining 67540 not shown) Histogram of bond angle deviations from ideal: 73.22 - 85.87: 76 85.87 - 98.53: 4 98.53 - 111.19: 29100 111.19 - 123.85: 60329 123.85 - 136.50: 1942 Bond angle restraints: 91451 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 139.87 120.11 19.76 1.00e+00 1.00e+00 3.90e+02 angle pdb=" PA ATP O 401 " pdb=" O3A ATP O 401 " pdb=" PB ATP O 401 " ideal model delta sigma weight residual 136.83 121.12 15.71 1.00e+00 1.00e+00 2.47e+02 angle pdb=" C5 ATP O 401 " pdb=" C4 ATP O 401 " pdb=" N3 ATP O 401 " ideal model delta sigma weight residual 126.80 118.85 7.95 1.00e+00 1.00e+00 6.33e+01 angle pdb=" C51 CDL d 201 " pdb=" CB5 CDL d 201 " pdb=" OB6 CDL d 201 " ideal model delta sigma weight residual 111.33 120.50 -9.17 1.32e+00 5.72e-01 4.81e+01 angle pdb=" C51 CDL L 702 " pdb=" CB5 CDL L 702 " pdb=" OB6 CDL L 702 " ideal model delta sigma weight residual 111.33 120.38 -9.05 1.32e+00 5.72e-01 4.69e+01 ... (remaining 91446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.64: 39065 29.64 - 59.27: 1637 59.27 - 88.91: 119 88.91 - 118.55: 7 118.55 - 148.18: 4 Dihedral angle restraints: 40832 sinusoidal: 17296 harmonic: 23536 Sorted by residual: 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 93.00 170.84 -77.84 1 1.00e+01 1.00e-02 7.58e+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 -149.69 63.69 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CB CYS X 77 " pdb=" SG CYS X 77 " pdb=" SG CYS X 109 " pdb=" CB CYS X 109 " ideal model delta sinusoidal sigma weight residual 93.00 152.65 -59.65 1 1.00e+01 1.00e-02 4.75e+01 ... (remaining 40829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.258: 9979 4.258 - 8.515: 0 8.515 - 12.773: 0 12.773 - 17.031: 0 17.031 - 21.289: 24 Chirality restraints: 10003 Sorted by residual: chirality pdb="FE3 SF4 I 203 " pdb=" S1 SF4 I 203 " pdb=" S2 SF4 I 203 " pdb=" S4 SF4 I 203 " both_signs ideal model delta sigma weight residual False -10.55 10.73 -21.29 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE3 SF4 I 204 " pdb=" S1 SF4 I 204 " pdb=" S2 SF4 I 204 " pdb=" S4 SF4 I 204 " both_signs ideal model delta sigma weight residual False -10.55 10.72 -21.28 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE1 SF4 I 203 " pdb=" S2 SF4 I 203 " pdb=" S3 SF4 I 203 " pdb=" S4 SF4 I 203 " both_signs ideal model delta sigma weight residual False -10.55 10.72 -21.28 2.00e-01 2.50e+01 1.13e+04 ... (remaining 10000 not shown) Planarity restraints: 11456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS m 84 " -0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C LYS m 84 " 0.065 2.00e-02 2.50e+03 pdb=" O LYS m 84 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN m 85 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 111 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" C MET D 111 " 0.059 2.00e-02 2.50e+03 pdb=" O MET D 111 " -0.022 2.00e-02 2.50e+03 pdb=" N MET D 112 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS V 20 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C HIS V 20 " -0.059 2.00e-02 2.50e+03 pdb=" O HIS V 20 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU V 21 " 0.020 2.00e-02 2.50e+03 ... (remaining 11453 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 433 2.47 - 3.08: 48590 3.08 - 3.69: 97164 3.69 - 4.29: 152356 4.29 - 4.90: 253979 Nonbonded interactions: 552522 Sorted by model distance: nonbonded pdb=" O ALA L 245 " pdb=" OG SER L 249 " model vdw 1.865 2.440 nonbonded pdb=" O PHE H 293 " pdb=" OG1 THR H 297 " model vdw 1.871 2.440 nonbonded pdb=" O LEU H 307 " pdb=" OG1 THR H 311 " model vdw 1.898 2.440 nonbonded pdb=" OD2 ASP G 528 " pdb=" OH TYR G 545 " model vdw 1.937 2.440 nonbonded pdb=" OH TYR A 4 " pdb=" OH TYR J 4 " model vdw 1.942 2.440 ... (remaining 552517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.730 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: 0.060 Extract box with map and model: 12.360 Check model and map are aligned: 0.760 Set scattering table: 0.480 Process input model: 156.260 Find NCS groups from input model: 2.040 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 177.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 67545 Z= 0.323 Angle : 0.733 19.761 91451 Z= 0.376 Chirality : 1.040 21.289 10003 Planarity : 0.005 0.058 11456 Dihedral : 15.538 148.181 25625 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.94 % Favored : 94.05 % Rotamer: Outliers : 0.01 % Allowed : 2.28 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -3.68 (0.08), residues: 7948 helix: -1.53 (0.07), residues: 4249 sheet: -2.12 (0.23), residues: 417 loop : -3.76 (0.08), residues: 3282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.006 0.001 HIS L 264 PHE 0.039 0.001 PHE l 115 TYR 0.020 0.001 TYR B 135 ARG 0.007 0.000 ARG G 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1413 time to evaluate : 5.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7995 (mmtp) cc_final: 0.7600 (mmtm) REVERT: B 64 CYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8382 (p) REVERT: B 183 LEU cc_start: 0.8176 (mt) cc_final: 0.7854 (mp) REVERT: C 147 ASP cc_start: 0.6895 (p0) cc_final: 0.6672 (p0) REVERT: C 200 ASN cc_start: 0.8236 (m110) cc_final: 0.7989 (m110) REVERT: E 112 ASP cc_start: 0.6647 (t0) cc_final: 0.6151 (t0) REVERT: I 112 ASP cc_start: 0.7806 (m-30) cc_final: 0.7591 (m-30) REVERT: I 174 ASP cc_start: 0.7829 (t70) cc_final: 0.7455 (t0) REVERT: L 206 ASN cc_start: 0.6972 (m-40) cc_final: 0.6584 (p0) REVERT: L 574 THR cc_start: 0.8204 (m) cc_final: 0.7660 (m) REVERT: M 437 MET cc_start: 0.7961 (mmt) cc_final: 0.7610 (mmt) REVERT: N 153 ILE cc_start: 0.7647 (pt) cc_final: 0.7432 (mt) REVERT: N 208 TYR cc_start: 0.8634 (t80) cc_final: 0.8425 (t80) REVERT: N 229 SER cc_start: 0.8049 (m) cc_final: 0.7801 (t) REVERT: O 185 LYS cc_start: 0.8016 (mtmt) cc_final: 0.7641 (ptmm) REVERT: P 287 ILE cc_start: 0.8275 (mt) cc_final: 0.7913 (mm) REVERT: Q 42 ARG cc_start: 0.8291 (ttp-170) cc_final: 0.7955 (ttp-110) REVERT: R 21 LYS cc_start: 0.8461 (mmtm) cc_final: 0.8177 (tptp) REVERT: S 30 GLN cc_start: 0.6848 (tp40) cc_final: 0.6576 (tp40) REVERT: S 34 ASP cc_start: 0.7478 (m-30) cc_final: 0.6856 (m-30) REVERT: U 20 LYS cc_start: 0.8127 (mttt) cc_final: 0.7832 (mttp) REVERT: W 67 GLU cc_start: 0.7402 (tt0) cc_final: 0.7183 (tt0) REVERT: W 96 ILE cc_start: 0.8539 (pt) cc_final: 0.8026 (pt) REVERT: b 59 ASP cc_start: 0.7579 (p0) cc_final: 0.7291 (p0) REVERT: c 41 GLU cc_start: 0.6752 (tt0) cc_final: 0.6324 (tt0) REVERT: d 25 LYS cc_start: 0.8231 (pttt) cc_final: 0.7975 (pttm) REVERT: d 55 ARG cc_start: 0.7057 (mtm110) cc_final: 0.6605 (mtt90) REVERT: e 12 SER cc_start: 0.8463 (t) cc_final: 0.8082 (p) REVERT: e 14 ASP cc_start: 0.7817 (p0) cc_final: 0.7373 (p0) REVERT: h 10 VAL cc_start: 0.9329 (t) cc_final: 0.9044 (m) REVERT: h 106 LYS cc_start: 0.8194 (mtmt) cc_final: 0.7967 (mtmt) REVERT: l 49 LEU cc_start: 0.8395 (mt) cc_final: 0.8137 (mt) REVERT: l 102 LYS cc_start: 0.7691 (ttmt) cc_final: 0.6923 (tmtt) REVERT: l 140 GLU cc_start: 0.7805 (mp0) cc_final: 0.7316 (mp0) REVERT: l 148 GLU cc_start: 0.6432 (mm-30) cc_final: 0.6178 (mm-30) REVERT: m 43 LYS cc_start: 0.8325 (tttm) cc_final: 0.8103 (tttm) REVERT: n 10 THR cc_start: 0.7212 (m) cc_final: 0.6564 (p) REVERT: n 52 ASN cc_start: 0.6200 (m110) cc_final: 0.5793 (m-40) REVERT: n 64 ARG cc_start: 0.7902 (ttm170) cc_final: 0.7250 (mtt180) REVERT: n 65 GLU cc_start: 0.7372 (tt0) cc_final: 0.6346 (tp30) REVERT: o 30 PHE cc_start: 0.6024 (m-80) cc_final: 0.5780 (m-80) REVERT: p 144 ASP cc_start: 0.8318 (m-30) cc_final: 0.8091 (m-30) REVERT: q 53 LYS cc_start: 0.8364 (mtpt) cc_final: 0.8161 (mtmt) REVERT: q 81 MET cc_start: 0.8039 (mtt) cc_final: 0.7792 (mtt) REVERT: r 9 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7904 (mtmt) REVERT: s 48 LEU cc_start: 0.7704 (mt) cc_final: 0.7253 (mt) REVERT: s 52 LEU cc_start: 0.8076 (mt) cc_final: 0.7872 (mt) outliers start: 1 outliers final: 0 residues processed: 1414 average time/residue: 0.6913 time to fit residues: 1605.7733 Evaluate side-chains 996 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 995 time to evaluate : 5.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 662 optimal weight: 0.9980 chunk 594 optimal weight: 8.9990 chunk 330 optimal weight: 5.9990 chunk 203 optimal weight: 0.0370 chunk 401 optimal weight: 6.9990 chunk 317 optimal weight: 1.9990 chunk 615 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 374 optimal weight: 10.0000 chunk 457 optimal weight: 4.9990 chunk 712 optimal weight: 1.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN C 39 GLN C 200 ASN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN D 398 HIS D 421 GLN E 55 GLN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS F 250 ASN F 257 ASN F 356 HIS F 435 GLN G 421 HIS G 437 HIS G 475 GLN G 491 ASN G 535 GLN G 546 GLN ** G 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN K 91 GLN K 92 ASN ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 230 HIS L 320 ASN L 446 ASN ** L 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 605 ASN M 48 ASN M 139 GLN M 144 ASN M 374 ASN N 63 GLN N 174 GLN N 222 ASN N 342 GLN O 97 GLN O 180 GLN P 93 ASN P 131 HIS Q 44 ASN Q 46 GLN R 36 ASN R 46 GLN S 79 ASN W 101 GLN X 34 GLN Y 80 GLN a 58 ASN d 61 GLN e 76 HIS e 97 HIS g 43 HIS g 55 ASN g 109 ASN j 42 HIS j 50 HIS j 58 GLN l 77 HIS l 154 HIS m 74 ASN n 140 GLN o 42 GLN o 53 GLN ** o 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 84 HIS q 13 GLN q 87 HIS r 28 GLN r 46 HIS s 34 ASN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.265 67545 Z= 0.547 Angle : 1.583 51.028 91451 Z= 1.024 Chirality : 0.315 6.587 10003 Planarity : 0.005 0.054 11456 Dihedral : 11.031 154.026 9702 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.19 % Allowed : 8.51 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -1.54 (0.09), residues: 7948 helix: 0.14 (0.08), residues: 4246 sheet: -1.31 (0.24), residues: 431 loop : -2.60 (0.10), residues: 3271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 85 HIS 0.009 0.001 HIS j 50 PHE 0.027 0.001 PHE M 151 TYR 0.021 0.001 TYR L 422 ARG 0.006 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1094 time to evaluate : 5.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8021 (mmtp) cc_final: 0.7723 (mmtt) REVERT: D 189 MET cc_start: 0.8953 (ttm) cc_final: 0.8665 (ttp) REVERT: E 161 TYR cc_start: 0.8434 (m-80) cc_final: 0.8032 (m-10) REVERT: F 50 LEU cc_start: 0.8000 (pp) cc_final: 0.7599 (mt) REVERT: F 257 ASN cc_start: 0.7704 (m-40) cc_final: 0.7393 (t0) REVERT: G 283 MET cc_start: 0.8468 (mtp) cc_final: 0.8177 (mtm) REVERT: G 521 MET cc_start: 0.8021 (ttt) cc_final: 0.7575 (ttt) REVERT: H 116 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8361 (mm) REVERT: I 112 ASP cc_start: 0.7904 (m-30) cc_final: 0.7591 (m-30) REVERT: I 174 ASP cc_start: 0.8019 (t70) cc_final: 0.7585 (t0) REVERT: J 63 MET cc_start: 0.7369 (tpp) cc_final: 0.6982 (ttp) REVERT: L 206 ASN cc_start: 0.7065 (m-40) cc_final: 0.6609 (p0) REVERT: L 393 ASP cc_start: 0.5608 (t0) cc_final: 0.5266 (t0) REVERT: L 482 MET cc_start: 0.7567 (ptp) cc_final: 0.7295 (ptp) REVERT: L 574 THR cc_start: 0.8543 (m) cc_final: 0.8216 (m) REVERT: M 231 LEU cc_start: 0.8546 (mt) cc_final: 0.8337 (mp) REVERT: M 361 MET cc_start: 0.7692 (mtp) cc_final: 0.7394 (mtm) REVERT: M 437 MET cc_start: 0.8234 (mmt) cc_final: 0.7792 (mmt) REVERT: M 441 MET cc_start: 0.8121 (tpt) cc_final: 0.7696 (tpt) REVERT: N 153 ILE cc_start: 0.7764 (pt) cc_final: 0.7562 (mt) REVERT: P 244 TYR cc_start: 0.7562 (t80) cc_final: 0.7168 (t80) REVERT: P 287 ILE cc_start: 0.8381 (mt) cc_final: 0.7988 (mm) REVERT: Q 42 ARG cc_start: 0.8373 (ttp-170) cc_final: 0.7911 (ttt-90) REVERT: R 21 LYS cc_start: 0.8328 (mmtm) cc_final: 0.7910 (tptp) REVERT: R 55 ARG cc_start: 0.8502 (ptm-80) cc_final: 0.8246 (ptm160) REVERT: T 18 VAL cc_start: 0.6339 (t) cc_final: 0.5881 (m) REVERT: T 54 MET cc_start: 0.6328 (mmt) cc_final: 0.5686 (mmt) REVERT: W 44 GLU cc_start: 0.7562 (tp30) cc_final: 0.7323 (tp30) REVERT: W 96 ILE cc_start: 0.8694 (pt) cc_final: 0.8293 (pt) REVERT: W 106 MET cc_start: 0.7666 (mmt) cc_final: 0.7253 (mmt) REVERT: b 9 LYS cc_start: 0.7428 (mtpt) cc_final: 0.7050 (ttpt) REVERT: d 55 ARG cc_start: 0.7082 (mtm110) cc_final: 0.6671 (mtt90) REVERT: e 14 ASP cc_start: 0.8091 (p0) cc_final: 0.7867 (p0) REVERT: h 10 VAL cc_start: 0.9278 (t) cc_final: 0.9041 (m) REVERT: l 49 LEU cc_start: 0.8625 (mt) cc_final: 0.8352 (mt) REVERT: l 62 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7694 (mt0) REVERT: l 102 LYS cc_start: 0.7688 (ttmt) cc_final: 0.6974 (tmtt) REVERT: l 140 GLU cc_start: 0.7778 (mp0) cc_final: 0.7354 (mp0) REVERT: l 148 GLU cc_start: 0.6616 (mm-30) cc_final: 0.6315 (mm-30) REVERT: m 43 LYS cc_start: 0.8335 (tttm) cc_final: 0.8110 (tttm) REVERT: n 52 ASN cc_start: 0.6428 (m110) cc_final: 0.5834 (m-40) REVERT: n 64 ARG cc_start: 0.7876 (ttm170) cc_final: 0.7441 (mtt180) REVERT: n 65 GLU cc_start: 0.7292 (tt0) cc_final: 0.6364 (tp30) REVERT: o 96 LYS cc_start: 0.7554 (mttt) cc_final: 0.7276 (mtpt) REVERT: p 34 LYS cc_start: 0.6565 (mtpt) cc_final: 0.6245 (mttp) REVERT: p 144 ASP cc_start: 0.8343 (m-30) cc_final: 0.8142 (m-30) REVERT: r 9 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7924 (mtmt) REVERT: r 27 TYR cc_start: 0.7852 (m-80) cc_final: 0.7648 (m-80) outliers start: 84 outliers final: 50 residues processed: 1141 average time/residue: 0.6405 time to fit residues: 1234.2684 Evaluate side-chains 1012 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 961 time to evaluate : 5.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 181 MET Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain L residue 298 ILE Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain N residue 187 MET Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 250 LYS Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 36 ASN Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain W residue 72 ASN Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 91 SER Chi-restraints excluded: chain Y residue 96 CYS Chi-restraints excluded: chain Y residue 130 LYS Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain a residue 35 GLU Chi-restraints excluded: chain b residue 29 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain d residue 119 VAL Chi-restraints excluded: chain i residue 78 MET Chi-restraints excluded: chain l residue 82 MET Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain n residue 80 ILE Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain n residue 157 ARG Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 45 MET Chi-restraints excluded: chain o residue 46 MET Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 106 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 396 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 593 optimal weight: 0.9980 chunk 485 optimal weight: 8.9990 chunk 196 optimal weight: 5.9990 chunk 714 optimal weight: 9.9990 chunk 771 optimal weight: 3.9990 chunk 636 optimal weight: 5.9990 chunk 708 optimal weight: 0.3980 chunk 243 optimal weight: 7.9990 chunk 572 optimal weight: 10.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 HIS ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 HIS E 91 ASN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 HIS G 475 GLN G 546 GLN ** G 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN K 83 ASN K 91 GLN L 209 ASN ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 ASN ** L 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 594 ASN L 605 ASN M 48 ASN M 175 ASN N 2 ASN N 125 HIS Q 44 ASN R 36 ASN R 46 GLN S 38 GLN V 52 ASN X 63 ASN X 102 GLN Y 80 GLN b 10 ASN e 28 ASN g 109 ASN i 12 GLN l 2 HIS ** o 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.246 67545 Z= 0.608 Angle : 1.607 50.635 91451 Z= 1.033 Chirality : 0.314 6.457 10003 Planarity : 0.005 0.060 11456 Dihedral : 10.734 152.312 9701 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.15 % Allowed : 11.13 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.90 (0.09), residues: 7948 helix: 0.55 (0.08), residues: 4220 sheet: -0.93 (0.24), residues: 442 loop : -2.10 (0.10), residues: 3286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP X 85 HIS 0.007 0.001 HIS R 68 PHE 0.034 0.002 PHE M 151 TYR 0.024 0.002 TYR I 120 ARG 0.010 0.001 ARG j 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 996 time to evaluate : 5.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8135 (mmtp) cc_final: 0.7839 (mmtt) REVERT: C 45 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8356 (pp) REVERT: C 47 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7910 (mt-10) REVERT: E 109 MET cc_start: 0.7911 (ppp) cc_final: 0.7601 (ppp) REVERT: F 129 MET cc_start: 0.8228 (mtt) cc_final: 0.8025 (mtt) REVERT: F 149 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9038 (mt) REVERT: F 272 MET cc_start: 0.8157 (mmm) cc_final: 0.7903 (mmt) REVERT: G 283 MET cc_start: 0.8600 (mtp) cc_final: 0.8240 (mtm) REVERT: G 306 MET cc_start: 0.7622 (tpp) cc_final: 0.7251 (tpp) REVERT: G 473 MET cc_start: 0.8244 (ttp) cc_final: 0.7999 (ttm) REVERT: H 22 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8684 (tt) REVERT: H 59 GLU cc_start: 0.7197 (mp0) cc_final: 0.6966 (mp0) REVERT: H 116 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8336 (mm) REVERT: I 28 MET cc_start: 0.8439 (mmm) cc_final: 0.7945 (mmt) REVERT: I 112 ASP cc_start: 0.7963 (m-30) cc_final: 0.7644 (m-30) REVERT: I 174 ASP cc_start: 0.8351 (t70) cc_final: 0.7911 (t0) REVERT: J 63 MET cc_start: 0.7692 (tpp) cc_final: 0.7472 (tpp) REVERT: L 27 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8110 (mt) REVERT: L 206 ASN cc_start: 0.7035 (m-40) cc_final: 0.6662 (p0) REVERT: L 482 MET cc_start: 0.7447 (ptp) cc_final: 0.7115 (ptp) REVERT: L 574 THR cc_start: 0.8619 (m) cc_final: 0.8243 (m) REVERT: M 17 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8488 (pp) REVERT: M 243 MET cc_start: 0.8599 (mtm) cc_final: 0.8368 (ttm) REVERT: M 269 MET cc_start: 0.7815 (ptm) cc_final: 0.7589 (ptm) REVERT: M 437 MET cc_start: 0.8536 (mmt) cc_final: 0.7954 (mmt) REVERT: M 441 MET cc_start: 0.8109 (tpt) cc_final: 0.7637 (tpt) REVERT: N 68 MET cc_start: 0.8028 (mmt) cc_final: 0.7386 (mmt) REVERT: N 190 MET cc_start: 0.8321 (mtt) cc_final: 0.7940 (mtt) REVERT: P 239 PHE cc_start: 0.7650 (t80) cc_final: 0.7170 (t80) REVERT: P 244 TYR cc_start: 0.7705 (t80) cc_final: 0.7437 (t80) REVERT: P 287 ILE cc_start: 0.8254 (mt) cc_final: 0.7870 (mm) REVERT: Q 42 ARG cc_start: 0.8733 (ttp-170) cc_final: 0.8293 (ttt-90) REVERT: R 21 LYS cc_start: 0.8303 (mmtm) cc_final: 0.7917 (tptp) REVERT: S 34 ASP cc_start: 0.7671 (m-30) cc_final: 0.7370 (m-30) REVERT: S 45 LYS cc_start: 0.7561 (mtmt) cc_final: 0.7317 (mtmt) REVERT: S 61 GLN cc_start: 0.7182 (mp10) cc_final: 0.6921 (mp10) REVERT: U 72 CYS cc_start: 0.7230 (m) cc_final: 0.6749 (t) REVERT: W 106 MET cc_start: 0.7772 (mmt) cc_final: 0.7210 (mmt) REVERT: W 119 ASP cc_start: 0.6889 (t0) cc_final: 0.6680 (t0) REVERT: Y 62 PHE cc_start: 0.7494 (t80) cc_final: 0.6685 (m-10) REVERT: b 9 LYS cc_start: 0.7602 (mtpt) cc_final: 0.7242 (ttpt) REVERT: e 5 ILE cc_start: 0.8382 (tp) cc_final: 0.8174 (tp) REVERT: e 14 ASP cc_start: 0.8333 (p0) cc_final: 0.8130 (p0) REVERT: h 10 VAL cc_start: 0.9269 (t) cc_final: 0.9050 (m) REVERT: l 102 LYS cc_start: 0.7872 (ttmt) cc_final: 0.7123 (tmtt) REVERT: l 111 MET cc_start: 0.7642 (mmt) cc_final: 0.7281 (mmm) REVERT: l 140 GLU cc_start: 0.7666 (mp0) cc_final: 0.7124 (mp0) REVERT: l 148 GLU cc_start: 0.6445 (mm-30) cc_final: 0.6176 (mm-30) REVERT: m 102 TYR cc_start: 0.7678 (m-80) cc_final: 0.7469 (m-10) REVERT: n 64 ARG cc_start: 0.7938 (ttm170) cc_final: 0.7561 (mtt180) REVERT: n 65 GLU cc_start: 0.7627 (tt0) cc_final: 0.6729 (tp30) REVERT: n 67 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6909 (mm-30) REVERT: o 96 LYS cc_start: 0.7753 (mttt) cc_final: 0.7433 (mtmt) REVERT: p 140 ASP cc_start: 0.8074 (m-30) cc_final: 0.7660 (m-30) REVERT: p 144 ASP cc_start: 0.8542 (m-30) cc_final: 0.8123 (m-30) REVERT: r 9 LYS cc_start: 0.8425 (mtpt) cc_final: 0.8042 (mtmm) outliers start: 152 outliers final: 87 residues processed: 1096 average time/residue: 0.6522 time to fit residues: 1223.9104 Evaluate side-chains 1026 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 933 time to evaluate : 5.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 181 MET Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 298 ILE Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain M residue 201 MET Chi-restraints excluded: chain N residue 187 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 160 LEU Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 250 LYS Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 295 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain S residue 47 HIS Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain W residue 72 ASN Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 91 SER Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain Y residue 96 CYS Chi-restraints excluded: chain Y residue 130 LYS Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain a residue 35 GLU Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 29 ILE Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain d residue 119 VAL Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain g residue 109 ASN Chi-restraints excluded: chain i residue 98 SER Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain l residue 64 ASP Chi-restraints excluded: chain l residue 82 MET Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain m residue 86 SER Chi-restraints excluded: chain n residue 80 ILE Chi-restraints excluded: chain n residue 113 MET Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain n residue 157 ARG Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 45 MET Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 39 VAL Chi-restraints excluded: chain p residue 83 CYS Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 100 THR Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 106 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 705 optimal weight: 5.9990 chunk 536 optimal weight: 10.0000 chunk 370 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 340 optimal weight: 7.9990 chunk 479 optimal weight: 7.9990 chunk 716 optimal weight: 0.7980 chunk 758 optimal weight: 3.9990 chunk 374 optimal weight: 3.9990 chunk 679 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN ** G 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 ASN L 446 ASN ** L 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 366 ASN N 2 ASN S 38 GLN T 74 GLN X 102 GLN Y 80 GLN b 10 ASN k 26 GLN l 2 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.242 67545 Z= 0.562 Angle : 1.580 50.588 91451 Z= 1.024 Chirality : 0.312 6.376 10003 Planarity : 0.005 0.058 11456 Dihedral : 10.444 153.275 9701 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.14 % Allowed : 13.10 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.10), residues: 7948 helix: 0.82 (0.08), residues: 4230 sheet: -0.67 (0.25), residues: 430 loop : -1.76 (0.11), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 85 HIS 0.007 0.001 HIS F 283 PHE 0.031 0.001 PHE M 151 TYR 0.026 0.001 TYR P 244 ARG 0.006 0.000 ARG k 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 981 time to evaluate : 5.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8058 (mmtp) cc_final: 0.7716 (mmtm) REVERT: B 135 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.7008 (t80) REVERT: E 43 GLN cc_start: 0.8256 (pm20) cc_final: 0.8007 (pm20) REVERT: E 109 MET cc_start: 0.7977 (ppp) cc_final: 0.7775 (ppp) REVERT: E 161 TYR cc_start: 0.8413 (m-80) cc_final: 0.8178 (m-10) REVERT: F 372 MET cc_start: 0.9037 (mtm) cc_final: 0.8829 (mtm) REVERT: G 18 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8399 (p) REVERT: G 109 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8061 (m-30) REVERT: G 283 MET cc_start: 0.8510 (mtp) cc_final: 0.8163 (mtm) REVERT: G 473 MET cc_start: 0.8310 (ttp) cc_final: 0.7996 (ttm) REVERT: H 22 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8714 (tt) REVERT: H 59 GLU cc_start: 0.7125 (mp0) cc_final: 0.6879 (mp0) REVERT: H 116 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8301 (mm) REVERT: H 151 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8366 (tt) REVERT: H 271 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8287 (mt) REVERT: I 28 MET cc_start: 0.8437 (mmm) cc_final: 0.7934 (mmt) REVERT: I 38 MET cc_start: 0.8955 (tpt) cc_final: 0.8736 (mmp) REVERT: I 112 ASP cc_start: 0.7940 (m-30) cc_final: 0.7599 (m-30) REVERT: L 206 ASN cc_start: 0.7029 (m-40) cc_final: 0.6643 (p0) REVERT: L 313 MET cc_start: 0.8383 (mtt) cc_final: 0.8159 (mtt) REVERT: L 410 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7595 (tp) REVERT: L 482 MET cc_start: 0.7490 (ptp) cc_final: 0.7154 (ptp) REVERT: L 574 THR cc_start: 0.8543 (m) cc_final: 0.8192 (m) REVERT: M 17 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8461 (pp) REVERT: M 243 MET cc_start: 0.8536 (mtm) cc_final: 0.8209 (ttm) REVERT: N 68 MET cc_start: 0.8073 (mmt) cc_final: 0.7667 (mmt) REVERT: N 190 MET cc_start: 0.8216 (mtt) cc_final: 0.7879 (mtt) REVERT: P 239 PHE cc_start: 0.7603 (t80) cc_final: 0.7130 (t80) REVERT: P 287 ILE cc_start: 0.8251 (mt) cc_final: 0.7868 (mm) REVERT: Q 42 ARG cc_start: 0.8753 (ttp-170) cc_final: 0.8288 (ttt-90) REVERT: R 21 LYS cc_start: 0.8446 (mmtm) cc_final: 0.8049 (tptp) REVERT: S 34 ASP cc_start: 0.7655 (m-30) cc_final: 0.7315 (m-30) REVERT: S 61 GLN cc_start: 0.6982 (mp10) cc_final: 0.6746 (mp10) REVERT: T 71 MET cc_start: 0.5759 (mmm) cc_final: 0.5370 (mmt) REVERT: U 49 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: U 68 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6143 (tt0) REVERT: U 72 CYS cc_start: 0.6937 (m) cc_final: 0.6712 (t) REVERT: W 106 MET cc_start: 0.7753 (mmt) cc_final: 0.7194 (mmt) REVERT: W 119 ASP cc_start: 0.6819 (t0) cc_final: 0.6617 (t0) REVERT: X 102 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: Y 52 GLU cc_start: 0.6027 (mp0) cc_final: 0.5524 (mp0) REVERT: Y 62 PHE cc_start: 0.7599 (t80) cc_final: 0.6757 (m-10) REVERT: b 9 LYS cc_start: 0.7618 (mtpt) cc_final: 0.7349 (ttpt) REVERT: b 61 ASN cc_start: 0.6521 (t0) cc_final: 0.6250 (t0) REVERT: e 5 ILE cc_start: 0.8413 (tp) cc_final: 0.8194 (tp) REVERT: h 10 VAL cc_start: 0.9263 (t) cc_final: 0.9061 (m) REVERT: k 23 ASP cc_start: 0.8198 (p0) cc_final: 0.7974 (p0) REVERT: k 70 SER cc_start: 0.8872 (t) cc_final: 0.8532 (m) REVERT: l 102 LYS cc_start: 0.7929 (ttmt) cc_final: 0.7140 (tmtt) REVERT: l 111 MET cc_start: 0.7619 (mmt) cc_final: 0.7181 (mmm) REVERT: l 140 GLU cc_start: 0.7831 (mp0) cc_final: 0.7312 (mp0) REVERT: l 148 GLU cc_start: 0.6484 (mm-30) cc_final: 0.6198 (mm-30) REVERT: n 64 ARG cc_start: 0.7946 (ttm170) cc_final: 0.7539 (mtt180) REVERT: n 67 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6934 (mm-30) REVERT: n 104 ASP cc_start: 0.7180 (m-30) cc_final: 0.6972 (m-30) REVERT: o 80 LYS cc_start: 0.8329 (mmtm) cc_final: 0.7838 (mmtm) REVERT: o 96 LYS cc_start: 0.7484 (mttt) cc_final: 0.7075 (mtpt) REVERT: p 140 ASP cc_start: 0.8016 (m-30) cc_final: 0.7591 (m-30) REVERT: p 144 ASP cc_start: 0.8442 (m-30) cc_final: 0.8029 (m-30) REVERT: p 163 LEU cc_start: 0.7823 (mt) cc_final: 0.7598 (mt) REVERT: r 9 LYS cc_start: 0.8418 (mtpt) cc_final: 0.8050 (mtmm) REVERT: s 54 LYS cc_start: 0.6844 (ptmm) cc_final: 0.6602 (pttp) outliers start: 151 outliers final: 95 residues processed: 1083 average time/residue: 0.6480 time to fit residues: 1196.8964 Evaluate side-chains 1034 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 928 time to evaluate : 5.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 362 CYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 181 MET Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 585 VAL Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 298 ILE Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 531 SER Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 423 MET Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 187 MET Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 160 LEU Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 250 LYS Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 227 THR Chi-restraints excluded: chain P residue 295 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain S residue 47 HIS Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 56 ASP Chi-restraints excluded: chain W residue 72 ASN Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 91 SER Chi-restraints excluded: chain X residue 102 GLN Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain Y residue 96 CYS Chi-restraints excluded: chain Y residue 130 LYS Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain a residue 35 GLU Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 87 ASP Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain d residue 119 VAL Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain i residue 98 SER Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain k residue 48 ASP Chi-restraints excluded: chain l residue 64 ASP Chi-restraints excluded: chain l residue 82 MET Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain m residue 86 SER Chi-restraints excluded: chain n residue 80 ILE Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain n residue 157 ARG Chi-restraints excluded: chain o residue 11 ASP Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 45 MET Chi-restraints excluded: chain o residue 46 MET Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 100 THR Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 106 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 631 optimal weight: 0.6980 chunk 430 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 564 optimal weight: 8.9990 chunk 313 optimal weight: 6.9990 chunk 647 optimal weight: 0.9990 chunk 524 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 387 optimal weight: 3.9990 chunk 681 optimal weight: 0.0970 chunk 191 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN ** G 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 ASN L 446 ASN L 580 GLN N 2 ASN P 44 GLN X 102 GLN Y 80 GLN a 31 ASN b 10 ASN g 84 GLN g 109 ASN l 2 HIS s 49 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 67545 Z= 0.546 Angle : 1.570 50.594 91451 Z= 1.019 Chirality : 0.312 6.365 10003 Planarity : 0.004 0.056 11456 Dihedral : 10.148 154.893 9701 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.44 % Allowed : 13.93 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.10), residues: 7948 helix: 1.06 (0.08), residues: 4219 sheet: -0.55 (0.25), residues: 432 loop : -1.50 (0.11), residues: 3297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.006 0.001 HIS F 283 PHE 0.029 0.001 PHE M 151 TYR 0.022 0.001 TYR P 244 ARG 0.007 0.000 ARG k 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 985 time to evaluate : 5.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 TRP cc_start: 0.7561 (t60) cc_final: 0.7194 (t60) REVERT: A 54 LYS cc_start: 0.8046 (mmtp) cc_final: 0.7802 (mmtt) REVERT: B 135 TYR cc_start: 0.8737 (OUTLIER) cc_final: 0.6988 (t80) REVERT: E 43 GLN cc_start: 0.8205 (pm20) cc_final: 0.7991 (pm20) REVERT: E 161 TYR cc_start: 0.8394 (m-80) cc_final: 0.8115 (m-10) REVERT: F 50 LEU cc_start: 0.8003 (pp) cc_final: 0.7480 (mt) REVERT: F 60 MET cc_start: 0.8487 (mmm) cc_final: 0.8249 (mmt) REVERT: F 372 MET cc_start: 0.9029 (mtm) cc_final: 0.8782 (mtm) REVERT: G 109 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7740 (m-30) REVERT: G 231 MET cc_start: 0.8953 (mmp) cc_final: 0.8724 (mmp) REVERT: G 283 MET cc_start: 0.8469 (mtp) cc_final: 0.8142 (mtm) REVERT: G 306 MET cc_start: 0.7550 (tpp) cc_final: 0.7277 (tpp) REVERT: G 473 MET cc_start: 0.8347 (ttp) cc_final: 0.7992 (ttm) REVERT: G 654 GLN cc_start: 0.6998 (mt0) cc_final: 0.6788 (mt0) REVERT: H 22 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8742 (tt) REVERT: H 59 GLU cc_start: 0.7450 (mp0) cc_final: 0.7178 (mp0) REVERT: H 116 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8328 (mm) REVERT: H 271 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8330 (mt) REVERT: I 28 MET cc_start: 0.8462 (mmm) cc_final: 0.7937 (mmt) REVERT: I 112 ASP cc_start: 0.7845 (m-30) cc_final: 0.7530 (m-30) REVERT: L 27 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8080 (mt) REVERT: L 313 MET cc_start: 0.8402 (mtt) cc_final: 0.8136 (mtt) REVERT: L 482 MET cc_start: 0.7506 (ptp) cc_final: 0.7203 (ptp) REVERT: L 574 THR cc_start: 0.8541 (m) cc_final: 0.8196 (m) REVERT: M 17 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8487 (pp) REVERT: N 34 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7523 (mm-30) REVERT: N 68 MET cc_start: 0.8126 (mmt) cc_final: 0.7568 (mmt) REVERT: N 190 MET cc_start: 0.8295 (mtt) cc_final: 0.7984 (mtt) REVERT: O 214 MET cc_start: 0.7914 (mmm) cc_final: 0.7641 (mmm) REVERT: P 239 PHE cc_start: 0.7563 (t80) cc_final: 0.7096 (t80) REVERT: P 287 ILE cc_start: 0.8264 (mt) cc_final: 0.7882 (mm) REVERT: Q 42 ARG cc_start: 0.8730 (ttp-170) cc_final: 0.8300 (ttt-90) REVERT: R 21 LYS cc_start: 0.8422 (mmtm) cc_final: 0.8026 (tptp) REVERT: S 34 ASP cc_start: 0.7673 (m-30) cc_final: 0.7467 (m-30) REVERT: S 38 GLN cc_start: 0.6458 (mm-40) cc_final: 0.6243 (mm-40) REVERT: T 47 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7078 (tm-30) REVERT: U 72 CYS cc_start: 0.6929 (m) cc_final: 0.6684 (t) REVERT: X 93 MET cc_start: 0.8125 (mmm) cc_final: 0.7902 (mmm) REVERT: Y 62 PHE cc_start: 0.7610 (t80) cc_final: 0.6790 (m-10) REVERT: Z 18 ILE cc_start: 0.7742 (mm) cc_final: 0.7339 (mt) REVERT: Z 97 MET cc_start: 0.8019 (mtp) cc_final: 0.7730 (mtp) REVERT: b 61 ASN cc_start: 0.6604 (t0) cc_final: 0.6312 (t0) REVERT: e 5 ILE cc_start: 0.8401 (tp) cc_final: 0.8184 (tp) REVERT: h 10 VAL cc_start: 0.9230 (t) cc_final: 0.9002 (m) REVERT: j 13 GLU cc_start: 0.7739 (mp0) cc_final: 0.7082 (mp0) REVERT: k 23 ASP cc_start: 0.8185 (p0) cc_final: 0.7920 (p0) REVERT: k 70 SER cc_start: 0.8855 (t) cc_final: 0.8546 (m) REVERT: l 102 LYS cc_start: 0.7945 (ttmt) cc_final: 0.7156 (tmtt) REVERT: l 111 MET cc_start: 0.7577 (mmt) cc_final: 0.7101 (mmm) REVERT: l 140 GLU cc_start: 0.7819 (mp0) cc_final: 0.7372 (mp0) REVERT: l 148 GLU cc_start: 0.6501 (mm-30) cc_final: 0.6226 (mm-30) REVERT: m 5 TYR cc_start: 0.8407 (t80) cc_final: 0.8022 (t80) REVERT: n 64 ARG cc_start: 0.7949 (ttm170) cc_final: 0.7560 (mtt180) REVERT: o 96 LYS cc_start: 0.7494 (mttt) cc_final: 0.7241 (mtmt) REVERT: p 140 ASP cc_start: 0.8108 (m-30) cc_final: 0.7758 (m-30) REVERT: p 144 ASP cc_start: 0.8399 (m-30) cc_final: 0.8020 (m-30) REVERT: q 68 MET cc_start: 0.8653 (ttt) cc_final: 0.8291 (ttt) REVERT: r 9 LYS cc_start: 0.8477 (mtpt) cc_final: 0.8084 (mtmm) REVERT: s 49 ASN cc_start: 0.8176 (t0) cc_final: 0.7968 (t0) outliers start: 172 outliers final: 109 residues processed: 1105 average time/residue: 0.6220 time to fit residues: 1171.2687 Evaluate side-chains 1050 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 934 time to evaluate : 5.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 362 CYS Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 74 MET 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 181 MET Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 585 VAL Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 298 ILE Chi-restraints excluded: chain L residue 496 LEU Chi-restraints excluded: chain L residue 531 SER Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain M residue 177 MET Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 423 MET Chi-restraints excluded: chain N residue 187 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 160 LEU Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 250 LYS Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 227 THR Chi-restraints excluded: chain P residue 295 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain S residue 47 HIS Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain V residue 76 VAL Chi-restraints excluded: chain W residue 72 ASN Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 35 CYS Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain Y residue 96 CYS Chi-restraints excluded: chain Y residue 130 LYS Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 29 ILE Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain d residue 119 VAL Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain i residue 98 SER Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain k residue 48 ASP Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain l residue 82 MET Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain m residue 86 SER Chi-restraints excluded: chain n residue 80 ILE Chi-restraints excluded: chain n residue 113 MET Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain n residue 157 ARG Chi-restraints excluded: chain o residue 11 ASP Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 45 MET Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 39 VAL Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 31 ASN Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 106 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 255 optimal weight: 0.9990 chunk 683 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 445 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 759 optimal weight: 10.0000 chunk 630 optimal weight: 0.6980 chunk 351 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 398 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN ** G 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 ASN L 446 ASN L 580 GLN N 2 ASN P 112 ASN Y 80 GLN b 10 ASN g 84 GLN k 38 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 67545 Z= 0.549 Angle : 1.570 50.590 91451 Z= 1.019 Chirality : 0.312 6.353 10003 Planarity : 0.004 0.056 11456 Dihedral : 9.984 155.931 9701 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.46 % Allowed : 14.44 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.07 (0.10), residues: 7948 helix: 1.16 (0.08), residues: 4222 sheet: -0.47 (0.26), residues: 422 loop : -1.36 (0.11), residues: 3304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.006 0.001 HIS l 2 PHE 0.029 0.001 PHE M 151 TYR 0.026 0.001 TYR P 244 ARG 0.008 0.000 ARG k 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 963 time to evaluate : 6.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 TRP cc_start: 0.7546 (t60) cc_final: 0.7172 (t60) REVERT: A 54 LYS cc_start: 0.8067 (mmtp) cc_final: 0.7803 (mmtt) REVERT: A 68 GLU cc_start: 0.7384 (tp30) cc_final: 0.7177 (tp30) REVERT: B 58 MET cc_start: 0.7200 (tpt) cc_final: 0.6719 (tpt) REVERT: B 135 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.6991 (t80) REVERT: E 43 GLN cc_start: 0.8179 (pm20) cc_final: 0.7967 (pm20) REVERT: E 161 TYR cc_start: 0.8394 (m-80) cc_final: 0.8094 (m-10) REVERT: F 50 LEU cc_start: 0.7995 (pp) cc_final: 0.7468 (mt) REVERT: F 60 MET cc_start: 0.8503 (mmm) cc_final: 0.8220 (mmt) REVERT: G 18 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8446 (p) REVERT: G 109 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: G 231 MET cc_start: 0.8973 (mmp) cc_final: 0.8728 (mmp) REVERT: G 283 MET cc_start: 0.8518 (mtp) cc_final: 0.8192 (mtm) REVERT: G 306 MET cc_start: 0.7555 (tpp) cc_final: 0.7218 (tpp) REVERT: G 473 MET cc_start: 0.8264 (ttp) cc_final: 0.7875 (ttm) REVERT: H 22 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8799 (tt) REVERT: H 59 GLU cc_start: 0.7329 (mp0) cc_final: 0.7079 (mp0) REVERT: H 116 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8291 (mm) REVERT: H 151 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8420 (tt) REVERT: H 192 GLU cc_start: 0.7489 (tp30) cc_final: 0.7169 (tp30) REVERT: H 271 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8329 (mt) REVERT: I 28 MET cc_start: 0.8459 (mmm) cc_final: 0.7923 (mmt) REVERT: I 112 ASP cc_start: 0.7843 (m-30) cc_final: 0.7548 (m-30) REVERT: K 23 ARG cc_start: 0.7091 (ttt-90) cc_final: 0.6060 (mmt180) REVERT: L 27 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8176 (mt) REVERT: L 298 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7936 (tt) REVERT: L 313 MET cc_start: 0.8393 (mtt) cc_final: 0.8150 (mtt) REVERT: L 319 MET cc_start: 0.8029 (ptp) cc_final: 0.7742 (ptm) REVERT: L 482 MET cc_start: 0.7589 (ptp) cc_final: 0.7285 (ptp) REVERT: L 574 THR cc_start: 0.8547 (m) cc_final: 0.8200 (m) REVERT: M 17 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8497 (pp) REVERT: N 34 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7408 (mm-30) REVERT: N 68 MET cc_start: 0.8101 (mmt) cc_final: 0.7623 (mmt) REVERT: N 190 MET cc_start: 0.8333 (mtt) cc_final: 0.8053 (mtt) REVERT: O 214 MET cc_start: 0.7915 (mmm) cc_final: 0.7651 (mmm) REVERT: P 179 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7762 (mp) REVERT: P 239 PHE cc_start: 0.7649 (t80) cc_final: 0.7214 (t80) REVERT: P 244 TYR cc_start: 0.7693 (t80) cc_final: 0.7238 (t80) REVERT: P 287 ILE cc_start: 0.8260 (mt) cc_final: 0.7885 (mm) REVERT: Q 42 ARG cc_start: 0.8758 (ttp-170) cc_final: 0.8334 (ttt-90) REVERT: R 7 SER cc_start: 0.7610 (OUTLIER) cc_final: 0.7369 (t) REVERT: R 21 LYS cc_start: 0.8409 (mmtm) cc_final: 0.8029 (tptp) REVERT: S 34 ASP cc_start: 0.7645 (m-30) cc_final: 0.7351 (m-30) REVERT: S 63 LYS cc_start: 0.7946 (mptt) cc_final: 0.7688 (mptt) REVERT: U 72 CYS cc_start: 0.6952 (m) cc_final: 0.6675 (t) REVERT: W 106 MET cc_start: 0.7934 (mmp) cc_final: 0.7710 (mmp) REVERT: Y 52 GLU cc_start: 0.6173 (mp0) cc_final: 0.5677 (mp0) REVERT: Y 62 PHE cc_start: 0.7598 (t80) cc_final: 0.6739 (m-10) REVERT: Z 18 ILE cc_start: 0.7843 (mm) cc_final: 0.7433 (mt) REVERT: Z 97 MET cc_start: 0.8004 (mtp) cc_final: 0.7745 (mtp) REVERT: a 17 VAL cc_start: 0.9129 (OUTLIER) cc_final: 0.8839 (t) REVERT: b 61 ASN cc_start: 0.6597 (t0) cc_final: 0.6298 (t0) REVERT: e 5 ILE cc_start: 0.8417 (tp) cc_final: 0.8195 (tp) REVERT: g 22 MET cc_start: 0.7383 (tpt) cc_final: 0.6771 (tpp) REVERT: h 10 VAL cc_start: 0.9213 (t) cc_final: 0.9008 (m) REVERT: j 13 GLU cc_start: 0.7850 (mp0) cc_final: 0.7181 (mp0) REVERT: k 23 ASP cc_start: 0.8268 (p0) cc_final: 0.7991 (p0) REVERT: k 70 SER cc_start: 0.8845 (t) cc_final: 0.8556 (m) REVERT: l 70 MET cc_start: 0.8184 (ttm) cc_final: 0.7953 (mtp) REVERT: l 102 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7182 (tmtt) REVERT: l 111 MET cc_start: 0.7615 (mmt) cc_final: 0.7087 (mmm) REVERT: l 140 GLU cc_start: 0.7828 (mp0) cc_final: 0.7406 (mp0) REVERT: l 148 GLU cc_start: 0.6678 (mm-30) cc_final: 0.6396 (mm-30) REVERT: m 5 TYR cc_start: 0.8377 (t80) cc_final: 0.7948 (t80) REVERT: n 64 ARG cc_start: 0.7956 (ttm170) cc_final: 0.7559 (mtt180) REVERT: o 100 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7494 (tp30) REVERT: p 140 ASP cc_start: 0.8108 (m-30) cc_final: 0.7750 (m-30) REVERT: p 144 ASP cc_start: 0.8390 (m-30) cc_final: 0.8032 (m-30) REVERT: q 68 MET cc_start: 0.8674 (ttt) cc_final: 0.8302 (ttt) REVERT: r 9 LYS cc_start: 0.8475 (mtpt) cc_final: 0.8256 (mtmt) REVERT: r 90 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.5059 (pp20) outliers start: 174 outliers final: 131 residues processed: 1088 average time/residue: 0.6240 time to fit residues: 1159.5709 Evaluate side-chains 1078 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 933 time to evaluate : 6.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 362 CYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 74 MET 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 181 MET Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 585 VAL Chi-restraints excluded: chain G residue 606 ILE Chi-restraints excluded: chain G residue 609 ILE Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 298 ILE Chi-restraints excluded: chain L residue 496 LEU Chi-restraints excluded: chain L residue 531 SER Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 177 MET Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 423 MET Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 187 MET Chi-restraints excluded: chain N residue 333 SER Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 160 LEU Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 250 LYS Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain P residue 179 LEU Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 295 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain S residue 47 HIS Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 56 ASP Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain W residue 72 ASN Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 35 CYS Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain Y residue 96 CYS Chi-restraints excluded: chain Y residue 130 LYS Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 35 GLU Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 29 ILE Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 87 ASP Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain d residue 119 VAL Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain i residue 98 SER Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain k residue 48 ASP Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain l residue 64 ASP Chi-restraints excluded: chain l residue 82 MET Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain l residue 131 GLN Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain m residue 86 SER Chi-restraints excluded: chain n residue 80 ILE Chi-restraints excluded: chain n residue 113 MET Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain o residue 11 ASP Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 45 MET Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 39 VAL Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 31 ASN Chi-restraints excluded: chain q residue 100 THR Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 90 GLU Chi-restraints excluded: chain r residue 106 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 732 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 432 optimal weight: 9.9990 chunk 554 optimal weight: 3.9990 chunk 429 optimal weight: 9.9990 chunk 639 optimal weight: 2.9990 chunk 424 optimal weight: 4.9990 chunk 756 optimal weight: 4.9990 chunk 473 optimal weight: 20.0000 chunk 461 optimal weight: 2.9990 chunk 349 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN ** G 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 ASN L 580 GLN ** M 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 2 ASN Y 80 GLN b 10 ASN g 84 GLN ** k 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 2 HIS s 49 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.239 67545 Z= 0.602 Angle : 1.600 50.668 91451 Z= 1.030 Chirality : 0.313 6.481 10003 Planarity : 0.005 0.063 11456 Dihedral : 10.148 155.052 9701 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.72 % Allowed : 14.51 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 7948 helix: 0.97 (0.08), residues: 4240 sheet: -0.50 (0.26), residues: 420 loop : -1.39 (0.11), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 254 HIS 0.010 0.001 HIS l 2 PHE 0.035 0.002 PHE M 151 TYR 0.027 0.002 TYR P 244 ARG 0.009 0.001 ARG k 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1139 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 947 time to evaluate : 5.937 Fit side-chains revert: symmetry clash REVERT: A 23 TRP cc_start: 0.7567 (t60) cc_final: 0.7178 (t60) REVERT: A 68 GLU cc_start: 0.7583 (tp30) cc_final: 0.7291 (tp30) REVERT: B 58 MET cc_start: 0.7189 (tpt) cc_final: 0.6921 (tpt) REVERT: B 135 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.7000 (t80) REVERT: D 72 MET cc_start: 0.8024 (mmm) cc_final: 0.7819 (mmm) REVERT: E 43 GLN cc_start: 0.8119 (pm20) cc_final: 0.7916 (pm20) REVERT: E 161 TYR cc_start: 0.8459 (m-80) cc_final: 0.8177 (m-10) REVERT: F 50 LEU cc_start: 0.8056 (pp) cc_final: 0.7512 (mt) REVERT: F 60 MET cc_start: 0.8612 (mmm) cc_final: 0.8304 (mmt) REVERT: G 18 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8453 (p) REVERT: G 74 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7554 (mtm) REVERT: G 109 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7706 (m-30) REVERT: G 231 MET cc_start: 0.9045 (mmp) cc_final: 0.8833 (mmp) REVERT: G 283 MET cc_start: 0.8544 (mtp) cc_final: 0.8142 (mtm) REVERT: G 473 MET cc_start: 0.8261 (ttp) cc_final: 0.7935 (ttm) REVERT: H 22 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8754 (tt) REVERT: H 59 GLU cc_start: 0.7425 (mp0) cc_final: 0.7150 (mp0) REVERT: H 116 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8345 (mm) REVERT: H 126 LYS cc_start: 0.7873 (pttt) cc_final: 0.6790 (tppt) REVERT: H 151 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8419 (tt) REVERT: H 271 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8341 (mt) REVERT: I 28 MET cc_start: 0.8491 (mmm) cc_final: 0.7987 (mmt) REVERT: I 112 ASP cc_start: 0.7964 (m-30) cc_final: 0.7640 (m-30) REVERT: K 23 ARG cc_start: 0.7160 (ttt-90) cc_final: 0.6604 (tpp-160) REVERT: L 27 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8341 (mt) REVERT: L 298 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8161 (tt) REVERT: L 482 MET cc_start: 0.7715 (ptp) cc_final: 0.7421 (ptp) REVERT: M 17 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8505 (pp) REVERT: N 34 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7563 (mm-30) REVERT: N 68 MET cc_start: 0.8123 (mmt) cc_final: 0.7674 (mmt) REVERT: N 156 MET cc_start: 0.7541 (mmm) cc_final: 0.7335 (mmm) REVERT: N 190 MET cc_start: 0.8288 (mtt) cc_final: 0.7968 (mtt) REVERT: N 332 MET cc_start: 0.7552 (mmp) cc_final: 0.7218 (mmt) REVERT: P 239 PHE cc_start: 0.7386 (t80) cc_final: 0.7101 (t80) REVERT: P 287 ILE cc_start: 0.8274 (mt) cc_final: 0.7903 (mm) REVERT: R 7 SER cc_start: 0.7699 (OUTLIER) cc_final: 0.7438 (t) REVERT: R 21 LYS cc_start: 0.8425 (mmtm) cc_final: 0.8032 (tptp) REVERT: S 63 LYS cc_start: 0.7956 (mptt) cc_final: 0.7653 (mptt) REVERT: T 47 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7311 (tm-30) REVERT: U 49 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: U 72 CYS cc_start: 0.7152 (m) cc_final: 0.6783 (t) REVERT: V 43 TYR cc_start: 0.7882 (t80) cc_final: 0.7486 (t80) REVERT: V 72 GLN cc_start: 0.7821 (mm110) cc_final: 0.7544 (mm-40) REVERT: W 106 MET cc_start: 0.8012 (mmp) cc_final: 0.7508 (mmt) REVERT: Y 52 GLU cc_start: 0.6148 (mp0) cc_final: 0.5601 (mp0) REVERT: Z 18 ILE cc_start: 0.7862 (mm) cc_final: 0.7459 (mt) REVERT: Z 97 MET cc_start: 0.7937 (mtp) cc_final: 0.7677 (mtp) REVERT: a 17 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8802 (t) REVERT: e 5 ILE cc_start: 0.8479 (tp) cc_final: 0.8275 (tp) REVERT: g 22 MET cc_start: 0.7406 (tpt) cc_final: 0.6794 (tpp) REVERT: k 23 ASP cc_start: 0.8290 (p0) cc_final: 0.8037 (p0) REVERT: k 70 SER cc_start: 0.8802 (t) cc_final: 0.8427 (m) REVERT: l 102 LYS cc_start: 0.8065 (ttmt) cc_final: 0.7231 (tmtt) REVERT: l 111 MET cc_start: 0.7731 (mmt) cc_final: 0.7166 (mmm) REVERT: l 140 GLU cc_start: 0.7872 (mp0) cc_final: 0.7332 (mp0) REVERT: l 148 GLU cc_start: 0.6717 (mm-30) cc_final: 0.6427 (mm-30) REVERT: m 5 TYR cc_start: 0.8416 (t80) cc_final: 0.8032 (t80) REVERT: m 33 VAL cc_start: 0.8335 (t) cc_final: 0.8068 (p) REVERT: n 64 ARG cc_start: 0.8010 (ttm170) cc_final: 0.7583 (mtt180) REVERT: o 8 TYR cc_start: 0.7276 (m-80) cc_final: 0.6995 (m-80) REVERT: o 45 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7852 (ttm) REVERT: p 140 ASP cc_start: 0.8132 (m-30) cc_final: 0.7744 (m-30) REVERT: p 144 ASP cc_start: 0.8498 (m-30) cc_final: 0.8078 (m-30) REVERT: q 68 MET cc_start: 0.8656 (ttt) cc_final: 0.8220 (ttt) REVERT: q 78 ASP cc_start: 0.8109 (m-30) cc_final: 0.7817 (m-30) REVERT: r 90 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.5060 (pp20) REVERT: s 47 ASP cc_start: 0.7251 (m-30) cc_final: 0.7039 (m-30) outliers start: 192 outliers final: 143 residues processed: 1087 average time/residue: 0.6628 time to fit residues: 1233.3788 Evaluate side-chains 1071 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 912 time to evaluate : 6.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 362 CYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 585 VAL Chi-restraints excluded: chain G residue 606 ILE Chi-restraints excluded: chain G residue 609 ILE Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 298 ILE Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 496 LEU Chi-restraints excluded: chain L residue 531 SER Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain M residue 177 MET Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 201 MET Chi-restraints excluded: chain M residue 344 MET Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 423 MET Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 187 MET Chi-restraints excluded: chain N residue 333 SER Chi-restraints excluded: chain N residue 334 THR Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 160 LEU Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 250 LYS Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 295 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain S residue 47 HIS Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 56 ASP Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 76 VAL Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 72 ASN Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 35 CYS Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 91 SER Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain Y residue 43 SER Chi-restraints excluded: chain Y residue 96 CYS Chi-restraints excluded: chain Y residue 130 LYS Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 35 GLU Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 29 ILE Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 87 ASP Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain e residue 42 CYS Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain g residue 35 VAL Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 98 SER Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain k residue 48 ASP Chi-restraints excluded: chain l residue 64 ASP Chi-restraints excluded: chain l residue 82 MET Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain l residue 131 GLN Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain m residue 57 SER Chi-restraints excluded: chain m residue 86 SER Chi-restraints excluded: chain n residue 113 MET Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain o residue 11 ASP Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 45 MET Chi-restraints excluded: chain o residue 46 MET Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 39 VAL Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 31 ASN Chi-restraints excluded: chain q residue 100 THR Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 28 GLN Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 90 GLU Chi-restraints excluded: chain r residue 106 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 468 optimal weight: 9.9990 chunk 302 optimal weight: 4.9990 chunk 451 optimal weight: 0.9990 chunk 227 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 481 optimal weight: 10.0000 chunk 515 optimal weight: 9.9990 chunk 374 optimal weight: 6.9990 chunk 70 optimal weight: 0.0000 chunk 594 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 ASN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN G 546 GLN ** G 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 ASN L 580 GLN M 89 ASN Y 80 GLN b 10 ASN g 84 GLN ** k 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 168 HIS s 49 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 67545 Z= 0.543 Angle : 1.569 50.599 91451 Z= 1.019 Chirality : 0.311 6.383 10003 Planarity : 0.004 0.058 11456 Dihedral : 9.800 157.198 9701 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.28 % Allowed : 15.12 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.10), residues: 7948 helix: 1.20 (0.08), residues: 4206 sheet: -0.42 (0.26), residues: 423 loop : -1.18 (0.11), residues: 3319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 85 HIS 0.007 0.001 HIS F 283 PHE 0.029 0.001 PHE M 151 TYR 0.019 0.001 TYR L 422 ARG 0.005 0.000 ARG k 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 965 time to evaluate : 6.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7686 (mmtt) cc_final: 0.7439 (mmtp) REVERT: A 68 GLU cc_start: 0.7499 (tp30) cc_final: 0.7232 (tp30) REVERT: B 58 MET cc_start: 0.7175 (tpt) cc_final: 0.6855 (tpt) REVERT: B 135 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.6998 (t80) REVERT: D 72 MET cc_start: 0.7964 (mmm) cc_final: 0.7748 (mmm) REVERT: E 43 GLN cc_start: 0.8018 (pm20) cc_final: 0.7815 (pm20) REVERT: E 161 TYR cc_start: 0.8446 (m-80) cc_final: 0.8132 (m-10) REVERT: F 50 LEU cc_start: 0.8025 (pp) cc_final: 0.7479 (mt) REVERT: F 60 MET cc_start: 0.8608 (mmm) cc_final: 0.8354 (mmt) REVERT: F 317 MET cc_start: 0.8066 (tpt) cc_final: 0.7785 (tpt) REVERT: G 18 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8548 (p) REVERT: G 283 MET cc_start: 0.8443 (mtp) cc_final: 0.8084 (mtm) REVERT: G 306 MET cc_start: 0.7660 (tpp) cc_final: 0.7431 (tpp) REVERT: G 473 MET cc_start: 0.8250 (ttp) cc_final: 0.7856 (ttm) REVERT: H 51 ASP cc_start: 0.8317 (m-30) cc_final: 0.8116 (m-30) REVERT: H 59 GLU cc_start: 0.7392 (mp0) cc_final: 0.7130 (mp0) REVERT: H 116 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8310 (mm) REVERT: H 126 LYS cc_start: 0.7877 (pttt) cc_final: 0.6842 (tppt) REVERT: H 151 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8399 (tt) REVERT: H 271 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8309 (mt) REVERT: I 28 MET cc_start: 0.8468 (mmm) cc_final: 0.7934 (mmt) REVERT: I 112 ASP cc_start: 0.7914 (m-30) cc_final: 0.7552 (m-30) REVERT: K 23 ARG cc_start: 0.7122 (ttt-90) cc_final: 0.6571 (tpp-160) REVERT: L 27 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8104 (mt) REVERT: L 252 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.5905 (tpp) REVERT: L 313 MET cc_start: 0.8371 (mtt) cc_final: 0.8163 (mtt) REVERT: L 383 MET cc_start: 0.7618 (tpp) cc_final: 0.7289 (tpp) REVERT: L 482 MET cc_start: 0.7682 (ptp) cc_final: 0.7379 (ptp) REVERT: M 17 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8511 (pp) REVERT: M 98 MET cc_start: 0.8428 (mmp) cc_final: 0.8058 (mmm) REVERT: N 34 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7407 (mm-30) REVERT: N 68 MET cc_start: 0.8148 (mmt) cc_final: 0.7333 (mmp) REVERT: N 156 MET cc_start: 0.7473 (mmm) cc_final: 0.7258 (mmm) REVERT: N 190 MET cc_start: 0.8286 (mtt) cc_final: 0.7987 (mtt) REVERT: O 214 MET cc_start: 0.7944 (mmm) cc_final: 0.7672 (mmm) REVERT: P 179 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7310 (mp) REVERT: P 239 PHE cc_start: 0.7339 (t80) cc_final: 0.7061 (t80) REVERT: P 287 ILE cc_start: 0.8249 (mt) cc_final: 0.7873 (mm) REVERT: R 7 SER cc_start: 0.7576 (OUTLIER) cc_final: 0.7342 (t) REVERT: R 21 LYS cc_start: 0.8468 (mmtm) cc_final: 0.8076 (tptp) REVERT: S 63 LYS cc_start: 0.7909 (mptt) cc_final: 0.7613 (mptt) REVERT: T 47 GLN cc_start: 0.7594 (tm-30) cc_final: 0.7183 (tm-30) REVERT: U 72 CYS cc_start: 0.7020 (m) cc_final: 0.6666 (t) REVERT: V 6 LYS cc_start: 0.6608 (mptt) cc_final: 0.6374 (mmtp) REVERT: V 72 GLN cc_start: 0.7816 (mm110) cc_final: 0.7502 (mm-40) REVERT: Y 62 PHE cc_start: 0.7464 (t80) cc_final: 0.6708 (m-10) REVERT: Z 18 ILE cc_start: 0.7855 (mm) cc_final: 0.7437 (mt) REVERT: Z 97 MET cc_start: 0.7942 (mtp) cc_final: 0.7691 (mtp) REVERT: a 17 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8787 (t) REVERT: e 5 ILE cc_start: 0.8442 (tp) cc_final: 0.8220 (tp) REVERT: g 22 MET cc_start: 0.7518 (tpt) cc_final: 0.6733 (tpp) REVERT: j 13 GLU cc_start: 0.7793 (mp0) cc_final: 0.7066 (mp0) REVERT: k 47 ARG cc_start: 0.6027 (mmm-85) cc_final: 0.5687 (ttt-90) REVERT: k 70 SER cc_start: 0.8783 (t) cc_final: 0.8460 (m) REVERT: l 70 MET cc_start: 0.8214 (ttm) cc_final: 0.7995 (mtp) REVERT: l 102 LYS cc_start: 0.8055 (ttmt) cc_final: 0.7236 (tmtt) REVERT: l 111 MET cc_start: 0.7685 (mmt) cc_final: 0.7349 (mmm) REVERT: l 123 SER cc_start: 0.9115 (t) cc_final: 0.8799 (t) REVERT: l 140 GLU cc_start: 0.7857 (mp0) cc_final: 0.7393 (mp0) REVERT: l 148 GLU cc_start: 0.6731 (mm-30) cc_final: 0.6451 (mm-30) REVERT: m 5 TYR cc_start: 0.8413 (t80) cc_final: 0.8052 (t80) REVERT: m 33 VAL cc_start: 0.8307 (t) cc_final: 0.8042 (p) REVERT: n 64 ARG cc_start: 0.7982 (ttm170) cc_final: 0.7538 (mtt180) REVERT: o 8 TYR cc_start: 0.7142 (m-80) cc_final: 0.6914 (m-80) REVERT: o 100 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7539 (tp30) REVERT: p 140 ASP cc_start: 0.8125 (m-30) cc_final: 0.7742 (m-30) REVERT: p 144 ASP cc_start: 0.8393 (m-30) cc_final: 0.8013 (m-30) REVERT: q 68 MET cc_start: 0.8691 (ttt) cc_final: 0.8256 (ttt) REVERT: q 78 ASP cc_start: 0.8085 (m-30) cc_final: 0.7827 (m-30) REVERT: r 52 TYR cc_start: 0.8857 (m-80) cc_final: 0.8575 (m-80) REVERT: r 90 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.5080 (pp20) outliers start: 161 outliers final: 120 residues processed: 1077 average time/residue: 0.6238 time to fit residues: 1145.9598 Evaluate side-chains 1068 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 936 time to evaluate : 5.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 362 CYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 181 MET Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 585 VAL Chi-restraints excluded: chain G residue 609 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 252 MET Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 496 LEU Chi-restraints excluded: chain L residue 531 SER Chi-restraints excluded: chain L residue 559 GLU Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 423 MET Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 187 MET Chi-restraints excluded: chain N residue 333 SER Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 160 LEU Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 250 LYS Chi-restraints excluded: chain P residue 179 LEU Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 295 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain S residue 47 HIS Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 56 ASP Chi-restraints excluded: chain V residue 76 VAL Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 72 ASN Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain Y residue 96 CYS Chi-restraints excluded: chain Y residue 114 MET Chi-restraints excluded: chain Y residue 130 LYS Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 29 ILE Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 87 ASP Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain g residue 35 VAL Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 98 SER Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain k residue 48 ASP Chi-restraints excluded: chain l residue 82 MET Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain m residue 86 SER Chi-restraints excluded: chain n residue 113 MET Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain o residue 11 ASP Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 45 MET Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 39 VAL Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 31 ASN Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 90 GLU Chi-restraints excluded: chain r residue 106 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 688 optimal weight: 0.0370 chunk 724 optimal weight: 5.9990 chunk 661 optimal weight: 7.9990 chunk 705 optimal weight: 7.9990 chunk 424 optimal weight: 0.2980 chunk 307 optimal weight: 0.7980 chunk 553 optimal weight: 40.0000 chunk 216 optimal weight: 2.9990 chunk 637 optimal weight: 2.9990 chunk 666 optimal weight: 0.9990 chunk 702 optimal weight: 0.6980 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN G 110 GLN ** G 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 ASN ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 ASN M 89 ASN N 46 ASN Y 80 GLN b 10 ASN b 70 GLN g 84 GLN s 49 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 67545 Z= 0.535 Angle : 1.563 50.595 91451 Z= 1.016 Chirality : 0.311 6.339 10003 Planarity : 0.004 0.056 11456 Dihedral : 9.356 160.186 9701 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.80 % Allowed : 15.87 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.48 (0.10), residues: 7948 helix: 1.40 (0.08), residues: 4208 sheet: -0.36 (0.27), residues: 403 loop : -1.00 (0.11), residues: 3337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 144 HIS 0.006 0.001 HIS F 283 PHE 0.027 0.001 PHE M 151 TYR 0.025 0.001 TYR T 79 ARG 0.008 0.000 ARG k 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 991 time to evaluate : 6.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7884 (mmtt) cc_final: 0.7504 (mmtp) REVERT: A 68 GLU cc_start: 0.7371 (tp30) cc_final: 0.7108 (tp30) REVERT: B 58 MET cc_start: 0.7280 (tpt) cc_final: 0.6914 (tpt) REVERT: B 135 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.6906 (t80) REVERT: C 43 SER cc_start: 0.9107 (p) cc_final: 0.8598 (m) REVERT: E 161 TYR cc_start: 0.8310 (m-80) cc_final: 0.7947 (m-10) REVERT: F 50 LEU cc_start: 0.8043 (pp) cc_final: 0.7544 (mt) REVERT: F 60 MET cc_start: 0.8515 (mmm) cc_final: 0.8252 (mmt) REVERT: G 18 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8518 (p) REVERT: G 71 MET cc_start: 0.8770 (tpp) cc_final: 0.8459 (tpp) REVERT: G 306 MET cc_start: 0.7659 (tpp) cc_final: 0.7409 (tpp) REVERT: G 473 MET cc_start: 0.8147 (ttp) cc_final: 0.7704 (ttm) REVERT: H 59 GLU cc_start: 0.7434 (mp0) cc_final: 0.7182 (mp0) REVERT: H 116 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8373 (mm) REVERT: H 126 LYS cc_start: 0.7776 (pttt) cc_final: 0.6757 (tppt) REVERT: H 151 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8416 (tt) REVERT: H 271 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8319 (mt) REVERT: I 28 MET cc_start: 0.8432 (mmm) cc_final: 0.7871 (mmt) REVERT: I 112 ASP cc_start: 0.7837 (m-30) cc_final: 0.7504 (m-30) REVERT: K 23 ARG cc_start: 0.6936 (ttt-90) cc_final: 0.6453 (tpp-160) REVERT: L 23 MET cc_start: 0.8299 (mmt) cc_final: 0.7762 (mmt) REVERT: L 27 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8019 (mt) REVERT: L 383 MET cc_start: 0.7722 (tpp) cc_final: 0.7391 (tpp) REVERT: L 482 MET cc_start: 0.7639 (ptp) cc_final: 0.7347 (ptp) REVERT: M 17 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8331 (pp) REVERT: M 98 MET cc_start: 0.8352 (mmp) cc_final: 0.7985 (mmm) REVERT: M 210 TYR cc_start: 0.7994 (t80) cc_final: 0.7324 (t80) REVERT: M 441 MET cc_start: 0.8022 (tpt) cc_final: 0.7577 (tpt) REVERT: N 34 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7608 (mm-30) REVERT: N 68 MET cc_start: 0.8169 (mmt) cc_final: 0.7328 (mmp) REVERT: N 190 MET cc_start: 0.8366 (mtt) cc_final: 0.8093 (mtt) REVERT: O 214 MET cc_start: 0.7931 (mmm) cc_final: 0.7688 (mmm) REVERT: P 239 PHE cc_start: 0.7415 (t80) cc_final: 0.7124 (t80) REVERT: P 287 ILE cc_start: 0.8251 (mt) cc_final: 0.7868 (mm) REVERT: R 21 LYS cc_start: 0.8407 (mmtm) cc_final: 0.8019 (tptp) REVERT: S 63 LYS cc_start: 0.7857 (mptt) cc_final: 0.7594 (mptt) REVERT: T 47 GLN cc_start: 0.7641 (tm-30) cc_final: 0.7211 (tm-30) REVERT: U 29 LYS cc_start: 0.6620 (mmmt) cc_final: 0.6411 (tptt) REVERT: U 72 CYS cc_start: 0.7037 (m) cc_final: 0.6698 (t) REVERT: V 6 LYS cc_start: 0.6211 (mptt) cc_final: 0.5993 (mmtp) REVERT: W 68 MET cc_start: 0.8080 (mmt) cc_final: 0.7707 (mmm) REVERT: Y 52 GLU cc_start: 0.6508 (mp0) cc_final: 0.6082 (mp0) REVERT: Y 62 PHE cc_start: 0.7375 (t80) cc_final: 0.6651 (m-10) REVERT: Z 18 ILE cc_start: 0.7826 (mm) cc_final: 0.7432 (mt) REVERT: a 17 VAL cc_start: 0.9105 (OUTLIER) cc_final: 0.8851 (t) REVERT: c 38 ASP cc_start: 0.8338 (m-30) cc_final: 0.7984 (m-30) REVERT: e 5 ILE cc_start: 0.8454 (tp) cc_final: 0.8228 (tp) REVERT: g 22 MET cc_start: 0.7658 (tpt) cc_final: 0.7137 (tpp) REVERT: j 13 GLU cc_start: 0.7792 (mp0) cc_final: 0.7048 (mp0) REVERT: k 47 ARG cc_start: 0.5941 (mmm-85) cc_final: 0.5676 (ttt-90) REVERT: k 70 SER cc_start: 0.8752 (t) cc_final: 0.8509 (m) REVERT: l 70 MET cc_start: 0.8090 (ttm) cc_final: 0.7807 (mtp) REVERT: l 74 GLU cc_start: 0.7990 (tt0) cc_final: 0.7756 (tt0) REVERT: l 102 LYS cc_start: 0.8050 (ttmt) cc_final: 0.7221 (tmtt) REVERT: l 111 MET cc_start: 0.7658 (mmt) cc_final: 0.7352 (mmm) REVERT: l 123 SER cc_start: 0.9129 (t) cc_final: 0.8834 (t) REVERT: l 140 GLU cc_start: 0.7938 (mp0) cc_final: 0.7458 (mp0) REVERT: l 148 GLU cc_start: 0.6602 (mm-30) cc_final: 0.6363 (mm-30) REVERT: m 5 TYR cc_start: 0.8396 (t80) cc_final: 0.8038 (t80) REVERT: m 33 VAL cc_start: 0.8279 (t) cc_final: 0.8005 (p) REVERT: n 64 ARG cc_start: 0.7956 (ttm170) cc_final: 0.7554 (mtt180) REVERT: o 100 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7473 (tp30) REVERT: p 140 ASP cc_start: 0.7984 (m-30) cc_final: 0.7642 (m-30) REVERT: p 144 ASP cc_start: 0.8225 (m-30) cc_final: 0.7875 (m-30) REVERT: q 68 MET cc_start: 0.8733 (ttt) cc_final: 0.8273 (ttt) REVERT: q 78 ASP cc_start: 0.7929 (m-30) cc_final: 0.7683 (m-30) REVERT: r 52 TYR cc_start: 0.8869 (m-80) cc_final: 0.8585 (m-80) REVERT: r 90 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.5076 (pp20) outliers start: 127 outliers final: 90 residues processed: 1076 average time/residue: 0.6336 time to fit residues: 1160.8725 Evaluate side-chains 1031 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 932 time to evaluate : 5.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 362 CYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 181 MET Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 461 ASP Chi-restraints excluded: chain G residue 585 VAL Chi-restraints excluded: chain G residue 609 ILE Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 502 LEU Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain N residue 333 SER Chi-restraints excluded: chain N residue 334 THR Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 160 LEU Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 295 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain S residue 47 HIS Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 56 ASP Chi-restraints excluded: chain V residue 76 VAL Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain Y residue 96 CYS Chi-restraints excluded: chain Y residue 114 MET Chi-restraints excluded: chain Y residue 130 LYS Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 29 ILE Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain g residue 35 VAL Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 98 SER Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain k residue 48 ASP Chi-restraints excluded: chain l residue 82 MET Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain m residue 57 SER Chi-restraints excluded: chain m residue 86 SER Chi-restraints excluded: chain n residue 113 MET Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 39 VAL Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 90 GLU Chi-restraints excluded: chain s residue 54 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 462 optimal weight: 7.9990 chunk 745 optimal weight: 9.9990 chunk 455 optimal weight: 0.8980 chunk 353 optimal weight: 5.9990 chunk 518 optimal weight: 10.0000 chunk 782 optimal weight: 10.0000 chunk 719 optimal weight: 10.0000 chunk 622 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 481 optimal weight: 7.9990 chunk 381 optimal weight: 0.4980 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN G 110 GLN ** G 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN H 93 HIS L 209 ASN ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN R 46 GLN Y 80 GLN b 10 ASN g 84 GLN ** k 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.240 67545 Z= 0.624 Angle : 1.612 50.627 91451 Z= 1.035 Chirality : 0.314 6.432 10003 Planarity : 0.005 0.064 11456 Dihedral : 9.868 158.362 9701 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.80 % Allowed : 16.16 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.10), residues: 7948 helix: 1.04 (0.08), residues: 4239 sheet: -0.34 (0.26), residues: 410 loop : -1.15 (0.11), residues: 3299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Z 103 HIS 0.010 0.001 HIS L 323 PHE 0.034 0.002 PHE M 151 TYR 0.027 0.002 TYR P 244 ARG 0.008 0.001 ARG k 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15896 Ramachandran restraints generated. 7948 Oldfield, 0 Emsley, 7948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 915 time to evaluate : 6.080 Fit side-chains revert: symmetry clash REVERT: A 23 TRP cc_start: 0.7575 (t60) cc_final: 0.7188 (t60) REVERT: A 54 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7640 (mmtp) REVERT: B 58 MET cc_start: 0.7272 (tpt) cc_final: 0.6876 (tpt) REVERT: D 72 MET cc_start: 0.8300 (mmt) cc_final: 0.8088 (mmt) REVERT: D 405 MET cc_start: 0.8282 (mtm) cc_final: 0.8071 (mtp) REVERT: E 161 TYR cc_start: 0.8493 (m-80) cc_final: 0.8156 (m-10) REVERT: F 50 LEU cc_start: 0.8060 (pp) cc_final: 0.7581 (mt) REVERT: F 60 MET cc_start: 0.8636 (mmm) cc_final: 0.8297 (mmt) REVERT: F 99 GLU cc_start: 0.6025 (tt0) cc_final: 0.5780 (tt0) REVERT: G 18 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8382 (p) REVERT: G 306 MET cc_start: 0.7724 (tpp) cc_final: 0.7464 (tpp) REVERT: H 59 GLU cc_start: 0.7493 (mp0) cc_final: 0.7187 (mp0) REVERT: H 116 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8277 (mm) REVERT: H 126 LYS cc_start: 0.7871 (pttt) cc_final: 0.6769 (tppt) REVERT: H 151 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8414 (tt) REVERT: H 271 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8336 (mt) REVERT: I 28 MET cc_start: 0.8488 (mmm) cc_final: 0.7987 (mmt) REVERT: I 112 ASP cc_start: 0.7945 (m-30) cc_final: 0.7617 (m-30) REVERT: K 23 ARG cc_start: 0.6977 (ttt-90) cc_final: 0.6337 (tpp-160) REVERT: K 43 MET cc_start: 0.8660 (mtp) cc_final: 0.8457 (ttm) REVERT: L 482 MET cc_start: 0.7778 (ptp) cc_final: 0.7477 (ptp) REVERT: M 17 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8509 (pp) REVERT: M 98 MET cc_start: 0.8487 (mmp) cc_final: 0.8151 (mmm) REVERT: N 34 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7574 (mm-30) REVERT: N 68 MET cc_start: 0.8136 (mmt) cc_final: 0.7676 (mmt) REVERT: N 190 MET cc_start: 0.8266 (mtt) cc_final: 0.7985 (mtt) REVERT: P 57 MET cc_start: 0.7665 (mmt) cc_final: 0.7330 (mmt) REVERT: P 239 PHE cc_start: 0.7429 (t80) cc_final: 0.7132 (t80) REVERT: P 287 ILE cc_start: 0.8259 (mt) cc_final: 0.7978 (mt) REVERT: R 21 LYS cc_start: 0.8396 (mmtm) cc_final: 0.8000 (tptp) REVERT: S 63 LYS cc_start: 0.7920 (mptt) cc_final: 0.7659 (mptt) REVERT: T 47 GLN cc_start: 0.7679 (tm-30) cc_final: 0.7334 (tm-30) REVERT: U 49 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: U 72 CYS cc_start: 0.7192 (m) cc_final: 0.6788 (t) REVERT: V 6 LYS cc_start: 0.6320 (mptt) cc_final: 0.6055 (mmtp) REVERT: V 43 TYR cc_start: 0.7940 (t80) cc_final: 0.7539 (t80) REVERT: X 93 MET cc_start: 0.8222 (mmm) cc_final: 0.7999 (mmm) REVERT: Z 18 ILE cc_start: 0.7963 (mm) cc_final: 0.7552 (mt) REVERT: a 68 ASN cc_start: 0.6713 (t0) cc_final: 0.6491 (t0) REVERT: e 5 ILE cc_start: 0.8530 (tp) cc_final: 0.8328 (tp) REVERT: g 22 MET cc_start: 0.7605 (tpt) cc_final: 0.6829 (tpp) REVERT: j 13 GLU cc_start: 0.7780 (mp0) cc_final: 0.7343 (mp0) REVERT: k 35 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7104 (mt-10) REVERT: k 40 LYS cc_start: 0.6939 (mmmt) cc_final: 0.6705 (mmmt) REVERT: l 102 LYS cc_start: 0.8111 (ttmt) cc_final: 0.7218 (tmtt) REVERT: l 111 MET cc_start: 0.7752 (mmt) cc_final: 0.7380 (mmm) REVERT: l 140 GLU cc_start: 0.7902 (mp0) cc_final: 0.7432 (mp0) REVERT: l 148 GLU cc_start: 0.6620 (mm-30) cc_final: 0.6334 (mm-30) REVERT: m 5 TYR cc_start: 0.8425 (t80) cc_final: 0.8077 (t80) REVERT: m 33 VAL cc_start: 0.8276 (t) cc_final: 0.7982 (p) REVERT: n 64 ARG cc_start: 0.8022 (ttm170) cc_final: 0.7554 (mtt180) REVERT: p 140 ASP cc_start: 0.8025 (m-30) cc_final: 0.7821 (m-30) REVERT: q 78 ASP cc_start: 0.7999 (m-30) cc_final: 0.7740 (m-30) REVERT: r 90 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.5079 (pp20) outliers start: 127 outliers final: 102 residues processed: 1009 average time/residue: 0.6487 time to fit residues: 1115.3967 Evaluate side-chains 1007 residues out of total 7075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 898 time to evaluate : 6.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 362 CYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 585 VAL Chi-restraints excluded: chain G residue 609 ILE Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 502 LEU Chi-restraints excluded: chain L residue 531 SER Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 201 MET Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 423 MET Chi-restraints excluded: chain N residue 333 SER Chi-restraints excluded: chain N residue 334 THR Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 160 LEU Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 295 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain S residue 47 HIS Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain V residue 76 VAL Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain X residue 91 SER Chi-restraints excluded: chain Y residue 96 CYS Chi-restraints excluded: chain Y residue 130 LYS Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 29 ILE Chi-restraints excluded: chain b residue 64 ASP Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 87 ASP Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain g residue 35 VAL Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 98 SER Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain k residue 48 ASP Chi-restraints excluded: chain l residue 64 ASP Chi-restraints excluded: chain l residue 82 MET Chi-restraints excluded: chain l residue 131 GLN Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain m residue 86 SER Chi-restraints excluded: chain n residue 113 MET Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 39 VAL Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 90 GLU Chi-restraints excluded: chain s residue 54 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 494 optimal weight: 9.9990 chunk 663 optimal weight: 6.9990 chunk 190 optimal weight: 0.0670 chunk 574 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 623 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 640 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN G 459 GLN ** G 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN Y 80 GLN b 10 ASN ** k 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.093725 restraints weight = 102958.716| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.35 r_work: 0.3079 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 67545 Z= 0.540 Angle : 1.570 50.577 91451 Z= 1.019 Chirality : 0.311 6.339 10003 Planarity : 0.004 0.058 11456 Dihedral : 9.424 160.803 9701 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.57 % Allowed : 16.53 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.43 (0.10), residues: 7948 helix: 1.31 (0.08), residues: 4217 sheet: -0.38 (0.27), residues: 399 loop : -0.95 (0.11), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP X 85 HIS 0.006 0.001 HIS F 283 PHE 0.028 0.001 PHE M 151 TYR 0.028 0.001 TYR P 244 ARG 0.007 0.000 ARG k 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18595.26 seconds wall clock time: 325 minutes 43.54 seconds (19543.54 seconds total)