Starting phenix.real_space_refine on Mon Feb 19 14:44:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvi_11457/02_2024/6zvi_11457.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvi_11457/02_2024/6zvi_11457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvi_11457/02_2024/6zvi_11457.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvi_11457/02_2024/6zvi_11457.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvi_11457/02_2024/6zvi_11457.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvi_11457/02_2024/6zvi_11457.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1945 5.49 5 S 87 5.16 5 C 42916 2.51 5 N 14524 2.21 5 O 20614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "i PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 8": "OD1" <-> "OD2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 41": "NH1" <-> "NH2" Residue "i GLU 55": "OE1" <-> "OE2" Residue "i TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 117": "OE1" <-> "OE2" Residue "i ASP 125": "OD1" <-> "OD2" Residue "i GLU 135": "OE1" <-> "OE2" Residue "i ASP 148": "OD1" <-> "OD2" Residue "i ASP 150": "OD1" <-> "OD2" Residue "j GLU 28": "OE1" <-> "OE2" Residue "j PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 78": "OD1" <-> "OD2" Residue "j PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 87": "NH1" <-> "NH2" Residue "j GLU 122": "OE1" <-> "OE2" Residue "j PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 144": "NH1" <-> "NH2" Residue "j ARG 152": "NH1" <-> "NH2" Residue "j GLU 196": "OE1" <-> "OE2" Residue "j ARG 213": "NH1" <-> "NH2" Residue "k GLU 54": "OE1" <-> "OE2" Residue "k GLU 55": "OE1" <-> "OE2" Residue "k PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 78": "OD1" <-> "OD2" Residue "k GLU 79": "OE1" <-> "OE2" Residue "k GLU 120": "OE1" <-> "OE2" Residue "k ARG 141": "NH1" <-> "NH2" Residue "k GLU 194": "OE1" <-> "OE2" Residue "k PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 232": "OE1" <-> "OE2" Residue "k ASP 245": "OD1" <-> "OD2" Residue "k GLU 246": "OE1" <-> "OE2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "l PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 68": "OE1" <-> "OE2" Residue "l ARG 90": "NH1" <-> "NH2" Residue "l ARG 94": "NH1" <-> "NH2" Residue "l ARG 124": "NH1" <-> "NH2" Residue "l ARG 143": "NH1" <-> "NH2" Residue "l ARG 146": "NH1" <-> "NH2" Residue "l ASP 169": "OD1" <-> "OD2" Residue "l ASP 191": "OD1" <-> "OD2" Residue "m ARG 11": "NH1" <-> "NH2" Residue "m PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 49": "NH1" <-> "NH2" Residue "m TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 108": "NH1" <-> "NH2" Residue "m PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 117": "OE1" <-> "OE2" Residue "m TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 148": "NH1" <-> "NH2" Residue "m ASP 163": "OD1" <-> "OD2" Residue "m ARG 200": "NH1" <-> "NH2" Residue "m PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 251": "OE1" <-> "OE2" Residue "m ARG 252": "NH1" <-> "NH2" Residue "n GLU 31": "OE1" <-> "OE2" Residue "n GLU 39": "OE1" <-> "OE2" Residue "n PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 55": "OD1" <-> "OD2" Residue "n ARG 65": "NH1" <-> "NH2" Residue "n ARG 76": "NH1" <-> "NH2" Residue "n TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 119": "OD1" <-> "OD2" Residue "n ARG 148": "NH1" <-> "NH2" Residue "n ASP 161": "OD1" <-> "OD2" Residue "n ARG 219": "NH1" <-> "NH2" Residue "o TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 23": "NH1" <-> "NH2" Residue "o PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 29": "OD1" <-> "OD2" Residue "o ASP 43": "OD1" <-> "OD2" Residue "o TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 92": "NH1" <-> "NH2" Residue "o ARG 98": "NH1" <-> "NH2" Residue "o ASP 105": "OD1" <-> "OD2" Residue "o ARG 137": "NH1" <-> "NH2" Residue "o GLU 166": "OE1" <-> "OE2" Residue "o TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 191": "NH1" <-> "NH2" Residue "p ARG 39": "NH1" <-> "NH2" Residue "p PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 104": "NH1" <-> "NH2" Residue "p ASP 163": "OD1" <-> "OD2" Residue "p TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 6": "OD1" <-> "OD2" Residue "q ARG 22": "NH1" <-> "NH2" Residue "q GLU 28": "OE1" <-> "OE2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ARG 49": "NH1" <-> "NH2" Residue "q TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 110": "NH1" <-> "NH2" Residue "q TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 164": "NH1" <-> "NH2" Residue "q ARG 178": "NH1" <-> "NH2" Residue "q PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 3": "NH1" <-> "NH2" Residue "r TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 17": "NH1" <-> "NH2" Residue "r ASP 25": "OD1" <-> "OD2" Residue "r PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 53": "NH1" <-> "NH2" Residue "r ARG 54": "NH1" <-> "NH2" Residue "r ARG 62": "NH1" <-> "NH2" Residue "r ASP 66": "OD1" <-> "OD2" Residue "r PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 72": "OE1" <-> "OE2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 151": "OD1" <-> "OD2" Residue "r PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 168": "NH1" <-> "NH2" Residue "r ARG 171": "NH1" <-> "NH2" Residue "s TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 18": "OE1" <-> "OE2" Residue "s PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 36": "OD1" <-> "OD2" Residue "s TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 10": "OE1" <-> "OE2" Residue "t ARG 33": "NH1" <-> "NH2" Residue "t TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 101": "OE1" <-> "OE2" Residue "t PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "v GLU 86": "OE1" <-> "OE2" Residue "v TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "v ARG 106": "NH1" <-> "NH2" Residue "v GLU 142": "OE1" <-> "OE2" Residue "x ASP 32": "OD1" <-> "OD2" Residue "x PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 110": "OE1" <-> "OE2" Residue "x TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 118": "OE1" <-> "OE2" Residue "y GLU 42": "OE1" <-> "OE2" Residue "y PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 99": "OE1" <-> "OE2" Residue "y ASP 113": "OD1" <-> "OD2" Residue "y ARG 123": "NH1" <-> "NH2" Residue "y GLU 125": "OE1" <-> "OE2" Residue "y PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 143": "NH1" <-> "NH2" Residue "z ARG 3": "NH1" <-> "NH2" Residue "z ASP 27": "OD1" <-> "OD2" Residue "z ARG 33": "NH1" <-> "NH2" Residue "z ASP 36": "OD1" <-> "OD2" Residue "z ARG 67": "NH1" <-> "NH2" Residue "z PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 80": "NH1" <-> "NH2" Residue "z ARG 95": "NH1" <-> "NH2" Residue "z ASP 103": "OD1" <-> "OD2" Residue "A PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 23": "OD1" <-> "OD2" Residue "A TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A ASP 112": "OD1" <-> "OD2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ARG 145": "NH1" <-> "NH2" Residue "B ASP 8": "OD1" <-> "OD2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B ASP 131": "OD1" <-> "OD2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C ASP 92": "OD1" <-> "OD2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "D GLU 2": "OE1" <-> "OE2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "D ASP 27": "OD1" <-> "OD2" Residue "D ASP 28": "OD1" <-> "OD2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D ASP 66": "OD1" <-> "OD2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 16": "NH1" <-> "NH2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "H PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 141": "OE1" <-> "OE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 20": "NH1" <-> "NH2" Residue "I PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 38": "OD1" <-> "OD2" Residue "I GLU 42": "OE1" <-> "OE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I ASP 53": "OD1" <-> "OD2" Residue "I PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 86": "OE1" <-> "OE2" Residue "J GLU 45": "OE1" <-> "OE2" Residue "J ARG 49": "NH1" <-> "NH2" Residue "J ARG 58": "NH1" <-> "NH2" Residue "J ARG 68": "NH1" <-> "NH2" Residue "J ARG 103": "NH1" <-> "NH2" Residue "L GLU 15": "OE1" <-> "OE2" Residue "N GLU 31": "OE1" <-> "OE2" Residue "N ASP 52": "OD1" <-> "OD2" Residue "N ARG 65": "NH1" <-> "NH2" Residue "P TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 109": "OD1" <-> "OD2" Residue "Q ARG 119": "NH1" <-> "NH2" Residue "Q TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 14": "OE1" <-> "OE2" Residue "R PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 76": "OD1" <-> "OD2" Residue "R TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 165": "OD1" <-> "OD2" Residue "R PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 191": "OD1" <-> "OD2" Residue "R PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 219": "OE1" <-> "OE2" Residue "R TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 286": "OE1" <-> "OE2" Residue "R PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 54": "NH1" <-> "NH2" Residue "T ARG 67": "NH1" <-> "NH2" Residue "T ARG 83": "NH1" <-> "NH2" Residue "T ARG 87": "NH1" <-> "NH2" Residue "T GLU 105": "OE1" <-> "OE2" Residue "T ASP 112": "OD1" <-> "OD2" Residue "T ARG 117": "NH1" <-> "NH2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T ARG 137": "NH1" <-> "NH2" Residue "O ARG 12": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 32": "NH1" <-> "NH2" Residue "O ASP 49": "OD1" <-> "OD2" Residue "w PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 37": "OE1" <-> "OE2" Residue "w ASP 51": "OD1" <-> "OD2" Residue "w ASP 53": "OD1" <-> "OD2" Residue "w ASP 66": "OD1" <-> "OD2" Residue "w ARG 90": "NH1" <-> "NH2" Residue "w ARG 107": "NH1" <-> "NH2" Residue "w ASP 117": "OD1" <-> "OD2" Residue "K ARG 10": "NH1" <-> "NH2" Residue "K ARG 42": "NH1" <-> "NH2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K ARG 51": "NH1" <-> "NH2" Residue "K ASP 52": "OD1" <-> "OD2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 90": "OE1" <-> "OE2" Residue "K ASP 91": "OD1" <-> "OD2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 80088 Number of models: 1 Model: "" Number of chains: 40 Chain: "d" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1620 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 13, 'rna3p': 62} Chain: "e" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 66} Chain: "f" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 724 Classifications: {'RNA': 35} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 8, 'rna3p_pur': 7, 'rna3p_pyr': 17} Link IDs: {'rna2p': 10, 'rna3p': 24} Chain breaks: 1 Chain: "h" Number of atoms: 37455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1758, 37455 Classifications: {'RNA': 1758} Modifications used: {'rna2p_pur': 160, 'rna2p_pyr': 159, 'rna3p_pur': 763, 'rna3p_pyr': 676} Link IDs: {'rna2p': 318, 'rna3p': 1439} Chain breaks: 3 Chain: "i" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1583 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 189} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "j" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1722 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain: "k" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1635 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 13, 'TRANS': 203} Chain: "l" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1734 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain: "m" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2068 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "n" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1609 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 8, 'TRANS': 197} Chain: "o" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1755 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 9, 'TRANS': 208} Chain: "p" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1486 Classifications: {'peptide': 185} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 172} Chain: "q" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "r" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "s" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 741 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 88} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "t" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1168 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain: "u" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 890 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 121} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "v" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "x" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 939 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "y" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1105 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "z" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1001 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "A" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1192 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "B" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "C" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 805 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "D" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 684 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "E" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "H" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 137} Chain: "I" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1073 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "J" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 558 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "L" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "N" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 497 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "P" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 3, 'TRANS': 42} Chain: "Q" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 556 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2403 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 304} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "T" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 870 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "O" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 442 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "w" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 949 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "K" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 769 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 72905 SG CYS L 37 131.695 137.283 13.608 1.00 84.30 S ATOM 73040 SG CYS L 56 131.313 138.938 16.262 1.00 81.20 S ATOM 78219 SG CYS O 39 86.835 63.630 119.914 1.00 30.18 S Time building chain proxies: 33.94, per 1000 atoms: 0.42 Number of scatterers: 80088 At special positions: 0 Unit cell: (238.275, 224.508, 201.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 87 16.00 P 1945 15.00 O 20614 8.00 N 14524 7.00 C 42916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 29.65 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 56 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 37 " pdb=" ZN O 101 " pdb="ZN ZN O 101 " - pdb=" SG CYS O 39 " 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9146 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 58 sheets defined 34.1% alpha, 17.8% beta 547 base pairs and 960 stacking pairs defined. Time for finding SS restraints: 25.76 Creating SS restraints... Processing helix chain 'i' and resid 4 through 8 removed outlier: 3.900A pdb=" N ASP i 8 " --> pdb=" O ALA i 5 " (cutoff:3.500A) Processing helix chain 'i' and resid 13 through 20 Processing helix chain 'i' and resid 30 through 35 Proline residue: i 35 - end of helix Processing helix chain 'i' and resid 42 through 44 No H-bonds generated for 'chain 'i' and resid 42 through 44' Processing helix chain 'i' and resid 49 through 65 Processing helix chain 'i' and resid 69 through 71 No H-bonds generated for 'chain 'i' and resid 69 through 71' Processing helix chain 'i' and resid 79 through 81 No H-bonds generated for 'chain 'i' and resid 79 through 81' Processing helix chain 'i' and resid 82 through 88 Processing helix chain 'i' and resid 88 through 93 Processing helix chain 'i' and resid 129 through 137 Processing helix chain 'i' and resid 166 through 184 removed outlier: 4.097A pdb=" N ILE i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY i 171 " --> pdb=" O LYS i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 198 through 203 removed outlier: 3.627A pdb=" N PHE i 203 " --> pdb=" O ASP i 200 " (cutoff:3.500A) Processing helix chain 'j' and resid 70 through 75 Processing helix chain 'j' and resid 76 through 80 removed outlier: 3.690A pdb=" N HIS j 79 " --> pdb=" O SER j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 106 through 114 removed outlier: 3.625A pdb=" N ARG j 111 " --> pdb=" O THR j 107 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL j 114 " --> pdb=" O LEU j 110 " (cutoff:3.500A) Processing helix chain 'j' and resid 157 through 178 removed outlier: 3.551A pdb=" N ARG j 162 " --> pdb=" O SER j 158 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL j 176 " --> pdb=" O LEU j 172 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY j 178 " --> pdb=" O LYS j 174 " (cutoff:3.500A) Processing helix chain 'j' and resid 180 through 188 removed outlier: 3.915A pdb=" N SER j 186 " --> pdb=" O ALA j 182 " (cutoff:3.500A) Processing helix chain 'j' and resid 191 through 199 removed outlier: 3.511A pdb=" N LYS j 195 " --> pdb=" O GLU j 191 " (cutoff:3.500A) Processing helix chain 'j' and resid 224 through 232 removed outlier: 3.858A pdb=" N LEU j 228 " --> pdb=" O ASP j 224 " (cutoff:3.500A) Processing helix chain 'k' and resid 39 through 47 Processing helix chain 'k' and resid 53 through 60 Processing helix chain 'k' and resid 65 through 69 Processing helix chain 'k' and resid 120 through 135 Processing helix chain 'k' and resid 181 through 192 removed outlier: 3.548A pdb=" N LYS k 186 " --> pdb=" O PRO k 182 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU k 190 " --> pdb=" O LYS k 186 " (cutoff:3.500A) Processing helix chain 'k' and resid 206 through 220 Processing helix chain 'k' and resid 226 through 230 removed outlier: 3.714A pdb=" N TRP k 230 " --> pdb=" O PRO k 227 " (cutoff:3.500A) Processing helix chain 'k' and resid 238 through 243 Processing helix chain 'k' and resid 243 through 248 Processing helix chain 'l' and resid 6 through 29 Processing helix chain 'l' and resid 54 through 59 Processing helix chain 'l' and resid 60 through 64 removed outlier: 3.638A pdb=" N GLY l 63 " --> pdb=" O GLY l 60 " (cutoff:3.500A) Processing helix chain 'l' and resid 66 through 77 Processing helix chain 'l' and resid 93 through 96 Processing helix chain 'l' and resid 97 through 111 Processing helix chain 'l' and resid 114 through 129 removed outlier: 3.627A pdb=" N VAL l 122 " --> pdb=" O ALA l 118 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR l 125 " --> pdb=" O GLY l 121 " (cutoff:3.500A) Processing helix chain 'l' and resid 161 through 167 removed outlier: 4.021A pdb=" N ASN l 165 " --> pdb=" O GLY l 161 " (cutoff:3.500A) Processing helix chain 'm' and resid 15 through 19 Processing helix chain 'm' and resid 37 through 41 removed outlier: 4.047A pdb=" N SER m 41 " --> pdb=" O LEU m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 50 Processing helix chain 'm' and resid 58 through 66 removed outlier: 3.657A pdb=" N LYS m 62 " --> pdb=" O GLY m 58 " (cutoff:3.500A) Processing helix chain 'm' and resid 133 through 135 No H-bonds generated for 'chain 'm' and resid 133 through 135' Processing helix chain 'm' and resid 247 through 259 Processing helix chain 'n' and resid 30 through 35 removed outlier: 4.013A pdb=" N GLN n 34 " --> pdb=" O PRO n 30 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN n 35 " --> pdb=" O GLU n 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 30 through 35' Processing helix chain 'n' and resid 82 through 87 Processing helix chain 'n' and resid 88 through 95 Processing helix chain 'n' and resid 106 through 125 removed outlier: 3.847A pdb=" N ARG n 112 " --> pdb=" O LEU n 108 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP n 119 " --> pdb=" O LYS n 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 128 through 140 Processing helix chain 'n' and resid 163 through 183 Processing helix chain 'n' and resid 189 through 203 removed outlier: 3.708A pdb=" N LYS n 203 " --> pdb=" O ILE n 199 " (cutoff:3.500A) Processing helix chain 'n' and resid 208 through 224 removed outlier: 3.511A pdb=" N GLU n 216 " --> pdb=" O LYS n 212 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 26 removed outlier: 4.018A pdb=" N VAL o 26 " --> pdb=" O HIS o 22 " (cutoff:3.500A) Processing helix chain 'o' and resid 39 through 41 No H-bonds generated for 'chain 'o' and resid 39 through 41' Processing helix chain 'o' and resid 137 through 143 Processing helix chain 'o' and resid 152 through 156 removed outlier: 3.722A pdb=" N ASP o 155 " --> pdb=" O ASP o 152 " (cutoff:3.500A) Processing helix chain 'o' and resid 180 through 216 removed outlier: 3.506A pdb=" N VAL o 195 " --> pdb=" O ARG o 191 " (cutoff:3.500A) Processing helix chain 'p' and resid 14 through 29 removed outlier: 4.207A pdb=" N LEU p 27 " --> pdb=" O ALA p 23 " (cutoff:3.500A) Processing helix chain 'p' and resid 33 through 37 Processing helix chain 'p' and resid 66 through 71 Processing helix chain 'p' and resid 73 through 83 removed outlier: 3.741A pdb=" N ARG p 79 " --> pdb=" O THR p 75 " (cutoff:3.500A) Processing helix chain 'p' and resid 113 through 116 Processing helix chain 'p' and resid 117 through 130 removed outlier: 3.809A pdb=" N ASP p 123 " --> pdb=" O THR p 119 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL p 130 " --> pdb=" O LEU p 126 " (cutoff:3.500A) Processing helix chain 'p' and resid 158 through 164 removed outlier: 3.818A pdb=" N GLN p 161 " --> pdb=" O ASP p 158 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP p 163 " --> pdb=" O GLN p 160 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N TYR p 164 " --> pdb=" O GLN p 161 " (cutoff:3.500A) Processing helix chain 'p' and resid 165 through 178 removed outlier: 3.885A pdb=" N ALA p 171 " --> pdb=" O GLU p 167 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 27 No H-bonds generated for 'chain 'q' and resid 25 through 27' Processing helix chain 'q' and resid 88 through 94 removed outlier: 3.550A pdb=" N ARG q 92 " --> pdb=" O ASN q 88 " (cutoff:3.500A) Processing helix chain 'q' and resid 106 through 117 removed outlier: 3.705A pdb=" N TRP q 112 " --> pdb=" O PRO q 108 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU q 114 " --> pdb=" O ARG q 110 " (cutoff:3.500A) Processing helix chain 'q' and resid 136 through 138 No H-bonds generated for 'chain 'q' and resid 136 through 138' Processing helix chain 'q' and resid 139 through 146 removed outlier: 3.645A pdb=" N TRP q 143 " --> pdb=" O ALA q 139 " (cutoff:3.500A) Processing helix chain 'q' and resid 153 through 158 Processing helix chain 'q' and resid 159 through 162 Processing helix chain 'q' and resid 172 through 177 Processing helix chain 'q' and resid 186 through 200 removed outlier: 3.670A pdb=" N ARG q 194 " --> pdb=" O ALA q 190 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS q 199 " --> pdb=" O ARG q 195 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 33 removed outlier: 4.196A pdb=" N LEU r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) Processing helix chain 'r' and resid 39 through 62 removed outlier: 3.839A pdb=" N ILE r 45 " --> pdb=" O GLU r 41 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA r 55 " --> pdb=" O LYS r 51 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 83 Processing helix chain 'r' and resid 92 through 97 removed outlier: 3.797A pdb=" N LEU r 97 " --> pdb=" O LEU r 93 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 106 removed outlier: 3.687A pdb=" N LEU r 105 " --> pdb=" O VAL r 101 " (cutoff:3.500A) Processing helix chain 'r' and resid 108 through 116 removed outlier: 4.303A pdb=" N TYR r 114 " --> pdb=" O GLN r 110 " (cutoff:3.500A) Processing helix chain 'r' and resid 121 through 131 removed outlier: 3.747A pdb=" N ARG r 126 " --> pdb=" O VAL r 122 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL r 127 " --> pdb=" O HIS r 123 " (cutoff:3.500A) Processing helix chain 'r' and resid 162 through 166 Processing helix chain 'r' and resid 170 through 182 removed outlier: 3.631A pdb=" N LYS r 180 " --> pdb=" O ASN r 176 " (cutoff:3.500A) Processing helix chain 's' and resid 4 through 19 removed outlier: 3.801A pdb=" N LYS s 10 " --> pdb=" O GLU s 6 " (cutoff:3.500A) Processing helix chain 's' and resid 38 through 53 removed outlier: 3.544A pdb=" N LEU s 46 " --> pdb=" O VAL s 42 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS s 52 " --> pdb=" O SER s 48 " (cutoff:3.500A) Processing helix chain 's' and resid 69 through 81 removed outlier: 4.024A pdb=" N GLU s 74 " --> pdb=" O GLU s 70 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR s 75 " --> pdb=" O GLU s 71 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU s 78 " --> pdb=" O GLU s 74 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR s 79 " --> pdb=" O TYR s 75 " (cutoff:3.500A) Processing helix chain 't' and resid 45 through 51 removed outlier: 3.627A pdb=" N ILE t 49 " --> pdb=" O PRO t 45 " (cutoff:3.500A) Processing helix chain 'u' and resid 27 through 37 removed outlier: 3.650A pdb=" N THR u 34 " --> pdb=" O VAL u 30 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 44 through 53 removed outlier: 3.662A pdb=" N SER u 48 " --> pdb=" O GLY u 44 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR u 53 " --> pdb=" O THR u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 71 through 80 removed outlier: 3.617A pdb=" N LEU u 78 " --> pdb=" O LEU u 74 " (cutoff:3.500A) Processing helix chain 'u' and resid 93 through 98 removed outlier: 3.714A pdb=" N GLN u 96 " --> pdb=" O ASP u 93 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY u 98 " --> pdb=" O LYS u 95 " (cutoff:3.500A) Processing helix chain 'u' and resid 130 through 142 removed outlier: 5.394A pdb=" N ILE u 136 " --> pdb=" O GLU u 132 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET u 137 " --> pdb=" O LEU u 133 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU u 138 " --> pdb=" O SER u 134 " (cutoff:3.500A) Processing helix chain 'v' and resid 31 through 42 Processing helix chain 'v' and resid 46 through 58 removed outlier: 3.543A pdb=" N VAL v 52 " --> pdb=" O SER v 48 " (cutoff:3.500A) Processing helix chain 'v' and resid 62 through 68 removed outlier: 3.881A pdb=" N ILE v 66 " --> pdb=" O GLN v 62 " (cutoff:3.500A) Processing helix chain 'v' and resid 70 through 78 Processing helix chain 'v' and resid 85 through 105 removed outlier: 3.899A pdb=" N LEU v 91 " --> pdb=" O ASP v 87 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG v 104 " --> pdb=" O LYS v 100 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN v 105 " --> pdb=" O HIS v 101 " (cutoff:3.500A) Processing helix chain 'v' and resid 108 through 132 removed outlier: 3.509A pdb=" N ILE v 116 " --> pdb=" O LYS v 112 " (cutoff:3.500A) Processing helix chain 'v' and resid 145 through 151 removed outlier: 3.668A pdb=" N LEU v 149 " --> pdb=" O THR v 145 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL v 150 " --> pdb=" O ALA v 146 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN v 151 " --> pdb=" O SER v 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 145 through 151' Processing helix chain 'x' and resid 21 through 27 removed outlier: 3.997A pdb=" N GLU x 27 " --> pdb=" O GLU x 23 " (cutoff:3.500A) Processing helix chain 'x' and resid 29 through 35 removed outlier: 3.580A pdb=" N VAL x 34 " --> pdb=" O THR x 30 " (cutoff:3.500A) Processing helix chain 'x' and resid 38 through 47 Processing helix chain 'x' and resid 53 through 65 removed outlier: 3.517A pdb=" N MET x 57 " --> pdb=" O PRO x 53 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS x 59 " --> pdb=" O GLY x 55 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG x 61 " --> pdb=" O MET x 57 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU x 65 " --> pdb=" O ARG x 61 " (cutoff:3.500A) Processing helix chain 'x' and resid 86 through 90 Processing helix chain 'x' and resid 108 through 112 removed outlier: 3.895A pdb=" N LEU x 112 " --> pdb=" O PRO x 109 " (cutoff:3.500A) Processing helix chain 'x' and resid 115 through 120 removed outlier: 3.709A pdb=" N SER x 120 " --> pdb=" O GLY x 117 " (cutoff:3.500A) Processing helix chain 'y' and resid 37 through 39 No H-bonds generated for 'chain 'y' and resid 37 through 39' Processing helix chain 'y' and resid 44 through 49 removed outlier: 3.591A pdb=" N VAL y 48 " --> pdb=" O ARG y 45 " (cutoff:3.500A) Processing helix chain 'y' and resid 56 through 61 removed outlier: 3.756A pdb=" N LYS y 59 " --> pdb=" O GLY y 56 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE y 60 " --> pdb=" O LEU y 57 " (cutoff:3.500A) Processing helix chain 'y' and resid 73 through 97 removed outlier: 3.659A pdb=" N VAL y 78 " --> pdb=" O HIS y 74 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG y 82 " --> pdb=" O VAL y 78 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN y 83 " --> pdb=" O TYR y 79 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS y 95 " --> pdb=" O ALA y 91 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL y 97 " --> pdb=" O HIS y 93 " (cutoff:3.500A) Processing helix chain 'y' and resid 98 through 112 removed outlier: 3.565A pdb=" N LYS y 102 " --> pdb=" O ASP y 98 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN y 103 " --> pdb=" O GLU y 99 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU y 104 " --> pdb=" O GLN y 100 " (cutoff:3.500A) Processing helix chain 'z' and resid 6 through 18 removed outlier: 3.554A pdb=" N ARG z 11 " --> pdb=" O LYS z 7 " (cutoff:3.500A) Processing helix chain 'z' and resid 20 through 24 Processing helix chain 'z' and resid 31 through 38 removed outlier: 3.635A pdb=" N ASP z 36 " --> pdb=" O LYS z 32 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 43 through 60 removed outlier: 3.617A pdb=" N ARG z 60 " --> pdb=" O HIS z 56 " (cutoff:3.500A) Processing helix chain 'z' and resid 73 through 81 removed outlier: 3.678A pdb=" N GLU z 77 " --> pdb=" O LEU z 73 " (cutoff:3.500A) Processing helix chain 'z' and resid 82 through 84 No H-bonds generated for 'chain 'z' and resid 82 through 84' Processing helix chain 'z' and resid 103 through 114 Processing helix chain 'A' and resid 27 through 33 removed outlier: 3.844A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 62 through 75 Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.669A pdb=" N LYS A 80 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 116 removed outlier: 3.835A pdb=" N SER A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 10 through 26 removed outlier: 3.521A pdb=" N ALA B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 68 removed outlier: 3.582A pdb=" N LYS B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.515A pdb=" N LYS B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 111 removed outlier: 3.889A pdb=" N ASN B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 141 removed outlier: 3.523A pdb=" N ARG B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 140 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 141 " --> pdb=" O ALA B 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 48 removed outlier: 3.903A pdb=" N ASN C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL C 37 " --> pdb=" O GLN C 33 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS C 48 " --> pdb=" O ASN C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 107 removed outlier: 3.640A pdb=" N VAL C 100 " --> pdb=" O PRO C 96 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR C 107 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 63 Processing helix chain 'D' and resid 64 through 75 Processing helix chain 'E' and resid 5 through 21 removed outlier: 3.750A pdb=" N ASP E 9 " --> pdb=" O SER E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 44 removed outlier: 3.553A pdb=" N HIS E 44 " --> pdb=" O VAL E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 94 removed outlier: 3.664A pdb=" N ASN E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 94 " --> pdb=" O THR E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 118 removed outlier: 3.506A pdb=" N ARG E 118 " --> pdb=" O GLU E 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 24 removed outlier: 3.544A pdb=" N LEU H 15 " --> pdb=" O SER H 11 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TRP H 24 " --> pdb=" O ARG H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 35 removed outlier: 3.596A pdb=" N LYS H 31 " --> pdb=" O ASN H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 40 Processing helix chain 'H' and resid 91 through 96 Processing helix chain 'H' and resid 132 through 137 Processing helix chain 'I' and resid 16 through 18 No H-bonds generated for 'chain 'I' and resid 16 through 18' Processing helix chain 'I' and resid 36 through 49 removed outlier: 3.955A pdb=" N LEU I 40 " --> pdb=" O SER I 36 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL I 47 " --> pdb=" O LYS I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 85 removed outlier: 3.592A pdb=" N PHE I 85 " --> pdb=" O GLU I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 94 removed outlier: 3.599A pdb=" N ARG I 93 " --> pdb=" O TYR I 89 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR I 94 " --> pdb=" O ARG I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 116 removed outlier: 3.709A pdb=" N LYS I 112 " --> pdb=" O ARG I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 135 removed outlier: 3.745A pdb=" N LYS I 127 " --> pdb=" O LYS I 123 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS I 128 " --> pdb=" O ARG I 124 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG I 131 " --> pdb=" O LYS I 127 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG I 132 " --> pdb=" O LYS I 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 52 Processing helix chain 'J' and resid 53 through 57 Processing helix chain 'J' and resid 61 through 69 Processing helix chain 'J' and resid 75 through 86 removed outlier: 4.176A pdb=" N ARG J 81 " --> pdb=" O ARG J 77 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU J 84 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU J 86 " --> pdb=" O HIS J 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 18 Processing helix chain 'P' and resid 32 through 43 removed outlier: 3.698A pdb=" N LYS P 36 " --> pdb=" O GLY P 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 164 removed outlier: 4.115A pdb=" N ASP R 163 " --> pdb=" O GLU R 160 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP R 164 " --> pdb=" O ALA R 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 160 through 164' Processing helix chain 'T' and resid 33 through 37 removed outlier: 4.001A pdb=" N ARG T 37 " --> pdb=" O ALA T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 68 removed outlier: 3.663A pdb=" N LYS T 64 " --> pdb=" O GLN T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 91 removed outlier: 4.125A pdb=" N ARG T 83 " --> pdb=" O PRO T 79 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE T 85 " --> pdb=" O VAL T 81 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG T 87 " --> pdb=" O ARG T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 95 through 103 removed outlier: 3.563A pdb=" N THR T 101 " --> pdb=" O LYS T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 110 through 114 Processing helix chain 'T' and resid 121 through 133 removed outlier: 3.784A pdb=" N LEU T 132 " --> pdb=" O LEU T 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 36 removed outlier: 3.810A pdb=" N GLY O 35 " --> pdb=" O ARG O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 46 removed outlier: 3.538A pdb=" N GLU O 45 " --> pdb=" O GLN O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 51 Processing helix chain 'w' and resid 45 through 47 No H-bonds generated for 'chain 'w' and resid 45 through 47' Processing helix chain 'w' and resid 56 through 75 removed outlier: 3.551A pdb=" N ALA w 63 " --> pdb=" O ALA w 59 " (cutoff:3.500A) Processing helix chain 'w' and resid 96 through 108 removed outlier: 4.437A pdb=" N ALA w 100 " --> pdb=" O PRO w 96 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA w 106 " --> pdb=" O LEU w 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 56 removed outlier: 4.467A pdb=" N GLU K 55 " --> pdb=" O ARG K 51 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 51 through 56' Processing helix chain 'K' and resid 74 through 81 Processing helix chain 'K' and resid 90 through 94 removed outlier: 3.551A pdb=" N LYS K 93 " --> pdb=" O GLU K 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'i' and resid 37 through 40 removed outlier: 6.673A pdb=" N VAL i 47 " --> pdb=" O PHE i 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'i' and resid 97 through 99 removed outlier: 7.462A pdb=" N ILE i 98 " --> pdb=" O VAL i 73 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA i 75 " --> pdb=" O ILE i 98 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL i 74 " --> pdb=" O ILE i 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'j' and resid 42 through 46 removed outlier: 4.052A pdb=" N GLY j 44 " --> pdb=" O ILE j 32 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU j 96 " --> pdb=" O VAL j 91 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL j 91 " --> pdb=" O LEU j 96 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N THR j 98 " --> pdb=" O ASP j 89 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASP j 89 " --> pdb=" O THR j 98 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE j 100 " --> pdb=" O ARG j 87 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ARG j 87 " --> pdb=" O PHE j 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'j' and resid 42 through 46 removed outlier: 4.052A pdb=" N GLY j 44 " --> pdb=" O ILE j 32 " (cutoff:3.500A) removed outlier: 13.457A pdb=" N ASN j 99 " --> pdb=" O LYS j 219 " (cutoff:3.500A) removed outlier: 13.454A pdb=" N LYS j 219 " --> pdb=" O ASN j 99 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N HIS j 101 " --> pdb=" O LEU j 217 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU j 217 " --> pdb=" O HIS j 101 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET j 103 " --> pdb=" O VAL j 215 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ARG j 213 " --> pdb=" O PHE j 105 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE j 210 " --> pdb=" O PHE j 142 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N PHE j 142 " --> pdb=" O ILE j 210 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL j 212 " --> pdb=" O ILE j 140 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE j 140 " --> pdb=" O VAL j 212 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS j 214 " --> pdb=" O PHE j 138 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL j 134 " --> pdb=" O LEU j 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'k' and resid 77 through 89 removed outlier: 3.679A pdb=" N GLN k 77 " --> pdb=" O GLY k 105 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL k 101 " --> pdb=" O MET k 81 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE k 83 " --> pdb=" O LYS k 99 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS k 99 " --> pdb=" O ILE k 83 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG k 97 " --> pdb=" O PRO k 85 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLN k 87 " --> pdb=" O ARG k 95 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG k 95 " --> pdb=" O GLN k 87 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'k' and resid 141 through 142 Processing sheet with id=AA7, first strand: chain 'k' and resid 158 through 162 removed outlier: 3.623A pdb=" N VAL k 165 " --> pdb=" O CYS k 162 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR k 166 " --> pdb=" O ASN k 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'l' and resid 34 through 40 removed outlier: 6.499A pdb=" N ARG l 51 " --> pdb=" O SER l 35 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL l 37 " --> pdb=" O ILE l 49 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE l 49 " --> pdb=" O VAL l 37 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL l 39 " --> pdb=" O GLU l 47 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU l 47 " --> pdb=" O VAL l 39 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR l 46 " --> pdb=" O VAL l 85 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N TYR l 87 " --> pdb=" O THR l 46 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL l 48 " --> pdb=" O TYR l 87 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLU l 89 " --> pdb=" O VAL l 48 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE l 50 " --> pdb=" O GLU l 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'l' and resid 148 through 155 Processing sheet with id=AB1, first strand: chain 'l' and resid 207 through 208 Processing sheet with id=AB2, first strand: chain 'l' and resid 221 through 224 removed outlier: 6.639A pdb=" N ALA R 180 " --> pdb=" O GLU R 189 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP R 191 " --> pdb=" O VAL R 178 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL R 178 " --> pdb=" O ASP R 191 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR R 168 " --> pdb=" O VAL R 157 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN R 153 " --> pdb=" O ALA R 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'm' and resid 42 through 43 Processing sheet with id=AB4, first strand: chain 'm' and resid 75 through 76 removed outlier: 4.192A pdb=" N ASN m 98 " --> pdb=" O ILE m 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'm' and resid 146 through 148 removed outlier: 5.654A pdb=" N VAL m 136 " --> pdb=" O LEU m 131 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU m 131 " --> pdb=" O VAL m 136 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR m 138 " --> pdb=" O VAL m 129 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL m 129 " --> pdb=" O TYR m 138 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL m 140 " --> pdb=" O LYS m 127 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N THR m 159 " --> pdb=" O PHE m 172 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N PHE m 172 " --> pdb=" O THR m 159 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS m 161 " --> pdb=" O THR m 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'm' and resid 179 through 183 removed outlier: 3.722A pdb=" N GLY m 229 " --> pdb=" O LEU m 180 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR m 182 " --> pdb=" O VAL m 227 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL m 227 " --> pdb=" O TYR m 182 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'm' and resid 197 through 199 removed outlier: 3.525A pdb=" N HIS m 197 " --> pdb=" O HIS m 209 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'n' and resid 145 through 148 Processing sheet with id=AB9, first strand: chain 'o' and resid 12 through 17 removed outlier: 6.280A pdb=" N LYS o 2 " --> pdb=" O LEU o 109 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU o 111 " --> pdb=" O LYS o 2 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASN o 4 " --> pdb=" O LEU o 111 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE o 113 " --> pdb=" O ASN o 4 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N SER o 6 " --> pdb=" O ILE o 113 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N LYS o 115 " --> pdb=" O SER o 6 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL o 112 " --> pdb=" O ILE o 52 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE o 52 " --> pdb=" O VAL o 112 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL o 114 " --> pdb=" O PHE o 50 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N PHE o 50 " --> pdb=" O VAL o 114 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'o' and resid 73 through 77 Processing sheet with id=AC2, first strand: chain 'o' and resid 160 through 163 Processing sheet with id=AC3, first strand: chain 'p' and resid 45 through 50 removed outlier: 3.940A pdb=" N SER p 45 " --> pdb=" O PHE p 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG p 47 " --> pdb=" O ALA p 59 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'p' and resid 180 through 184 removed outlier: 4.487A pdb=" N GLN p 180 " --> pdb=" O LYS p 148 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY p 137 " --> pdb=" O LEU p 153 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS p 138 " --> pdb=" O ASP E 54 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE E 50 " --> pdb=" O TYR p 142 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'q' and resid 3 through 4 removed outlier: 3.669A pdb=" N ILE q 3 " --> pdb=" O GLY q 30 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'q' and resid 37 through 38 removed outlier: 6.537A pdb=" N ARG q 42 " --> pdb=" O LEU q 58 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'q' and resid 72 through 76 removed outlier: 3.563A pdb=" N ILE q 72 " --> pdb=" O TRP q 67 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN q 64 " --> pdb=" O GLY q 181 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE q 183 " --> pdb=" O ASN q 64 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER q 66 " --> pdb=" O ILE q 183 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE q 101 " --> pdb=" O VAL q 82 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY q 80 " --> pdb=" O GLN q 103 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASP q 105 " --> pdb=" O ILE q 78 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE q 78 " --> pdb=" O ASP q 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'r' and resid 139 through 140 Processing sheet with id=AC9, first strand: chain 's' and resid 20 through 21 Processing sheet with id=AD1, first strand: chain 't' and resid 70 through 77 removed outlier: 17.903A pdb=" N ILE t 70 " --> pdb=" O LEU t 91 " (cutoff:3.500A) removed outlier: 15.404A pdb=" N LEU t 91 " --> pdb=" O ILE t 70 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N THR t 72 " --> pdb=" O ALA t 89 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA t 89 " --> pdb=" O THR t 72 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL t 85 " --> pdb=" O VAL t 76 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG t 99 " --> pdb=" O ILE t 94 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N PHE t 137 " --> pdb=" O PRO t 108 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR t 124 " --> pdb=" O VAL t 140 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL t 142 " --> pdb=" O ILE t 122 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE t 122 " --> pdb=" O VAL t 142 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ASP t 121 " --> pdb=" O VAL t 75 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL t 75 " --> pdb=" O ASP t 121 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'u' and resid 41 through 43 removed outlier: 3.696A pdb=" N VAL u 121 " --> pdb=" O VAL u 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL u 123 " --> pdb=" O LEU u 59 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU u 59 " --> pdb=" O VAL u 123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'x' and resid 76 through 78 Processing sheet with id=AD4, first strand: chain 'y' and resid 6 through 13 removed outlier: 3.631A pdb=" N THR y 70 " --> pdb=" O THR y 17 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LYS y 30 " --> pdb=" O VAL y 67 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N VAL y 69 " --> pdb=" O LYS y 30 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 15 through 16 Processing sheet with id=AD6, first strand: chain 'A' and resid 88 through 89 Processing sheet with id=AD7, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.778A pdb=" N LYS B 92 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ARG B 86 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AD9, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AE1, first strand: chain 'C' and resid 56 through 57 removed outlier: 3.726A pdb=" N TYR C 90 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 56 through 57 removed outlier: 3.726A pdb=" N TYR C 90 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 32 through 37 Processing sheet with id=AE4, first strand: chain 'E' and resid 72 through 74 Processing sheet with id=AE5, first strand: chain 'E' and resid 72 through 74 removed outlier: 6.716A pdb=" N ILE E 103 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE E 128 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR E 101 " --> pdb=" O PHE E 128 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 48 through 57 removed outlier: 6.703A pdb=" N ARG H 73 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LYS H 56 " --> pdb=" O CYS H 71 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N CYS H 71 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE H 122 " --> pdb=" O THR H 84 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU H 103 " --> pdb=" O VAL H 125 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 6 through 15 removed outlier: 3.524A pdb=" N THR I 6 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL I 12 " --> pdb=" O GLN I 22 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN I 22 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N SER I 14 " --> pdb=" O ARG I 20 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ARG I 20 " --> pdb=" O SER I 14 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 6 through 15 removed outlier: 3.524A pdb=" N THR I 6 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL I 12 " --> pdb=" O GLN I 22 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN I 22 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N SER I 14 " --> pdb=" O ARG I 20 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ARG I 20 " --> pdb=" O SER I 14 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 89 through 95 removed outlier: 7.097A pdb=" N ILE J 100 " --> pdb=" O ILE J 92 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYS J 94 " --> pdb=" O GLN J 98 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLN J 98 " --> pdb=" O LYS J 94 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 44 through 47 removed outlier: 4.013A pdb=" N THR L 44 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER L 78 " --> pdb=" O LYS L 36 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 64 through 65 Processing sheet with id=AF3, first strand: chain 'N' and resid 39 through 44 removed outlier: 7.208A pdb=" N VAL N 25 " --> pdb=" O GLY N 17 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY N 17 " --> pdb=" O VAL N 25 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLN N 27 " --> pdb=" O VAL N 15 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL N 15 " --> pdb=" O GLN N 27 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG N 29 " --> pdb=" O ILE N 13 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 8 through 13 removed outlier: 3.802A pdb=" N ARG R 10 " --> pdb=" O VAL R 312 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL R 312 " --> pdb=" O ARG R 10 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR R 12 " --> pdb=" O ILE R 310 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE R 310 " --> pdb=" O THR R 12 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR R 300 " --> pdb=" O TRP R 294 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP R 294 " --> pdb=" O THR R 300 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE R 302 " --> pdb=" O LEU R 292 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU R 292 " --> pdb=" O PHE R 302 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY R 304 " --> pdb=" O VAL R 290 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 20 through 25 removed outlier: 3.958A pdb=" N LEU R 33 " --> pdb=" O TRP R 45 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR R 41 " --> pdb=" O SER R 37 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG R 59 " --> pdb=" O SER R 44 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS R 46 " --> pdb=" O PRO R 57 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 68 through 73 removed outlier: 3.549A pdb=" N SER R 84 " --> pdb=" O THR R 88 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR R 88 " --> pdb=" O SER R 84 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN R 101 " --> pdb=" O LEU R 91 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP R 93 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR R 99 " --> pdb=" O ASP R 93 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'R' and resid 110 through 115 removed outlier: 3.654A pdb=" N SER R 112 " --> pdb=" O GLY R 125 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE R 131 " --> pdb=" O THR R 143 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR R 143 " --> pdb=" O ILE R 131 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL R 133 " --> pdb=" O LEU R 141 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 201 through 204 removed outlier: 3.505A pdb=" N THR R 201 " --> pdb=" O ALA R 214 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR R 232 " --> pdb=" O LEU R 222 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN R 224 " --> pdb=" O ALA R 230 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ALA R 230 " --> pdb=" O ASN R 224 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 240 through 245 removed outlier: 3.676A pdb=" N ASP R 272 " --> pdb=" O VAL R 262 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N SER R 264 " --> pdb=" O LEU R 270 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU R 270 " --> pdb=" O SER R 264 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 30 through 31 Processing sheet with id=AG2, first strand: chain 'w' and resid 40 through 43 removed outlier: 6.302A pdb=" N GLY w 15 " --> pdb=" O HIS w 80 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LYS w 82 " --> pdb=" O GLY w 15 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA w 17 " --> pdb=" O LYS w 82 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ARG w 84 " --> pdb=" O ALA w 17 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE w 19 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL w 81 " --> pdb=" O GLY w 113 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE w 115 " --> pdb=" O VAL w 81 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE w 83 " --> pdb=" O ILE w 115 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASP w 117 " --> pdb=" O ILE w 83 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 20 through 22 Processing sheet with id=AG4, first strand: chain 'K' and resid 37 through 43 1344 hydrogen bonds defined for protein. 3750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1345 hydrogen bonds 2172 hydrogen bond angles 0 basepair planarities 547 basepair parallelities 960 stacking parallelities Total time for adding SS restraints: 65.22 Time building geometry restraints manager: 32.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 10217 1.32 - 1.45: 33654 1.45 - 1.57: 37728 1.57 - 1.70: 3883 1.70 - 1.83: 137 Bond restraints: 85619 Sorted by residual: bond pdb=" CA LYS B 27 " pdb=" CB LYS B 27 " ideal model delta sigma weight residual 1.528 1.635 -0.107 2.61e-02 1.47e+03 1.67e+01 bond pdb=" CA LEU I 28 " pdb=" CB LEU I 28 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.75e-02 3.27e+03 6.49e+00 bond pdb=" C2 G h 976 " pdb=" N3 G h 976 " ideal model delta sigma weight residual 1.323 1.280 0.043 2.00e-02 2.50e+03 4.66e+00 bond pdb=" CB VAL t 135 " pdb=" CG2 VAL t 135 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.25e+00 bond pdb=" N3 U h1012 " pdb=" C4 U h1012 " ideal model delta sigma weight residual 1.380 1.339 0.041 2.00e-02 2.50e+03 4.21e+00 ... (remaining 85614 not shown) Histogram of bond angle deviations from ideal: 96.91 - 105.36: 9677 105.36 - 113.80: 53303 113.80 - 122.24: 45081 122.24 - 130.69: 16195 130.69 - 139.13: 829 Bond angle restraints: 125085 Sorted by residual: angle pdb=" C ILE u 89 " pdb=" N LYS u 90 " pdb=" CA LYS u 90 " ideal model delta sigma weight residual 121.54 132.84 -11.30 1.91e+00 2.74e-01 3.50e+01 angle pdb=" N THR w 91 " pdb=" CA THR w 91 " pdb=" C THR w 91 " ideal model delta sigma weight residual 111.28 117.42 -6.14 1.09e+00 8.42e-01 3.17e+01 angle pdb=" CA GLU N 62 " pdb=" CB GLU N 62 " pdb=" CG GLU N 62 " ideal model delta sigma weight residual 114.10 124.58 -10.48 2.00e+00 2.50e-01 2.75e+01 angle pdb=" C ASN I 34 " pdb=" N VAL I 35 " pdb=" CA VAL I 35 " ideal model delta sigma weight residual 122.14 116.63 5.51 1.11e+00 8.12e-01 2.46e+01 angle pdb=" CA LYS Q 136 " pdb=" CB LYS Q 136 " pdb=" CG LYS Q 136 " ideal model delta sigma weight residual 114.10 123.95 -9.85 2.00e+00 2.50e-01 2.43e+01 ... (remaining 125080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 48860 35.96 - 71.92: 4819 71.92 - 107.88: 517 107.88 - 143.83: 26 143.83 - 179.79: 56 Dihedral angle restraints: 54278 sinusoidal: 40108 harmonic: 14170 Sorted by residual: dihedral pdb=" CA VAL p 64 " pdb=" C VAL p 64 " pdb=" N PRO p 65 " pdb=" CA PRO p 65 " ideal model delta harmonic sigma weight residual 180.00 123.55 56.45 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA SER u 119 " pdb=" C SER u 119 " pdb=" N VAL u 120 " pdb=" CA VAL u 120 " ideal model delta harmonic sigma weight residual 180.00 124.39 55.61 0 5.00e+00 4.00e-02 1.24e+02 dihedral pdb=" CA ALA s 23 " pdb=" C ALA s 23 " pdb=" N LYS s 24 " pdb=" CA LYS s 24 " ideal model delta harmonic sigma weight residual 180.00 130.09 49.91 0 5.00e+00 4.00e-02 9.96e+01 ... (remaining 54275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 14582 0.097 - 0.194: 1019 0.194 - 0.291: 80 0.291 - 0.388: 24 0.388 - 0.485: 3 Chirality restraints: 15708 Sorted by residual: chirality pdb=" C3' C h 408 " pdb=" C4' C h 408 " pdb=" O3' C h 408 " pdb=" C2' C h 408 " both_signs ideal model delta sigma weight residual False -2.74 -2.26 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" C3' G h 925 " pdb=" C4' G h 925 " pdb=" O3' G h 925 " pdb=" C2' G h 925 " both_signs ideal model delta sigma weight residual False -2.48 -2.06 -0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" CB VAL p 64 " pdb=" CA VAL p 64 " pdb=" CG1 VAL p 64 " pdb=" CG2 VAL p 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 15705 not shown) Planarity restraints: 8721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G h 287 " -0.059 2.00e-02 2.50e+03 2.66e-02 2.13e+01 pdb=" N9 G h 287 " 0.068 2.00e-02 2.50e+03 pdb=" C8 G h 287 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G h 287 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G h 287 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G h 287 " -0.009 2.00e-02 2.50e+03 pdb=" O6 G h 287 " -0.011 2.00e-02 2.50e+03 pdb=" N1 G h 287 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G h 287 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G h 287 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G h 287 " 0.008 2.00e-02 2.50e+03 pdb=" C4 G h 287 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL p 64 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO p 65 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO p 65 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO p 65 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A h1039 " -0.055 2.00e-02 2.50e+03 2.53e-02 1.76e+01 pdb=" N9 A h1039 " 0.060 2.00e-02 2.50e+03 pdb=" C8 A h1039 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A h1039 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A h1039 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A h1039 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A h1039 " -0.019 2.00e-02 2.50e+03 pdb=" N1 A h1039 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A h1039 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A h1039 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A h1039 " 0.008 2.00e-02 2.50e+03 ... (remaining 8718 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 489 2.51 - 3.11: 53166 3.11 - 3.71: 142295 3.71 - 4.30: 206722 4.30 - 4.90: 295020 Nonbonded interactions: 697692 Sorted by model distance: nonbonded pdb=" N1 G h 976 " pdb=" C2 A h1027 " model vdw 1.914 3.420 nonbonded pdb=" CA CYS O 39 " pdb="ZN ZN O 101 " model vdw 2.037 2.128 nonbonded pdb=" O2' G h 991 " pdb=" O2' U h1785 " model vdw 2.157 2.440 nonbonded pdb=" OP1 G h 925 " pdb=" O2' G h 986 " model vdw 2.180 2.440 nonbonded pdb=" O2' C h1729 " pdb=" O GLY q 2 " model vdw 2.182 2.440 ... (remaining 697687 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 16.240 Check model and map are aligned: 1.280 Set scattering table: 0.810 Process input model: 226.640 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 262.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 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 0.107 85619 Z= 0.444 Angle : 0.973 14.996 125085 Z= 0.504 Chirality : 0.053 0.485 15708 Planarity : 0.006 0.113 8721 Dihedral : 23.039 179.792 45132 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.16 % Favored : 94.64 % Rotamer: Outliers : 0.02 % Allowed : 0.48 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 2.04 % Twisted General : 0.45 % 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: -2.84 (0.11), residues: 4848 helix: -2.56 (0.10), residues: 1387 sheet: -0.80 (0.17), residues: 885 loop : -1.86 (0.11), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP v 139 HIS 0.023 0.002 HIS R 288 PHE 0.066 0.003 PHE H 107 TYR 0.065 0.003 TYR Q 148 ARG 0.019 0.001 ARG j 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 656 time to evaluate : 4.584 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: o 89 ASP cc_start: 0.7201 (p0) cc_final: 0.6878 (p0) REVERT: J 67 ASP cc_start: 0.8079 (t0) cc_final: 0.7777 (t0) outliers start: 1 outliers final: 0 residues processed: 657 average time/residue: 1.5239 time to fit residues: 1350.8595 Evaluate side-chains 538 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 538 time to evaluate : 4.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 564 optimal weight: 8.9990 chunk 506 optimal weight: 0.0770 chunk 280 optimal weight: 0.9980 chunk 172 optimal weight: 9.9990 chunk 341 optimal weight: 10.0000 chunk 270 optimal weight: 1.9990 chunk 523 optimal weight: 0.2980 chunk 202 optimal weight: 7.9990 chunk 318 optimal weight: 7.9990 chunk 389 optimal weight: 5.9990 chunk 606 optimal weight: 7.9990 overall best weight: 1.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 228 ASN l 67 ASN m 98 ASN m 223 ASN n 66 GLN n 127 GLN n 131 GLN ** p 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 110 GLN r 48 GLN t 16 GLN v 58 HIS v 62 GLN ** z 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 ASN A 71 GLN B 129 GLN E 15 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 ASN L 5 GLN N 51 ASN ** T 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 85619 Z= 0.166 Angle : 0.651 17.292 125085 Z= 0.334 Chirality : 0.039 0.309 15708 Planarity : 0.005 0.087 8721 Dihedral : 23.951 179.930 35509 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.69 % Favored : 92.12 % Rotamer: Outliers : 1.67 % Allowed : 11.49 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 1.53 % Twisted General : 0.15 % 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: -1.93 (0.11), residues: 4848 helix: -0.91 (0.13), residues: 1457 sheet: -0.69 (0.17), residues: 902 loop : -1.72 (0.12), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP q 112 HIS 0.005 0.001 HIS p 122 PHE 0.022 0.001 PHE H 107 TYR 0.033 0.001 TYR R 250 ARG 0.008 0.000 ARG l 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 640 time to evaluate : 4.662 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: n 41 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7511 (ptmm) REVERT: n 65 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7106 (mmt180) REVERT: t 121 ASP cc_start: 0.7761 (m-30) cc_final: 0.7494 (m-30) REVERT: z 82 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7406 (t0) REVERT: A 23 ASP cc_start: 0.8763 (t0) cc_final: 0.8552 (t70) REVERT: B 35 ASP cc_start: 0.8176 (p0) cc_final: 0.7966 (p0) REVERT: J 67 ASP cc_start: 0.7912 (t0) cc_final: 0.7706 (t0) REVERT: K 87 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8147 (ptm160) outliers start: 69 outliers final: 21 residues processed: 665 average time/residue: 1.5365 time to fit residues: 1381.0055 Evaluate side-chains 594 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 569 time to evaluate : 4.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 9 LEU Chi-restraints excluded: chain i residue 169 SER Chi-restraints excluded: chain i residue 196 SER Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain p residue 157 LYS Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain r residue 138 LYS Chi-restraints excluded: chain r residue 161 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain y residue 70 THR Chi-restraints excluded: chain z residue 25 THR Chi-restraints excluded: chain z residue 79 GLU Chi-restraints excluded: chain z residue 82 ASP Chi-restraints excluded: chain z residue 113 LEU Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain L residue 34 ASP Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain K residue 87 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 337 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 504 optimal weight: 9.9990 chunk 413 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 607 optimal weight: 30.0000 chunk 656 optimal weight: 5.9990 chunk 541 optimal weight: 9.9990 chunk 602 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 487 optimal weight: 0.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** j 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 189 GLN ** m 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 GLN t 16 GLN z 48 ASN A 19 ASN A 71 GLN B 129 GLN D 33 GLN E 15 ASN ** E 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 ASN I 107 GLN L 26 GLN R 17 ASN R 288 HIS ** T 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 85619 Z= 0.360 Angle : 0.716 21.034 125085 Z= 0.365 Chirality : 0.043 0.316 15708 Planarity : 0.005 0.094 8721 Dihedral : 23.867 179.729 35509 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.46 % Favored : 91.38 % Rotamer: Outliers : 2.96 % Allowed : 15.42 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 1.53 % Twisted General : 0.15 % 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: -1.72 (0.12), residues: 4848 helix: -0.43 (0.13), residues: 1477 sheet: -0.73 (0.17), residues: 900 loop : -1.74 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP q 112 HIS 0.006 0.001 HIS p 122 PHE 0.035 0.002 PHE H 107 TYR 0.017 0.002 TYR y 79 ARG 0.010 0.001 ARG t 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 593 time to evaluate : 4.592 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: i 135 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: n 65 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7092 (mmt180) REVERT: q 111 GLN cc_start: 0.8487 (pm20) cc_final: 0.8137 (pm20) REVERT: t 121 ASP cc_start: 0.7947 (m-30) cc_final: 0.7732 (m-30) REVERT: x 24 LYS cc_start: 0.9335 (tppp) cc_final: 0.9053 (mmtm) REVERT: z 82 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7525 (t0) REVERT: A 23 ASP cc_start: 0.8806 (t0) cc_final: 0.8593 (t70) REVERT: B 35 ASP cc_start: 0.8207 (p0) cc_final: 0.7989 (p0) REVERT: B 127 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8308 (m110) REVERT: C 48 HIS cc_start: 0.7916 (OUTLIER) cc_final: 0.7331 (p-80) REVERT: J 67 ASP cc_start: 0.7952 (t0) cc_final: 0.7680 (t0) REVERT: R 250 TYR cc_start: 0.6530 (t80) cc_final: 0.5543 (t80) REVERT: T 68 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7822 (tm-30) REVERT: K 87 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7999 (ptm-80) outliers start: 122 outliers final: 52 residues processed: 650 average time/residue: 1.5235 time to fit residues: 1342.5558 Evaluate side-chains 619 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 561 time to evaluate : 4.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 9 LEU Chi-restraints excluded: chain i residue 114 SER Chi-restraints excluded: chain i residue 135 GLU Chi-restraints excluded: chain i residue 169 SER Chi-restraints excluded: chain i residue 196 SER Chi-restraints excluded: chain j residue 24 PHE Chi-restraints excluded: chain k residue 51 THR Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 146 THR Chi-restraints excluded: chain l residue 47 GLU Chi-restraints excluded: chain l residue 139 SER Chi-restraints excluded: chain l residue 175 VAL Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain n residue 119 ASP Chi-restraints excluded: chain o residue 6 SER Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain r residue 138 LYS Chi-restraints excluded: chain r residue 161 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 51 SER Chi-restraints excluded: chain t residue 21 ASN Chi-restraints excluded: chain v residue 145 THR Chi-restraints excluded: chain y residue 58 ASP Chi-restraints excluded: chain z residue 17 ILE Chi-restraints excluded: chain z residue 25 THR Chi-restraints excluded: chain z residue 79 GLU Chi-restraints excluded: chain z residue 82 ASP Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain L residue 34 ASP Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 87 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 600 optimal weight: 30.0000 chunk 456 optimal weight: 5.9990 chunk 315 optimal weight: 10.0000 chunk 67 optimal weight: 40.0000 chunk 290 optimal weight: 10.0000 chunk 408 optimal weight: 2.9990 chunk 609 optimal weight: 20.0000 chunk 645 optimal weight: 6.9990 chunk 318 optimal weight: 5.9990 chunk 578 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** j 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 ASN m 67 GLN ** m 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 GLN ** o 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 65 GLN ** q 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 74 ASN A 19 ASN A 71 GLN B 129 GLN ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN E 15 ASN ** E 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 85619 Z= 0.269 Angle : 0.665 20.817 125085 Z= 0.340 Chirality : 0.041 0.307 15708 Planarity : 0.005 0.082 8721 Dihedral : 23.813 179.975 35509 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.46 % Favored : 91.40 % Rotamer: Outliers : 3.30 % Allowed : 17.07 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 1.53 % Twisted General : 0.15 % 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: -1.52 (0.12), residues: 4848 helix: -0.11 (0.14), residues: 1476 sheet: -0.65 (0.17), residues: 891 loop : -1.71 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP u 100 HIS 0.008 0.001 HIS l 159 PHE 0.020 0.001 PHE R 241 TYR 0.020 0.001 TYR r 95 ARG 0.009 0.000 ARG u 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 593 time to evaluate : 4.713 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: i 88 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8313 (mtpp) REVERT: i 164 ASN cc_start: 0.7991 (p0) cc_final: 0.7731 (p0) REVERT: m 133 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7736 (mttm) REVERT: n 41 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7696 (ptmm) REVERT: n 65 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7052 (mmt180) REVERT: q 20 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7216 (tt0) REVERT: r 176 ASN cc_start: 0.8589 (t0) cc_final: 0.8280 (t0) REVERT: t 121 ASP cc_start: 0.7951 (m-30) cc_final: 0.7712 (m-30) REVERT: x 24 LYS cc_start: 0.9287 (tppp) cc_final: 0.9036 (mptp) REVERT: x 104 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7267 (mt0) REVERT: z 82 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7541 (t0) REVERT: B 35 ASP cc_start: 0.8281 (p0) cc_final: 0.8043 (p0) REVERT: B 131 ASP cc_start: 0.8336 (m-30) cc_final: 0.8126 (t0) REVERT: C 48 HIS cc_start: 0.7913 (OUTLIER) cc_final: 0.7339 (p-80) REVERT: J 67 ASP cc_start: 0.7930 (t0) cc_final: 0.7667 (t0) REVERT: T 68 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7735 (tm-30) REVERT: O 32 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.7604 (ptt90) REVERT: K 87 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8034 (ptm-80) outliers start: 136 outliers final: 67 residues processed: 667 average time/residue: 1.5584 time to fit residues: 1404.8792 Evaluate side-chains 642 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 565 time to evaluate : 4.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 88 LYS Chi-restraints excluded: chain i residue 114 SER Chi-restraints excluded: chain i residue 158 VAL Chi-restraints excluded: chain i residue 169 SER Chi-restraints excluded: chain i residue 196 SER Chi-restraints excluded: chain j residue 24 PHE Chi-restraints excluded: chain k residue 51 THR Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 146 THR Chi-restraints excluded: chain l residue 134 CYS Chi-restraints excluded: chain l residue 139 SER Chi-restraints excluded: chain l residue 175 VAL Chi-restraints excluded: chain m residue 133 LYS Chi-restraints excluded: chain m residue 253 ASP Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain o residue 6 SER Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain o residue 22 HIS Chi-restraints excluded: chain q residue 20 GLN Chi-restraints excluded: chain q residue 88 ASN Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 138 LYS Chi-restraints excluded: chain r residue 161 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain t residue 60 PHE Chi-restraints excluded: chain x residue 104 GLN Chi-restraints excluded: chain y residue 58 ASP Chi-restraints excluded: chain z residue 17 ILE Chi-restraints excluded: chain z residue 25 THR Chi-restraints excluded: chain z residue 79 GLU Chi-restraints excluded: chain z residue 82 ASP Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain T residue 51 THR Chi-restraints excluded: chain O residue 32 ARG Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 87 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 537 optimal weight: 7.9990 chunk 366 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 480 optimal weight: 0.5980 chunk 266 optimal weight: 0.9990 chunk 550 optimal weight: 0.7980 chunk 446 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 329 optimal weight: 6.9990 chunk 579 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: j 40 ASN k 189 GLN l 74 GLN l 111 ASN l 159 HIS ** m 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 GLN n 127 GLN ** o 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 74 ASN s 32 HIS u 96 GLN A 19 ASN A 71 GLN C 72 ASN D 33 GLN E 15 ASN ** E 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 85619 Z= 0.213 Angle : 0.638 20.882 125085 Z= 0.326 Chirality : 0.039 0.292 15708 Planarity : 0.005 0.081 8721 Dihedral : 23.755 179.712 35509 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.40 % Favored : 91.46 % Rotamer: Outliers : 3.47 % Allowed : 18.57 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 1.53 % Twisted General : 0.13 % 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: -1.34 (0.12), residues: 4848 helix: 0.11 (0.14), residues: 1476 sheet: -0.59 (0.17), residues: 887 loop : -1.64 (0.12), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 100 HIS 0.004 0.001 HIS r 124 PHE 0.025 0.001 PHE L 79 TYR 0.020 0.001 TYR y 96 ARG 0.009 0.000 ARG k 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 591 time to evaluate : 4.675 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: n 65 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7072 (mmt180) REVERT: n 99 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7988 (mmt) REVERT: q 20 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7175 (tt0) REVERT: r 176 ASN cc_start: 0.8485 (t0) cc_final: 0.7912 (m-40) REVERT: t 121 ASP cc_start: 0.7921 (m-30) cc_final: 0.7677 (m-30) REVERT: u 135 MET cc_start: 0.8121 (ppp) cc_final: 0.7496 (ppp) REVERT: x 24 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.9041 (mmtm) REVERT: x 57 MET cc_start: 0.8018 (mmm) cc_final: 0.7789 (mmm) REVERT: x 104 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7254 (mt0) REVERT: z 82 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7500 (t0) REVERT: B 35 ASP cc_start: 0.8313 (p0) cc_final: 0.8082 (p0) REVERT: B 131 ASP cc_start: 0.8254 (m-30) cc_final: 0.8044 (t0) REVERT: C 48 HIS cc_start: 0.7805 (OUTLIER) cc_final: 0.7274 (p-80) REVERT: J 52 LYS cc_start: 0.8410 (ptpp) cc_final: 0.8156 (pttm) REVERT: J 67 ASP cc_start: 0.7926 (t0) cc_final: 0.7675 (t0) REVERT: Q 118 ARG cc_start: 0.5094 (mtm180) cc_final: 0.4839 (mtm180) REVERT: T 68 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7647 (tm-30) REVERT: O 32 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7584 (ptt90) REVERT: K 87 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8050 (ptm-80) outliers start: 143 outliers final: 64 residues processed: 678 average time/residue: 1.5220 time to fit residues: 1399.9370 Evaluate side-chains 637 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 564 time to evaluate : 4.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 114 SER Chi-restraints excluded: chain i residue 158 VAL Chi-restraints excluded: chain i residue 169 SER Chi-restraints excluded: chain j residue 24 PHE Chi-restraints excluded: chain k residue 51 THR Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 146 THR Chi-restraints excluded: chain k residue 166 THR Chi-restraints excluded: chain l residue 134 CYS Chi-restraints excluded: chain l residue 175 VAL Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain n residue 99 MET Chi-restraints excluded: chain q residue 20 GLN Chi-restraints excluded: chain q residue 46 VAL Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 138 LYS Chi-restraints excluded: chain r residue 161 THR Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain t residue 21 ASN Chi-restraints excluded: chain t residue 60 PHE Chi-restraints excluded: chain x residue 24 LYS Chi-restraints excluded: chain x residue 104 GLN Chi-restraints excluded: chain y residue 58 ASP Chi-restraints excluded: chain y residue 70 THR Chi-restraints excluded: chain z residue 17 ILE Chi-restraints excluded: chain z residue 25 THR Chi-restraints excluded: chain z residue 82 ASP Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 25 GLN Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain H residue 89 ASN Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 43 ASN Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain T residue 51 THR Chi-restraints excluded: chain O residue 32 ARG Chi-restraints excluded: chain w residue 43 THR Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 87 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 217 optimal weight: 7.9990 chunk 581 optimal weight: 0.3980 chunk 127 optimal weight: 10.0000 chunk 379 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 646 optimal weight: 10.0000 chunk 536 optimal weight: 9.9990 chunk 299 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 339 optimal weight: 10.0000 overall best weight: 6.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 74 GLN l 159 HIS ** m 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 127 GLN ** o 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 58 GLN A 19 ASN A 71 GLN C 72 ASN D 33 GLN E 15 ASN I 107 GLN N 51 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 85619 Z= 0.342 Angle : 0.706 21.101 125085 Z= 0.359 Chirality : 0.043 0.285 15708 Planarity : 0.005 0.077 8721 Dihedral : 23.752 179.679 35509 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.22 % Favored : 90.61 % Rotamer: Outliers : 4.15 % Allowed : 19.56 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 1.02 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.12), residues: 4848 helix: 0.08 (0.14), residues: 1482 sheet: -0.64 (0.17), residues: 889 loop : -1.65 (0.12), residues: 2477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP u 100 HIS 0.005 0.001 HIS p 122 PHE 0.030 0.002 PHE L 79 TYR 0.029 0.002 TYR y 96 ARG 0.014 0.001 ARG r 179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 578 time to evaluate : 4.659 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: l 159 HIS cc_start: 0.7942 (OUTLIER) cc_final: 0.7491 (p-80) REVERT: m 133 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7803 (mttm) REVERT: n 65 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7082 (mmt180) REVERT: o 89 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.6802 (p0) REVERT: q 20 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: x 24 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.9050 (mmtm) REVERT: x 57 MET cc_start: 0.8062 (mmm) cc_final: 0.7819 (mmm) REVERT: x 104 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7266 (mt0) REVERT: z 79 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7420 (pt0) REVERT: z 82 ASP cc_start: 0.7990 (t70) cc_final: 0.7695 (t0) REVERT: B 35 ASP cc_start: 0.8314 (p0) cc_final: 0.8099 (p0) REVERT: B 127 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8226 (m110) REVERT: C 48 HIS cc_start: 0.7834 (OUTLIER) cc_final: 0.7283 (p-80) REVERT: C 109 GLU cc_start: 0.7774 (tt0) cc_final: 0.7547 (tt0) REVERT: I 22 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8478 (pt0) REVERT: J 49 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7477 (mtp-110) REVERT: J 67 ASP cc_start: 0.7959 (t0) cc_final: 0.7674 (t0) REVERT: T 68 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7659 (tm-30) REVERT: O 32 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7560 (ptt90) REVERT: K 87 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8110 (ptm-80) outliers start: 171 outliers final: 95 residues processed: 684 average time/residue: 1.5040 time to fit residues: 1397.7976 Evaluate side-chains 668 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 559 time to evaluate : 4.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 6 THR Chi-restraints excluded: chain i residue 9 LEU Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 114 SER Chi-restraints excluded: chain i residue 158 VAL Chi-restraints excluded: chain i residue 169 SER Chi-restraints excluded: chain i residue 188 LEU Chi-restraints excluded: chain j residue 24 PHE Chi-restraints excluded: chain k residue 51 THR Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 146 THR Chi-restraints excluded: chain k residue 166 THR Chi-restraints excluded: chain k residue 206 THR Chi-restraints excluded: chain l residue 67 ASN Chi-restraints excluded: chain l residue 134 CYS Chi-restraints excluded: chain l residue 139 SER Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 175 VAL Chi-restraints excluded: chain m residue 133 LYS Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 253 ASP Chi-restraints excluded: chain n residue 23 VAL Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain n residue 119 ASP Chi-restraints excluded: chain o residue 6 SER Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain o residue 89 ASP Chi-restraints excluded: chain p residue 166 LEU Chi-restraints excluded: chain q residue 20 GLN Chi-restraints excluded: chain q residue 46 VAL Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 138 LYS Chi-restraints excluded: chain r residue 161 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain s residue 51 SER Chi-restraints excluded: chain t residue 21 ASN Chi-restraints excluded: chain t residue 60 PHE Chi-restraints excluded: chain t residue 83 THR Chi-restraints excluded: chain x residue 24 LYS Chi-restraints excluded: chain x residue 70 ASN Chi-restraints excluded: chain x residue 104 GLN Chi-restraints excluded: chain y residue 58 ASP Chi-restraints excluded: chain z residue 17 ILE Chi-restraints excluded: chain z residue 25 THR Chi-restraints excluded: chain z residue 79 GLU Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain B residue 25 GLN Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain H residue 89 ASN Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain J residue 49 ARG Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 43 ASN Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain Q residue 137 ASP Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain T residue 51 THR Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain O residue 32 ARG Chi-restraints excluded: chain w residue 43 THR Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 91 THR Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 87 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 623 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 368 optimal weight: 6.9990 chunk 471 optimal weight: 6.9990 chunk 365 optimal weight: 9.9990 chunk 544 optimal weight: 1.9990 chunk 360 optimal weight: 9.9990 chunk 643 optimal weight: 1.9990 chunk 402 optimal weight: 7.9990 chunk 392 optimal weight: 6.9990 chunk 297 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: j 40 ASN l 74 GLN l 159 HIS ** m 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 127 GLN ** o 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 32 HIS A 19 ASN A 71 GLN C 72 ASN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN N 51 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 85619 Z= 0.234 Angle : 0.656 21.007 125085 Z= 0.334 Chirality : 0.039 0.270 15708 Planarity : 0.005 0.078 8721 Dihedral : 23.725 179.164 35509 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.68 % Favored : 91.17 % Rotamer: Outliers : 3.66 % Allowed : 21.31 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 1.53 % Twisted General : 0.13 % 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: -1.29 (0.12), residues: 4848 helix: 0.22 (0.14), residues: 1478 sheet: -0.62 (0.17), residues: 890 loop : -1.62 (0.12), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 100 HIS 0.009 0.001 HIS l 159 PHE 0.030 0.001 PHE L 79 TYR 0.030 0.001 TYR y 96 ARG 0.012 0.000 ARG o 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 581 time to evaluate : 4.836 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: m 133 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7709 (mttm) REVERT: n 65 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7109 (mmt180) REVERT: n 66 GLN cc_start: 0.7825 (mp10) cc_final: 0.7548 (mp10) REVERT: n 99 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.8006 (mmt) REVERT: o 89 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6713 (p0) REVERT: o 101 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8419 (mp) REVERT: q 20 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7222 (tt0) REVERT: r 180 LYS cc_start: 0.7938 (mmpt) cc_final: 0.7513 (mmtm) REVERT: x 24 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.9042 (mmtm) REVERT: x 104 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7276 (mt0) REVERT: z 82 ASP cc_start: 0.8115 (t70) cc_final: 0.7596 (t0) REVERT: B 35 ASP cc_start: 0.8289 (p0) cc_final: 0.8052 (p0) REVERT: B 127 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8193 (m110) REVERT: C 48 HIS cc_start: 0.7781 (OUTLIER) cc_final: 0.7282 (p-80) REVERT: C 109 GLU cc_start: 0.7675 (tt0) cc_final: 0.7402 (tt0) REVERT: J 67 ASP cc_start: 0.7918 (t0) cc_final: 0.7660 (t0) REVERT: Q 149 LYS cc_start: 0.7642 (mmmm) cc_final: 0.6870 (mppt) REVERT: T 68 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7693 (tm-30) REVERT: O 32 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7455 (ptt90) REVERT: K 87 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8038 (ptm-80) REVERT: K 91 ASP cc_start: 0.8066 (m-30) cc_final: 0.7766 (m-30) outliers start: 151 outliers final: 102 residues processed: 669 average time/residue: 1.5357 time to fit residues: 1395.1475 Evaluate side-chains 674 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 560 time to evaluate : 4.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 114 SER Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain i residue 158 VAL Chi-restraints excluded: chain i residue 169 SER Chi-restraints excluded: chain i residue 188 LEU Chi-restraints excluded: chain j residue 24 PHE Chi-restraints excluded: chain j residue 113 MET Chi-restraints excluded: chain k residue 51 THR Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 146 THR Chi-restraints excluded: chain k residue 166 THR Chi-restraints excluded: chain l residue 134 CYS Chi-restraints excluded: chain l residue 139 SER Chi-restraints excluded: chain l residue 175 VAL Chi-restraints excluded: chain m residue 38 LEU Chi-restraints excluded: chain m residue 133 LYS Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 162 ILE Chi-restraints excluded: chain n residue 23 VAL Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain n residue 99 MET Chi-restraints excluded: chain n residue 119 ASP Chi-restraints excluded: chain o residue 6 SER Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 89 ASP Chi-restraints excluded: chain o residue 101 ILE Chi-restraints excluded: chain o residue 111 LEU Chi-restraints excluded: chain p residue 157 LYS Chi-restraints excluded: chain p residue 166 LEU Chi-restraints excluded: chain q residue 20 GLN Chi-restraints excluded: chain q residue 46 VAL Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain q residue 121 LEU Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 138 LYS Chi-restraints excluded: chain r residue 161 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain t residue 21 ASN Chi-restraints excluded: chain t residue 60 PHE Chi-restraints excluded: chain t residue 83 THR Chi-restraints excluded: chain u residue 137 MET Chi-restraints excluded: chain x residue 24 LYS Chi-restraints excluded: chain x residue 104 GLN Chi-restraints excluded: chain y residue 58 ASP Chi-restraints excluded: chain y residue 70 THR Chi-restraints excluded: chain z residue 17 ILE Chi-restraints excluded: chain z residue 25 THR Chi-restraints excluded: chain z residue 79 GLU Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain H residue 89 ASN Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 43 ASN Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 137 ASP Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain T residue 51 THR Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain O residue 32 ARG Chi-restraints excluded: chain w residue 43 THR Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 91 THR Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 87 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 398 optimal weight: 10.0000 chunk 257 optimal weight: 8.9990 chunk 384 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 409 optimal weight: 5.9990 chunk 438 optimal weight: 6.9990 chunk 318 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 506 optimal weight: 0.2980 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 74 GLN l 159 HIS ** m 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 127 GLN ** o 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 32 HIS A 19 ASN A 71 GLN C 72 ASN D 33 GLN E 15 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 GLN N 51 ASN w 99 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 85619 Z= 0.215 Angle : 0.648 20.982 125085 Z= 0.330 Chirality : 0.039 0.377 15708 Planarity : 0.005 0.078 8721 Dihedral : 23.671 179.923 35509 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.83 % Favored : 91.03 % Rotamer: Outliers : 3.61 % Allowed : 22.18 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 1.53 % Twisted General : 0.09 % 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: -1.22 (0.12), residues: 4848 helix: 0.29 (0.14), residues: 1481 sheet: -0.58 (0.18), residues: 867 loop : -1.59 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP u 100 HIS 0.004 0.001 HIS l 159 PHE 0.029 0.001 PHE L 79 TYR 0.034 0.001 TYR y 96 ARG 0.013 0.000 ARG r 179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 585 time to evaluate : 4.600 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: m 133 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7698 (mttm) REVERT: n 65 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7108 (mmt180) REVERT: n 66 GLN cc_start: 0.7866 (mp10) cc_final: 0.7644 (mp10) REVERT: o 101 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8424 (mp) REVERT: q 20 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7200 (tt0) REVERT: r 180 LYS cc_start: 0.7916 (mmpt) cc_final: 0.7658 (mppt) REVERT: x 24 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8991 (mmtm) REVERT: x 104 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7295 (mt0) REVERT: z 82 ASP cc_start: 0.8104 (t70) cc_final: 0.7579 (t0) REVERT: B 35 ASP cc_start: 0.8278 (p0) cc_final: 0.8063 (p0) REVERT: B 127 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8189 (m110) REVERT: C 48 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.7251 (p-80) REVERT: J 67 ASP cc_start: 0.7875 (t0) cc_final: 0.7635 (t0) REVERT: Q 149 LYS cc_start: 0.7626 (mmmm) cc_final: 0.6998 (mppt) REVERT: T 68 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7673 (tm-30) REVERT: O 32 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7483 (ptt90) REVERT: K 87 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8079 (ptm-80) REVERT: K 91 ASP cc_start: 0.8066 (m-30) cc_final: 0.7774 (m-30) outliers start: 149 outliers final: 103 residues processed: 671 average time/residue: 1.5493 time to fit residues: 1406.5108 Evaluate side-chains 677 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 564 time to evaluate : 4.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 6 THR Chi-restraints excluded: chain i residue 9 LEU Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 114 SER Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain i residue 158 VAL Chi-restraints excluded: chain i residue 188 LEU Chi-restraints excluded: chain j residue 24 PHE Chi-restraints excluded: chain k residue 51 THR Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 146 THR Chi-restraints excluded: chain k residue 166 THR Chi-restraints excluded: chain l residue 134 CYS Chi-restraints excluded: chain l residue 139 SER Chi-restraints excluded: chain l residue 175 VAL Chi-restraints excluded: chain m residue 38 LEU Chi-restraints excluded: chain m residue 133 LYS Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 162 ILE Chi-restraints excluded: chain n residue 23 VAL Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain o residue 6 SER Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 101 ILE Chi-restraints excluded: chain o residue 111 LEU Chi-restraints excluded: chain p residue 90 VAL Chi-restraints excluded: chain p residue 166 LEU Chi-restraints excluded: chain q residue 20 GLN Chi-restraints excluded: chain q residue 46 VAL Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain q residue 121 LEU Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 138 LYS Chi-restraints excluded: chain r residue 161 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain t residue 21 ASN Chi-restraints excluded: chain t residue 60 PHE Chi-restraints excluded: chain t residue 83 THR Chi-restraints excluded: chain u residue 137 MET Chi-restraints excluded: chain u residue 138 GLU Chi-restraints excluded: chain x residue 24 LYS Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain x residue 70 ASN Chi-restraints excluded: chain x residue 104 GLN Chi-restraints excluded: chain y residue 58 ASP Chi-restraints excluded: chain z residue 17 ILE Chi-restraints excluded: chain z residue 25 THR Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain H residue 89 ASN Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 43 ASN Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain T residue 51 THR Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain O residue 32 ARG Chi-restraints excluded: chain w residue 43 THR Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 91 THR Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 87 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 585 optimal weight: 9.9990 chunk 616 optimal weight: 20.0000 chunk 562 optimal weight: 10.0000 chunk 599 optimal weight: 20.0000 chunk 361 optimal weight: 10.0000 chunk 261 optimal weight: 0.8980 chunk 471 optimal weight: 9.9990 chunk 184 optimal weight: 30.0000 chunk 542 optimal weight: 8.9990 chunk 567 optimal weight: 7.9990 chunk 597 optimal weight: 30.0000 overall best weight: 7.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** j 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 159 HIS ** m 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 127 GLN ** o 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 32 HIS t 110 HIS t 138 ASN A 19 ASN A 71 GLN C 72 ASN D 33 GLN E 15 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 85619 Z= 0.387 Angle : 0.749 21.344 125085 Z= 0.380 Chirality : 0.045 0.379 15708 Planarity : 0.006 0.080 8721 Dihedral : 23.711 179.748 35509 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.55 % Favored : 90.26 % Rotamer: Outliers : 3.39 % Allowed : 22.86 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 1.02 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.12), residues: 4848 helix: 0.13 (0.14), residues: 1471 sheet: -0.64 (0.17), residues: 882 loop : -1.65 (0.12), residues: 2495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 100 HIS 0.006 0.001 HIS m 17 PHE 0.032 0.002 PHE L 79 TYR 0.043 0.002 TYR y 96 ARG 0.014 0.001 ARG k 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 580 time to evaluate : 4.638 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: k 117 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8781 (m) REVERT: l 105 MET cc_start: 0.8126 (tpp) cc_final: 0.7896 (ttm) REVERT: m 133 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7873 (mttm) REVERT: n 65 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7071 (mmt180) REVERT: n 66 GLN cc_start: 0.7861 (mp10) cc_final: 0.7593 (mp10) REVERT: o 89 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.6709 (p0) REVERT: o 101 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8507 (mp) REVERT: q 20 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: u 33 ARG cc_start: 0.8384 (mmp80) cc_final: 0.8095 (mmp80) REVERT: x 104 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7290 (mt0) REVERT: z 82 ASP cc_start: 0.8158 (t70) cc_final: 0.7543 (t0) REVERT: z 104 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.8011 (p0) REVERT: A 16 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7597 (ttm110) REVERT: B 35 ASP cc_start: 0.8272 (p0) cc_final: 0.8072 (p0) REVERT: B 126 GLU cc_start: 0.7153 (tp30) cc_final: 0.6825 (mm-30) REVERT: B 127 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8217 (m110) REVERT: C 48 HIS cc_start: 0.7864 (OUTLIER) cc_final: 0.7273 (p-80) REVERT: J 67 ASP cc_start: 0.8009 (t0) cc_final: 0.7737 (t0) REVERT: N 54 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8235 (mp) REVERT: Q 116 LYS cc_start: 0.7228 (mmmt) cc_final: 0.6009 (mmmt) REVERT: Q 149 LYS cc_start: 0.7849 (mmmm) cc_final: 0.7311 (mppt) REVERT: T 68 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7935 (tm-30) REVERT: O 32 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.7586 (ptt90) REVERT: K 87 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8104 (ptm-80) outliers start: 140 outliers final: 100 residues processed: 670 average time/residue: 1.5540 time to fit residues: 1408.6105 Evaluate side-chains 672 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 558 time to evaluate : 4.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 6 THR Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 114 SER Chi-restraints excluded: chain i residue 169 SER Chi-restraints excluded: chain i residue 188 LEU Chi-restraints excluded: chain i residue 196 SER Chi-restraints excluded: chain j residue 24 PHE Chi-restraints excluded: chain j residue 113 MET Chi-restraints excluded: chain k residue 51 THR Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 117 THR Chi-restraints excluded: chain k residue 146 THR Chi-restraints excluded: chain k residue 166 THR Chi-restraints excluded: chain l residue 67 ASN Chi-restraints excluded: chain l residue 134 CYS Chi-restraints excluded: chain l residue 139 SER Chi-restraints excluded: chain l residue 175 VAL Chi-restraints excluded: chain m residue 133 LYS Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 162 ILE Chi-restraints excluded: chain n residue 23 VAL Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain o residue 6 SER Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 89 ASP Chi-restraints excluded: chain o residue 101 ILE Chi-restraints excluded: chain o residue 111 LEU Chi-restraints excluded: chain p residue 90 VAL Chi-restraints excluded: chain p residue 157 LYS Chi-restraints excluded: chain p residue 166 LEU Chi-restraints excluded: chain q residue 20 GLN Chi-restraints excluded: chain q residue 46 VAL Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain q residue 121 LEU Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 138 LYS Chi-restraints excluded: chain r residue 161 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain t residue 21 ASN Chi-restraints excluded: chain t residue 60 PHE Chi-restraints excluded: chain t residue 83 THR Chi-restraints excluded: chain u residue 137 MET Chi-restraints excluded: chain u residue 138 GLU Chi-restraints excluded: chain x residue 70 ASN Chi-restraints excluded: chain x residue 104 GLN Chi-restraints excluded: chain y residue 58 ASP Chi-restraints excluded: chain z residue 17 ILE Chi-restraints excluded: chain z residue 25 THR Chi-restraints excluded: chain z residue 104 ASN Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain H residue 89 ASN Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 43 ASN Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 137 ASP Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain T residue 51 THR Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain O residue 32 ARG Chi-restraints excluded: chain w residue 43 THR Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 91 THR Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 87 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 393 optimal weight: 9.9990 chunk 634 optimal weight: 0.0040 chunk 387 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 chunk 441 optimal weight: 2.9990 chunk 665 optimal weight: 5.9990 chunk 612 optimal weight: 5.9990 chunk 529 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 409 optimal weight: 9.9990 chunk 324 optimal weight: 7.9990 overall best weight: 4.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 159 HIS ** m 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 127 GLN ** o 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 32 HIS u 96 GLN A 19 ASN A 71 GLN ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 ASN D 33 GLN E 15 ASN N 51 ASN ** w 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 85619 Z= 0.261 Angle : 0.687 21.159 125085 Z= 0.349 Chirality : 0.041 0.357 15708 Planarity : 0.005 0.078 8721 Dihedral : 23.692 178.794 35509 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.89 % Favored : 90.99 % Rotamer: Outliers : 3.27 % Allowed : 23.22 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 1.02 % Twisted General : 0.13 % 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: -1.27 (0.12), residues: 4848 helix: 0.25 (0.14), residues: 1472 sheet: -0.62 (0.17), residues: 883 loop : -1.61 (0.12), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 100 HIS 0.004 0.001 HIS t 110 PHE 0.031 0.001 PHE L 79 TYR 0.038 0.002 TYR y 96 ARG 0.019 0.000 ARG r 179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 565 time to evaluate : 4.710 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: m 133 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7733 (mttm) REVERT: n 65 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7063 (mmt180) REVERT: n 66 GLN cc_start: 0.7804 (mp10) cc_final: 0.7537 (mp10) REVERT: o 89 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.6683 (p0) REVERT: o 101 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8472 (mp) REVERT: q 20 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7256 (tt0) REVERT: u 33 ARG cc_start: 0.8346 (mmp80) cc_final: 0.7942 (mmp80) REVERT: x 104 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7289 (mt0) REVERT: z 82 ASP cc_start: 0.8121 (t70) cc_final: 0.7584 (t0) REVERT: z 104 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7995 (p0) REVERT: B 35 ASP cc_start: 0.8272 (p0) cc_final: 0.8064 (p0) REVERT: B 126 GLU cc_start: 0.7106 (tp30) cc_final: 0.6756 (mm-30) REVERT: B 127 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8198 (m110) REVERT: C 48 HIS cc_start: 0.7710 (OUTLIER) cc_final: 0.7243 (p-80) REVERT: J 67 ASP cc_start: 0.8047 (t0) cc_final: 0.7780 (t0) REVERT: Q 116 LYS cc_start: 0.7249 (mmmt) cc_final: 0.6060 (mmmt) REVERT: Q 149 LYS cc_start: 0.7773 (mmmm) cc_final: 0.7275 (mppt) REVERT: T 68 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7652 (tm-30) REVERT: O 32 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7526 (ptt90) REVERT: K 87 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8062 (ptm-80) outliers start: 135 outliers final: 103 residues processed: 654 average time/residue: 1.4909 time to fit residues: 1326.9592 Evaluate side-chains 672 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 558 time to evaluate : 4.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 6 THR Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 114 SER Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain i residue 169 SER Chi-restraints excluded: chain i residue 188 LEU Chi-restraints excluded: chain j residue 24 PHE Chi-restraints excluded: chain k residue 51 THR Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 146 THR Chi-restraints excluded: chain k residue 166 THR Chi-restraints excluded: chain k residue 206 THR Chi-restraints excluded: chain l residue 134 CYS Chi-restraints excluded: chain l residue 139 SER Chi-restraints excluded: chain l residue 175 VAL Chi-restraints excluded: chain m residue 133 LYS Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 162 ILE Chi-restraints excluded: chain n residue 23 VAL Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain o residue 6 SER Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 89 ASP Chi-restraints excluded: chain o residue 101 ILE Chi-restraints excluded: chain o residue 111 LEU Chi-restraints excluded: chain p residue 90 VAL Chi-restraints excluded: chain p residue 157 LYS Chi-restraints excluded: chain p residue 166 LEU Chi-restraints excluded: chain q residue 3 ILE Chi-restraints excluded: chain q residue 20 GLN Chi-restraints excluded: chain q residue 46 VAL Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain q residue 121 LEU Chi-restraints excluded: chain r residue 65 LYS Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 138 LYS Chi-restraints excluded: chain r residue 161 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain t residue 21 ASN Chi-restraints excluded: chain t residue 60 PHE Chi-restraints excluded: chain t residue 83 THR Chi-restraints excluded: chain u residue 70 ASN Chi-restraints excluded: chain u residue 138 GLU Chi-restraints excluded: chain x residue 104 GLN Chi-restraints excluded: chain y residue 58 ASP Chi-restraints excluded: chain z residue 17 ILE Chi-restraints excluded: chain z residue 25 THR Chi-restraints excluded: chain z residue 104 ASN Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain H residue 89 ASN Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 43 ASN Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 137 ASP Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain O residue 32 ARG Chi-restraints excluded: chain w residue 43 THR Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 91 THR Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 74 CYS Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 87 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 420 optimal weight: 50.0000 chunk 564 optimal weight: 0.7980 chunk 162 optimal weight: 10.0000 chunk 488 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 530 optimal weight: 6.9990 chunk 222 optimal weight: 20.0000 chunk 545 optimal weight: 9.9990 chunk 67 optimal weight: 40.0000 chunk 97 optimal weight: 40.0000 overall best weight: 6.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 127 GLN ** o 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 ASN A 71 GLN ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN E 15 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 ASN w 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.094244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.065643 restraints weight = 205528.446| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.54 r_work: 0.2932 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.273 85619 Z= 0.324 Angle : 0.744 59.184 125085 Z= 0.386 Chirality : 0.042 0.699 15708 Planarity : 0.005 0.159 8721 Dihedral : 23.692 178.773 35509 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.99 % Favored : 90.88 % Rotamer: Outliers : 3.08 % Allowed : 23.44 % Favored : 73.48 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 1.53 % Twisted General : 0.15 % 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: -1.27 (0.12), residues: 4848 helix: 0.24 (0.14), residues: 1472 sheet: -0.61 (0.17), residues: 883 loop : -1.61 (0.12), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 100 HIS 0.004 0.001 HIS t 110 PHE 0.030 0.001 PHE L 79 TYR 0.032 0.002 TYR y 96 ARG 0.015 0.000 ARG r 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21661.45 seconds wall clock time: 380 minutes 5.70 seconds (22805.70 seconds total)