Starting phenix.real_space_refine on Sun Mar 17 01:36:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psa_13611/03_2024/7psa_13611_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psa_13611/03_2024/7psa_13611.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psa_13611/03_2024/7psa_13611_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psa_13611/03_2024/7psa_13611_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psa_13611/03_2024/7psa_13611_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psa_13611/03_2024/7psa_13611.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psa_13611/03_2024/7psa_13611.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psa_13611/03_2024/7psa_13611_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psa_13611/03_2024/7psa_13611_trim_updated.pdb" } resolution = 3.4 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: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 36 5.49 5 S 493 5.16 5 C 43364 2.51 5 N 11104 2.21 5 O 12056 1.98 5 H 65942 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 165": "OD1" <-> "OD2" Residue "C ASP 178": "OD1" <-> "OD2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 209": "OD1" <-> "OD2" Residue "D ASP 223": "OD1" <-> "OD2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D ASP 276": "OD1" <-> "OD2" Residue "D PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F GLU 145": "OE1" <-> "OE2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 320": "OD1" <-> "OD2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "F ASP 428": "OD1" <-> "OD2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 221": "OE1" <-> "OE2" Residue "G GLU 281": "OE1" <-> "OE2" Residue "G TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 346": "OE1" <-> "OE2" Residue "G PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 462": "OD1" <-> "OD2" Residue "G ASP 558": "OD1" <-> "OD2" Residue "G TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 624": "OE1" <-> "OE2" Residue "G ASP 675": "OD1" <-> "OD2" Residue "H PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I ASP 112": "OD1" <-> "OD2" Residue "I ASP 131": "OD1" <-> "OD2" Residue "I GLU 154": "OE1" <-> "OE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 53": "OE1" <-> "OE2" Residue "O GLU 72": "OE1" <-> "OE2" Residue "O ASP 90": "OD1" <-> "OD2" Residue "O GLU 113": "OE1" <-> "OE2" Residue "O GLU 125": "OE1" <-> "OE2" Residue "O GLU 136": "OE1" <-> "OE2" Residue "O GLU 162": "OE1" <-> "OE2" Residue "O ASP 253": "OD1" <-> "OD2" Residue "O TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 311": "OE1" <-> "OE2" Residue "P TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 72": "OE1" <-> "OE2" Residue "P GLU 98": "OE1" <-> "OE2" Residue "P PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R GLU 53": "OE1" <-> "OE2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "S PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 73": "OE1" <-> "OE2" Residue "T TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T ASP 26": "OD1" <-> "OD2" Residue "U GLU 49": "OE1" <-> "OE2" Residue "U ASP 56": "OD1" <-> "OD2" Residue "U ASP 66": "OD1" <-> "OD2" Residue "V GLU 53": "OE1" <-> "OE2" Residue "V GLU 86": "OE1" <-> "OE2" Residue "W TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 67": "OE1" <-> "OE2" Residue "W PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X GLU 49": "OE1" <-> "OE2" Residue "X GLU 58": "OE1" <-> "OE2" Residue "X GLU 83": "OE1" <-> "OE2" Residue "Y TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 4": "OE1" <-> "OE2" Residue "a GLU 67": "OE1" <-> "OE2" Residue "c TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 9": "OE1" <-> "OE2" Residue "d GLU 17": "OE1" <-> "OE2" Residue "d TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 114": "OE1" <-> "OE2" Residue "f TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f GLU 46": "OE1" <-> "OE2" Residue "g GLU 107": "OE1" <-> "OE2" Residue "g ASP 112": "OD1" <-> "OD2" Residue "h GLU 54": "OE1" <-> "OE2" Residue "h TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "i PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i GLU 111": "OE1" <-> "OE2" Residue "k GLU 20": "OE1" <-> "OE2" Residue "k ASP 48": "OD1" <-> "OD2" Residue "l TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l GLU 34": "OE1" <-> "OE2" Residue "l TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l ASP 58": "OD1" <-> "OD2" Residue "l TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l ASP 79": "OD1" <-> "OD2" Residue "l ASP 89": "OD1" <-> "OD2" Residue "l TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n GLU 27": "OE1" <-> "OE2" Residue "n GLU 69": "OE1" <-> "OE2" Residue "n TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n ASP 116": "OD1" <-> "OD2" Residue "n ASP 133": "OD1" <-> "OD2" Residue "n GLU 135": "OE1" <-> "OE2" Residue "o GLU 15": "OE1" <-> "OE2" Residue "o ASP 47": "OD1" <-> "OD2" Residue "o GLU 90": "OE1" <-> "OE2" Residue "p TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p GLU 11": "OE1" <-> "OE2" Residue "p TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p ASP 37": "OD1" <-> "OD2" Residue "p TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p GLU 86": "OE1" <-> "OE2" Residue "p GLU 116": "OE1" <-> "OE2" Residue "q PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "q GLU 41": "OE1" <-> "OE2" Residue "q TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "q GLU 67": "OE1" <-> "OE2" Residue "q ASP 95": "OD1" <-> "OD2" Residue "r ASP 18": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 133024 Number of models: 1 Model: "" Number of chains: 67 Chain: "A" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1892 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2502 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "C" Number of atoms: 3402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3402 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 15, 'TRANS': 191} Chain: "D" Number of atoms: 6863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 6863 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 26, 'TRANS': 403} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3287 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 21, 'TRANS': 190} Chain: "F" Number of atoms: 6559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6559 Classifications: {'peptide': 428} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 406} Chain: "G" Number of atoms: 10618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 10618 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 31, 'TRANS': 656} Chain: "H" Number of atoms: 5156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5156 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2812 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 9, 'TRANS': 168} Chain: "J" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2605 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 3, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1495 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: 9775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 9775 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: 7475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 7475 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: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5581 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: 5171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 5171 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 16, 'TRANS': 303} Chain: "P" Number of atoms: 5514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 5514 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain: "Q" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2031 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "R" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1453 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "S" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1353 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1213 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "U" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1378 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Chain: "V" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1895 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 105} Chain: "W" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1961 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2773 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 11, 'TRANS': 159} Chain: "Y" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2062 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "Z" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2333 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "a" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1124 Classifications: {'peptide': 68} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "b" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1256 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "c" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 797 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "d" Number of atoms: 1997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1997 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 107} Chain: "e" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1746 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "f" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 908 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "g" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1633 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "h" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2325 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain: "i" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1578 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 12, 'TRANS': 81} Chain breaks: 1 Chain: "j" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1033 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 6, 'TRANS': 55} Chain: "k" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1213 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 4, 'TRANS': 70} Chain: "l" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 2481 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 18, 'TRANS': 135} Chain: "m" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2111 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 11, 'TRANS': 114} Chain: "n" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2998 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "o" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1894 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "p" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 2832 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 10, 'TRANS': 158} Chain: "q" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2349 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1630 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 11, 'TRANS': 88} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 668 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 86 Unusual residues: {'PC1': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "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: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 138 Unusual residues: {'3PE': 2, '88I': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "L" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 214 Unusual residues: {'3PE': 3, 'CDL': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "M" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "N" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 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 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 Chain: "X" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 67 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "Y" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "Z" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "d" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 122 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "i" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 70 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "r" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3396 SG CYS B 129 97.832 94.530 200.218 1.00 35.73 S ATOM 2399 SG CYS B 65 92.157 96.946 201.839 1.00 42.19 S ATOM 2389 SG CYS B 64 91.962 91.205 199.813 1.00 42.60 S ATOM 3838 SG CYS B 159 95.242 91.959 205.173 1.00 37.78 S ATOM 16245 SG CYS E 103 117.054 45.417 253.804 1.00 57.98 S ATOM 16311 SG CYS E 108 115.592 42.611 255.411 1.00 60.06 S ATOM 16894 SG CYS E 144 119.953 42.472 250.398 1.00 57.45 S ATOM 16940 SG CYS E 148 118.743 39.574 251.334 1.00 64.23 S ATOM 23328 SG CYS F 362 121.878 52.597 230.214 1.00 39.78 S ATOM 23366 SG CYS F 365 119.027 51.902 235.225 1.00 41.98 S ATOM 24004 SG CYS F 405 122.903 47.535 233.863 1.00 44.81 S ATOM 23294 SG CYS F 359 125.576 53.197 235.493 1.00 43.32 S ATOM 26152 SG CYS G 114 117.825 70.962 221.668 1.00 38.01 S ATOM 26041 SG CYS G 105 112.153 73.447 223.916 1.00 37.11 S ATOM 26084 SG CYS G 108 117.818 75.888 225.672 1.00 37.67 S ATOM 25044 SG CYS G 41 126.087 59.423 224.332 1.00 40.76 S ATOM 25208 SG CYS G 52 123.858 59.648 223.715 1.00 39.31 S ATOM 25259 SG CYS G 55 124.565 54.695 219.377 1.00 40.89 S ATOM 25473 SG CYS G 69 127.278 54.843 220.459 1.00 41.23 S ATOM 26820 SG CYS G 156 126.336 64.907 226.068 1.00 38.21 S ATOM 26774 SG CYS G 153 123.711 67.040 231.633 1.00 37.76 S ATOM 26868 SG CYS G 159 129.840 68.048 230.300 1.00 41.33 S ATOM 27516 SG CYS G 203 125.291 70.779 226.424 1.00 38.40 S ATOM 42295 SG CYS I 128 103.853 84.987 223.516 1.00 36.37 S ATOM 41654 SG CYS I 85 106.852 87.667 218.378 1.00 35.16 S ATOM 41564 SG CYS I 79 108.554 89.439 224.249 1.00 36.15 S ATOM 41603 SG CYS I 82 109.119 83.080 221.824 1.00 35.67 S ATOM 42206 SG CYS I 121 99.096 86.246 210.631 1.00 38.13 S ATOM 42156 SG CYS I 118 99.461 92.798 211.592 1.00 36.72 S ATOM 42243 SG CYS I 124 100.825 88.403 216.068 1.00 35.85 S ATOM 41708 SG CYS I 89 104.618 89.159 210.791 1.00 36.76 S ATOM 83682 SG CYS R 59 106.258 80.334 238.634 1.00 40.87 S ATOM 84030 SG CYS R 84 108.881 80.860 236.342 1.00 39.70 S ATOM 84068 SG CYS R 87 106.528 83.741 237.184 1.00 38.61 S Time building chain proxies: 40.97, per 1000 atoms: 0.31 Number of scatterers: 133024 At special positions: 0 Unit cell: (189.826, 187.74, 287.868, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 493 16.00 P 36 15.00 O 12056 8.00 N 11104 7.00 C 43364 6.00 H 65942 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS X 35 " - pdb=" SG CYS X 65 " distance=2.03 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.04 Simple disulfide: pdb=" SG CYS X 77 " - pdb=" SG CYS X 109 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 94 " - pdb=" SG CYS Y 114 " distance=2.03 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.03 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.03 Simple disulfide: pdb=" SG CYS o 68 " - pdb=" SG CYS o 79 " distance=2.03 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: 79.34 Conformation dependent library (CDL) restraints added in 9.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " 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=" FES G 802 " pdb="FE1 FES G 802 " - pdb=" SG CYS G 52 " pdb="FE2 FES G 802 " - pdb=" SG CYS G 55 " pdb="FE1 FES G 802 " - pdb=" SG CYS G 41 " pdb="FE2 FES G 802 " - pdb=" SG CYS G 69 " pdb=" SF4 B 201 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 129 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 159 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 64 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 65 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 365 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 405 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 359 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 362 " 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 803 " pdb="FE2 SF4 G 803 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G 803 " - pdb=" SG CYS G 203 " pdb="FE3 SF4 G 803 " - pdb=" SG CYS G 159 " pdb="FE1 SF4 G 803 " - pdb=" SG CYS G 156 " pdb=" SF4 I 201 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 128 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 82 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 85 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 79 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 118 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 124 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 89 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 121 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15408 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 330 helices and 29 sheets defined 61.9% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 47.76 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 removed outlier: 3.507A pdb=" N VAL A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 7 " --> pdb=" O LEU A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 35 Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.613A pdb=" N LEU A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.447A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR A 81 " --> pdb=" O TRP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 109 removed outlier: 6.455A pdb=" N MET A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N MET A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 55 removed outlier: 4.127A pdb=" N VAL B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU B 55 " --> pdb=" O ARG B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 75 removed outlier: 6.160A pdb=" N VAL B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 73 " --> pdb=" O MET B 69 " (cutoff:3.500A) Proline residue: B 75 - end of helix Processing helix chain 'B' and resid 78 through 83 removed outlier: 4.900A pdb=" N PHE B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY B 83 " --> pdb=" O MET B 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 78 through 83' Processing helix chain 'B' and resid 89 through 94 removed outlier: 3.574A pdb=" N ALA B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASP B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 94' Processing helix chain 'B' and resid 103 through 117 Proline residue: B 108 - end of helix removed outlier: 3.590A pdb=" N MET B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 145 through 150 removed outlier: 4.583A pdb=" N ILE B 149 " --> pdb=" O GLY B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 189 removed outlier: 3.643A pdb=" N ARG B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLN B 181 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N LYS B 182 " --> pdb=" O LYS B 178 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N LEU B 183 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 34 removed outlier: 4.253A pdb=" N HIS C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS C 20 " --> pdb=" O ASP C 16 " (cutoff:3.500A) Proline residue: C 34 - end of helix Processing helix chain 'C' and resid 56 through 67 Processing helix chain 'C' and resid 124 through 138 removed outlier: 4.482A pdb=" N ASN C 128 " --> pdb=" O HIS C 124 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TRP C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP C 135 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.297A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY D 16 " --> pdb=" O GLU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 95 removed outlier: 3.513A pdb=" N LEU D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N THR D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 108 removed outlier: 3.560A pdb=" N LEU D 100 " --> pdb=" O TYR D 96 " (cutoff:3.500A) Proline residue: D 101 - end of helix removed outlier: 3.726A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP D 107 " --> pdb=" O PHE D 103 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 127 removed outlier: 3.647A pdb=" N ASN D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU D 115 " --> pdb=" O MET D 111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN D 116 " --> pdb=" O MET D 112 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA D 117 " --> pdb=" O CYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 162 removed outlier: 3.665A pdb=" N ARG D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 185 removed outlier: 4.664A pdb=" N PHE D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE D 168 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR D 181 " --> pdb=" O MET D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 229 removed outlier: 3.825A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 240 Processing helix chain 'D' and resid 246 through 254 removed outlier: 3.582A pdb=" N LEU D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 264 Processing helix chain 'D' and resid 268 through 273 Processing helix chain 'D' and resid 277 through 282 removed outlier: 5.488A pdb=" N GLU D 282 " --> pdb=" O TYR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 318 removed outlier: 3.798A pdb=" N GLU D 312 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET D 318 " --> pdb=" O CYS D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 341 removed outlier: 3.556A pdb=" N THR D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 354 Processing helix chain 'D' and resid 393 through 407 removed outlier: 4.442A pdb=" N ALA D 397 " --> pdb=" O ALA D 393 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS D 398 " --> pdb=" O PRO D 394 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 422 removed outlier: 3.868A pdb=" N GLY D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR D 420 " --> pdb=" O ALA D 416 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN D 421 " --> pdb=" O ILE D 417 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP D 422 " --> pdb=" O ILE D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 430 removed outlier: 3.734A pdb=" N ILE D 428 " --> pdb=" O VAL D 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 38 removed outlier: 3.867A pdb=" N LYS E 29 " --> pdb=" O PRO E 25 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG E 30 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 59 removed outlier: 4.960A pdb=" N ALA E 46 " --> pdb=" O HIS E 42 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU E 48 " --> pdb=" O ALA E 44 " (cutoff:3.500A) Proline residue: E 49 - end of helix Processing helix chain 'E' and resid 62 through 74 Processing helix chain 'E' and resid 76 through 88 removed outlier: 3.890A pdb=" N VAL E 80 " --> pdb=" O PRO E 76 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N THR E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 112 removed outlier: 4.507A pdb=" N ARG E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP E 112 " --> pdb=" O CYS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 125 removed outlier: 3.675A pdb=" N LEU E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 179 removed outlier: 3.792A pdb=" N GLU E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU E 171 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 21 removed outlier: 3.936A pdb=" N ARG F 20 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE F 21 " --> pdb=" O ASP F 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 16 through 21' Processing helix chain 'F' and resid 32 through 40 removed outlier: 6.644A pdb=" N ARG F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG F 39 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 52 removed outlier: 4.013A pdb=" N GLY F 52 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 64 removed outlier: 3.578A pdb=" N GLY F 64 " --> pdb=" O MET F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 84 removed outlier: 3.577A pdb=" N LYS F 78 " --> pdb=" O PRO F 74 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N TRP F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N MET F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASN F 83 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LYS F 84 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 114 removed outlier: 3.541A pdb=" N ILE F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG F 112 " --> pdb=" O ARG F 108 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N HIS F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 130 removed outlier: 3.704A pdb=" N GLY F 126 " --> pdb=" O CYS F 122 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET F 129 " --> pdb=" O GLY F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 160 Processing helix chain 'F' and resid 183 through 188 removed outlier: 4.210A pdb=" N GLY F 187 " --> pdb=" O ALA F 183 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU F 188 " --> pdb=" O TYR F 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 183 through 188' Processing helix chain 'F' and resid 189 through 198 removed outlier: 3.978A pdb=" N ILE F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 238 removed outlier: 3.641A pdb=" N SER F 231 " --> pdb=" O THR F 227 " (cutoff:3.500A) Proline residue: F 232 - end of helix Processing helix chain 'F' and resid 239 through 245 removed outlier: 4.702A pdb=" N PHE F 245 " --> pdb=" O TRP F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 282 Processing helix chain 'F' and resid 308 through 313 removed outlier: 7.128A pdb=" N CYS F 312 " --> pdb=" O PRO F 308 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLU F 313 " --> pdb=" O LYS F 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 308 through 313' Processing helix chain 'F' and resid 318 through 326 removed outlier: 3.500A pdb=" N LEU F 322 " --> pdb=" O ASP F 318 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL F 323 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN F 324 " --> pdb=" O ASP F 320 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN F 326 " --> pdb=" O LEU F 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 318 through 326' Processing helix chain 'F' and resid 342 through 358 Processing helix chain 'F' and resid 362 through 382 removed outlier: 3.587A pdb=" N VAL F 369 " --> pdb=" O CYS F 365 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG F 378 " --> pdb=" O LYS F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 402 removed outlier: 3.963A pdb=" N ILE F 389 " --> pdb=" O ARG F 385 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP F 390 " --> pdb=" O PRO F 386 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE F 399 " --> pdb=" O ILE F 395 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLY F 401 " --> pdb=" O LYS F 397 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N HIS F 402 " --> pdb=" O GLN F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 422 Proline residue: F 414 - end of helix Processing helix chain 'F' and resid 423 through 436 Processing helix chain 'G' and resid 25 through 34 removed outlier: 3.833A pdb=" N VAL G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 101 removed outlier: 4.226A pdb=" N ASN G 100 " --> pdb=" O PHE G 96 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS G 101 " --> pdb=" O LEU G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 123 Processing helix chain 'G' and resid 149 through 154 removed outlier: 4.534A pdb=" N CYS G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE G 154 " --> pdb=" O MET G 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 149 through 154' Processing helix chain 'G' and resid 157 through 166 Processing helix chain 'G' and resid 195 through 203 removed outlier: 5.846A pdb=" N VAL G 199 " --> pdb=" O LEU G 195 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 223 removed outlier: 3.614A pdb=" N THR G 222 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ARG G 223 " --> pdb=" O PRO G 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 218 through 223' Processing helix chain 'G' and resid 264 through 277 removed outlier: 3.541A pdb=" N ARG G 268 " --> pdb=" O SER G 264 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASP G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS G 275 " --> pdb=" O TYR G 271 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG G 276 " --> pdb=" O ASP G 272 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLN G 277 " --> pdb=" O GLY G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 311 removed outlier: 3.970A pdb=" N ASN G 309 " --> pdb=" O GLY G 305 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE G 310 " --> pdb=" O MET G 306 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLU G 311 " --> pdb=" O LEU G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 339 removed outlier: 4.419A pdb=" N LEU G 328 " --> pdb=" O ASP G 324 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL G 338 " --> pdb=" O LEU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 363 removed outlier: 4.554A pdb=" N TYR G 362 " --> pdb=" O LEU G 358 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU G 363 " --> pdb=" O ARG G 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 358 through 363' Processing helix chain 'G' and resid 367 through 375 removed outlier: 3.597A pdb=" N VAL G 371 " --> pdb=" O THR G 367 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU G 372 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU G 373 " --> pdb=" O ALA G 369 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA G 374 " --> pdb=" O GLY G 370 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ASP G 375 " --> pdb=" O VAL G 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 367 through 375' Processing helix chain 'G' and resid 383 through 388 removed outlier: 4.191A pdb=" N ALA G 388 " --> pdb=" O PRO G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 389 through 402 removed outlier: 3.588A pdb=" N ARG G 394 " --> pdb=" O LEU G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 435 removed outlier: 4.880A pdb=" N LEU G 429 " --> pdb=" O SER G 425 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN G 430 " --> pdb=" O PRO G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 447 removed outlier: 4.019A pdb=" N GLU G 441 " --> pdb=" O HIS G 437 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL G 442 " --> pdb=" O SER G 438 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP G 445 " --> pdb=" O GLU G 441 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA G 446 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LYS G 447 " --> pdb=" O LEU G 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 454 through 460 removed outlier: 3.903A pdb=" N LEU G 458 " --> pdb=" O GLY G 454 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ARG G 460 " --> pdb=" O SER G 456 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 482 removed outlier: 3.732A pdb=" N GLN G 475 " --> pdb=" O SER G 471 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS G 476 " --> pdb=" O ASN G 472 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY G 482 " --> pdb=" O ARG G 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 506 removed outlier: 4.533A pdb=" N ALA G 502 " --> pdb=" O SER G 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 518 removed outlier: 3.697A pdb=" N ARG G 515 " --> pdb=" O VAL G 511 " (cutoff:3.500A) Proline residue: G 518 - end of helix Processing helix chain 'G' and resid 533 through 538 removed outlier: 3.542A pdb=" N LEU G 537 " --> pdb=" O THR G 533 " (cutoff:3.500A) Proline residue: G 538 - end of helix No H-bonds generated for 'chain 'G' and resid 533 through 538' Processing helix chain 'G' and resid 551 through 557 Proline residue: G 555 - end of helix No H-bonds generated for 'chain 'G' and resid 551 through 557' Processing helix chain 'G' and resid 565 through 570 removed outlier: 3.890A pdb=" N LYS G 569 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N SER G 570 " --> pdb=" O TYR G 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 565 through 570' Processing helix chain 'G' and resid 595 through 608 removed outlier: 3.829A pdb=" N ILE G 600 " --> pdb=" O ASP G 596 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA G 607 " --> pdb=" O LEU G 603 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY G 608 " --> pdb=" O SER G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 615 through 627 Processing helix chain 'G' and resid 628 through 633 removed outlier: 3.718A pdb=" N ARG G 632 " --> pdb=" O PRO G 628 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TYR G 633 " --> pdb=" O ASN G 629 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 628 through 633' Processing helix chain 'G' and resid 641 through 652 removed outlier: 3.790A pdb=" N ALA G 645 " --> pdb=" O TYR G 641 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU G 651 " --> pdb=" O GLU G 647 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL G 652 " --> pdb=" O LEU G 648 " (cutoff:3.500A) Processing helix chain 'G' and resid 667 through 674 removed outlier: 3.974A pdb=" N PHE G 671 " --> pdb=" O THR G 667 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR G 672 " --> pdb=" O ILE G 668 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N MET G 673 " --> pdb=" O LYS G 669 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N THR G 674 " --> pdb=" O ASP G 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 667 through 674' Processing helix chain 'G' and resid 675 through 682 removed outlier: 5.475A pdb=" N GLN G 682 " --> pdb=" O SER G 678 " (cutoff:3.500A) Processing helix chain 'G' and resid 683 through 693 Processing helix chain 'H' and resid 1 through 33 removed outlier: 3.672A pdb=" N ASN H 5 " --> pdb=" O FME H 1 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU H 7 " --> pdb=" O PHE H 3 " (cutoff:3.500A) Proline residue: H 12 - end of helix removed outlier: 3.719A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 58 Processing helix chain 'H' and resid 67 through 86 Proline residue: H 75 - end of helix removed outlier: 4.273A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 123 removed outlier: 4.085A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 158 removed outlier: 4.320A pdb=" N ALA H 137 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR H 142 " --> pdb=" O GLN H 138 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN H 157 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 170 removed outlier: 4.147A pdb=" N LEU H 165 " --> pdb=" O SER H 161 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR H 167 " --> pdb=" O GLN H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 179 Proline residue: H 177 - end of helix No H-bonds generated for 'chain 'H' and resid 173 through 179' Processing helix chain 'H' and resid 180 through 194 removed outlier: 3.595A pdb=" N LEU H 190 " --> pdb=" O PHE H 186 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR H 193 " --> pdb=" O THR H 189 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN H 194 " --> pdb=" O LEU H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 242 removed outlier: 3.968A pdb=" N LEU H 222 " --> pdb=" O GLY H 218 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE H 223 " --> pdb=" O PRO H 219 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE H 224 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR H 229 " --> pdb=" O MET H 225 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE H 231 " --> pdb=" O GLU H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 277 removed outlier: 3.987A pdb=" N TYR H 255 " --> pdb=" O LEU H 251 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER H 256 " --> pdb=" O PRO H 252 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER H 276 " --> pdb=" O TRP H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 311 removed outlier: 4.164A pdb=" N PHE H 293 " --> pdb=" O LEU H 289 " (cutoff:3.500A) removed outlier: 5.155A 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 'H' and resid 203 through 208 removed outlier: 4.154A pdb=" N VAL H 208 " --> pdb=" O GLY H 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 203 through 208' Processing helix chain 'I' and resid 15 through 28 Processing helix chain 'I' and resid 29 through 46 removed outlier: 3.922A pdb=" N GLY I 35 " --> pdb=" O GLU I 31 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET I 38 " --> pdb=" O ARG I 34 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR I 39 " --> pdb=" O GLY I 35 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE I 44 " --> pdb=" O LEU I 40 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG I 45 " --> pdb=" O SER I 41 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLU I 46 " --> pdb=" O TYR I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 89 removed outlier: 3.858A pdb=" N ALA I 87 " --> pdb=" O LYS I 83 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE I 88 " --> pdb=" O LEU I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 119 removed outlier: 5.772A pdb=" N ILE I 119 " --> pdb=" O MET I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 129 removed outlier: 3.570A pdb=" N GLU I 126 " --> pdb=" O GLY I 122 " (cutoff:3.500A) Proline residue: I 129 - end of helix Processing helix chain 'I' and resid 145 through 151 removed outlier: 4.500A pdb=" N LEU I 149 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU I 150 " --> pdb=" O HIS I 146 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N TYR I 151 " --> pdb=" O GLU I 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 145 through 151' Processing helix chain 'I' and resid 152 through 164 removed outlier: 4.240A pdb=" N GLY I 160 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TRP I 163 " --> pdb=" O ASN I 159 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU I 164 " --> pdb=" O GLY I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 175 removed outlier: 4.369A pdb=" N ALA I 169 " --> pdb=" O ALA I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 56 removed outlier: 4.530A pdb=" N LYS I 56 " --> pdb=" O ASN I 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 51 through 56' Processing helix chain 'J' and resid 3 through 22 removed outlier: 3.931A pdb=" N VAL J 7 " --> pdb=" O ASN J 3 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS J 22 " --> pdb=" O GLY J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 47 removed outlier: 3.869A pdb=" N GLY J 47 " --> pdb=" O VAL J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 71 removed outlier: 4.295A pdb=" N GLY J 52 " --> pdb=" O GLY J 48 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU J 60 " --> pdb=" O PHE J 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY J 61 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU J 64 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL J 65 " --> pdb=" O GLY J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 110 removed outlier: 3.606A pdb=" N VAL J 100 " --> pdb=" O VAL J 96 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN J 107 " --> pdb=" O ILE J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 146 removed outlier: 6.906A pdb=" N VAL J 141 " --> pdb=" O GLY J 137 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N MET J 144 " --> pdb=" O GLY J 140 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR J 145 " --> pdb=" O VAL J 141 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER J 146 " --> pdb=" O ALA J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 171 removed outlier: 3.884A pdb=" N MET J 152 " --> pdb=" O ALA J 148 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE J 164 " --> pdb=" O PHE J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 1 through 22 removed outlier: 3.602A pdb=" N PHE K 6 " --> pdb=" O PRO K 2 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN K 7 " --> pdb=" O SER K 3 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET K 21 " --> pdb=" O LEU K 17 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 52 removed outlier: 4.266A pdb=" N THR K 29 " --> pdb=" O HIS K 25 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU K 30 " --> pdb=" O LEU K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 86 Proline residue: K 58 - end of helix removed outlier: 4.152A pdb=" N ILE K 61 " --> pdb=" O MET K 57 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU K 64 " --> pdb=" O PRO K 60 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS K 69 " --> pdb=" O VAL K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 94 removed outlier: 4.737A pdb=" N LEU K 93 " --> pdb=" O TYR K 89 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ASN K 94 " --> pdb=" O VAL K 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 89 through 94' Processing helix chain 'L' and resid 3 through 21 removed outlier: 3.721A 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 31 through 58 removed outlier: 3.929A pdb=" N LEU L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.877A pdb=" N ASN L 57 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 108 removed outlier: 3.616A pdb=" N SER L 91 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP L 106 " --> pdb=" O GLN L 102 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N MET L 108 " --> pdb=" O SER L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 134 removed outlier: 4.174A pdb=" N PHE L 117 " --> pdb=" O ASN L 113 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA L 134 " --> pdb=" O ILE L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 157 removed outlier: 3.590A pdb=" N GLY L 143 " --> pdb=" O GLN L 139 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP L 157 " --> pdb=" O LEU L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 193 removed outlier: 3.667A pdb=" N ASN L 165 " --> pdb=" O ARG L 161 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR L 166 " --> pdb=" O THR L 162 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY L 178 " --> pdb=" O TYR L 174 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP L 179 " --> pdb=" O ASN L 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE L 180 " --> pdb=" O ARG L 176 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 205 removed outlier: 4.605A pdb=" N PHE L 203 " --> pdb=" O GLN L 199 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASN L 205 " --> pdb=" O ILE L 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 224 removed outlier: 4.040A pdb=" N LEU L 213 " --> pdb=" O ASN L 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 236 Proline residue: L 234 - end of helix No H-bonds generated for 'chain 'L' and resid 230 through 236' Processing helix chain 'L' and resid 240 through 247 Processing helix chain 'L' and resid 250 through 264 removed outlier: 5.523A pdb=" N VAL L 254 " --> pdb=" O SER L 250 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA L 255 " --> pdb=" O THR L 251 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY L 256 " --> pdb=" O MET L 252 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ILE L 257 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 265 through 271 removed outlier: 4.134A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN L 270 " --> pdb=" O LEU L 266 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ASN L 271 " --> pdb=" O THR L 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 265 through 271' Processing helix chain 'L' and resid 272 through 295 removed outlier: 3.571A pdb=" N LEU L 278 " --> pdb=" O LEU L 274 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR L 294 " --> pdb=" O ILE L 290 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN L 295 " --> pdb=" O CYS L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 320 removed outlier: 3.598A pdb=" N LEU L 317 " --> pdb=" O MET L 313 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET L 319 " --> pdb=" O VAL L 315 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ASN L 320 " --> pdb=" O THR L 316 " (cutoff:3.500A) Processing helix chain 'L' and resid 321 through 351 removed outlier: 3.625A pdb=" N ALA L 325 " --> pdb=" O GLN L 321 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS L 332 " --> pdb=" O HIS L 328 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA L 337 " --> pdb=" O ALA L 333 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET L 338 " --> pdb=" O PHE L 334 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA L 351 " --> pdb=" O ILE L 347 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 360 removed outlier: 3.863A pdb=" N MET L 359 " --> pdb=" O ASP L 355 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY L 360 " --> pdb=" O ILE L 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 355 through 360' Processing helix chain 'L' and resid 361 through 366 removed outlier: 4.856A pdb=" N ILE L 365 " --> pdb=" O ASN L 361 " (cutoff:3.500A) Processing helix chain 'L' and resid 367 through 382 removed outlier: 3.553A pdb=" N THR L 381 " --> pdb=" O SER L 377 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLY L 382 " --> pdb=" O LEU L 378 " (cutoff:3.500A) Processing helix chain 'L' and resid 386 through 402 removed outlier: 6.428A pdb=" N TYR L 390 " --> pdb=" O LEU L 386 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N SER L 391 " --> pdb=" O THR L 387 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS L 402 " --> pdb=" O ALA L 398 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 430 removed outlier: 3.615A pdb=" N LEU L 409 " --> pdb=" O ASN L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 447 through 472 removed outlier: 3.524A pdb=" N ASN L 452 " --> pdb=" O PRO L 448 " (cutoff:3.500A) Proline residue: L 453 - end of helix removed outlier: 3.510A pdb=" N ILE L 462 " --> pdb=" O ALA L 458 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N PHE L 466 " --> pdb=" O ILE L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 483 through 511 removed outlier: 4.167A pdb=" N THR L 489 " --> pdb=" O PHE L 485 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ALA L 490 " --> pdb=" O LEU L 486 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU L 491 " --> pdb=" O LYS L 487 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU L 507 " --> pdb=" O GLU L 503 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR L 508 " --> pdb=" O LEU L 504 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET L 509 " --> pdb=" O ASN L 505 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS L 510 " --> pdb=" O ASN L 506 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU L 511 " --> pdb=" O LEU L 507 " (cutoff:3.500A) Processing helix chain 'L' and resid 517 through 526 removed outlier: 6.320A pdb=" N SER L 523 " --> pdb=" O TYR L 519 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU L 526 " --> pdb=" O PHE L 522 " (cutoff:3.500A) Processing helix chain 'L' and resid 528 through 547 removed outlier: 3.537A pdb=" N ILE L 532 " --> pdb=" O PHE L 528 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG L 535 " --> pdb=" O SER L 531 " (cutoff:3.500A) Proline residue: L 538 - end of helix Processing helix chain 'L' and resid 556 through 579 removed outlier: 4.091A pdb=" N ILE L 562 " --> pdb=" O LEU L 558 " (cutoff:3.500A) Proline residue: L 563 - end of helix removed outlier: 3.652A pdb=" N THR L 575 " --> pdb=" O THR L 571 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN L 579 " --> pdb=" O THR L 575 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 606 removed outlier: 3.789A pdb=" N TYR L 587 " --> pdb=" O LEU L 583 " (cutoff:3.500A) Processing helix chain 'M' and resid 1 through 18 removed outlier: 3.637A pdb=" N LEU M 6 " --> pdb=" O LEU M 2 " (cutoff:3.500A) Proline residue: M 7 - end of helix removed outlier: 3.966A 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 22 through 44 removed outlier: 3.748A pdb=" N LEU M 33 " --> pdb=" O SER M 29 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TRP M 43 " --> pdb=" O LEU M 39 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLN M 44 " --> pdb=" O THR M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 85 Proline residue: M 64 - end of helix removed outlier: 3.592A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix removed outlier: 3.507A pdb=" N GLN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASN M 82 " --> pdb=" O MET M 78 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N HIS M 83 " --> pdb=" O ALA M 79 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU M 84 " --> pdb=" O SER M 80 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS M 85 " --> pdb=" O GLN M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 112 removed outlier: 3.905A pdb=" N TYR M 95 " --> pdb=" O LEU M 91 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA M 112 " --> pdb=" O MET M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 135 removed outlier: 4.554A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.049A 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 141 through 171 removed outlier: 3.670A pdb=" N ALA M 145 " --> pdb=" O GLU M 141 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR M 153 " --> pdb=" O PHE M 149 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.527A pdb=" N GLN M 168 " --> pdb=" O LEU M 164 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN M 169 " --> pdb=" O ILE M 165 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS M 170 " --> pdb=" O LEU M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 183 removed outlier: 3.537A pdb=" N PHE M 181 " --> pdb=" O MET M 177 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR M 183 " --> pdb=" O LEU M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 208 removed outlier: 3.577A pdb=" N ASN M 193 " --> pdb=" O SER M 189 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU M 194 " --> pdb=" O TRP M 190 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE M 205 " --> pdb=" O MET M 201 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS M 206 " --> pdb=" O ALA M 202 " (cutoff:3.500A) Proline residue: M 208 - end of helix Processing helix chain 'M' and resid 213 through 223 Proline residue: M 217 - end of helix Processing helix chain 'M' and resid 224 through 233 removed outlier: 3.855A pdb=" N ILE M 230 " --> pdb=" O ALA M 226 " (cutoff:3.500A) Processing helix chain 'M' and resid 235 through 251 removed outlier: 3.822A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE M 248 " --> pdb=" O ILE M 244 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU M 250 " --> pdb=" O ILE M 246 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP M 251 " --> pdb=" O SER M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 279 removed outlier: 4.623A pdb=" N TYR M 256 " --> pdb=" O PRO M 252 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR M 259 " --> pdb=" O LYS M 255 " (cutoff:3.500A) Proline residue: M 260 - end of helix removed outlier: 3.793A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 304 removed outlier: 3.586A pdb=" N VAL M 291 " --> pdb=" O ALA M 287 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 305 through 338 removed outlier: 3.588A pdb=" N ILE M 317 " --> pdb=" O THR M 313 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER M 324 " --> pdb=" O GLY M 320 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN M 333 " --> pdb=" O LEU M 329 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 341 through 346 removed outlier: 4.766A pdb=" N ALA M 345 " --> pdb=" O THR M 341 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ARG M 346 " --> pdb=" O MET M 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 341 through 346' Processing helix chain 'M' and resid 348 through 353 removed outlier: 6.262A pdb=" N PHE M 352 " --> pdb=" O LEU M 348 " (cutoff:3.500A) Proline residue: M 353 - end of helix No H-bonds generated for 'chain 'M' and resid 348 through 353' Processing helix chain 'M' and resid 354 through 368 removed outlier: 3.670A pdb=" N TRP M 358 " --> pdb=" O LEU M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 372 through 389 removed outlier: 3.903A pdb=" N GLU M 378 " --> pdb=" O ASN M 374 " (cutoff:3.500A) Processing helix chain 'M' and resid 391 through 415 removed outlier: 4.219A pdb=" N LEU M 395 " --> pdb=" O PHE M 391 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE M 411 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR M 414 " --> pdb=" O MET M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 430 through 451 Proline residue: M 443 - end of helix Proline residue: M 451 - end of helix Processing helix chain 'N' and resid 2 through 23 Proline residue: N 17 - end of helix Processing helix chain 'N' and resid 25 through 46 removed outlier: 3.534A pdb=" N SER N 36 " --> pdb=" O GLY N 32 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE N 41 " --> pdb=" O LEU N 37 " (cutoff:3.500A) Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 49 through 81 removed outlier: 3.509A pdb=" N THR N 65 " --> pdb=" O VAL N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 107 Processing helix chain 'N' and resid 112 through 123 Proline residue: N 116 - end of helix removed outlier: 3.573A pdb=" N GLN N 120 " --> pdb=" O PRO N 116 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY N 121 " --> pdb=" O GLU N 117 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE N 122 " --> pdb=" O VAL N 118 " (cutoff:3.500A) Proline residue: N 123 - end of helix Processing helix chain 'N' and resid 124 through 146 removed outlier: 3.556A pdb=" N LEU N 128 " --> pdb=" O LEU N 124 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE N 129 " --> pdb=" O HIS N 125 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU N 130 " --> pdb=" O MET N 126 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.669A pdb=" N GLN N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE N 145 " --> pdb=" O ILE N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 173 removed outlier: 3.866A pdb=" N LEU N 155 " --> pdb=" O SER N 151 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA N 158 " --> pdb=" O ILE N 154 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR N 160 " --> pdb=" O MET N 156 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN N 172 " --> pdb=" O GLY N 168 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR N 173 " --> pdb=" O GLY N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 174 through 195 removed outlier: 3.886A pdb=" N TRP N 189 " --> pdb=" O ALA N 185 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) Proline residue: N 195 - end of helix Processing helix chain 'N' and resid 197 through 223 removed outlier: 4.378A pdb=" N THR N 201 " --> pdb=" O ASN N 197 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU N 202 " --> pdb=" O PRO N 198 " (cutoff:3.500A) Proline residue: N 214 - end of helix removed outlier: 4.955A pdb=" N ASN N 222 " --> pdb=" O ALA N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 237 removed outlier: 3.539A pdb=" N LEU N 232 " --> pdb=" O ASN N 228 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TRP N 234 " --> pdb=" O ILE N 230 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 253 removed outlier: 4.464A pdb=" N THR N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N MET N 243 " --> pdb=" O ALA N 239 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU N 246 " --> pdb=" O THR N 242 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY N 253 " --> pdb=" O LEU N 249 " (cutoff:3.500A) Processing helix chain 'N' and resid 257 through 274 removed outlier: 4.511A pdb=" N LEU N 261 " --> pdb=" O LEU N 257 " (cutoff:3.500A) Proline residue: N 262 - end of helix removed outlier: 3.623A pdb=" N ASN N 273 " --> pdb=" O GLU N 269 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN N 274 " --> pdb=" O LEU N 270 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 301 removed outlier: 3.677A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU N 288 " --> pdb=" O MET N 284 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN N 289 " --> pdb=" O MET N 285 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE N 292 " --> pdb=" O LEU N 288 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR N 293 " --> pdb=" O ASN N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 318 removed outlier: 4.279A pdb=" N LYS N 312 " --> pdb=" O ASN N 308 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N MET N 313 " --> pdb=" O ASN N 309 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET N 314 " --> pdb=" O ASN N 310 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR N 315 " --> pdb=" O SER N 311 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS N 316 " --> pdb=" O LYS N 312 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN N 317 " --> pdb=" O MET N 313 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N THR N 318 " --> pdb=" O MET N 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 308 through 318' Processing helix chain 'N' and resid 324 through 335 removed outlier: 3.739A pdb=" N THR N 328 " --> pdb=" O LEU N 324 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR N 334 " --> pdb=" O ALA N 330 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET N 335 " --> pdb=" O ILE N 331 " (cutoff:3.500A) Processing helix chain 'N' and resid 336 through 344 removed outlier: 3.503A pdb=" N ALA N 340 " --> pdb=" O THR N 336 " (cutoff:3.500A) Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 4 through 11 Processing helix chain 'O' and resid 13 through 18 removed outlier: 4.424A pdb=" N LYS O 17 " --> pdb=" O LYS O 13 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU O 18 " --> pdb=" O THR O 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 13 through 18' Processing helix chain 'O' and resid 34 through 47 removed outlier: 3.769A pdb=" N LEU O 38 " --> pdb=" O GLY O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 63 removed outlier: 4.455A pdb=" N THR O 61 " --> pdb=" O GLN O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 75 removed outlier: 4.318A pdb=" N GLY O 75 " --> pdb=" O ILE O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 85 Processing helix chain 'O' and resid 91 through 118 Processing helix chain 'O' and resid 127 through 142 removed outlier: 4.363A pdb=" N PHE O 132 " --> pdb=" O ILE O 128 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL O 133 " --> pdb=" O TYR O 129 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE O 134 " --> pdb=" O SER O 130 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU O 135 " --> pdb=" O ASP O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 164 removed outlier: 3.757A pdb=" N VAL O 149 " --> pdb=" O ARG O 145 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP O 150 " --> pdb=" O LYS O 146 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS O 151 " --> pdb=" O GLN O 147 " (cutoff:3.500A) Proline residue: O 161 - end of helix removed outlier: 5.423A pdb=" N LEU O 164 " --> pdb=" O LEU O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 175 through 187 removed outlier: 3.818A pdb=" N SER O 181 " --> pdb=" O PRO O 177 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN O 184 " --> pdb=" O GLN O 180 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS O 185 " --> pdb=" O SER O 181 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS O 186 " --> pdb=" O ARG O 182 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY O 187 " --> pdb=" O ILE O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 194 removed outlier: 4.542A pdb=" N LYS O 193 " --> pdb=" O PRO O 189 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL O 194 " --> pdb=" O HIS O 190 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 218 removed outlier: 3.505A pdb=" N LEU O 199 " --> pdb=" O THR O 195 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR O 209 " --> pdb=" O ALA O 205 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU O 211 " --> pdb=" O LYS O 207 " (cutoff:3.500A) Proline residue: O 212 - end of helix removed outlier: 3.603A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET O 217 " --> pdb=" O LYS O 213 " (cutoff:3.500A) Processing helix chain 'O' and resid 224 through 231 removed outlier: 3.513A pdb=" N GLU O 229 " --> pdb=" O SER O 225 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ASP O 230 " --> pdb=" O TRP O 226 " (cutoff:3.500A) Proline residue: O 231 - end of helix Processing helix chain 'O' and resid 232 through 241 removed outlier: 3.667A pdb=" N LEU O 241 " --> pdb=" O ASP O 237 " (cutoff:3.500A) Processing helix chain 'O' and resid 246 through 252 removed outlier: 4.655A pdb=" N LYS O 250 " --> pdb=" O GLY O 246 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN O 251 " --> pdb=" O PRO O 247 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASP O 252 " --> pdb=" O TRP O 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 246 through 252' Processing helix chain 'O' and resid 253 through 266 removed outlier: 3.654A pdb=" N HIS O 257 " --> pdb=" O ASP O 253 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS O 266 " --> pdb=" O LEU O 262 " (cutoff:3.500A) Processing helix chain 'O' and resid 267 through 275 removed outlier: 5.550A pdb=" N TYR O 272 " --> pdb=" O GLU O 268 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N THR O 273 " --> pdb=" O VAL O 269 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR O 274 " --> pdb=" O LEU O 270 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE O 275 " --> pdb=" O ASN O 271 " (cutoff:3.500A) Processing helix chain 'O' and resid 285 through 299 removed outlier: 3.611A pdb=" N ARG O 291 " --> pdb=" O HIS O 287 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU O 299 " --> pdb=" O SER O 295 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 42 removed outlier: 4.325A pdb=" N ARG P 32 " --> pdb=" O GLY P 28 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET P 41 " --> pdb=" O HIS P 37 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY P 42 " --> pdb=" O LEU P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 61 removed outlier: 3.513A pdb=" N MET P 57 " --> pdb=" O VAL P 53 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N HIS P 58 " --> pdb=" O TYR P 54 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU P 59 " --> pdb=" O ASP P 55 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG P 60 " --> pdb=" O ILE P 56 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU P 61 " --> pdb=" O MET P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 86 removed outlier: 6.862A pdb=" N ARG P 82 " --> pdb=" O LYS P 78 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS P 83 " --> pdb=" O ASP P 79 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA P 84 " --> pdb=" O SER P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 125 removed outlier: 3.557A pdb=" N VAL P 109 " --> pdb=" O ASP P 105 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASN P 112 " --> pdb=" O ASP P 108 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE P 113 " --> pdb=" O VAL P 109 " (cutoff:3.500A) Proline residue: P 114 - end of helix removed outlier: 3.515A pdb=" N ALA P 124 " --> pdb=" O ALA P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 161 Proline residue: P 161 - end of helix Processing helix chain 'P' and resid 176 through 189 removed outlier: 4.924A pdb=" N ASN P 180 " --> pdb=" O ASP P 176 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N HIS P 181 " --> pdb=" O ARG P 177 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN P 184 " --> pdb=" O ASN P 180 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N TRP P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N PHE P 188 " --> pdb=" O ASN P 184 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU P 189 " --> pdb=" O TYR P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 220 removed outlier: 3.612A pdb=" N THR P 218 " --> pdb=" O ILE P 214 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS P 219 " --> pdb=" O VAL P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 237 through 250 removed outlier: 3.642A pdb=" N HIS P 250 " --> pdb=" O PHE P 246 " (cutoff:3.500A) Processing helix chain 'P' and resid 259 through 273 removed outlier: 3.635A pdb=" N GLY P 267 " --> pdb=" O TYR P 263 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU P 272 " --> pdb=" O LYS P 268 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER P 273 " --> pdb=" O LEU P 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 280 through 289 removed outlier: 3.550A pdb=" N GLU P 285 " --> pdb=" O LYS P 281 " (cutoff:3.500A) Processing helix chain 'P' and resid 299 through 304 removed outlier: 4.153A pdb=" N LEU P 303 " --> pdb=" O GLY P 299 " (cutoff:3.500A) Processing helix chain 'P' and resid 309 through 319 removed outlier: 3.675A pdb=" N LYS P 313 " --> pdb=" O PRO P 309 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ILE P 315 " --> pdb=" O GLU P 311 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLU P 316 " --> pdb=" O LEU P 312 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N VAL P 317 " --> pdb=" O LYS P 313 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 24 removed outlier: 3.825A pdb=" N GLY Q 24 " --> pdb=" O THR Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 32 removed outlier: 3.681A pdb=" N ILE Q 30 " --> pdb=" O PRO Q 26 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR Q 32 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 26 through 32' Processing helix chain 'Q' and resid 88 through 100 Processing helix chain 'Q' and resid 117 through 123 removed outlier: 4.285A pdb=" N ASN Q 121 " --> pdb=" O SER Q 117 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE Q 122 " --> pdb=" O TYR Q 118 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER Q 123 " --> pdb=" O GLY Q 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 117 through 123' Processing helix chain 'R' and resid 25 through 30 removed outlier: 3.745A pdb=" N VAL R 29 " --> pdb=" O ARG R 25 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASP R 30 " --> pdb=" O VAL R 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 25 through 30' Processing helix chain 'R' and resid 39 through 47 removed outlier: 3.834A pdb=" N LEU R 43 " --> pdb=" O PHE R 39 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA R 45 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN R 47 " --> pdb=" O LEU R 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 39 removed outlier: 3.825A pdb=" N GLN S 30 " --> pdb=" O SER S 26 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLY S 31 " --> pdb=" O PRO S 27 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL S 32 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASP S 34 " --> pdb=" O GLN S 30 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL S 37 " --> pdb=" O ARG S 33 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 48 removed outlier: 3.542A pdb=" N LYS S 45 " --> pdb=" O VAL S 41 " (cutoff:3.500A) Proline residue: S 48 - end of helix Processing helix chain 'S' and resid 82 through 95 removed outlier: 3.663A pdb=" N VAL S 93 " --> pdb=" O ALA S 89 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 23 removed outlier: 3.569A pdb=" N LYS T 20 " --> pdb=" O LEU T 16 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU T 21 " --> pdb=" O TYR T 17 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TYR T 22 " --> pdb=" O VAL T 18 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP T 23 " --> pdb=" O LEU T 19 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 31 removed outlier: 3.579A pdb=" N LEU T 30 " --> pdb=" O ASP T 26 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N SER T 31 " --> pdb=" O PRO T 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 26 through 31' Processing helix chain 'T' and resid 43 through 59 removed outlier: 3.957A pdb=" N GLY T 59 " --> pdb=" O GLU T 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 63 through 71 removed outlier: 3.905A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N MET T 71 " --> pdb=" O ALA T 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 72 through 82 Processing helix chain 'T' and resid 35 through 40 Processing helix chain 'U' and resid 7 through 23 removed outlier: 3.599A pdb=" N LEU U 21 " --> pdb=" O TYR U 17 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR U 22 " --> pdb=" O VAL U 18 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 59 Processing helix chain 'U' and resid 63 through 71 removed outlier: 3.621A pdb=" N GLU U 68 " --> pdb=" O ASP U 64 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS U 69 " --> pdb=" O ILE U 65 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N MET U 71 " --> pdb=" O ALA U 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 85 Processing helix chain 'U' and resid 36 through 41 Processing helix chain 'V' and resid 18 through 37 removed outlier: 4.220A pdb=" N ARG V 22 " --> pdb=" O THR V 18 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU V 23 " --> pdb=" O PRO V 19 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR V 24 " --> pdb=" O HIS V 20 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE V 37 " --> pdb=" O ILE V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 41 through 62 removed outlier: 3.649A pdb=" N GLU V 53 " --> pdb=" O GLN V 49 " (cutoff:3.500A) Proline residue: V 62 - end of helix Processing helix chain 'V' and resid 63 through 72 removed outlier: 3.899A pdb=" N GLN V 72 " --> pdb=" O GLU V 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 75 through 97 removed outlier: 3.570A pdb=" N ARG V 91 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 26 through 53 removed outlier: 3.632A pdb=" N ARG W 33 " --> pdb=" O GLU W 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU W 44 " --> pdb=" O ALA W 40 " (cutoff:3.500A) Proline residue: W 46 - end of helix removed outlier: 4.195A pdb=" N HIS W 50 " --> pdb=" O PRO W 46 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN W 53 " --> pdb=" O VAL W 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 57 through 74 removed outlier: 3.557A pdb=" N ASP W 63 " --> pdb=" O LYS W 59 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN W 72 " --> pdb=" O MET W 68 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N HIS W 74 " --> pdb=" O MET W 70 " (cutoff:3.500A) Processing helix chain 'W' and resid 77 through 98 removed outlier: 3.571A pdb=" N THR W 95 " --> pdb=" O GLU W 91 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL W 98 " --> pdb=" O GLU W 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 101 through 110 removed outlier: 3.661A pdb=" N ARG W 107 " --> pdb=" O THR W 103 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE W 108 " --> pdb=" O HIS W 104 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE W 109 " --> pdb=" O VAL W 105 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS W 110 " --> pdb=" O MET W 106 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 127 removed outlier: 4.239A pdb=" N GLY W 127 " --> pdb=" O LYS W 123 " (cutoff:3.500A) Processing helix chain 'X' and resid 8 through 14 removed outlier: 3.583A pdb=" N LEU X 12 " --> pdb=" O THR X 8 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS X 13 " --> pdb=" O LEU X 9 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL X 14 " --> pdb=" O GLU X 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 8 through 14' Processing helix chain 'X' and resid 20 through 29 removed outlier: 3.528A pdb=" N LEU X 24 " --> pdb=" O SER X 20 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N HIS X 29 " --> pdb=" O LYS X 25 " (cutoff:3.500A) Processing helix chain 'X' and resid 30 through 35 removed outlier: 4.568A pdb=" N CYS X 35 " --> pdb=" O TYR X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 49 Processing helix chain 'X' and resid 51 through 77 removed outlier: 4.143A pdb=" N CYS X 55 " --> pdb=" O ASP X 51 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU X 56 " --> pdb=" O PRO X 52 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LYS X 57 " --> pdb=" O ARG X 53 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLU X 58 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY X 59 " --> pdb=" O CYS X 55 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN X 72 " --> pdb=" O ASN X 68 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE X 73 " --> pdb=" O PHE X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 92 removed outlier: 4.069A pdb=" N TYR X 84 " --> pdb=" O PRO X 80 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS X 87 " --> pdb=" O GLU X 83 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR X 90 " --> pdb=" O THR X 86 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER X 91 " --> pdb=" O CYS X 87 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASN X 92 " --> pdb=" O LEU X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 95 through 100 removed outlier: 5.283A pdb=" N CYS X 99 " --> pdb=" O LEU X 95 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG X 100 " --> pdb=" O PHE X 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 95 through 100' Processing helix chain 'X' and resid 101 through 113 removed outlier: 3.948A pdb=" N LYS X 105 " --> pdb=" O GLN X 101 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE X 106 " --> pdb=" O GLN X 102 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1 through 11 removed outlier: 3.738A pdb=" N PHE Y 5 " --> pdb=" O VAL Y 1 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR Y 8 " --> pdb=" O PHE Y 4 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N HIS Y 9 " --> pdb=" O PHE Y 5 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU Y 10 " --> pdb=" O GLU Y 6 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL Y 11 " --> pdb=" O SER Y 7 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 42 removed outlier: 3.784A pdb=" N TYR Y 38 " --> pdb=" O ILE Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 47 through 81 removed outlier: 4.775A pdb=" N ARG Y 80 " --> pdb=" O SER Y 76 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU Y 81 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 105 removed outlier: 4.400A pdb=" N TYR Y 89 " --> pdb=" O ASP Y 85 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY Y 96 " --> pdb=" O GLY Y 92 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY Y 97 " --> pdb=" O GLY Y 93 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N HIS Y 105 " --> pdb=" O GLY Y 101 " (cutoff:3.500A) Processing helix chain 'Y' and resid 106 through 131 removed outlier: 3.697A pdb=" N ALA Y 110 " --> pdb=" O SER Y 106 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS Y 114 " --> pdb=" O ALA Y 110 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL Y 115 " --> pdb=" O ALA Y 111 " (cutoff:3.500A) Processing helix chain 'Z' and resid 30 through 72 removed outlier: 6.831A pdb=" N MET Z 34 " --> pdb=" O SER Z 30 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE Z 35 " --> pdb=" O GLY Z 31 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR Z 46 " --> pdb=" O LEU Z 42 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU Z 55 " --> pdb=" O ARG Z 51 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU Z 62 " --> pdb=" O ARG Z 58 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG Z 67 " --> pdb=" O ASP Z 63 " (cutoff:3.500A) Proline residue: Z 72 - end of helix Processing helix chain 'Z' and resid 73 through 98 removed outlier: 3.752A pdb=" N GLU Z 77 " --> pdb=" O LEU Z 73 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE Z 95 " --> pdb=" O GLU Z 91 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE Z 96 " --> pdb=" O GLU Z 92 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS Z 98 " --> pdb=" O ALA Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 119 through 124 removed outlier: 4.242A pdb=" N TYR Z 124 " --> pdb=" O ILE Z 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 128 through 137 removed outlier: 3.657A pdb=" N MET Z 132 " --> pdb=" O THR Z 128 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE Z 137 " --> pdb=" O SER Z 133 " (cutoff:3.500A) Processing helix chain 'a' and resid 1 through 32 removed outlier: 4.442A pdb=" N ILE a 5 " --> pdb=" O MET a 1 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU a 6 " --> pdb=" O TRP a 2 " (cutoff:3.500A) Proline residue: a 7 - end of helix removed outlier: 3.739A pdb=" N ILE a 11 " --> pdb=" O PRO a 7 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET a 12 " --> pdb=" O GLY a 8 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.809A pdb=" N THR a 23 " --> pdb=" O PRO a 19 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA a 24 " --> pdb=" O GLY a 20 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY a 32 " --> pdb=" O LYS a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 56 removed outlier: 5.772A pdb=" N GLY a 56 " --> pdb=" O ARG a 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 4 through 15 Processing helix chain 'b' and resid 16 through 35 removed outlier: 3.722A pdb=" N PHE b 22 " --> pdb=" O LEU b 18 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE b 29 " --> pdb=" O TRP b 25 " (cutoff:3.500A) Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 37 through 48 removed outlier: 3.536A pdb=" N ALA b 41 " --> pdb=" O TYR b 37 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET b 43 " --> pdb=" O LYS b 39 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN b 45 " --> pdb=" O ALA b 41 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR b 48 " --> pdb=" O ILE b 44 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 83 removed outlier: 3.552A pdb=" N LYS b 81 " --> pdb=" O LEU b 77 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN b 82 " --> pdb=" O ASP b 78 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU b 83 " --> pdb=" O TRP b 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 77 through 83' Processing helix chain 'c' and resid 13 through 46 Processing helix chain 'd' and resid 15 through 20 removed outlier: 4.034A pdb=" N ARG d 19 " --> pdb=" O PRO d 15 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER d 20 " --> pdb=" O ASP d 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 15 through 20' Processing helix chain 'd' and resid 28 through 50 removed outlier: 3.732A pdb=" N TYR d 33 " --> pdb=" O PRO d 29 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG d 49 " --> pdb=" O ASP d 45 " (cutoff:3.500A) Processing helix chain 'd' and resid 57 through 102 removed outlier: 3.810A pdb=" N LEU d 62 " --> pdb=" O LEU d 58 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU d 96 " --> pdb=" O GLY d 92 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS d 97 " --> pdb=" O TYR d 93 " (cutoff:3.500A) Proline residue: d 98 - end of helix removed outlier: 3.558A pdb=" N PHE d 101 " --> pdb=" O HIS d 97 " (cutoff:3.500A) Proline residue: d 102 - end of helix Processing helix chain 'd' and resid 108 through 113 removed outlier: 3.612A pdb=" N ILE d 112 " --> pdb=" O THR d 108 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU d 113 " --> pdb=" O TYR d 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 108 through 113' Processing helix chain 'e' and resid 4 through 10 Processing helix chain 'e' and resid 32 through 44 removed outlier: 3.948A pdb=" N HIS e 44 " --> pdb=" O ILE e 40 " (cutoff:3.500A) Processing helix chain 'e' and resid 47 through 55 removed outlier: 4.841A pdb=" N ALA e 51 " --> pdb=" O GLY e 47 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LYS e 53 " --> pdb=" O THR e 49 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU e 54 " --> pdb=" O ARG e 50 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS e 55 " --> pdb=" O ALA e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 67 removed outlier: 3.571A pdb=" N ASP e 61 " --> pdb=" O ILE e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 68 through 89 Processing helix chain 'e' and resid 94 through 99 removed outlier: 3.542A pdb=" N SER e 98 " --> pdb=" O PRO e 94 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 34 removed outlier: 4.700A pdb=" N VAL f 15 " --> pdb=" O VAL f 11 " (cutoff:3.500A) Proline residue: f 16 - end of helix removed outlier: 3.936A pdb=" N LEU f 33 " --> pdb=" O ASP f 29 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR f 34 " --> pdb=" O ASP f 30 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 40 removed outlier: 4.881A pdb=" N LYS g 38 " --> pdb=" O ASN g 34 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASN g 39 " --> pdb=" O VAL g 35 " (cutoff:3.500A) Proline residue: g 40 - end of helix No H-bonds generated for 'chain 'g' and resid 34 through 40' Processing helix chain 'g' and resid 48 through 63 Processing helix chain 'g' and resid 68 through 78 removed outlier: 4.763A pdb=" N THR g 72 " --> pdb=" O LEU g 68 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL g 78 " --> pdb=" O PHE g 74 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 102 removed outlier: 3.577A pdb=" N ASN g 101 " --> pdb=" O TYR g 97 " (cutoff:3.500A) Processing helix chain 'g' and resid 112 through 117 removed outlier: 4.425A pdb=" N ILE g 116 " --> pdb=" O ASP g 112 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN g 117 " --> pdb=" O PRO g 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 112 through 117' Processing helix chain 'h' and resid 15 through 47 removed outlier: 4.005A pdb=" N ALA h 19 " --> pdb=" O LEU h 15 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE h 27 " --> pdb=" O ARG h 23 " (cutoff:3.500A) removed outlier: 3.675A 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 62 through 67 removed outlier: 3.727A pdb=" N TYR h 66 " --> pdb=" O GLU h 62 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR h 67 " --> pdb=" O HIS h 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 62 through 67' Processing helix chain 'h' and resid 69 through 79 removed outlier: 3.714A pdb=" N ARG h 77 " --> pdb=" O ARG h 73 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN h 78 " --> pdb=" O TRP h 74 " (cutoff:3.500A) Processing helix chain 'h' and resid 82 through 118 removed outlier: 4.149A pdb=" N ASN h 86 " --> pdb=" O GLY h 82 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS h 100 " --> pdb=" O ILE h 96 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU h 113 " --> pdb=" O GLU h 109 " (cutoff:3.500A) Processing helix chain 'i' and resid 4 through 26 removed outlier: 3.513A pdb=" N ARG i 10 " --> pdb=" O ASP i 6 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU i 16 " --> pdb=" O GLN i 12 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU i 17 " --> pdb=" O GLN i 13 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU i 26 " --> pdb=" O LEU i 22 " (cutoff:3.500A) Processing helix chain 'i' and resid 66 through 93 removed outlier: 4.648A pdb=" N ALA i 70 " --> pdb=" O SER i 66 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE i 76 " --> pdb=" O SER i 72 " (cutoff:3.500A) Proline residue: i 77 - end of helix removed outlier: 3.577A pdb=" N TYR i 87 " --> pdb=" O TYR i 83 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ALA i 90 " --> pdb=" O LYS i 86 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N THR i 91 " --> pdb=" O TYR i 87 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS i 92 " --> pdb=" O HIS i 88 " (cutoff:3.500A) Proline residue: i 93 - end of helix Processing helix chain 'j' and resid 18 through 43 removed outlier: 4.255A pdb=" N LEU j 28 " --> pdb=" O GLN j 24 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER j 29 " --> pdb=" O GLY j 25 " (cutoff:3.500A) Processing helix chain 'j' and resid 44 through 49 removed outlier: 3.865A pdb=" N LEU j 48 " --> pdb=" O SER j 44 " (cutoff:3.500A) Processing helix chain 'j' and resid 60 through 65 removed outlier: 3.619A pdb=" N LEU j 64 " --> pdb=" O THR j 60 " (cutoff:3.500A) Processing helix chain 'k' and resid 32 through 45 removed outlier: 4.205A pdb=" N THR k 36 " --> pdb=" O THR k 32 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG k 44 " --> pdb=" O LYS k 40 " (cutoff:3.500A) Processing helix chain 'k' and resid 50 through 60 removed outlier: 4.800A pdb=" N TRP k 56 " --> pdb=" O ARG k 52 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG k 57 " --> pdb=" O ASN k 53 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR k 58 " --> pdb=" O GLU k 54 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET k 59 " --> pdb=" O ALA k 55 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLY k 60 " --> pdb=" O TRP k 56 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 93 removed outlier: 4.315A pdb=" N LYS k 74 " --> pdb=" O SER k 70 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY k 75 " --> pdb=" O VAL k 71 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE k 76 " --> pdb=" O ILE k 72 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LYS k 77 " --> pdb=" O LEU k 73 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N TRP k 78 " --> pdb=" O LYS k 74 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE k 92 " --> pdb=" O GLY k 88 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 9 Proline residue: l 9 - end of helix Processing helix chain 'l' and resid 15 through 27 Processing helix chain 'l' and resid 79 through 84 removed outlier: 3.589A pdb=" N TYR l 83 " --> pdb=" O ASP l 79 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE l 84 " --> pdb=" O LEU l 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 79 through 84' Processing helix chain 'l' and resid 96 through 122 Proline residue: l 122 - end of helix Processing helix chain 'l' and resid 133 through 142 removed outlier: 5.327A pdb=" N LEU l 137 " --> pdb=" O PRO l 133 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LEU l 139 " --> pdb=" O ASN l 135 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLU l 140 " --> pdb=" O ASN l 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG l 141 " --> pdb=" O LEU l 137 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY l 142 " --> pdb=" O TYR l 138 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 52 Processing helix chain 'm' and resid 61 through 73 removed outlier: 3.797A pdb=" N ILE m 65 " --> pdb=" O ASP m 61 " (cutoff:3.500A) Processing helix chain 'm' and resid 74 through 79 removed outlier: 4.063A pdb=" N ASN m 78 " --> pdb=" O ASN m 74 " (cutoff:3.500A) Processing helix chain 'm' and resid 82 through 118 removed outlier: 6.539A pdb=" N LEU m 87 " --> pdb=" O PRO m 83 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU m 88 " --> pdb=" O LYS m 84 " (cutoff:3.500A) Proline residue: m 96 - end of helix removed outlier: 3.727A pdb=" N GLN m 116 " --> pdb=" O GLU m 112 " (cutoff:3.500A) Processing helix chain 'n' and resid 10 through 31 removed outlier: 3.679A pdb=" N LYS n 14 " --> pdb=" O THR n 10 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE n 31 " --> pdb=" O GLU n 27 " (cutoff:3.500A) Processing helix chain 'n' and resid 32 through 51 removed outlier: 5.060A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS n 51 " --> pdb=" O PHE n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 74 removed outlier: 4.818A pdb=" N THR n 60 " --> pdb=" O MET n 56 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN n 61 " --> pdb=" O MET n 57 " (cutoff:3.500A) Processing helix chain 'n' and resid 93 through 98 removed outlier: 5.062A pdb=" N VAL n 98 " --> pdb=" O GLU n 94 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 106 removed outlier: 4.788A pdb=" N TYR n 105 " --> pdb=" O TRP n 101 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP n 106 " --> pdb=" O CYS n 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 101 through 106' Processing helix chain 'n' and resid 107 through 115 removed outlier: 3.673A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR n 114 " --> pdb=" O GLU n 110 " (cutoff:3.500A) Proline residue: n 115 - end of helix Processing helix chain 'n' and resid 116 through 143 removed outlier: 4.363A pdb=" N GLN n 123 " --> pdb=" O SER n 119 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP n 124 " --> pdb=" O LYS n 120 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASP n 133 " --> pdb=" O MET n 129 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS n 137 " --> pdb=" O ASP n 133 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N THR n 143 " --> pdb=" O LEU n 139 " (cutoff:3.500A) Processing helix chain 'n' and resid 166 through 171 removed outlier: 4.588A pdb=" N THR n 171 " --> pdb=" O TRP n 167 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 9 removed outlier: 6.123A pdb=" N ARG o 6 " --> pdb=" O ALA o 2 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ARG o 7 " --> pdb=" O HIS o 3 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR o 8 " --> pdb=" O LEU o 4 " (cutoff:3.500A) Processing helix chain 'o' and resid 41 through 49 removed outlier: 3.572A pdb=" N MET o 45 " --> pdb=" O THR o 41 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET o 46 " --> pdb=" O GLN o 42 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP o 47 " --> pdb=" O GLN o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 51 through 56 removed outlier: 5.076A pdb=" N ASP o 56 " --> pdb=" O LEU o 52 " (cutoff:3.500A) Processing helix chain 'o' and resid 58 through 73 removed outlier: 4.283A pdb=" N LEU o 62 " --> pdb=" O CYS o 58 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG o 64 " --> pdb=" O HIS o 60 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE o 73 " --> pdb=" O LYS o 69 " (cutoff:3.500A) Processing helix chain 'o' and resid 79 through 112 removed outlier: 4.063A pdb=" N GLN o 83 " --> pdb=" O CYS o 79 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS o 111 " --> pdb=" O LEU o 107 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS o 112 " --> pdb=" O LEU o 108 " (cutoff:3.500A) Processing helix chain 'p' and resid 5 through 10 Proline residue: p 10 - end of helix Processing helix chain 'p' and resid 27 through 59 removed outlier: 3.894A pdb=" N TYR p 31 " --> pdb=" O ASN p 27 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP p 41 " --> pdb=" O ASP p 37 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N TRP p 42 " --> pdb=" O LEU p 38 " (cutoff:3.500A) Proline residue: p 43 - end of helix Processing helix chain 'p' and resid 80 through 117 removed outlier: 3.680A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 119 through 124 removed outlier: 3.699A pdb=" N ASN p 123 " --> pdb=" O ASN p 119 " (cutoff:3.500A) Processing helix chain 'p' and resid 125 through 142 Processing helix chain 'p' and resid 150 through 171 removed outlier: 4.195A pdb=" N GLN p 171 " --> pdb=" O LYS p 167 " (cutoff:3.500A) Processing helix chain 'q' and resid 1 through 16 removed outlier: 4.214A pdb=" N GLU q 5 " --> pdb=" O AME q 1 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 28 removed outlier: 3.745A pdb=" N VAL q 26 " --> pdb=" O GLY q 22 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 92 removed outlier: 4.375A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS q 92 " --> pdb=" O ARG q 88 " (cutoff:3.500A) Processing helix chain 'q' and resid 97 through 102 Proline residue: q 102 - end of helix Processing helix chain 'r' and resid 4 through 16 removed outlier: 5.939A pdb=" N GLN r 8 " --> pdb=" O THR r 4 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS r 9 " --> pdb=" O ARG r 5 " (cutoff:3.500A) Processing helix chain 'r' and resid 52 through 57 removed outlier: 4.253A pdb=" N ARG r 56 " --> pdb=" O TYR r 52 " (cutoff:3.500A) Processing helix chain 's' and resid 43 through 54 removed outlier: 4.682A pdb=" N ASP s 47 " --> pdb=" O TYR s 43 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU s 48 " --> pdb=" O THR s 44 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) Processing helix chain 's' and resid 34 through 39 removed outlier: 4.434A pdb=" N HIS s 37 " --> pdb=" O ASN s 34 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS s 38 " --> pdb=" O LEU s 35 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP s 39 " --> pdb=" O GLN s 36 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 34 through 39' Processing sheet with id= 1, first strand: chain 'B' and resid 95 through 98 removed outlier: 3.549A pdb=" N ILE B 154 " --> pdb=" O VAL B 123 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 39 through 42 removed outlier: 4.564A pdb=" N GLN C 39 " --> pdb=" O CYS C 51 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS C 51 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR C 110 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER C 103 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 98 " --> pdb=" O SER C 103 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C 90 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG C 89 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 83 " --> pdb=" O ARG C 89 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 171 through 177 removed outlier: 7.475A pdb=" N TYR C 171 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 188 " --> pdb=" O TYR C 171 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 62 through 68 removed outlier: 3.809A pdb=" N ARG D 63 " --> pdb=" O HIS D 79 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 65 " --> pdb=" O ASP D 77 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS D 75 " --> pdb=" O GLU D 67 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 361 through 368 removed outlier: 3.710A pdb=" N GLY D 361 " --> pdb=" O SER D 380 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG D 388 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 97 through 104 Processing sheet with id= 7, first strand: chain 'F' and resid 173 through 180 removed outlier: 4.224A pdb=" N ALA F 133 " --> pdb=" O LYS F 91 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG F 139 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR F 221 " --> pdb=" O TYR F 92 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'F' and resid 265 through 269 removed outlier: 5.482A pdb=" N ALA F 332 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA F 296 " --> pdb=" O MET F 337 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'G' and resid 8 through 12 Processing sheet with id= 10, first strand: chain 'G' and resid 57 through 60 removed outlier: 3.694A pdb=" N GLU G 58 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN G 78 " --> pdb=" O GLU G 60 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 173 through 176 removed outlier: 3.770A pdb=" N GLY G 173 " --> pdb=" O GLY G 184 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'G' and resid 224 through 227 removed outlier: 5.642A pdb=" N ASN G 237 " --> pdb=" O ARG G 253 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG G 253 " --> pdb=" O ASN G 237 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG G 249 " --> pdb=" O SER G 241 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 291 through 294 removed outlier: 6.733A pdb=" N GLU G 281 " --> pdb=" O PRO G 562 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ASP G 558 " --> pdb=" O ARG G 285 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 342 through 346 removed outlier: 5.108A pdb=" N ASN G 342 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA G 317 " --> pdb=" O ASN G 342 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU G 346 " --> pdb=" O ALA G 319 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE G 318 " --> pdb=" O PHE G 523 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY G 320 " --> pdb=" O LEU G 525 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE G 542 " --> pdb=" O LYS G 520 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU G 524 " --> pdb=" O VAL G 544 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN G 546 " --> pdb=" O LEU G 524 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 405 through 409 Processing sheet with id= 16, first strand: chain 'G' and resid 571 through 575 removed outlier: 3.813A pdb=" N ALA G 571 " --> pdb=" O THR G 583 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN G 575 " --> pdb=" O ARG G 579 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG G 579 " --> pdb=" O ASN G 575 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'I' and resid 66 through 70 removed outlier: 3.781A pdb=" N GLU I 66 " --> pdb=" O GLY I 136 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA I 132 " --> pdb=" O ARG I 70 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'I' and resid 94 through 98 removed outlier: 4.541A pdb=" N ARG I 110 " --> pdb=" O GLU I 97 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'L' and resid 61 through 65 removed outlier: 6.651A pdb=" N MET L 78 " --> pdb=" O THR L 65 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'O' and resid 24 through 29 Processing sheet with id= 21, first strand: chain 'O' and resid 48 through 51 Processing sheet with id= 22, first strand: chain 'P' and resid 67 through 73 removed outlier: 5.580A pdb=" N GLN P 67 " --> pdb=" O SER P 43 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP P 73 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLN P 44 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU P 94 " --> pdb=" O PHE P 24 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL P 91 " --> pdb=" O ARG P 128 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL P 132 " --> pdb=" O ASN P 93 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'P' and resid 190 through 193 No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 'Q' and resid 72 through 75 removed outlier: 4.606A pdb=" N TRP Q 72 " --> pdb=" O ASN Q 67 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE Q 38 " --> pdb=" O LYS Q 56 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS Q 34 " --> pdb=" O ASP Q 60 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL Q 39 " --> pdb=" O GLU Q 106 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Q' and resid 54 through 58 removed outlier: 3.515A pdb=" N LEU Q 84 " --> pdb=" O MET Q 57 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'R' and resid 49 through 52 removed outlier: 4.678A pdb=" N LEU R 89 " --> pdb=" O CYS R 84 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 56 through 60 removed outlier: 3.561A pdb=" N ILE R 57 " --> pdb=" O ILE R 73 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'S' and resid 51 through 57 removed outlier: 3.646A pdb=" N VAL S 20 " --> pdb=" O LEU S 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU S 22 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU S 17 " --> pdb=" O ARG S 67 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU S 78 " --> pdb=" O PRO S 62 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU S 64 " --> pdb=" O VAL S 76 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL S 76 " --> pdb=" O LEU S 64 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLN S 72 " --> pdb=" O TYR S 68 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'q' and resid 36 through 39 removed outlier: 8.082A pdb=" N GLY q 45 " --> pdb=" O THR q 65 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N THR q 65 " --> pdb=" O GLY q 45 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N HIS q 59 " --> pdb=" O ASP q 51 " (cutoff:3.500A) 2996 hydrogen bonds defined for protein. 8973 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: 42.17 Time building geometry restraints manager: 83.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.13: 65871 1.13 - 1.42: 28381 1.42 - 1.71: 39576 1.71 - 2.00: 807 2.00 - 2.29: 80 Bond restraints: 134715 Sorted by residual: bond pdb=" C4 88I H 402 " pdb=" C5 88I H 402 " ideal model delta sigma weight residual 1.525 1.318 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" CA7 CDL N 401 " pdb=" OA8 CDL N 401 " ideal model delta sigma weight residual 1.334 1.403 -0.069 1.10e-02 8.26e+03 3.95e+01 bond pdb=" CB7 CDL X 201 " pdb=" OB8 CDL X 201 " ideal model delta sigma weight residual 1.334 1.401 -0.067 1.10e-02 8.26e+03 3.68e+01 bond pdb=" CA7 CDL r 201 " pdb=" OA8 CDL r 201 " ideal model delta sigma weight residual 1.334 1.400 -0.066 1.10e-02 8.26e+03 3.61e+01 bond pdb=" CB7 CDL L 703 " pdb=" OB8 CDL L 703 " ideal model delta sigma weight residual 1.334 1.400 -0.066 1.10e-02 8.26e+03 3.59e+01 ... (remaining 134710 not shown) Histogram of bond angle deviations from ideal: 73.08 - 86.40: 95 86.40 - 99.72: 23 99.72 - 113.05: 159556 113.05 - 126.37: 81945 126.37 - 139.69: 1656 Bond angle restraints: 243275 Sorted by residual: angle pdb=" SD MET F 430 " pdb=" CE MET F 430 " pdb=" HE2 MET F 430 " ideal model delta sigma weight residual 109.00 79.31 29.69 3.00e+00 1.11e-01 9.80e+01 angle pdb=" SD MET F 430 " pdb=" CE MET F 430 " pdb=" HE3 MET F 430 " ideal model delta sigma weight residual 109.00 79.45 29.55 3.00e+00 1.11e-01 9.70e+01 angle pdb=" CA ALA L 236 " pdb=" CB ALA L 236 " pdb=" HB3 ALA L 236 " ideal model delta sigma weight residual 109.00 79.53 29.47 3.00e+00 1.11e-01 9.65e+01 angle pdb=" CA ALA L 236 " pdb=" CB ALA L 236 " pdb=" HB2 ALA L 236 " ideal model delta sigma weight residual 109.00 79.72 29.28 3.00e+00 1.11e-01 9.53e+01 angle pdb=" HB1 ALA L 236 " pdb=" CB ALA L 236 " pdb=" HB2 ALA L 236 " ideal model delta sigma weight residual 110.00 81.31 28.69 3.00e+00 1.11e-01 9.15e+01 ... (remaining 243270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 61801 35.08 - 70.16: 2055 70.16 - 105.25: 86 105.25 - 140.33: 3 140.33 - 175.41: 3 Dihedral angle restraints: 63948 sinusoidal: 35300 harmonic: 28648 Sorted by residual: 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 -159.99 73.99 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CB CYS p 112 " pdb=" SG CYS p 112 " pdb=" SG CYS p 124 " pdb=" CB CYS p 124 " ideal model delta sinusoidal sigma weight residual 93.00 162.47 -69.47 1 1.00e+01 1.00e-02 6.23e+01 dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual -102.41 73.00 -175.41 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 63945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.228: 10138 4.228 - 8.456: 2 8.456 - 12.684: 0 12.684 - 16.912: 0 16.912 - 21.140: 24 Chirality restraints: 10164 Sorted by residual: chirality pdb="FE2 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S3 SF4 G 801 " pdb=" S4 SF4 G 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.59 21.14 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE3 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.58 -21.13 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 F 501 " pdb=" S1 SF4 F 501 " pdb=" S2 SF4 F 501 " pdb=" S3 SF4 F 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.57 21.12 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10161 not shown) Planarity restraints: 19291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA AME q 1 " -0.070 2.00e-02 2.50e+03 1.30e-01 1.70e+02 pdb=" C AME q 1 " 0.226 2.00e-02 2.50e+03 pdb=" O AME q 1 " -0.081 2.00e-02 2.50e+03 pdb=" N GLU q 2 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP j 55 " -0.086 5.00e-02 4.00e+02 1.26e-01 2.54e+01 pdb=" N PRO j 56 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO j 56 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO j 56 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 73 " 0.025 2.00e-02 2.50e+03 2.03e-02 1.64e+01 pdb=" CG TRP P 73 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP P 73 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP P 73 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP P 73 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP P 73 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP P 73 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 73 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 73 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP P 73 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP P 73 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 TRP P 73 " 0.004 2.00e-02 2.50e+03 pdb=" HE3 TRP P 73 " -0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP P 73 " -0.005 2.00e-02 2.50e+03 pdb=" HZ3 TRP P 73 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP P 73 " 0.004 2.00e-02 2.50e+03 ... (remaining 19288 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 1439 2.06 - 2.69: 210811 2.69 - 3.33: 394849 3.33 - 3.96: 506221 3.96 - 4.60: 808610 Nonbonded interactions: 1921930 Sorted by model distance: nonbonded pdb=" O ASN L 207 " pdb="HD21 ASN L 207 " model vdw 1.419 1.850 nonbonded pdb="HE22 GLN L 580 " pdb=" HE1 PHE N 113 " model vdw 1.440 2.100 nonbonded pdb=" OE2 GLU X 48 " pdb="HH12 ARG X 134 " model vdw 1.551 1.850 nonbonded pdb=" O LYS L 77 " pdb="HD22 ASN L 136 " model vdw 1.562 1.850 nonbonded pdb=" OD1 ASN L 194 " pdb="HE22 GLN p 106 " model vdw 1.570 1.850 ... (remaining 1921925 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'T' selection = (chain 'U' and ((resid 7 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 8 through 82 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.350 Extract box with map and model: 22.580 Check model and map are aligned: 1.410 Set scattering table: 0.870 Process input model: 400.780 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.350 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:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 435.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.207 68773 Z= 0.428 Angle : 0.826 14.936 93122 Z= 0.404 Chirality : 1.028 21.140 10164 Planarity : 0.006 0.130 11649 Dihedral : 15.907 175.409 26194 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.01 % Allowed : 0.28 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.09), residues: 8076 helix: -0.09 (0.08), residues: 4038 sheet: -1.81 (0.27), residues: 363 loop : -1.19 (0.10), residues: 3675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP P 73 HIS 0.007 0.001 HIS P 250 PHE 0.027 0.002 PHE P 160 TYR 0.023 0.002 TYR P 263 ARG 0.010 0.001 ARG s 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 44 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Evaluate side-chains 1682 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1681 time to evaluate : 7.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 TYR cc_start: 0.6547 (m-80) cc_final: 0.5431 (m-80) REVERT: A 108 GLN cc_start: 0.7714 (mm110) cc_final: 0.7437 (mm-40) REVERT: B 72 MET cc_start: 0.7742 (ttp) cc_final: 0.7434 (ttp) REVERT: B 154 ILE cc_start: 0.8840 (tt) cc_final: 0.8639 (mt) REVERT: B 182 LYS cc_start: 0.8192 (ttmt) cc_final: 0.7862 (mtmt) REVERT: C 200 ASN cc_start: 0.7715 (m-40) cc_final: 0.7452 (m110) REVERT: D 75 LYS cc_start: 0.7118 (tppt) cc_final: 0.6867 (tttt) REVERT: D 118 TYR cc_start: 0.8633 (t80) cc_final: 0.8388 (t80) REVERT: D 226 GLU cc_start: 0.7432 (tt0) cc_final: 0.7134 (tt0) REVERT: E 93 LYS cc_start: 0.8083 (ptmt) cc_final: 0.7636 (mmtt) REVERT: F 272 MET cc_start: 0.6260 (mmm) cc_final: 0.6059 (mmm) REVERT: G 61 LYS cc_start: 0.7177 (mmtm) cc_final: 0.6013 (tptm) REVERT: G 375 ASP cc_start: 0.7398 (m-30) cc_final: 0.7147 (t0) REVERT: G 490 MET cc_start: 0.8196 (tpt) cc_final: 0.7935 (tpt) REVERT: G 659 ASP cc_start: 0.6192 (t70) cc_final: 0.5950 (t0) REVERT: H 31 MET cc_start: 0.8301 (mtt) cc_final: 0.8027 (mtt) REVERT: H 106 LEU cc_start: 0.7896 (mm) cc_final: 0.7613 (mp) REVERT: H 214 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7803 (mm-30) REVERT: L 12 PHE cc_start: 0.8190 (m-80) cc_final: 0.7850 (m-10) REVERT: L 297 ASP cc_start: 0.7619 (t0) cc_final: 0.7300 (t0) REVERT: L 319 MET cc_start: 0.7026 (mpp) cc_final: 0.6821 (mpp) REVERT: L 396 ILE cc_start: 0.7947 (mm) cc_final: 0.7725 (mt) REVERT: L 580 GLN cc_start: 0.7384 (mt0) cc_final: 0.6621 (mm-40) REVERT: L 589 MET cc_start: 0.7007 (ttt) cc_final: 0.6754 (ttt) REVERT: M 292 SER cc_start: 0.7867 (t) cc_final: 0.7562 (m) REVERT: M 376 MET cc_start: 0.7481 (mmm) cc_final: 0.7264 (tpp) REVERT: M 396 MET cc_start: 0.7007 (mmm) cc_final: 0.6687 (tpp) REVERT: M 409 TYR cc_start: 0.7586 (t80) cc_final: 0.7292 (t80) REVERT: M 445 ILE cc_start: 0.8702 (mm) cc_final: 0.8459 (mm) REVERT: N 47 LYS cc_start: 0.6492 (mmpt) cc_final: 0.5830 (mtmt) REVERT: N 68 MET cc_start: 0.7792 (mmt) cc_final: 0.7441 (mmp) REVERT: O 2 ARG cc_start: 0.6736 (mmm160) cc_final: 0.5707 (ptt-90) REVERT: O 37 LYS cc_start: 0.7321 (mttp) cc_final: 0.6984 (tptp) REVERT: O 113 GLU cc_start: 0.6851 (tm-30) cc_final: 0.6569 (tm-30) REVERT: O 129 TYR cc_start: 0.8340 (m-80) cc_final: 0.8127 (m-80) REVERT: O 308 TYR cc_start: 0.7857 (m-80) cc_final: 0.7475 (m-80) REVERT: P 57 MET cc_start: 0.8172 (tpt) cc_final: 0.7799 (tpp) REVERT: P 102 ARG cc_start: 0.5472 (mtp-110) cc_final: 0.4524 (mpt180) REVERT: P 122 LYS cc_start: 0.7289 (tppt) cc_final: 0.6551 (ttpp) REVERT: P 291 ASP cc_start: 0.6567 (m-30) cc_final: 0.6156 (m-30) REVERT: R 30 ASP cc_start: 0.7287 (t0) cc_final: 0.6984 (t0) REVERT: R 77 LYS cc_start: 0.6400 (mttt) cc_final: 0.6137 (mttp) REVERT: S 59 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6944 (tm-30) REVERT: T 33 ASN cc_start: 0.7093 (m-40) cc_final: 0.6236 (p0) REVERT: T 46 ASP cc_start: 0.6089 (m-30) cc_final: 0.5737 (m-30) REVERT: T 72 CYS cc_start: 0.6959 (m) cc_final: 0.6630 (p) REVERT: U 50 ILE cc_start: 0.8415 (mm) cc_final: 0.8167 (mt) REVERT: V 85 LYS cc_start: 0.7482 (mttt) cc_final: 0.7200 (mptt) REVERT: W 31 LYS cc_start: 0.7470 (mtpt) cc_final: 0.7114 (ttpt) REVERT: W 91 GLU cc_start: 0.7347 (tp30) cc_final: 0.7125 (tp30) REVERT: Y 16 GLN cc_start: 0.6575 (mt0) cc_final: 0.6184 (mp10) REVERT: Y 19 ARG cc_start: 0.6828 (ttm-80) cc_final: 0.6360 (ttt90) REVERT: Y 39 SER cc_start: 0.7614 (m) cc_final: 0.7273 (t) REVERT: Y 140 VAL cc_start: 0.8071 (t) cc_final: 0.7756 (t) REVERT: Z 133 SER cc_start: 0.7907 (m) cc_final: 0.7545 (p) REVERT: c 30 TYR cc_start: 0.7590 (t80) cc_final: 0.7007 (t80) REVERT: e 18 MET cc_start: 0.8348 (mmm) cc_final: 0.8055 (mmm) REVERT: g 109 ASN cc_start: 0.8126 (m-40) cc_final: 0.7905 (m-40) REVERT: h 7 ARG cc_start: 0.8013 (mtm-85) cc_final: 0.7336 (mtm180) REVERT: h 75 ILE cc_start: 0.8379 (mm) cc_final: 0.8171 (mt) REVERT: h 77 ARG cc_start: 0.7656 (ttp-170) cc_final: 0.7371 (ttp-170) REVERT: h 106 LYS cc_start: 0.7430 (mmmt) cc_final: 0.6993 (mttt) REVERT: i 97 VAL cc_start: 0.8847 (m) cc_final: 0.8643 (t) REVERT: j 10 ARG cc_start: 0.8008 (mtp85) cc_final: 0.7667 (mmm-85) REVERT: j 13 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7163 (mm-30) REVERT: j 58 GLN cc_start: 0.7088 (mm110) cc_final: 0.6491 (tm-30) REVERT: k 38 GLN cc_start: 0.5939 (mm-40) cc_final: 0.5447 (mt0) REVERT: k 44 ARG cc_start: 0.6563 (ttm-80) cc_final: 0.6323 (ttm170) REVERT: l 7 MET cc_start: 0.7075 (mmm) cc_final: 0.6813 (tpp) REVERT: l 39 ASP cc_start: 0.6887 (m-30) cc_final: 0.6539 (t0) REVERT: m 15 SER cc_start: 0.6798 (m) cc_final: 0.6450 (t) REVERT: m 61 ASP cc_start: 0.7004 (t0) cc_final: 0.6536 (p0) REVERT: n 158 ARG cc_start: 0.6323 (mtm180) cc_final: 0.5351 (ttm110) REVERT: o 10 TRP cc_start: 0.4919 (t-100) cc_final: 0.4412 (m100) REVERT: o 90 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7557 (mm-30) REVERT: o 112 LYS cc_start: 0.5327 (ptpt) cc_final: 0.5064 (tppt) REVERT: p 136 LYS cc_start: 0.7391 (ttpt) cc_final: 0.7047 (tppt) REVERT: q 21 ARG cc_start: 0.7202 (ttt180) cc_final: 0.6427 (mtm-85) REVERT: r 5 ARG cc_start: 0.7844 (tpp80) cc_final: 0.7343 (tmt170) outliers start: 1 outliers final: 0 residues processed: 1681 average time/residue: 1.6898 time to fit residues: 4711.8605 Evaluate side-chains 1073 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1073 time to evaluate : 7.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 674 optimal weight: 6.9990 chunk 605 optimal weight: 3.9990 chunk 336 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 408 optimal weight: 4.9990 chunk 323 optimal weight: 3.9990 chunk 626 optimal weight: 7.9990 chunk 242 optimal weight: 8.9990 chunk 380 optimal weight: 8.9990 chunk 466 optimal weight: 7.9990 chunk 725 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 ASN D 232 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 342 ASN H 93 HIS H 163 GLN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 ASN L 170 GLN L 192 ASN ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 308 ASN O 44 GLN Q 44 ASN R 36 ASN S 72 GLN X 98 HIS Z 54 GLN Z 136 ASN g 55 ASN j 58 GLN m 78 ASN p 58 ASN r 50 ASN s 59 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.258 68773 Z= 0.658 Angle : 1.625 50.782 93122 Z= 1.040 Chirality : 0.319 6.669 10164 Planarity : 0.006 0.072 11649 Dihedral : 11.502 169.434 10016 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.31 % Allowed : 8.36 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.09), residues: 8076 helix: 0.20 (0.08), residues: 4196 sheet: -1.85 (0.25), residues: 379 loop : -1.37 (0.11), residues: 3501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 106 HIS 0.010 0.001 HIS G 101 PHE 0.022 0.002 PHE D 218 TYR 0.025 0.002 TYR I 120 ARG 0.013 0.001 ARG Z 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 44 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Evaluate side-chains 1171 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1077 time to evaluate : 7.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7980 (mm110) cc_final: 0.7570 (mm110) REVERT: D 75 LYS cc_start: 0.7081 (tppt) cc_final: 0.6822 (tttt) REVERT: D 115 GLU cc_start: 0.7287 (pt0) cc_final: 0.6987 (pt0) REVERT: D 118 TYR cc_start: 0.8720 (t80) cc_final: 0.8451 (t80) REVERT: E 93 LYS cc_start: 0.8101 (ptmt) cc_final: 0.7658 (mmtt) REVERT: F 33 LEU cc_start: 0.7844 (tp) cc_final: 0.7376 (tt) REVERT: G 61 LYS cc_start: 0.7282 (mmtm) cc_final: 0.6109 (tptm) REVERT: G 375 ASP cc_start: 0.7236 (m-30) cc_final: 0.6938 (t0) REVERT: G 490 MET cc_start: 0.8297 (tpt) cc_final: 0.7920 (tpt) REVERT: G 659 ASP cc_start: 0.6087 (t70) cc_final: 0.5850 (t0) REVERT: H 31 MET cc_start: 0.8321 (mtt) cc_final: 0.8066 (mtt) REVERT: H 53 MET cc_start: 0.7196 (mtt) cc_final: 0.6942 (mtt) REVERT: H 209 SER cc_start: 0.8173 (t) cc_final: 0.7973 (m) REVERT: J 97 ILE cc_start: 0.7460 (mm) cc_final: 0.6967 (pt) REVERT: J 98 MET cc_start: 0.6534 (mmt) cc_final: 0.5842 (mtp) REVERT: J 108 TYR cc_start: 0.6469 (m-10) cc_final: 0.6206 (m-80) REVERT: L 62 MET cc_start: 0.7265 (tmm) cc_final: 0.7049 (tmm) REVERT: L 145 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6742 (mm-30) REVERT: L 150 MET cc_start: 0.7881 (mmp) cc_final: 0.7501 (mmt) REVERT: L 396 ILE cc_start: 0.7922 (mm) cc_final: 0.7635 (mt) REVERT: L 539 MET cc_start: 0.7419 (mmm) cc_final: 0.7213 (mmm) REVERT: L 580 GLN cc_start: 0.7342 (mt0) cc_final: 0.6612 (mm110) REVERT: L 589 MET cc_start: 0.6746 (ttt) cc_final: 0.6403 (ttt) REVERT: L 596 ILE cc_start: 0.8772 (mt) cc_final: 0.8428 (pt) REVERT: M 88 ASN cc_start: 0.7355 (t0) cc_final: 0.7120 (t0) REVERT: M 292 SER cc_start: 0.7933 (t) cc_final: 0.7628 (m) REVERT: N 173 THR cc_start: 0.8526 (m) cc_final: 0.8281 (p) REVERT: O 2 ARG cc_start: 0.6761 (mmm160) cc_final: 0.5733 (ptt-90) REVERT: O 129 TYR cc_start: 0.8365 (m-80) cc_final: 0.8019 (m-80) REVERT: P 102 ARG cc_start: 0.5632 (mtp-110) cc_final: 0.4525 (mpt180) REVERT: Q 45 MET cc_start: 0.7792 (mmm) cc_final: 0.7552 (mmm) REVERT: R 4 VAL cc_start: 0.7891 (m) cc_final: 0.7679 (m) REVERT: R 30 ASP cc_start: 0.7303 (t0) cc_final: 0.6927 (t0) REVERT: S 35 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.7133 (t80) REVERT: S 59 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6807 (tm-30) REVERT: T 33 ASN cc_start: 0.7117 (m-40) cc_final: 0.6284 (p0) REVERT: T 46 ASP cc_start: 0.6640 (m-30) cc_final: 0.6207 (m-30) REVERT: T 72 CYS cc_start: 0.6407 (m) cc_final: 0.6092 (p) REVERT: V 85 LYS cc_start: 0.7548 (mttt) cc_final: 0.7348 (mptt) REVERT: W 91 GLU cc_start: 0.7398 (tp30) cc_final: 0.6987 (tp30) REVERT: Y 60 PHE cc_start: 0.6405 (m-80) cc_final: 0.6184 (t80) REVERT: Z 120 ILE cc_start: 0.7961 (mt) cc_final: 0.7581 (pt) REVERT: a 29 PHE cc_start: 0.8191 (t80) cc_final: 0.7717 (t80) REVERT: c 30 TYR cc_start: 0.7383 (t80) cc_final: 0.6938 (t80) REVERT: e 14 ASP cc_start: 0.8231 (p0) cc_final: 0.7989 (p0) REVERT: e 88 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7219 (mt-10) REVERT: g 27 ASP cc_start: 0.7087 (m-30) cc_final: 0.6696 (p0) REVERT: h 7 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7511 (mtm-85) REVERT: h 75 ILE cc_start: 0.8401 (mm) cc_final: 0.8188 (mt) REVERT: h 106 LYS cc_start: 0.7436 (mmmt) cc_final: 0.6961 (mttt) REVERT: j 10 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7745 (mmm-85) REVERT: j 13 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7250 (mm-30) REVERT: j 58 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6632 (tm-30) REVERT: k 38 GLN cc_start: 0.5862 (mm-40) cc_final: 0.5564 (mt0) REVERT: k 77 LYS cc_start: 0.7582 (tppt) cc_final: 0.7379 (mmmt) REVERT: l 7 MET cc_start: 0.6991 (mmm) cc_final: 0.6777 (tpp) REVERT: l 39 ASP cc_start: 0.6832 (m-30) cc_final: 0.6513 (t0) REVERT: m 15 SER cc_start: 0.6713 (m) cc_final: 0.6477 (t) REVERT: m 61 ASP cc_start: 0.7248 (t0) cc_final: 0.6616 (p0) REVERT: m 125 ASN cc_start: 0.7978 (OUTLIER) cc_final: 0.7650 (m-40) REVERT: n 8 TYR cc_start: 0.6726 (OUTLIER) cc_final: 0.6329 (m-80) REVERT: n 12 GLN cc_start: 0.6700 (mp10) cc_final: 0.6493 (mp10) REVERT: n 158 ARG cc_start: 0.6322 (mtm180) cc_final: 0.5581 (ttm110) REVERT: p 136 LYS cc_start: 0.7617 (ttpt) cc_final: 0.7327 (tppt) REVERT: q 21 ARG cc_start: 0.7065 (ttt180) cc_final: 0.6108 (tpt170) REVERT: q 72 ASN cc_start: 0.7427 (t0) cc_final: 0.7183 (t0) REVERT: r 5 ARG cc_start: 0.8040 (tpp80) cc_final: 0.7490 (ttp80) outliers start: 94 outliers final: 75 residues processed: 1134 average time/residue: 1.6024 time to fit residues: 3063.8039 Evaluate side-chains 1062 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 984 time to evaluate : 6.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 194 GLU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 147 CYS Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 170 GLN Chi-restraints excluded: chain L residue 186 MET Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 320 ASN Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 411 ILE Chi-restraints excluded: chain N residue 308 ASN Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain P residue 103 ASN Chi-restraints excluded: chain P residue 231 THR Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain S residue 35 PHE Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain X residue 171 VAL Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain b residue 42 SER Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 21 VAL Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain h residue 41 THR Chi-restraints excluded: chain h residue 49 GLU Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain j residue 29 SER Chi-restraints excluded: chain j residue 43 ASP Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain m residue 125 ASN Chi-restraints excluded: chain n residue 8 TYR Chi-restraints excluded: chain n residue 30 CYS Chi-restraints excluded: chain n residue 113 MET Chi-restraints excluded: chain n residue 143 THR Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain r residue 15 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 403 optimal weight: 0.2980 chunk 225 optimal weight: 6.9990 chunk 603 optimal weight: 0.2980 chunk 494 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 chunk 726 optimal weight: 7.9990 chunk 785 optimal weight: 0.9990 chunk 647 optimal weight: 6.9990 chunk 720 optimal weight: 0.9980 chunk 247 optimal weight: 4.9990 chunk 583 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN H 230 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 323 HIS N 289 ASN S 72 GLN ** j 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.252 68773 Z= 0.520 Angle : 1.568 50.592 93122 Z= 1.017 Chirality : 0.311 6.400 10164 Planarity : 0.004 0.059 11649 Dihedral : 10.718 170.823 10016 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.13 % Allowed : 9.85 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.09), residues: 8076 helix: 0.67 (0.08), residues: 4214 sheet: -1.76 (0.25), residues: 382 loop : -1.20 (0.11), residues: 3480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP O 318 HIS 0.009 0.001 HIS H 93 PHE 0.016 0.001 PHE H 310 TYR 0.020 0.001 TYR L 422 ARG 0.007 0.000 ARG s 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 44 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Evaluate side-chains 1145 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1064 time to evaluate : 9.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7923 (mm110) cc_final: 0.7493 (mm110) REVERT: B 37 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7156 (tm-30) REVERT: D 75 LYS cc_start: 0.7107 (tppt) cc_final: 0.6768 (tttt) REVERT: D 115 GLU cc_start: 0.7283 (pt0) cc_final: 0.7045 (pt0) REVERT: D 118 TYR cc_start: 0.8629 (t80) cc_final: 0.8360 (t80) REVERT: D 182 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7651 (tm-30) REVERT: E 93 LYS cc_start: 0.8057 (ptmt) cc_final: 0.7648 (mmtt) REVERT: F 33 LEU cc_start: 0.7800 (tp) cc_final: 0.7348 (tt) REVERT: G 375 ASP cc_start: 0.7236 (m-30) cc_final: 0.6887 (t0) REVERT: G 490 MET cc_start: 0.8310 (tpt) cc_final: 0.7924 (tpt) REVERT: G 659 ASP cc_start: 0.6159 (t70) cc_final: 0.5946 (t0) REVERT: G 679 ARG cc_start: 0.7936 (ttm-80) cc_final: 0.7683 (mtm-85) REVERT: H 31 MET cc_start: 0.8270 (mtt) cc_final: 0.8047 (mtt) REVERT: I 112 ASP cc_start: 0.7348 (m-30) cc_final: 0.7132 (m-30) REVERT: J 97 ILE cc_start: 0.7406 (mm) cc_final: 0.6896 (pt) REVERT: J 108 TYR cc_start: 0.6409 (m-10) cc_final: 0.6029 (m-80) REVERT: K 66 PHE cc_start: 0.8556 (m-80) cc_final: 0.8003 (m-80) REVERT: L 396 ILE cc_start: 0.7909 (mm) cc_final: 0.7601 (mt) REVERT: L 539 MET cc_start: 0.7430 (mmm) cc_final: 0.7225 (mmm) REVERT: L 580 GLN cc_start: 0.7360 (mt0) cc_final: 0.6525 (mm-40) REVERT: L 589 MET cc_start: 0.6662 (ttt) cc_final: 0.6348 (ttt) REVERT: M 46 ASP cc_start: 0.6618 (t0) cc_final: 0.6270 (p0) REVERT: M 292 SER cc_start: 0.8025 (t) cc_final: 0.7752 (m) REVERT: M 441 MET cc_start: 0.7175 (mmt) cc_final: 0.6916 (tpp) REVERT: N 12 THR cc_start: 0.9096 (m) cc_final: 0.8731 (p) REVERT: N 117 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7081 (mp0) REVERT: N 173 THR cc_start: 0.8457 (m) cc_final: 0.8212 (p) REVERT: O 2 ARG cc_start: 0.6755 (mmm160) cc_final: 0.5721 (ptt-90) REVERT: O 215 SER cc_start: 0.8319 (m) cc_final: 0.8037 (p) REVERT: O 308 TYR cc_start: 0.7887 (m-80) cc_final: 0.7164 (m-80) REVERT: P 102 ARG cc_start: 0.5674 (mtp-110) cc_final: 0.4607 (mpt180) REVERT: R 4 VAL cc_start: 0.7893 (m) cc_final: 0.7663 (m) REVERT: R 30 ASP cc_start: 0.7269 (t0) cc_final: 0.6858 (t0) REVERT: S 35 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.7391 (t80) REVERT: S 59 GLU cc_start: 0.7156 (tm-30) cc_final: 0.6755 (tm-30) REVERT: T 33 ASN cc_start: 0.7112 (m-40) cc_final: 0.6265 (p0) REVERT: T 72 CYS cc_start: 0.6451 (m) cc_final: 0.6229 (p) REVERT: V 85 LYS cc_start: 0.7510 (mttt) cc_final: 0.7246 (mptt) REVERT: W 91 GLU cc_start: 0.7267 (tp30) cc_final: 0.6980 (tp30) REVERT: Y 16 GLN cc_start: 0.6278 (mt0) cc_final: 0.5852 (mp10) REVERT: Z 120 ILE cc_start: 0.7974 (mt) cc_final: 0.7665 (pt) REVERT: a 29 PHE cc_start: 0.8132 (t80) cc_final: 0.7876 (t80) REVERT: c 30 TYR cc_start: 0.7326 (t80) cc_final: 0.6876 (t80) REVERT: d 1 MET cc_start: 0.8310 (ptt) cc_final: 0.7974 (ptt) REVERT: d 45 ASP cc_start: 0.6876 (t0) cc_final: 0.6525 (t0) REVERT: g 27 ASP cc_start: 0.6996 (m-30) cc_final: 0.6661 (p0) REVERT: h 7 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7532 (mtm-85) REVERT: h 106 LYS cc_start: 0.7389 (mmmt) cc_final: 0.6945 (mttt) REVERT: j 10 ARG cc_start: 0.8013 (mtp85) cc_final: 0.7758 (mmm-85) REVERT: j 58 GLN cc_start: 0.7191 (mm-40) cc_final: 0.6641 (tm-30) REVERT: k 38 GLN cc_start: 0.6081 (mm-40) cc_final: 0.5555 (mt0) REVERT: l 7 MET cc_start: 0.6906 (mmm) cc_final: 0.6669 (tpp) REVERT: l 29 ARG cc_start: 0.7205 (ptm-80) cc_final: 0.6888 (ptm-80) REVERT: l 39 ASP cc_start: 0.6710 (m-30) cc_final: 0.6404 (t0) REVERT: m 15 SER cc_start: 0.6754 (m) cc_final: 0.6432 (t) REVERT: m 61 ASP cc_start: 0.7188 (t0) cc_final: 0.6683 (p0) REVERT: n 8 TYR cc_start: 0.6583 (OUTLIER) cc_final: 0.6271 (m-80) REVERT: n 12 GLN cc_start: 0.6717 (mp10) cc_final: 0.6507 (mp10) REVERT: n 158 ARG cc_start: 0.6242 (mtm180) cc_final: 0.5510 (ttm110) REVERT: p 136 LYS cc_start: 0.7535 (ttpt) cc_final: 0.7288 (tppt) REVERT: q 21 ARG cc_start: 0.7422 (ttt180) cc_final: 0.6089 (tpt170) REVERT: q 72 ASN cc_start: 0.7408 (t0) cc_final: 0.7110 (t0) REVERT: r 5 ARG cc_start: 0.7959 (tpp80) cc_final: 0.7241 (ttp80) outliers start: 81 outliers final: 56 residues processed: 1115 average time/residue: 1.5793 time to fit residues: 2986.5691 Evaluate side-chains 1045 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 987 time to evaluate : 7.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 194 GLU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 147 CYS Chi-restraints excluded: chain L residue 186 MET Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 320 ASN Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain M residue 411 ILE Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain P residue 103 ASN Chi-restraints excluded: chain P residue 231 THR Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain S residue 35 PHE Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain b residue 42 SER Chi-restraints excluded: chain c residue 9 ASN Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain h residue 41 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain n residue 8 TYR Chi-restraints excluded: chain n residue 113 MET Chi-restraints excluded: chain n residue 161 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 718 optimal weight: 10.0000 chunk 546 optimal weight: 0.9980 chunk 377 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 346 optimal weight: 7.9990 chunk 488 optimal weight: 6.9990 chunk 729 optimal weight: 8.9990 chunk 772 optimal weight: 9.9990 chunk 381 optimal weight: 6.9990 chunk 691 optimal weight: 0.3980 chunk 208 optimal weight: 9.9990 overall best weight: 3.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN S 72 GLN n 32 HIS ** q 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.244 68773 Z= 0.558 Angle : 1.577 50.683 93122 Z= 1.021 Chirality : 0.311 6.398 10164 Planarity : 0.005 0.059 11649 Dihedral : 10.567 171.179 10016 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.56 % Allowed : 10.73 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.09), residues: 8076 helix: 0.75 (0.08), residues: 4224 sheet: -1.73 (0.26), residues: 378 loop : -1.22 (0.11), residues: 3474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP g 54 HIS 0.006 0.001 HIS G 101 PHE 0.021 0.001 PHE M 380 TYR 0.020 0.001 TYR M 406 ARG 0.005 0.000 ARG a 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 44 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Evaluate side-chains 1118 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1006 time to evaluate : 7.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8040 (mm110) cc_final: 0.7640 (mm-40) REVERT: B 37 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7207 (tm-30) REVERT: D 75 LYS cc_start: 0.7124 (tppt) cc_final: 0.6784 (tttt) REVERT: D 118 TYR cc_start: 0.8643 (t80) cc_final: 0.8429 (t80) REVERT: E 93 LYS cc_start: 0.8155 (ptmt) cc_final: 0.7747 (mmtt) REVERT: E 175 GLU cc_start: 0.5394 (mt-10) cc_final: 0.4994 (mt-10) REVERT: F 33 LEU cc_start: 0.7821 (tp) cc_final: 0.7365 (tt) REVERT: F 307 ILE cc_start: 0.8210 (mm) cc_final: 0.7544 (mt) REVERT: G 61 LYS cc_start: 0.7477 (mmtp) cc_final: 0.6159 (tptm) REVERT: G 375 ASP cc_start: 0.7162 (m-30) cc_final: 0.6927 (t0) REVERT: G 490 MET cc_start: 0.8327 (tpt) cc_final: 0.7920 (tpt) REVERT: G 659 ASP cc_start: 0.6153 (t70) cc_final: 0.5934 (t0) REVERT: G 679 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7740 (mtm-85) REVERT: H 31 MET cc_start: 0.8269 (mtt) cc_final: 0.8031 (mtt) REVERT: J 97 ILE cc_start: 0.7407 (mm) cc_final: 0.6903 (pt) REVERT: L 396 ILE cc_start: 0.7945 (mm) cc_final: 0.7622 (mt) REVERT: L 539 MET cc_start: 0.7493 (mmm) cc_final: 0.7268 (mmm) REVERT: L 580 GLN cc_start: 0.7359 (mt0) cc_final: 0.6545 (mm-40) REVERT: L 589 MET cc_start: 0.6707 (ttt) cc_final: 0.6348 (ttt) REVERT: M 10 MET cc_start: 0.8022 (mmm) cc_final: 0.7639 (mpp) REVERT: M 292 SER cc_start: 0.7998 (t) cc_final: 0.7704 (m) REVERT: M 441 MET cc_start: 0.7231 (mmt) cc_final: 0.6987 (tpp) REVERT: N 12 THR cc_start: 0.9106 (m) cc_final: 0.8751 (p) REVERT: N 34 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6677 (mm-30) REVERT: N 117 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7137 (mp0) REVERT: N 134 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7462 (tp40) REVERT: O 2 ARG cc_start: 0.6777 (mmm160) cc_final: 0.5742 (ptt-90) REVERT: O 215 SER cc_start: 0.8339 (m) cc_final: 0.8054 (p) REVERT: P 102 ARG cc_start: 0.5707 (mtp-110) cc_final: 0.4620 (mpt180) REVERT: R 4 VAL cc_start: 0.7835 (m) cc_final: 0.7626 (m) REVERT: R 30 ASP cc_start: 0.7339 (t0) cc_final: 0.6939 (t0) REVERT: S 35 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7605 (t80) REVERT: S 59 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6723 (tm-30) REVERT: S 90 MET cc_start: 0.8169 (ttp) cc_final: 0.7854 (ttp) REVERT: T 33 ASN cc_start: 0.7104 (m-40) cc_final: 0.6229 (p0) REVERT: T 46 ASP cc_start: 0.6935 (m-30) cc_final: 0.6354 (m-30) REVERT: T 72 CYS cc_start: 0.6471 (m) cc_final: 0.6211 (p) REVERT: U 78 ASP cc_start: 0.7143 (m-30) cc_final: 0.6888 (t0) REVERT: V 85 LYS cc_start: 0.7607 (mttt) cc_final: 0.7330 (mptt) REVERT: W 91 GLU cc_start: 0.7275 (tp30) cc_final: 0.6888 (tp30) REVERT: Y 16 GLN cc_start: 0.5995 (mt0) cc_final: 0.5637 (mp10) REVERT: Y 60 PHE cc_start: 0.6291 (m-80) cc_final: 0.6071 (t80) REVERT: Z 97 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7296 (mtt) REVERT: Z 120 ILE cc_start: 0.8002 (mt) cc_final: 0.7772 (pt) REVERT: a 29 PHE cc_start: 0.8171 (t80) cc_final: 0.7928 (t80) REVERT: c 30 TYR cc_start: 0.7321 (t80) cc_final: 0.6898 (t80) REVERT: d 1 MET cc_start: 0.8343 (ptt) cc_final: 0.7959 (ptt) REVERT: e 14 ASP cc_start: 0.8197 (p0) cc_final: 0.7963 (p0) REVERT: g 27 ASP cc_start: 0.7238 (m-30) cc_final: 0.6654 (p0) REVERT: h 7 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7586 (mtm-85) REVERT: h 106 LYS cc_start: 0.7552 (mmmt) cc_final: 0.7104 (mttt) REVERT: j 10 ARG cc_start: 0.7994 (mtp85) cc_final: 0.7743 (mmm-85) REVERT: j 24 GLN cc_start: 0.7469 (tt0) cc_final: 0.7235 (tt0) REVERT: j 58 GLN cc_start: 0.7292 (mm-40) cc_final: 0.6711 (tm-30) REVERT: k 38 GLN cc_start: 0.6092 (mm-40) cc_final: 0.5610 (mt0) REVERT: l 7 MET cc_start: 0.6898 (mmm) cc_final: 0.6647 (tpp) REVERT: l 29 ARG cc_start: 0.7186 (ptm-80) cc_final: 0.6803 (ptm-80) REVERT: l 39 ASP cc_start: 0.6836 (m-30) cc_final: 0.6477 (t0) REVERT: l 113 PHE cc_start: 0.7962 (t80) cc_final: 0.7711 (t80) REVERT: m 15 SER cc_start: 0.6748 (m) cc_final: 0.6488 (t) REVERT: m 61 ASP cc_start: 0.7252 (t0) cc_final: 0.6729 (p0) REVERT: n 8 TYR cc_start: 0.6651 (OUTLIER) cc_final: 0.6339 (m-80) REVERT: n 158 ARG cc_start: 0.6240 (mtm180) cc_final: 0.5502 (ttm110) REVERT: p 136 LYS cc_start: 0.7661 (ttpt) cc_final: 0.7374 (tppt) REVERT: q 21 ARG cc_start: 0.7480 (ttt180) cc_final: 0.6272 (tpt170) REVERT: q 72 ASN cc_start: 0.7533 (t0) cc_final: 0.7222 (t0) REVERT: r 5 ARG cc_start: 0.7950 (tpp80) cc_final: 0.7416 (ttp80) outliers start: 112 outliers final: 91 residues processed: 1075 average time/residue: 1.5417 time to fit residues: 2813.0322 Evaluate side-chains 1058 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 964 time to evaluate : 7.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 194 GLU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 147 CYS Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain L residue 186 MET Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 320 ASN Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain M residue 411 ILE Chi-restraints excluded: chain N residue 151 SER Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain P residue 103 ASN Chi-restraints excluded: chain P residue 189 LEU Chi-restraints excluded: chain P residue 231 THR Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain S residue 35 PHE Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain W residue 24 SER Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain X residue 171 VAL Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain Y residue 106 SER Chi-restraints excluded: chain Z residue 50 MET Chi-restraints excluded: chain Z residue 63 ASP Chi-restraints excluded: chain Z residue 97 MET Chi-restraints excluded: chain b residue 42 SER Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain h residue 41 THR Chi-restraints excluded: chain h residue 49 GLU Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain j residue 29 SER Chi-restraints excluded: chain j residue 55 ASP Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain n residue 8 TYR Chi-restraints excluded: chain n residue 30 CYS Chi-restraints excluded: chain n residue 109 SER Chi-restraints excluded: chain n residue 113 MET Chi-restraints excluded: chain o residue 10 TRP Chi-restraints excluded: chain p residue 27 ASN Chi-restraints excluded: chain p residue 83 CYS Chi-restraints excluded: chain p residue 90 GLN Chi-restraints excluded: chain q residue 37 THR Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 15 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 643 optimal weight: 4.9990 chunk 438 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 575 optimal weight: 5.9990 chunk 318 optimal weight: 1.9990 chunk 659 optimal weight: 5.9990 chunk 533 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 394 optimal weight: 8.9990 chunk 693 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN H 230 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 ASN ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 72 GLN V 82 GLN e 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.242 68773 Z= 0.613 Angle : 1.600 50.669 93122 Z= 1.031 Chirality : 0.312 6.418 10164 Planarity : 0.005 0.064 11649 Dihedral : 10.840 171.022 10016 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.29 % Allowed : 11.55 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.09), residues: 8076 helix: 0.61 (0.08), residues: 4227 sheet: -1.82 (0.25), residues: 387 loop : -1.40 (0.11), residues: 3462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP O 318 HIS 0.009 0.001 HIS P 250 PHE 0.031 0.002 PHE B 60 TYR 0.028 0.002 TYR O 129 ARG 0.007 0.001 ARG E 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 44 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Evaluate side-chains 1120 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 956 time to evaluate : 8.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 SER cc_start: 0.8563 (t) cc_final: 0.8298 (m) REVERT: A 108 GLN cc_start: 0.8051 (mm110) cc_final: 0.7715 (mm-40) REVERT: B 37 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7195 (tm-30) REVERT: B 79 MET cc_start: 0.7097 (mmm) cc_final: 0.6858 (mmm) REVERT: B 182 LYS cc_start: 0.7869 (mttt) cc_final: 0.7657 (mttt) REVERT: D 75 LYS cc_start: 0.7118 (tppt) cc_final: 0.6772 (tttt) REVERT: D 228 MET cc_start: 0.8433 (mmm) cc_final: 0.8220 (mmm) REVERT: D 420 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7859 (t) REVERT: E 93 LYS cc_start: 0.8209 (ptmt) cc_final: 0.7739 (mmtt) REVERT: E 175 GLU cc_start: 0.5448 (mt-10) cc_final: 0.5141 (mt-10) REVERT: F 33 LEU cc_start: 0.7845 (tp) cc_final: 0.7409 (tt) REVERT: F 295 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7731 (tt) REVERT: G 27 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8044 (mp) REVERT: G 61 LYS cc_start: 0.7506 (mmtp) cc_final: 0.6124 (tptm) REVERT: G 375 ASP cc_start: 0.7161 (m-30) cc_final: 0.6878 (t0) REVERT: G 379 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8469 (mt) REVERT: G 490 MET cc_start: 0.8372 (tpt) cc_final: 0.7997 (tpt) REVERT: H 31 MET cc_start: 0.8313 (mtt) cc_final: 0.8062 (mtt) REVERT: I 174 ASP cc_start: 0.7707 (t0) cc_final: 0.7406 (t0) REVERT: J 97 ILE cc_start: 0.7459 (mm) cc_final: 0.6945 (pt) REVERT: L 59 MET cc_start: 0.6994 (mmm) cc_final: 0.6627 (mmm) REVERT: L 226 GLN cc_start: 0.6829 (mm-40) cc_final: 0.6532 (mp10) REVERT: L 387 THR cc_start: 0.7063 (OUTLIER) cc_final: 0.6652 (t) REVERT: L 396 ILE cc_start: 0.8018 (mm) cc_final: 0.7701 (mt) REVERT: L 545 SER cc_start: 0.8802 (m) cc_final: 0.8580 (t) REVERT: L 589 MET cc_start: 0.6786 (ttt) cc_final: 0.6351 (ttt) REVERT: M 10 MET cc_start: 0.7996 (mmm) cc_final: 0.7616 (mpp) REVERT: M 292 SER cc_start: 0.7943 (t) cc_final: 0.7620 (m) REVERT: M 441 MET cc_start: 0.7264 (mmt) cc_final: 0.7001 (tpp) REVERT: N 117 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7129 (mp0) REVERT: N 134 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7471 (tp40) REVERT: O 2 ARG cc_start: 0.6889 (mmm160) cc_final: 0.5839 (ppt170) REVERT: O 215 SER cc_start: 0.8359 (m) cc_final: 0.8102 (p) REVERT: P 102 ARG cc_start: 0.5891 (mtp-110) cc_final: 0.4723 (mpt180) REVERT: R 30 ASP cc_start: 0.7353 (t0) cc_final: 0.6946 (t0) REVERT: S 24 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.6341 (mp10) REVERT: S 35 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7787 (t80) REVERT: T 33 ASN cc_start: 0.6934 (m-40) cc_final: 0.6035 (p0) REVERT: U 78 ASP cc_start: 0.7123 (m-30) cc_final: 0.6867 (t0) REVERT: V 85 LYS cc_start: 0.7587 (mttt) cc_final: 0.7317 (mptt) REVERT: W 91 GLU cc_start: 0.7304 (tp30) cc_final: 0.6797 (tp30) REVERT: Y 16 GLN cc_start: 0.6053 (mt0) cc_final: 0.5676 (mp10) REVERT: Y 60 PHE cc_start: 0.6331 (m-80) cc_final: 0.6087 (t80) REVERT: Z 97 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7359 (mtt) REVERT: Z 120 ILE cc_start: 0.7994 (mt) cc_final: 0.7685 (pt) REVERT: a 51 ASP cc_start: 0.7199 (t0) cc_final: 0.6887 (t0) REVERT: c 30 TYR cc_start: 0.7368 (t80) cc_final: 0.6974 (t80) REVERT: d 1 MET cc_start: 0.8330 (ptt) cc_final: 0.7966 (ptt) REVERT: e 14 ASP cc_start: 0.8171 (p0) cc_final: 0.7947 (p0) REVERT: f 30 ASP cc_start: 0.7605 (m-30) cc_final: 0.7186 (m-30) REVERT: h 7 ARG cc_start: 0.7922 (mtm-85) cc_final: 0.7610 (mtm-85) REVERT: h 106 LYS cc_start: 0.7546 (mmmt) cc_final: 0.7010 (mttt) REVERT: j 10 ARG cc_start: 0.8067 (mtp85) cc_final: 0.7773 (mmm-85) REVERT: j 55 ASP cc_start: 0.7284 (OUTLIER) cc_final: 0.6925 (t0) REVERT: j 58 GLN cc_start: 0.7421 (mm-40) cc_final: 0.6761 (tm-30) REVERT: k 38 GLN cc_start: 0.6121 (mm-40) cc_final: 0.5658 (mt0) REVERT: l 39 ASP cc_start: 0.6786 (m-30) cc_final: 0.6479 (t0) REVERT: m 15 SER cc_start: 0.6682 (m) cc_final: 0.6443 (t) REVERT: m 128 TYR cc_start: 0.7266 (p90) cc_final: 0.7022 (p90) REVERT: n 8 TYR cc_start: 0.6767 (OUTLIER) cc_final: 0.6429 (m-80) REVERT: n 42 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6990 (tt) REVERT: n 158 ARG cc_start: 0.6159 (mtm180) cc_final: 0.5429 (ttm110) REVERT: p 136 LYS cc_start: 0.7622 (ttpt) cc_final: 0.7360 (tppt) REVERT: q 21 ARG cc_start: 0.7561 (ttt180) cc_final: 0.6368 (tpt170) REVERT: q 72 ASN cc_start: 0.7771 (t0) cc_final: 0.7410 (t0) REVERT: r 5 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7481 (ttp80) outliers start: 164 outliers final: 118 residues processed: 1072 average time/residue: 1.5400 time to fit residues: 2819.1715 Evaluate side-chains 1049 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 920 time to evaluate : 6.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 194 GLU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 52 CYS Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain I residue 36 LEU 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 24 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 147 CYS Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 186 MET Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 320 ASN Chi-restraints excluded: chain L residue 387 THR Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 201 MET Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain M residue 411 ILE Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 151 SER Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain P residue 103 ASN Chi-restraints excluded: chain P residue 189 LEU Chi-restraints excluded: chain P residue 231 THR Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain S residue 24 GLN Chi-restraints excluded: chain S residue 35 PHE Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain W residue 24 SER Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain X residue 171 VAL Chi-restraints excluded: chain Y residue 13 ASP Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 106 SER Chi-restraints excluded: chain Z residue 63 ASP Chi-restraints excluded: chain Z residue 97 MET Chi-restraints excluded: chain b residue 42 SER Chi-restraints excluded: chain b residue 48 THR Chi-restraints excluded: chain c residue 9 ASN Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain h residue 41 THR Chi-restraints excluded: chain h residue 49 GLU Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain j residue 29 SER Chi-restraints excluded: chain j residue 55 ASP Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain k residue 48 ASP Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain n residue 8 TYR Chi-restraints excluded: chain n residue 30 CYS Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain n residue 109 SER Chi-restraints excluded: chain n residue 113 MET Chi-restraints excluded: chain o residue 10 TRP Chi-restraints excluded: chain p residue 27 ASN Chi-restraints excluded: chain p residue 83 CYS Chi-restraints excluded: chain p residue 90 GLN Chi-restraints excluded: chain q residue 37 THR Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 15 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 259 optimal weight: 0.9980 chunk 695 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 453 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 773 optimal weight: 5.9990 chunk 641 optimal weight: 5.9990 chunk 357 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 chunk 405 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 580 GLN ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.242 68773 Z= 0.571 Angle : 1.584 50.667 93122 Z= 1.024 Chirality : 0.312 6.408 10164 Planarity : 0.005 0.065 11649 Dihedral : 10.682 169.297 10016 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.05 % Allowed : 12.87 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.09), residues: 8076 helix: 0.68 (0.08), residues: 4244 sheet: -1.83 (0.26), residues: 367 loop : -1.37 (0.11), residues: 3465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP O 318 HIS 0.011 0.001 HIS H 93 PHE 0.020 0.002 PHE H 310 TYR 0.022 0.002 TYR O 129 ARG 0.005 0.000 ARG E 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 44 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Evaluate side-chains 1102 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 955 time to evaluate : 7.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 SER cc_start: 0.8487 (t) cc_final: 0.8256 (m) REVERT: A 108 GLN cc_start: 0.8072 (mm110) cc_final: 0.7729 (mm-40) REVERT: B 37 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7196 (tm-30) REVERT: B 79 MET cc_start: 0.7099 (mmm) cc_final: 0.6839 (mmm) REVERT: D 75 LYS cc_start: 0.7108 (tppt) cc_final: 0.6712 (tptt) REVERT: E 93 LYS cc_start: 0.8212 (ptmt) cc_final: 0.7736 (mmtt) REVERT: E 175 GLU cc_start: 0.5457 (mt-10) cc_final: 0.5145 (mt-10) REVERT: F 33 LEU cc_start: 0.7872 (tp) cc_final: 0.7442 (tt) REVERT: F 295 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7737 (tt) REVERT: G 27 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8014 (mp) REVERT: G 61 LYS cc_start: 0.7622 (mmtp) cc_final: 0.6235 (tptm) REVERT: G 375 ASP cc_start: 0.7225 (m-30) cc_final: 0.6902 (t0) REVERT: G 379 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8400 (mt) REVERT: G 490 MET cc_start: 0.8376 (tpt) cc_final: 0.7937 (tpt) REVERT: H 31 MET cc_start: 0.8317 (mtt) cc_final: 0.8063 (mtt) REVERT: J 97 ILE cc_start: 0.7450 (mm) cc_final: 0.6927 (pt) REVERT: L 53 MET cc_start: 0.7674 (ttm) cc_final: 0.7203 (mtp) REVERT: L 226 GLN cc_start: 0.6814 (mm-40) cc_final: 0.6582 (mp10) REVERT: L 387 THR cc_start: 0.7017 (OUTLIER) cc_final: 0.6588 (t) REVERT: L 396 ILE cc_start: 0.8042 (mm) cc_final: 0.7692 (mt) REVERT: L 539 MET cc_start: 0.7407 (mmm) cc_final: 0.7185 (mmm) REVERT: L 589 MET cc_start: 0.6754 (ttt) cc_final: 0.6301 (ttt) REVERT: M 292 SER cc_start: 0.7933 (t) cc_final: 0.7621 (m) REVERT: M 441 MET cc_start: 0.7268 (mmt) cc_final: 0.7013 (tpp) REVERT: N 117 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7088 (mp0) REVERT: N 134 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7467 (tp40) REVERT: O 2 ARG cc_start: 0.6900 (mmm160) cc_final: 0.5828 (ptt-90) REVERT: O 318 TRP cc_start: 0.7923 (p-90) cc_final: 0.7531 (p-90) REVERT: P 102 ARG cc_start: 0.5911 (mtp-110) cc_final: 0.4715 (mpt180) REVERT: R 30 ASP cc_start: 0.7417 (t0) cc_final: 0.6990 (t0) REVERT: S 24 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6579 (mp10) REVERT: S 35 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.7734 (t80) REVERT: T 33 ASN cc_start: 0.6886 (m-40) cc_final: 0.6003 (p0) REVERT: V 85 LYS cc_start: 0.7624 (mttt) cc_final: 0.7356 (mptt) REVERT: W 91 GLU cc_start: 0.7207 (tp30) cc_final: 0.6747 (tp30) REVERT: Y 16 GLN cc_start: 0.6053 (mt0) cc_final: 0.5678 (mp10) REVERT: Y 60 PHE cc_start: 0.6388 (m-80) cc_final: 0.6017 (t80) REVERT: Z 97 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7344 (mtt) REVERT: Z 120 ILE cc_start: 0.8089 (mt) cc_final: 0.7799 (pt) REVERT: a 51 ASP cc_start: 0.7141 (t0) cc_final: 0.6771 (t0) REVERT: c 30 TYR cc_start: 0.7349 (t80) cc_final: 0.6957 (t80) REVERT: d 1 MET cc_start: 0.8314 (ptt) cc_final: 0.7994 (ptt) REVERT: f 30 ASP cc_start: 0.7646 (m-30) cc_final: 0.7258 (m-30) REVERT: h 7 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7641 (mtm-85) REVERT: h 106 LYS cc_start: 0.7532 (mmmt) cc_final: 0.7007 (mttt) REVERT: j 10 ARG cc_start: 0.8042 (mtp85) cc_final: 0.7731 (mmm-85) REVERT: j 55 ASP cc_start: 0.7289 (m-30) cc_final: 0.6924 (t0) REVERT: j 58 GLN cc_start: 0.7493 (mm-40) cc_final: 0.6715 (tm-30) REVERT: k 38 GLN cc_start: 0.6119 (mm-40) cc_final: 0.5691 (mt0) REVERT: l 39 ASP cc_start: 0.6746 (m-30) cc_final: 0.6433 (t0) REVERT: m 15 SER cc_start: 0.6717 (m) cc_final: 0.6475 (t) REVERT: m 128 TYR cc_start: 0.7358 (p90) cc_final: 0.7125 (p90) REVERT: n 8 TYR cc_start: 0.6734 (OUTLIER) cc_final: 0.6460 (m-80) REVERT: n 42 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6990 (tt) REVERT: n 120 LYS cc_start: 0.7519 (ttmt) cc_final: 0.7292 (ttmt) REVERT: n 158 ARG cc_start: 0.6155 (mtm180) cc_final: 0.5398 (ttm110) REVERT: p 136 LYS cc_start: 0.7709 (ttpt) cc_final: 0.7384 (tppt) REVERT: q 21 ARG cc_start: 0.7566 (ttt180) cc_final: 0.6375 (tpt170) REVERT: q 72 ASN cc_start: 0.7837 (t0) cc_final: 0.7433 (t0) REVERT: r 5 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7533 (ttp80) outliers start: 147 outliers final: 110 residues processed: 1056 average time/residue: 1.4792 time to fit residues: 2645.2697 Evaluate side-chains 1035 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 916 time to evaluate : 7.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 194 GLU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 357 ASP Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 479 VAL Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 147 CYS Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 186 MET Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain L residue 320 ASN Chi-restraints excluded: chain L residue 387 THR Chi-restraints excluded: chain L residue 526 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 201 MET Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain M residue 411 ILE Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 151 SER Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain P residue 103 ASN Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 231 THR Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain S residue 24 GLN Chi-restraints excluded: chain S residue 35 PHE Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain W residue 24 SER Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain X residue 171 VAL Chi-restraints excluded: chain Y residue 13 ASP Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain Y residue 106 SER Chi-restraints excluded: chain Z residue 63 ASP Chi-restraints excluded: chain Z residue 97 MET Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain b residue 42 SER Chi-restraints excluded: chain b residue 48 THR Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain h residue 41 THR Chi-restraints excluded: chain h residue 49 GLU Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain j residue 29 SER Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain n residue 8 TYR Chi-restraints excluded: chain n residue 30 CYS Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain o residue 10 TRP Chi-restraints excluded: chain p residue 90 GLN Chi-restraints excluded: chain p residue 142 TYR Chi-restraints excluded: chain q residue 37 THR Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain s residue 42 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 745 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 440 optimal weight: 7.9990 chunk 564 optimal weight: 0.8980 chunk 437 optimal weight: 2.9990 chunk 650 optimal weight: 4.9990 chunk 431 optimal weight: 0.9990 chunk 770 optimal weight: 5.9990 chunk 481 optimal weight: 0.6980 chunk 469 optimal weight: 5.9990 chunk 355 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 HIS ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 GLN ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 580 GLN ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 68773 Z= 0.515 Angle : 1.562 50.624 93122 Z= 1.014 Chirality : 0.310 6.374 10164 Planarity : 0.004 0.063 11649 Dihedral : 10.195 169.922 10016 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.46 % Allowed : 13.78 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.10), residues: 8076 helix: 1.04 (0.08), residues: 4224 sheet: -1.72 (0.26), residues: 367 loop : -1.21 (0.11), residues: 3485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 318 HIS 0.007 0.001 HIS H 93 PHE 0.018 0.001 PHE B 60 TYR 0.021 0.001 TYR L 422 ARG 0.005 0.000 ARG a 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 44 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Evaluate side-chains 1078 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 973 time to evaluate : 7.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.6880 (tmm) cc_final: 0.6630 (tmm) REVERT: A 108 GLN cc_start: 0.8059 (mm110) cc_final: 0.7706 (mm-40) REVERT: B 37 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7139 (tm-30) REVERT: B 79 MET cc_start: 0.7098 (mmm) cc_final: 0.6802 (mmm) REVERT: C 133 GLU cc_start: 0.7518 (tt0) cc_final: 0.7126 (tt0) REVERT: D 75 LYS cc_start: 0.7019 (tppt) cc_final: 0.6667 (tptt) REVERT: D 182 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7769 (tm-30) REVERT: E 93 LYS cc_start: 0.8189 (ptmt) cc_final: 0.7735 (mmtt) REVERT: E 175 GLU cc_start: 0.5464 (mt-10) cc_final: 0.5138 (mt-10) REVERT: F 33 LEU cc_start: 0.7817 (tp) cc_final: 0.7401 (tt) REVERT: F 295 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7586 (tt) REVERT: G 27 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7935 (mp) REVERT: G 61 LYS cc_start: 0.7572 (mmtp) cc_final: 0.6206 (tptm) REVERT: G 375 ASP cc_start: 0.7202 (m-30) cc_final: 0.6880 (t0) REVERT: G 379 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8362 (mt) REVERT: H 31 MET cc_start: 0.8265 (mtt) cc_final: 0.8014 (mtt) REVERT: J 97 ILE cc_start: 0.7418 (mm) cc_final: 0.6883 (pt) REVERT: L 53 MET cc_start: 0.7593 (ttm) cc_final: 0.7143 (mtp) REVERT: L 59 MET cc_start: 0.6928 (mmm) cc_final: 0.6614 (mmm) REVERT: L 387 THR cc_start: 0.7039 (OUTLIER) cc_final: 0.6612 (t) REVERT: L 396 ILE cc_start: 0.8052 (mm) cc_final: 0.7725 (mt) REVERT: L 539 MET cc_start: 0.7386 (mmm) cc_final: 0.7155 (mmm) REVERT: L 589 MET cc_start: 0.6651 (ttt) cc_final: 0.6198 (ttt) REVERT: M 212 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7809 (m) REVERT: M 292 SER cc_start: 0.8005 (t) cc_final: 0.7709 (m) REVERT: M 441 MET cc_start: 0.7240 (mmt) cc_final: 0.6994 (tpp) REVERT: N 12 THR cc_start: 0.9083 (m) cc_final: 0.8725 (p) REVERT: N 34 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6642 (mm-30) REVERT: N 117 GLU cc_start: 0.7412 (mm-30) cc_final: 0.6973 (mp0) REVERT: N 134 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7446 (tp40) REVERT: O 2 ARG cc_start: 0.6889 (mmm160) cc_final: 0.5801 (ptt-90) REVERT: P 102 ARG cc_start: 0.5908 (mtp-110) cc_final: 0.4716 (mpt180) REVERT: R 30 ASP cc_start: 0.7386 (t0) cc_final: 0.6957 (t0) REVERT: R 77 LYS cc_start: 0.7248 (mmmt) cc_final: 0.6894 (tptp) REVERT: S 24 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.6672 (mp10) REVERT: S 35 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7901 (t80) REVERT: T 33 ASN cc_start: 0.6791 (m-40) cc_final: 0.5914 (p0) REVERT: T 46 ASP cc_start: 0.6872 (m-30) cc_final: 0.6230 (m-30) REVERT: V 85 LYS cc_start: 0.7645 (mttt) cc_final: 0.7373 (mptt) REVERT: W 91 GLU cc_start: 0.7176 (tp30) cc_final: 0.6745 (tp30) REVERT: Y 16 GLN cc_start: 0.5850 (mt0) cc_final: 0.5507 (mp10) REVERT: Y 60 PHE cc_start: 0.6378 (m-80) cc_final: 0.6029 (t80) REVERT: Z 97 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7279 (mtt) REVERT: Z 120 ILE cc_start: 0.7998 (mt) cc_final: 0.7735 (pt) REVERT: a 51 ASP cc_start: 0.7175 (t0) cc_final: 0.6848 (t0) REVERT: c 30 TYR cc_start: 0.7321 (t80) cc_final: 0.6930 (t80) REVERT: d 1 MET cc_start: 0.8336 (ptt) cc_final: 0.7974 (ptt) REVERT: f 30 ASP cc_start: 0.7536 (m-30) cc_final: 0.7124 (m-30) REVERT: h 7 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7583 (mtm-85) REVERT: h 106 LYS cc_start: 0.7698 (mmmt) cc_final: 0.7151 (mttt) REVERT: j 10 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7754 (mmm-85) REVERT: j 58 GLN cc_start: 0.7391 (mm-40) cc_final: 0.6667 (tm-30) REVERT: k 38 GLN cc_start: 0.6118 (mm-40) cc_final: 0.5688 (mt0) REVERT: m 15 SER cc_start: 0.6762 (m) cc_final: 0.6458 (t) REVERT: m 122 ARG cc_start: 0.7011 (mtm180) cc_final: 0.6794 (ptp-170) REVERT: n 8 TYR cc_start: 0.6575 (OUTLIER) cc_final: 0.6350 (m-80) REVERT: n 42 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.6990 (tt) REVERT: n 56 MET cc_start: 0.6463 (mmt) cc_final: 0.5829 (mtt) REVERT: n 120 LYS cc_start: 0.7524 (ttmt) cc_final: 0.7303 (ttmt) REVERT: n 158 ARG cc_start: 0.6103 (mtm180) cc_final: 0.5350 (ttm110) REVERT: p 136 LYS cc_start: 0.7653 (ttpt) cc_final: 0.7305 (tppt) REVERT: q 21 ARG cc_start: 0.7511 (ttt180) cc_final: 0.6305 (tpt170) REVERT: q 72 ASN cc_start: 0.7755 (t0) cc_final: 0.7347 (t0) REVERT: r 5 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7493 (ttp80) outliers start: 105 outliers final: 79 residues processed: 1049 average time/residue: 1.4958 time to fit residues: 2651.7995 Evaluate side-chains 1024 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 935 time to evaluate : 7.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 52 CYS Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 147 CYS Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 320 ASN Chi-restraints excluded: chain L residue 387 THR Chi-restraints excluded: chain L residue 526 LEU Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 201 MET Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain M residue 411 ILE Chi-restraints excluded: chain N residue 151 SER Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 57 GLN Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain P residue 103 ASN Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 231 THR Chi-restraints excluded: chain S residue 24 GLN Chi-restraints excluded: chain S residue 35 PHE Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain X residue 171 VAL Chi-restraints excluded: chain Y residue 13 ASP Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain Z residue 97 MET Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain b residue 48 THR Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 86 MET Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain h residue 41 THR Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain n residue 8 TYR Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain o residue 27 ASP Chi-restraints excluded: chain p residue 142 TYR Chi-restraints excluded: chain q residue 37 THR Chi-restraints excluded: chain s residue 42 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 476 optimal weight: 3.9990 chunk 307 optimal weight: 6.9990 chunk 459 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 489 optimal weight: 4.9990 chunk 524 optimal weight: 10.0000 chunk 380 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 605 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 580 GLN ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.243 68773 Z= 0.547 Angle : 1.571 50.649 93122 Z= 1.018 Chirality : 0.311 6.384 10164 Planarity : 0.004 0.061 11649 Dihedral : 10.187 167.574 10016 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.70 % Allowed : 13.93 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.10), residues: 8076 helix: 1.05 (0.08), residues: 4229 sheet: -1.71 (0.26), residues: 367 loop : -1.24 (0.11), residues: 3480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP g 24 HIS 0.007 0.001 HIS H 93 PHE 0.048 0.001 PHE B 60 TYR 0.038 0.001 TYR H 282 ARG 0.006 0.000 ARG a 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 44 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Evaluate side-chains 1049 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 927 time to evaluate : 7.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.6939 (tmm) cc_final: 0.6677 (tmm) REVERT: A 108 GLN cc_start: 0.8067 (mm110) cc_final: 0.7658 (mm-40) REVERT: B 37 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7190 (tm-30) REVERT: C 133 GLU cc_start: 0.7531 (tt0) cc_final: 0.7144 (tt0) REVERT: D 75 LYS cc_start: 0.7064 (tppt) cc_final: 0.6702 (tptt) REVERT: D 182 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7785 (tm-30) REVERT: E 175 GLU cc_start: 0.5441 (mt-10) cc_final: 0.5129 (mt-10) REVERT: F 33 LEU cc_start: 0.7849 (tp) cc_final: 0.7431 (tt) REVERT: F 295 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7593 (tt) REVERT: G 27 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7978 (mp) REVERT: G 61 LYS cc_start: 0.7558 (mmtp) cc_final: 0.6197 (tptm) REVERT: G 375 ASP cc_start: 0.7216 (m-30) cc_final: 0.6888 (t0) REVERT: G 379 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8380 (mt) REVERT: H 31 MET cc_start: 0.8297 (mtt) cc_final: 0.8047 (mtt) REVERT: J 97 ILE cc_start: 0.7349 (mm) cc_final: 0.6825 (pt) REVERT: K 66 PHE cc_start: 0.8484 (m-80) cc_final: 0.7898 (m-80) REVERT: L 53 MET cc_start: 0.7602 (ttm) cc_final: 0.7178 (mtp) REVERT: L 387 THR cc_start: 0.7037 (OUTLIER) cc_final: 0.6595 (t) REVERT: L 396 ILE cc_start: 0.8045 (mm) cc_final: 0.7738 (mt) REVERT: L 482 MET cc_start: 0.8131 (ptt) cc_final: 0.7915 (ptt) REVERT: L 545 SER cc_start: 0.8773 (OUTLIER) cc_final: 0.8558 (t) REVERT: L 589 MET cc_start: 0.6683 (ttt) cc_final: 0.6206 (ttt) REVERT: M 292 SER cc_start: 0.8021 (t) cc_final: 0.7718 (m) REVERT: M 441 MET cc_start: 0.7244 (mmt) cc_final: 0.7000 (tpp) REVERT: N 117 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6951 (mp0) REVERT: N 134 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7449 (tp40) REVERT: O 2 ARG cc_start: 0.6906 (mmm160) cc_final: 0.5797 (ptt-90) REVERT: P 102 ARG cc_start: 0.5924 (mtp-110) cc_final: 0.4726 (mpt180) REVERT: R 30 ASP cc_start: 0.7410 (t0) cc_final: 0.6981 (t0) REVERT: R 77 LYS cc_start: 0.7271 (mmmt) cc_final: 0.6896 (tptp) REVERT: S 24 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7215 (mt0) REVERT: S 35 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7942 (t80) REVERT: T 20 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6833 (pptt) REVERT: T 33 ASN cc_start: 0.6840 (m-40) cc_final: 0.5967 (p0) REVERT: T 46 ASP cc_start: 0.6888 (m-30) cc_final: 0.6207 (m-30) REVERT: V 85 LYS cc_start: 0.7601 (mttt) cc_final: 0.7333 (mptt) REVERT: W 91 GLU cc_start: 0.7158 (tp30) cc_final: 0.6681 (tp30) REVERT: Y 16 GLN cc_start: 0.5874 (mt0) cc_final: 0.5531 (mp10) REVERT: Y 60 PHE cc_start: 0.6364 (m-80) cc_final: 0.6008 (t80) REVERT: Z 97 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7298 (mtt) REVERT: Z 120 ILE cc_start: 0.8069 (mt) cc_final: 0.7803 (pt) REVERT: a 51 ASP cc_start: 0.7179 (t0) cc_final: 0.6848 (t0) REVERT: c 30 TYR cc_start: 0.7334 (t80) cc_final: 0.6926 (t80) REVERT: d 1 MET cc_start: 0.8349 (ptt) cc_final: 0.7989 (ptt) REVERT: e 14 ASP cc_start: 0.8304 (p0) cc_final: 0.8036 (p0) REVERT: f 30 ASP cc_start: 0.7524 (m-30) cc_final: 0.7120 (m-30) REVERT: h 7 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7550 (mtm-85) REVERT: h 106 LYS cc_start: 0.7677 (mmmt) cc_final: 0.7108 (mttt) REVERT: j 10 ARG cc_start: 0.8015 (mtp85) cc_final: 0.7732 (mmm-85) REVERT: j 55 ASP cc_start: 0.7339 (m-30) cc_final: 0.6982 (t0) REVERT: j 58 GLN cc_start: 0.7410 (mm-40) cc_final: 0.6655 (tm-30) REVERT: k 38 GLN cc_start: 0.6179 (mm-40) cc_final: 0.5738 (mt0) REVERT: l 39 ASP cc_start: 0.6693 (m-30) cc_final: 0.6445 (t0) REVERT: l 41 MET cc_start: 0.6823 (mpp) cc_final: 0.6337 (mpp) REVERT: m 15 SER cc_start: 0.6756 (m) cc_final: 0.6487 (t) REVERT: m 122 ARG cc_start: 0.7069 (mtm180) cc_final: 0.6837 (ptp-170) REVERT: n 8 TYR cc_start: 0.6590 (OUTLIER) cc_final: 0.6332 (m-80) REVERT: n 42 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6970 (tt) REVERT: n 56 MET cc_start: 0.6503 (mmt) cc_final: 0.5892 (mtt) REVERT: n 120 LYS cc_start: 0.7549 (ttmt) cc_final: 0.7323 (ttmt) REVERT: n 158 ARG cc_start: 0.6158 (mtm180) cc_final: 0.5384 (ttm110) REVERT: p 136 LYS cc_start: 0.7651 (ttpt) cc_final: 0.7322 (tppt) REVERT: q 21 ARG cc_start: 0.7550 (ttt180) cc_final: 0.6371 (tpt170) REVERT: q 41 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7602 (mt-10) REVERT: q 72 ASN cc_start: 0.7806 (t0) cc_final: 0.7396 (t0) REVERT: r 5 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7481 (ttp80) outliers start: 122 outliers final: 92 residues processed: 1012 average time/residue: 1.5009 time to fit residues: 2571.1381 Evaluate side-chains 1020 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 917 time to evaluate : 7.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 52 CYS Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 636 ILE Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 36 LEU 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 24 SER Chi-restraints excluded: chain J residue 40 CYS Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 147 CYS Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain L residue 320 ASN Chi-restraints excluded: chain L residue 387 THR Chi-restraints excluded: chain L residue 526 LEU Chi-restraints excluded: chain L residue 545 SER Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 201 MET Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain M residue 411 ILE Chi-restraints excluded: chain N residue 151 SER Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain O residue 57 GLN Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain P residue 103 ASN Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 189 LEU Chi-restraints excluded: chain P residue 231 THR Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain S residue 24 GLN Chi-restraints excluded: chain S residue 35 PHE Chi-restraints excluded: chain T residue 20 LYS Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain W residue 24 SER Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain X residue 171 VAL Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain Z residue 63 ASP Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 97 MET Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain b residue 42 SER Chi-restraints excluded: chain b residue 48 THR Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain h residue 41 THR Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain n residue 8 TYR Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain o residue 10 TRP Chi-restraints excluded: chain p residue 142 TYR Chi-restraints excluded: chain q residue 37 THR Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain s residue 42 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 700 optimal weight: 7.9990 chunk 737 optimal weight: 8.9990 chunk 673 optimal weight: 4.9990 chunk 717 optimal weight: 0.7980 chunk 431 optimal weight: 0.3980 chunk 312 optimal weight: 5.9990 chunk 563 optimal weight: 10.0000 chunk 220 optimal weight: 7.9990 chunk 648 optimal weight: 5.9990 chunk 678 optimal weight: 10.0000 chunk 715 optimal weight: 6.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 580 GLN ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 274 ASN p 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.243 68773 Z= 0.559 Angle : 1.576 50.648 93122 Z= 1.020 Chirality : 0.311 6.393 10164 Planarity : 0.005 0.062 11649 Dihedral : 10.237 166.480 10016 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.74 % Allowed : 14.07 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.10), residues: 8076 helix: 1.02 (0.08), residues: 4220 sheet: -1.70 (0.26), residues: 367 loop : -1.28 (0.11), residues: 3489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP g 24 HIS 0.008 0.001 HIS H 93 PHE 0.044 0.002 PHE B 60 TYR 0.024 0.002 TYR H 282 ARG 0.007 0.000 ARG a 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 44 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Evaluate side-chains 1044 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 919 time to evaluate : 7.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.6990 (tmm) cc_final: 0.6754 (tmm) REVERT: A 108 GLN cc_start: 0.8067 (mm110) cc_final: 0.7659 (mm-40) REVERT: B 37 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7187 (tm-30) REVERT: B 72 MET cc_start: 0.8041 (ttp) cc_final: 0.7837 (ttp) REVERT: B 79 MET cc_start: 0.7009 (mmm) cc_final: 0.6694 (mmm) REVERT: C 133 GLU cc_start: 0.7536 (tt0) cc_final: 0.7151 (tt0) REVERT: D 75 LYS cc_start: 0.7064 (tppt) cc_final: 0.6777 (tttt) REVERT: E 175 GLU cc_start: 0.5441 (mt-10) cc_final: 0.5153 (mt-10) REVERT: F 33 LEU cc_start: 0.7867 (tp) cc_final: 0.7447 (tt) REVERT: F 295 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7712 (tt) REVERT: G 27 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8014 (mp) REVERT: G 61 LYS cc_start: 0.7613 (mmtp) cc_final: 0.6235 (tptm) REVERT: G 375 ASP cc_start: 0.7223 (m-30) cc_final: 0.6950 (t0) REVERT: G 379 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8375 (mt) REVERT: G 490 MET cc_start: 0.8367 (tpt) cc_final: 0.7896 (tpt) REVERT: H 31 MET cc_start: 0.8298 (mtt) cc_final: 0.8041 (mtt) REVERT: H 230 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8102 (m-40) REVERT: J 97 ILE cc_start: 0.7319 (mm) cc_final: 0.6793 (pt) REVERT: L 53 MET cc_start: 0.7658 (ttm) cc_final: 0.7198 (mtp) REVERT: L 59 MET cc_start: 0.7033 (mmm) cc_final: 0.6806 (mmm) REVERT: L 387 THR cc_start: 0.7011 (OUTLIER) cc_final: 0.6590 (t) REVERT: L 396 ILE cc_start: 0.8053 (mm) cc_final: 0.7724 (mt) REVERT: L 539 MET cc_start: 0.7427 (mmm) cc_final: 0.7152 (mmm) REVERT: L 545 SER cc_start: 0.8795 (OUTLIER) cc_final: 0.8593 (t) REVERT: L 589 MET cc_start: 0.6701 (ttt) cc_final: 0.6220 (ttt) REVERT: M 441 MET cc_start: 0.7205 (mmt) cc_final: 0.6962 (tpp) REVERT: N 117 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7009 (mp0) REVERT: N 134 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7446 (tp40) REVERT: O 2 ARG cc_start: 0.6952 (mmm160) cc_final: 0.5831 (ptt-90) REVERT: R 30 ASP cc_start: 0.7333 (t0) cc_final: 0.6931 (t0) REVERT: R 53 GLU cc_start: 0.7298 (tm-30) cc_final: 0.7086 (tm-30) REVERT: R 77 LYS cc_start: 0.7288 (mmmt) cc_final: 0.6908 (tptp) REVERT: S 24 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7215 (mt0) REVERT: S 35 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7858 (t80) REVERT: T 20 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6752 (pptt) REVERT: T 33 ASN cc_start: 0.6841 (m-40) cc_final: 0.5968 (p0) REVERT: T 46 ASP cc_start: 0.6816 (m-30) cc_final: 0.6135 (m-30) REVERT: V 85 LYS cc_start: 0.7605 (mttt) cc_final: 0.7343 (mptt) REVERT: W 91 GLU cc_start: 0.7186 (tp30) cc_final: 0.6687 (tp30) REVERT: Y 16 GLN cc_start: 0.5878 (mt0) cc_final: 0.5534 (mp10) REVERT: Y 60 PHE cc_start: 0.6345 (m-80) cc_final: 0.6024 (t80) REVERT: Z 97 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7280 (mtt) REVERT: Z 120 ILE cc_start: 0.8079 (mt) cc_final: 0.7812 (pt) REVERT: a 51 ASP cc_start: 0.7212 (t0) cc_final: 0.6844 (t0) REVERT: c 30 TYR cc_start: 0.7358 (t80) cc_final: 0.6937 (t80) REVERT: d 1 MET cc_start: 0.8342 (ptt) cc_final: 0.7973 (ptt) REVERT: f 30 ASP cc_start: 0.7622 (m-30) cc_final: 0.7206 (m-30) REVERT: h 7 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7599 (mtm-85) REVERT: h 37 ILE cc_start: 0.8498 (mt) cc_final: 0.8246 (tt) REVERT: h 106 LYS cc_start: 0.7808 (mmmt) cc_final: 0.7213 (mttt) REVERT: j 10 ARG cc_start: 0.8025 (mtp85) cc_final: 0.7733 (mmm-85) REVERT: j 55 ASP cc_start: 0.7337 (m-30) cc_final: 0.6992 (t0) REVERT: j 58 GLN cc_start: 0.7547 (mm-40) cc_final: 0.6708 (tm-30) REVERT: k 38 GLN cc_start: 0.6192 (mm-40) cc_final: 0.5745 (mt0) REVERT: l 41 MET cc_start: 0.6892 (mpp) cc_final: 0.6512 (mpp) REVERT: m 15 SER cc_start: 0.6715 (m) cc_final: 0.6451 (t) REVERT: n 42 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6963 (tt) REVERT: n 56 MET cc_start: 0.6529 (mmt) cc_final: 0.5934 (mtt) REVERT: n 158 ARG cc_start: 0.6128 (mtm180) cc_final: 0.5353 (ttm110) REVERT: p 136 LYS cc_start: 0.7678 (ttpt) cc_final: 0.7415 (tppt) REVERT: q 21 ARG cc_start: 0.7556 (ttt180) cc_final: 0.6372 (tpt170) REVERT: q 41 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7592 (mt-10) REVERT: q 72 ASN cc_start: 0.7851 (t0) cc_final: 0.7440 (t0) REVERT: r 5 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7464 (ttp80) outliers start: 125 outliers final: 96 residues processed: 1008 average time/residue: 1.5009 time to fit residues: 2554.1331 Evaluate side-chains 1015 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 908 time to evaluate : 7.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 357 ASP Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 636 ILE Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain I residue 36 LEU 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 40 CYS Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 147 CYS Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 320 ASN Chi-restraints excluded: chain L residue 387 THR Chi-restraints excluded: chain L residue 526 LEU Chi-restraints excluded: chain L residue 545 SER Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 201 MET Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain M residue 411 ILE Chi-restraints excluded: chain N residue 151 SER Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain O residue 57 GLN Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain P residue 103 ASN Chi-restraints excluded: chain P residue 231 THR Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain S residue 24 GLN Chi-restraints excluded: chain S residue 35 PHE Chi-restraints excluded: chain T residue 20 LYS Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain W residue 24 SER Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain X residue 171 VAL Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain Z residue 63 ASP Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 97 MET Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain b residue 42 SER Chi-restraints excluded: chain b residue 48 THR Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 86 MET Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain h residue 41 THR Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain n residue 109 SER Chi-restraints excluded: chain p residue 142 TYR Chi-restraints excluded: chain q residue 37 THR Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain s residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 471 optimal weight: 5.9990 chunk 758 optimal weight: 3.9990 chunk 463 optimal weight: 1.9990 chunk 359 optimal weight: 9.9990 chunk 527 optimal weight: 10.0000 chunk 796 optimal weight: 8.9990 chunk 732 optimal weight: 0.0020 chunk 633 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 489 optimal weight: 6.9990 chunk 388 optimal weight: 9.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 580 GLN ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 68773 Z= 0.535 Angle : 1.568 50.625 93122 Z= 1.016 Chirality : 0.311 6.380 10164 Planarity : 0.004 0.062 11649 Dihedral : 10.119 167.545 10016 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 1.45 % Allowed : 14.44 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.10), residues: 8076 helix: 1.10 (0.08), residues: 4214 sheet: -1.67 (0.26), residues: 367 loop : -1.24 (0.11), residues: 3495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 318 HIS 0.008 0.001 HIS H 93 PHE 0.039 0.001 PHE B 60 TYR 0.026 0.001 TYR H 282 ARG 0.006 0.000 ARG a 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 44 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Evaluate side-chains 1023 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 919 time to evaluate : 7.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.6978 (tmm) cc_final: 0.6739 (tmm) REVERT: A 108 GLN cc_start: 0.8062 (mm110) cc_final: 0.7655 (mm-40) REVERT: B 37 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7168 (tm-30) REVERT: C 133 GLU cc_start: 0.7519 (tt0) cc_final: 0.7135 (tt0) REVERT: D 75 LYS cc_start: 0.7048 (tppt) cc_final: 0.6772 (tttt) REVERT: D 182 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7814 (tm-30) REVERT: E 175 GLU cc_start: 0.5449 (mt-10) cc_final: 0.5163 (mt-10) REVERT: F 33 LEU cc_start: 0.7862 (tp) cc_final: 0.7440 (tt) REVERT: F 295 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7610 (tt) REVERT: G 27 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7970 (mp) REVERT: G 61 LYS cc_start: 0.7613 (mmtp) cc_final: 0.6234 (tptm) REVERT: G 375 ASP cc_start: 0.7205 (m-30) cc_final: 0.6933 (t0) REVERT: G 379 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8369 (mt) REVERT: H 31 MET cc_start: 0.8284 (mtt) cc_final: 0.8030 (mtt) REVERT: J 97 ILE cc_start: 0.7305 (mm) cc_final: 0.6779 (pt) REVERT: L 53 MET cc_start: 0.7655 (ttm) cc_final: 0.7198 (mtp) REVERT: L 59 MET cc_start: 0.6947 (mmm) cc_final: 0.6697 (mmm) REVERT: L 387 THR cc_start: 0.6992 (OUTLIER) cc_final: 0.6552 (t) REVERT: L 396 ILE cc_start: 0.8046 (mm) cc_final: 0.7706 (mt) REVERT: L 545 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8541 (t) REVERT: L 589 MET cc_start: 0.6688 (ttt) cc_final: 0.6206 (ttt) REVERT: M 441 MET cc_start: 0.7264 (mmt) cc_final: 0.7021 (tpp) REVERT: N 117 GLU cc_start: 0.7516 (mm-30) cc_final: 0.6985 (mp0) REVERT: N 134 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7432 (tp40) REVERT: O 2 ARG cc_start: 0.6947 (mmm160) cc_final: 0.5820 (ptt-90) REVERT: R 30 ASP cc_start: 0.7395 (t0) cc_final: 0.6955 (t0) REVERT: R 77 LYS cc_start: 0.7289 (mmmt) cc_final: 0.6913 (tptp) REVERT: S 24 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7145 (mt0) REVERT: S 35 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7918 (t80) REVERT: T 20 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6755 (pptt) REVERT: T 33 ASN cc_start: 0.6831 (m-40) cc_final: 0.5960 (p0) REVERT: T 46 ASP cc_start: 0.6808 (m-30) cc_final: 0.6117 (m-30) REVERT: V 85 LYS cc_start: 0.7650 (mttt) cc_final: 0.7366 (mptt) REVERT: W 91 GLU cc_start: 0.7167 (tp30) cc_final: 0.6666 (tp30) REVERT: Y 16 GLN cc_start: 0.5863 (mt0) cc_final: 0.5512 (mp10) REVERT: Y 60 PHE cc_start: 0.6383 (m-80) cc_final: 0.5995 (t80) REVERT: Y 112 MET cc_start: 0.6492 (tmm) cc_final: 0.6270 (tmm) REVERT: Z 97 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7245 (mtt) REVERT: Z 120 ILE cc_start: 0.8086 (mt) cc_final: 0.7817 (pt) REVERT: a 51 ASP cc_start: 0.7214 (t0) cc_final: 0.6845 (t0) REVERT: c 30 TYR cc_start: 0.7349 (t80) cc_final: 0.6934 (t80) REVERT: e 14 ASP cc_start: 0.8293 (p0) cc_final: 0.8071 (p0) REVERT: f 30 ASP cc_start: 0.7534 (m-30) cc_final: 0.7111 (m-30) REVERT: h 7 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7597 (mtm-85) REVERT: h 37 ILE cc_start: 0.8494 (mt) cc_final: 0.8247 (tt) REVERT: h 106 LYS cc_start: 0.7796 (mmmt) cc_final: 0.7201 (mttt) REVERT: j 10 ARG cc_start: 0.7999 (mtp85) cc_final: 0.7709 (mmm-85) REVERT: j 55 ASP cc_start: 0.7316 (m-30) cc_final: 0.6970 (t0) REVERT: j 58 GLN cc_start: 0.7519 (mm-40) cc_final: 0.6705 (tm-30) REVERT: k 38 GLN cc_start: 0.6194 (mm-40) cc_final: 0.5750 (mt0) REVERT: l 41 MET cc_start: 0.6982 (mpp) cc_final: 0.6633 (mpp) REVERT: m 15 SER cc_start: 0.6766 (m) cc_final: 0.6495 (t) REVERT: n 42 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6952 (tt) REVERT: n 56 MET cc_start: 0.6436 (mmt) cc_final: 0.5886 (mtt) REVERT: n 120 LYS cc_start: 0.7574 (ttmt) cc_final: 0.7325 (ttmt) REVERT: n 158 ARG cc_start: 0.6106 (mtm180) cc_final: 0.5337 (ttm110) REVERT: p 136 LYS cc_start: 0.7720 (ttpt) cc_final: 0.7397 (tppt) REVERT: q 21 ARG cc_start: 0.7538 (ttt180) cc_final: 0.6366 (tpt170) REVERT: q 41 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7589 (mt-10) REVERT: q 72 ASN cc_start: 0.7825 (t0) cc_final: 0.7417 (t0) REVERT: r 5 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7471 (ttp80) outliers start: 104 outliers final: 91 residues processed: 996 average time/residue: 1.4859 time to fit residues: 2497.9286 Evaluate side-chains 1008 residues out of total 7177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 907 time to evaluate : 7.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 36 LEU 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 40 CYS Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 147 CYS Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 320 ASN Chi-restraints excluded: chain L residue 387 THR Chi-restraints excluded: chain L residue 526 LEU Chi-restraints excluded: chain L residue 545 SER Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 201 MET Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain M residue 411 ILE Chi-restraints excluded: chain N residue 151 SER Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain O residue 57 GLN Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain P residue 103 ASN Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 231 THR Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain S residue 24 GLN Chi-restraints excluded: chain S residue 35 PHE Chi-restraints excluded: chain T residue 20 LYS Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain W residue 24 SER Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain X residue 171 VAL Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain Z residue 63 ASP Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 97 MET Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain b residue 42 SER Chi-restraints excluded: chain b residue 48 THR Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 86 MET Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain h residue 41 THR Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain n residue 109 SER Chi-restraints excluded: chain o residue 27 ASP Chi-restraints excluded: chain p residue 142 TYR Chi-restraints excluded: chain q residue 37 THR Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain s residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 503 optimal weight: 6.9990 chunk 675 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 584 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 634 optimal weight: 6.9990 chunk 265 optimal weight: 6.9990 chunk 651 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 580 GLN ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.108223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.097297 restraints weight = 342596.832| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.37 r_work: 0.3169 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.242 68773 Z= 0.561 Angle : 1.578 50.646 93122 Z= 1.021 Chirality : 0.311 6.394 10164 Planarity : 0.005 0.062 11649 Dihedral : 10.164 166.194 10016 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.66 % Allowed : 14.44 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.10), residues: 8076 helix: 1.05 (0.08), residues: 4214 sheet: -1.69 (0.26), residues: 367 loop : -1.30 (0.11), residues: 3495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP g 24 HIS 0.008 0.001 HIS H 93 PHE 0.041 0.002 PHE B 60 TYR 0.025 0.002 TYR H 282 ARG 0.006 0.000 ARG a 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 39934.47 seconds wall clock time: 685 minutes 12.14 seconds (41112.14 seconds total)