Starting phenix.real_space_refine on Sun Mar 24 09:15:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmw_29298/03_2024/8fmw_29298.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmw_29298/03_2024/8fmw_29298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmw_29298/03_2024/8fmw_29298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmw_29298/03_2024/8fmw_29298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmw_29298/03_2024/8fmw_29298.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmw_29298/03_2024/8fmw_29298.pdb" } resolution = 2.86 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= 0.039 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 4 6.06 5 P 4645 5.49 5 S 168 5.16 5 C 74854 2.51 5 N 27354 2.21 5 O 40885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 56": "OD1" <-> "OD2" Residue "C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D ASP 189": "OD1" <-> "OD2" Residue "D TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "F PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "F PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 141": "OD1" <-> "OD2" Residue "G PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 9": "OD1" <-> "OD2" Residue "H TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 136": "NH1" <-> "NH2" Residue "J TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 19": "OE1" <-> "OE2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 110": "NH1" <-> "NH2" Residue "N TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 36": "OD1" <-> "OD2" Residue "N PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 50": "OE1" <-> "OE2" Residue "O ASP 3": "OD1" <-> "OD2" Residue "O GLU 18": "OE1" <-> "OE2" Residue "O TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 8": "OE1" <-> "OE2" Residue "Q TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 64": "OE1" <-> "OE2" Residue "R PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 36": "OE1" <-> "OE2" Residue "U TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 61": "NH1" <-> "NH2" Residue "W TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AD TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AD TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AD ASP 67": "OD1" <-> "OD2" Residue "AD PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AD TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AD ASP 100": "OD1" <-> "OD2" Residue "AD GLU 102": "OE1" <-> "OE2" Residue "AD PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AD TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE ASP 54": "OD1" <-> "OD2" Residue "AE ASP 90": "OD1" <-> "OD2" Residue "AE ASP 107": "OD1" <-> "OD2" Residue "AE PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE GLU 181": "OE1" <-> "OE2" Residue "AE PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AF ASP 20": "OD1" <-> "OD2" Residue "AF PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AF GLU 55": "OE1" <-> "OE2" Residue "AF ASP 119": "OD1" <-> "OD2" Residue "AF PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AF ASP 160": "OD1" <-> "OD2" Residue "AF PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AF PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AF TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG GLU 45": "OE1" <-> "OE2" Residue "AG TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG GLU 150": "OE1" <-> "OE2" Residue "AG PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AH ARG 3": "NH1" <-> "NH2" Residue "AH GLU 27": "OE1" <-> "OE2" Residue "AH ASP 36": "OD1" <-> "OD2" Residue "AH ASP 58": "OD1" <-> "OD2" Residue "AH TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AH PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AH PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AH PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AH ASP 137": "OD1" <-> "OD2" Residue "AH ASP 165": "OD1" <-> "OD2" Residue "AI PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL ASP 25": "OD1" <-> "OD2" Residue "AL ASP 28": "OD1" <-> "OD2" Residue "AL TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL ASP 55": "OD1" <-> "OD2" Residue "AL TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM ASP 12": "OD1" <-> "OD2" Residue "AM ASP 56": "OD1" <-> "OD2" Residue "AM TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM ASP 88": "OD1" <-> "OD2" Residue "AM PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM GLU 120": "OE1" <-> "OE2" Residue "AN PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AN TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AN TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AO TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AO TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AO GLU 38": "OE1" <-> "OE2" Residue "AO PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AO ASP 91": "OD1" <-> "OD2" Residue "AO PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AP PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AP PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AP PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AP TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AP ASP 106": "OD1" <-> "OD2" Residue "AP GLU 117": "OE1" <-> "OE2" Residue "AQ PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ ASP 48": "OD1" <-> "OD2" Residue "AQ PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AR PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AR TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AR GLU 37": "OE1" <-> "OE2" Residue "AR GLU 43": "OE1" <-> "OE2" Residue "AR TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS ASP 49": "OD1" <-> "OD2" Residue "AS PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AT PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AT ASP 23": "OD1" <-> "OD2" Residue "AT GLU 29": "OE1" <-> "OE2" Residue "AT GLU 34": "OE1" <-> "OE2" Residue "AT TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AT TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AU ASP 26": "OD1" <-> "OD2" Residue "AU TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AU TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AU ASP 99": "OD1" <-> "OD2" Residue "AU PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AU ASP 113": "OD1" <-> "OD2" Residue "AV TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AV GLU 14": "OE1" <-> "OE2" Residue "AV TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AV GLU 45": "OE1" <-> "OE2" Residue "AV TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AV TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AV PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AW ASP 60": "OD1" <-> "OD2" Residue "AW GLU 62": "OE1" <-> "OE2" Residue "AW PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AX TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AX PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AX PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AX PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AX ASP 66": "OD1" <-> "OD2" Residue "AX PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AX TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AX TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AX GLU 119": "OE1" <-> "OE2" Residue "AX PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AY PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AY GLU 35": "OE1" <-> "OE2" Residue "AY ASP 56": "OD1" <-> "OD2" Residue "AY GLU 68": "OE1" <-> "OE2" Residue "AY PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AY TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AZ PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AZ PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AZ PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa ASP 11": "OD1" <-> "OD2" Residue "Ab PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ab PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ab PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac GLU 33": "OE1" <-> "OE2" Residue "Ac TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ad PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ad TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae GLU 11": "OE1" <-> "OE2" Residue "Ae GLU 36": "OE1" <-> "OE2" Residue "Ae GLU 39": "OE1" <-> "OE2" Residue "Ae TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Af PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ag TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ag PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ai GLU 15": "OE1" <-> "OE2" Residue "Ai GLU 31": "OE1" <-> "OE2" Residue "Ai PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 147910 Number of models: 1 Model: "" Number of chains: 62 Chain: "A" Number of atoms: 32780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1529, 32780 Classifications: {'RNA': 1529} Modifications used: {'5*END': 1, 'rna2p_pur': 121, 'rna2p_pyr': 83, 'rna3p_pur': 763, 'rna3p_pyr': 562} Link IDs: {'rna2p': 204, 'rna3p': 1324} Chain: "C" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1646 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 6, 'TRANS': 199} Chain: "D" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1689 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 199} Chain: "E" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1196 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 153} Chain: "F" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 814 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "G" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1282 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "H" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1039 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "I" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1043 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain: "J" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 817 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain: "K" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 876 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "L" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 968 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 114} Chain: "M" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 901 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "N" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 491 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "O" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 718 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 676 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "Q" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 678 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "R" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 521 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "S" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 669 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 697 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'TRANS': 84} Chain: "U" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 603 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "V" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 240 Classifications: {'peptide': 27} Modifications used: {'COO': 1} Link IDs: {'TRANS': 26} Chain: "W" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 818 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "X" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1618 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 31, 'rna3p_pyr': 32} Link IDs: {'rna2p': 12, 'rna3p': 63} Chain: "AA" Number of atoms: 62816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2929, 62816 Classifications: {'RNA': 2929} Modifications used: {'rna2p_pur': 307, 'rna2p_pyr': 150, 'rna3p_pur': 1409, 'rna3p_pyr': 1063} Link IDs: {'rna2p': 457, 'rna3p': 2471} Chain: "AB" Number of atoms: 2398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2398 Classifications: {'RNA': 112} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 53, 'rna3p_pyr': 40} Link IDs: {'rna2p': 19, 'rna3p': 92} Chain: "AC" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 884 Classifications: {'peptide': 221} Incomplete info: {'backbone_only': 208} Link IDs: {'PTRANS': 8, 'TRANS': 212} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 918 Unresolved non-hydrogen angles: 1306 Unresolved non-hydrogen dihedrals: 597 Unresolved non-hydrogen chiralities: 267 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 10, 'TYR:plan': 5, 'ASN:plan1': 16, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 14, 'GLU:plan': 12, 'ASP:plan': 18} Unresolved non-hydrogen planarities: 406 Chain: "AD" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2156 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 261} Chain: "AE" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1564 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain: "AF" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1658 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 203} Chain: "AG" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1439 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain: "AH" Number of atoms: 1405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1405 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 174} Chain: "AI" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 751 Classifications: {'peptide': 148} Incomplete info: {'backbone_only': 103} Link IDs: {'PTRANS': 1, 'TRANS': 146} Unresolved non-hydrogen bonds: 465 Unresolved non-hydrogen angles: 653 Unresolved non-hydrogen dihedrals: 303 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 193 Chain: "AJ" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 648 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 155} Link IDs: {'PTRANS': 3, 'TRANS': 158} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 638 Unresolved non-hydrogen angles: 914 Unresolved non-hydrogen dihedrals: 397 Unresolved non-hydrogen chiralities: 207 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 10, 'ASP:plan': 7, 'PHE:plan': 9, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 240 Chain: "AK" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 556 Classifications: {'peptide': 139} Incomplete info: {'backbone_only': 128} Link IDs: {'PTRANS': 8, 'TRANS': 130} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 708 Unresolved non-hydrogen dihedrals: 308 Unresolved non-hydrogen chiralities: 165 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 150 Chain: "AL" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1171 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 136} Chain: "AM" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 942 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "AN" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1129 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "AO" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1092 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 131} Chain: "AP" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1004 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "AQ" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 968 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain: "AR" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 951 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "AS" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 943 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'TRANS': 113} Chain: "AT" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 859 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 100} Chain: "AU" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 918 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "AV" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 784 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "AW" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 800 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain: "AX" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1432 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "AY" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 571 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'TRANS': 73} Chain: "AZ" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "Aa" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 553 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "Ab" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 814 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'TRANS': 99} Chain: "Ac" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 656 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "Ad" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 484 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain: "Ae" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "Af" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 422 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "Ag" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 548 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "Ah" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 305 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "Ai" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 375 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Ad" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Ah" 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 45245 SG CYS N 24 150.647 69.749 220.262 1.00148.58 S ATOM 45268 SG CYS N 27 149.495 72.893 218.448 1.00147.71 S ATOM 45375 SG CYS N 40 152.723 71.482 217.397 1.00142.60 S ATOM 45400 SG CYS N 43 152.400 72.984 220.857 1.00140.27 S ATOM 47626 SG CYS R 35 230.122 127.139 185.977 0.00120.71 S ATOM 47652 SG CYS R 38 231.024 129.341 187.498 1.00123.63 S ATOM A0Z6M SG CYSAd 31 117.830 196.474 80.067 1.00 87.69 S ATOM A0Z76 SG CYSAd 34 119.510 196.202 76.590 1.00 89.10 S ATOM A0Z9B SG CYSAd 44 121.210 194.702 79.475 1.00 84.18 S ATOM A0Z9Y SG CYSAd 47 120.958 198.456 79.284 1.00 87.38 S ATOM A10I7 SG CYSAh 11 84.638 107.926 143.814 1.00 95.45 S ATOM A10IV SG CYSAh 14 85.837 109.476 140.612 1.00 93.33 S ATOM A10LS SG CYSAh 27 83.303 111.400 142.705 1.00 92.55 S Residues with excluded nonbonded symmetry interactions: 196 residue: pdb=" N GLY C 2 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY C 2 " occ=0.00 residue: pdb=" N GLN C 3 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN C 3 " occ=0.00 residue: pdb=" N MET D 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET D 1 " occ=0.00 residue: pdb=" N ASN D 2 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN D 2 " occ=0.00 residue: pdb=" N ARG D 3 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG D 3 " occ=0.00 residue: pdb=" N LYS D 4 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS D 4 " occ=0.00 residue: pdb=" N GLN D 5 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN D 5 " occ=0.00 residue: pdb=" N ILE D 6 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE D 6 " occ=0.00 residue: pdb=" N ARG E 8 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG E 8 " occ=0.00 residue: pdb=" N LYS E 9 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS E 9 " occ=0.00 residue: pdb=" N GLN E 10 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN E 10 " occ=0.00 residue: pdb=" N THR E 21 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR E 21 " occ=0.00 ... (remaining 184 not shown) Time building chain proxies: 58.44, per 1000 atoms: 0.40 Number of scatterers: 147910 At special positions: 0 Unit cell: (272.929, 245.526, 272.929, 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 4 29.99 S 168 16.00 P 4645 15.00 O 40885 8.00 N 27354 7.00 C 74854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYSAe 17 " - pdb=" SG CYSAe 44 " distance=2.05 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: 66.71 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 27 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 43 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 24 " pdb=" ZN R 101 " pdb="ZN ZN R 101 " - pdb=" ND1 HIS R 74 " pdb="ZN ZN R 101 " - pdb=" SG CYS R 35 " pdb="ZN ZN R 101 " - pdb=" SG CYS R 38 " pdb=" ZNAd 101 " pdb="ZN ZNAd 101 " - pdb=" SG CYSAd 34 " pdb="ZN ZNAd 101 " - pdb=" SG CYSAd 44 " pdb="ZN ZNAd 101 " - pdb=" SG CYSAd 47 " pdb="ZN ZNAd 101 " - pdb=" SG CYSAd 31 " pdb=" ZNAh 101 " pdb="ZN ZNAh 101 " - pdb=" ND1 HISAh 32 " pdb="ZN ZNAh 101 " - pdb=" SG CYSAh 14 " pdb="ZN ZNAh 101 " - pdb=" SG CYSAh 11 " pdb="ZN ZNAh 101 " - pdb=" SG CYSAh 27 " Number of angles added : 15 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10598 Finding SS restraints... Secondary structure from input PDB file: 206 helices and 77 sheets defined 37.3% alpha, 21.6% beta 1346 base pairs and 2669 stacking pairs defined. Time for finding SS restraints: 55.25 Creating SS restraints... Processing helix chain 'C' and resid 6 through 12 Processing helix chain 'C' and resid 25 through 49 removed outlier: 4.816A pdb=" N SER C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ALA C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 81 Processing helix chain 'C' and resid 84 through 96 removed outlier: 3.585A pdb=" N LEU C 93 " --> pdb=" O LYS C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'C' and resid 132 through 148 removed outlier: 3.895A pdb=" N GLY C 148 " --> pdb=" O SER C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.501A pdb=" N ALA C 163 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.007A pdb=" N LEU D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 32 Processing helix chain 'D' and resid 48 through 65 Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 96 through 105 Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 147 through 165 removed outlier: 4.612A pdb=" N SER D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU D 164 " --> pdb=" O LYS D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 207 removed outlier: 3.506A pdb=" N LYS D 206 " --> pdb=" O GLU D 202 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG D 207 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 67 Processing helix chain 'E' and resid 107 through 118 Processing helix chain 'E' and resid 131 through 146 Processing helix chain 'E' and resid 148 through 156 Processing helix chain 'F' and resid 14 through 32 Processing helix chain 'F' and resid 69 through 79 removed outlier: 4.521A pdb=" N GLU F 73 " --> pdb=" O ASN F 69 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS F 79 " --> pdb=" O GLU F 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 removed outlier: 3.782A pdb=" N ALA G 24 " --> pdb=" O SER G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 54 Processing helix chain 'G' and resid 58 through 69 removed outlier: 3.901A pdb=" N VAL G 62 " --> pdb=" O ASP G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 112 Processing helix chain 'G' and resid 116 through 130 Processing helix chain 'G' and resid 133 through 149 Processing helix chain 'G' and resid 150 through 155 removed outlier: 4.455A pdb=" N HIS G 154 " --> pdb=" O ALA G 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 21 removed outlier: 4.030A pdb=" N MET H 10 " --> pdb=" O SER H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 96 through 101 removed outlier: 3.674A pdb=" N ASN H 99 " --> pdb=" O ARG H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 121 Processing helix chain 'I' and resid 41 through 45 Processing helix chain 'I' and resid 47 through 61 Proline residue: I 57 - end of helix Processing helix chain 'I' and resid 77 through 97 Processing helix chain 'I' and resid 100 through 108 Processing helix chain 'J' and resid 15 through 33 removed outlier: 3.502A pdb=" N ALA J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 91 Processing helix chain 'K' and resid 54 through 59 removed outlier: 4.164A pdb=" N LYS K 57 " --> pdb=" O LYS K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 74 Processing helix chain 'K' and resid 93 through 104 Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 21 through 25 removed outlier: 3.554A pdb=" N LEU L 24 " --> pdb=" O SER L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 117 Processing helix chain 'M' and resid 14 through 19 Processing helix chain 'M' and resid 20 through 22 No H-bonds generated for 'chain 'M' and resid 20 through 22' Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 64 removed outlier: 3.890A pdb=" N VAL M 53 " --> pdb=" O ASP M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.700A pdb=" N ILE M 84 " --> pdb=" O ARG M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 95 Processing helix chain 'M' and resid 107 through 112 Processing helix chain 'N' and resid 3 through 12 Processing helix chain 'N' and resid 16 through 20 Processing helix chain 'N' and resid 40 through 51 Processing helix chain 'O' and resid 3 through 15 Processing helix chain 'O' and resid 23 through 45 removed outlier: 3.558A pdb=" N ILE O 44 " --> pdb=" O GLU O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 73 Processing helix chain 'O' and resid 73 through 85 Processing helix chain 'P' and resid 52 through 63 Processing helix chain 'P' and resid 67 through 83 Processing helix chain 'R' and resid 35 through 41 Processing helix chain 'R' and resid 45 through 47 No H-bonds generated for 'chain 'R' and resid 45 through 47' Processing helix chain 'R' and resid 48 through 53 Processing helix chain 'R' and resid 54 through 56 No H-bonds generated for 'chain 'R' and resid 54 through 56' Processing helix chain 'R' and resid 64 through 69 Processing helix chain 'R' and resid 71 through 88 Processing helix chain 'S' and resid 4 through 8 Processing helix chain 'S' and resid 12 through 25 Processing helix chain 'S' and resid 41 through 45 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 70 through 75 Processing helix chain 'T' and resid 4 through 42 removed outlier: 3.570A pdb=" N ARG T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 64 Processing helix chain 'T' and resid 68 through 85 Processing helix chain 'U' and resid 11 through 27 Processing helix chain 'U' and resid 27 through 35 Processing helix chain 'U' and resid 40 through 68 Processing helix chain 'V' and resid 4 through 25 Processing helix chain 'W' and resid 13 through 25 Processing helix chain 'W' and resid 31 through 33 No H-bonds generated for 'chain 'W' and resid 31 through 33' Processing helix chain 'W' and resid 71 through 96 Processing helix chain 'AC' and resid 7 through 15 Processing helix chain 'AC' and resid 22 through 33 Processing helix chain 'AC' and resid 79 through 88 Processing helix chain 'AC' and resid 94 through 104 Processing helix chain 'AC' and resid 117 through 122 Processing helix chain 'AC' and resid 124 through 129 Processing helix chain 'AC' and resid 145 through 156 Processing helix chain 'AC' and resid 178 through 196 Processing helix chain 'AD' and resid 12 through 15 removed outlier: 4.079A pdb=" N TYRAD 15 " --> pdb=" O SERAD 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'AD' and resid 12 through 15' Processing helix chain 'AD' and resid 31 through 33 No H-bonds generated for 'chain 'AD' and resid 31 through 33' Processing helix chain 'AD' and resid 70 through 74 Processing helix chain 'AD' and resid 209 through 216 removed outlier: 3.544A pdb=" N SERAD 213 " --> pdb=" O LYSAD 209 " (cutoff:3.500A) Processing helix chain 'AD' and resid 265 through 269 removed outlier: 3.592A pdb=" N ASPAD 268 " --> pdb=" O ARGAD 265 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYSAD 269 " --> pdb=" O TYRAD 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'AD' and resid 265 through 269' Processing helix chain 'AE' and resid 56 through 60 removed outlier: 4.150A pdb=" N VALAE 60 " --> pdb=" O SERAE 57 " (cutoff:3.500A) Processing helix chain 'AE' and resid 61 through 68 removed outlier: 3.804A pdb=" N TYRAE 68 " --> pdb=" O ILEAE 64 " (cutoff:3.500A) Processing helix chain 'AE' and resid 96 through 101 removed outlier: 3.935A pdb=" N VALAE 99 " --> pdb=" O LYSAE 96 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHEAE 100 " --> pdb=" O VALAE 97 " (cutoff:3.500A) Processing helix chain 'AE' and resid 119 through 125 Processing helix chain 'AF' and resid 19 through 24 Processing helix chain 'AF' and resid 28 through 42 Processing helix chain 'AF' and resid 101 through 118 Processing helix chain 'AF' and resid 136 through 147 Processing helix chain 'AF' and resid 161 through 169 Processing helix chain 'AF' and resid 180 through 182 No H-bonds generated for 'chain 'AF' and resid 180 through 182' Processing helix chain 'AF' and resid 183 through 190 Processing helix chain 'AF' and resid 197 through 209 removed outlier: 4.099A pdb=" N LYSAF 209 " --> pdb=" O GLUAF 205 " (cutoff:3.500A) Processing helix chain 'AG' and resid 5 through 14 Processing helix chain 'AG' and resid 14 through 24 Processing helix chain 'AG' and resid 27 through 31 Processing helix chain 'AG' and resid 44 through 48 Processing helix chain 'AG' and resid 49 through 65 removed outlier: 3.789A pdb=" N LEUAG 53 " --> pdb=" O ASNAG 49 " (cutoff:3.500A) Processing helix chain 'AG' and resid 95 through 110 Processing helix chain 'AG' and resid 137 through 141 Processing helix chain 'AG' and resid 165 through 177 removed outlier: 3.766A pdb=" N SERAG 169 " --> pdb=" O ASNAG 165 " (cutoff:3.500A) Processing helix chain 'AH' and resid 2 through 7 removed outlier: 3.865A pdb=" N ARGAH 6 " --> pdb=" O SERAH 2 " (cutoff:3.500A) Processing helix chain 'AH' and resid 58 through 82 removed outlier: 3.843A pdb=" N GLYAH 66 " --> pdb=" O LYSAH 62 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VALAH 79 " --> pdb=" O METAH 75 " (cutoff:3.500A) Processing helix chain 'AH' and resid 137 through 152 removed outlier: 3.744A pdb=" N LYSAH 152 " --> pdb=" O ILEAH 148 " (cutoff:3.500A) Processing helix chain 'AH' and resid 175 through 179 Processing helix chain 'AI' and resid 22 through 29 Processing helix chain 'AI' and resid 29 through 34 Processing helix chain 'AI' and resid 43 through 54 Processing helix chain 'AI' and resid 60 through 74 removed outlier: 3.967A pdb=" N LEUAI 74 " --> pdb=" O SERAI 70 " (cutoff:3.500A) Processing helix chain 'AI' and resid 94 through 106 Processing helix chain 'AJ' and resid 2 through 23 Processing helix chain 'AJ' and resid 35 through 49 Processing helix chain 'AJ' and resid 57 through 68 Processing helix chain 'AJ' and resid 73 through 77 Processing helix chain 'AJ' and resid 89 through 104 Processing helix chain 'AJ' and resid 119 through 129 Processing helix chain 'AJ' and resid 131 through 160 Proline residue: AJ 146 - end of helix Processing helix chain 'AK' and resid 22 through 30 Processing helix chain 'AK' and resid 35 through 48 Processing helix chain 'AK' and resid 76 through 85 Processing helix chain 'AK' and resid 103 through 114 Processing helix chain 'AK' and resid 115 through 117 No H-bonds generated for 'chain 'AK' and resid 115 through 117' Processing helix chain 'AK' and resid 122 through 138 Processing helix chain 'AL' and resid 13 through 17 removed outlier: 3.624A pdb=" N VALAL 17 " --> pdb=" O PROAL 14 " (cutoff:3.500A) Processing helix chain 'AL' and resid 30 through 44 removed outlier: 3.733A pdb=" N GLYAL 44 " --> pdb=" O LYSAL 40 " (cutoff:3.500A) Processing helix chain 'AL' and resid 64 through 68 removed outlier: 4.103A pdb=" N VALAL 68 " --> pdb=" O ALAAL 65 " (cutoff:3.500A) Processing helix chain 'AL' and resid 73 through 78 Processing helix chain 'AL' and resid 95 through 102 Processing helix chain 'AL' and resid 104 through 115 Processing helix chain 'AL' and resid 118 through 127 Processing helix chain 'AL' and resid 138 through 142 removed outlier: 3.505A pdb=" N ASNAL 142 " --> pdb=" O LYSAL 139 " (cutoff:3.500A) Processing helix chain 'AM' and resid 104 through 109 removed outlier: 3.969A pdb=" N ASPAM 108 " --> pdb=" O ARGAM 104 " (cutoff:3.500A) Processing helix chain 'AM' and resid 111 through 118 Processing helix chain 'AN' and resid 36 through 40 removed outlier: 3.851A pdb=" N ASNAN 40 " --> pdb=" O LYSAN 37 " (cutoff:3.500A) Processing helix chain 'AN' and resid 53 through 58 Processing helix chain 'AN' and resid 77 through 84 Processing helix chain 'AN' and resid 91 through 98 Processing helix chain 'AN' and resid 128 through 139 Processing helix chain 'AO' and resid 44 through 58 Processing helix chain 'AO' and resid 110 through 123 Processing helix chain 'AP' and resid 8 through 12 removed outlier: 4.115A pdb=" N SERAP 11 " --> pdb=" O ASNAP 8 " (cutoff:3.500A) Processing helix chain 'AP' and resid 13 through 32 Processing helix chain 'AP' and resid 38 through 55 removed outlier: 3.690A pdb=" N ARGAP 50 " --> pdb=" O ARGAP 46 " (cutoff:3.500A) Processing helix chain 'AP' and resid 59 through 68 removed outlier: 3.657A pdb=" N LYSAP 68 " --> pdb=" O ARGAP 64 " (cutoff:3.500A) Processing helix chain 'AP' and resid 72 through 82 Processing helix chain 'AP' and resid 83 through 87 Processing helix chain 'AQ' and resid 2 through 23 Processing helix chain 'AQ' and resid 69 through 86 removed outlier: 3.788A pdb=" N GLUAQ 86 " --> pdb=" O LYSAQ 82 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 103 through 114 Processing helix chain 'AR' and resid 2 through 12 Processing helix chain 'AR' and resid 52 through 55 removed outlier: 3.595A pdb=" N GLYAR 55 " --> pdb=" O LYSAR 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'AR' and resid 52 through 55' Processing helix chain 'AR' and resid 96 through 101 Processing helix chain 'AR' and resid 103 through 108 removed outlier: 3.610A pdb=" N ALAAR 106 " --> pdb=" O ILEAR 103 " (cutoff:3.500A) Processing helix chain 'AS' and resid 9 through 21 Processing helix chain 'AS' and resid 25 through 30 removed outlier: 3.813A pdb=" N LYSAS 29 " --> pdb=" O GLYAS 26 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SERAS 30 " --> pdb=" O THRAS 27 " (cutoff:3.500A) Processing helix chain 'AS' and resid 31 through 69 removed outlier: 4.495A pdb=" N LYSAS 54 " --> pdb=" O ARGAS 50 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARGAS 55 " --> pdb=" O LYSAS 51 " (cutoff:3.500A) Processing helix chain 'AS' and resid 75 through 86 Processing helix chain 'AS' and resid 91 through 102 removed outlier: 3.720A pdb=" N ILEAS 100 " --> pdb=" O SERAS 96 " (cutoff:3.500A) Processing helix chain 'AS' and resid 102 through 115 removed outlier: 3.617A pdb=" N PHEAS 106 " --> pdb=" O ASPAS 102 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARGAS 115 " --> pdb=" O LEUAS 111 " (cutoff:3.500A) Processing helix chain 'AT' and resid 26 through 30 Processing helix chain 'AU' and resid 17 through 29 Proline residue: AU 23 - end of helix removed outlier: 3.545A pdb=" N ILEAU 28 " --> pdb=" O ILEAU 24 " (cutoff:3.500A) Processing helix chain 'AU' and resid 32 through 43 Processing helix chain 'AU' and resid 45 through 66 Processing helix chain 'AU' and resid 94 through 96 No H-bonds generated for 'chain 'AU' and resid 94 through 96' Processing helix chain 'AV' and resid 13 through 24 Processing helix chain 'AV' and resid 35 through 48 Processing helix chain 'AX' and resid 2 through 4 No H-bonds generated for 'chain 'AX' and resid 2 through 4' Processing helix chain 'AX' and resid 16 through 26 Processing helix chain 'AX' and resid 47 through 55 Processing helix chain 'AX' and resid 114 through 119 Processing helix chain 'AX' and resid 135 through 139 Processing helix chain 'AZ' and resid 24 through 28 Processing helix chain 'AZ' and resid 66 through 76 Processing helix chain 'AZ' and resid 76 through 84 Processing helix chain 'AZ' and resid 87 through 91 Processing helix chain 'Aa' and resid 8 through 33 Processing helix chain 'Aa' and resid 39 through 61 Processing helix chain 'Ab' and resid 3 through 18 Processing helix chain 'Ab' and resid 20 through 39 Processing helix chain 'Ab' and resid 57 through 68 Processing helix chain 'Ab' and resid 81 through 91 Processing helix chain 'Ac' and resid 69 through 78 removed outlier: 3.685A pdb=" N ARGAc 77 " --> pdb=" O LYSAc 73 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 9 through 21 Processing helix chain 'Af' and resid 9 through 17 Processing helix chain 'Af' and resid 17 through 23 Processing helix chain 'Af' and resid 24 through 38 Processing helix chain 'Af' and resid 43 through 47 Processing helix chain 'Ag' and resid 8 through 13 Processing helix chain 'Ag' and resid 38 through 47 removed outlier: 3.583A pdb=" N LYSAg 47 " --> pdb=" O ARGAg 43 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 55 through 63 Processing helix chain 'Ah' and resid 29 through 32 Processing helix chain 'Ai' and resid 50 through 55 removed outlier: 3.610A pdb=" N PHEAi 55 " --> pdb=" O ARGAi 52 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AA2, first strand: chain 'C' and resid 167 through 174 removed outlier: 3.784A pdb=" N GLY C 151 " --> pdb=" O PHE C 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 127 through 128 removed outlier: 3.616A pdb=" N ASP D 140 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 11 through 23 removed outlier: 5.460A pdb=" N GLU E 12 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLY E 39 " --> pdb=" O GLU E 12 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU E 14 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL E 37 " --> pdb=" O LEU E 14 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 84 through 87 Processing sheet with id=AA6, first strand: chain 'F' and resid 35 through 51 removed outlier: 9.318A pdb=" N THR F 35 " --> pdb=" O GLU F 67 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N GLU F 67 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL F 37 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N SER F 65 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N SER F 39 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU F 63 " --> pdb=" O SER F 39 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE F 41 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE F 61 " --> pdb=" O PHE F 41 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG F 86 " --> pdb=" O LEU F 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 74 through 81 Processing sheet with id=AA8, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.932A pdb=" N ASP H 48 " --> pdb=" O LEU H 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 76 through 79 Processing sheet with id=AB1, first strand: chain 'H' and resid 76 through 79 removed outlier: 5.585A pdb=" N LEU H 127 " --> pdb=" O SER H 107 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER H 107 " --> pdb=" O LEU H 127 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 12 through 17 removed outlier: 3.707A pdb=" N SER I 12 " --> pdb=" O ILE I 27 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS I 35 " --> pdb=" O ILE I 71 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL I 73 " --> pdb=" O LYS I 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 37 through 53 removed outlier: 7.800A pdb=" N LYS J 38 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU J 78 " --> pdb=" O LYS J 38 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ASP J 76 " --> pdb=" O PRO J 40 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU J 74 " --> pdb=" O PRO J 42 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LYS J 72 " --> pdb=" O PRO J 44 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 37 through 53 removed outlier: 7.800A pdb=" N LYS J 38 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU J 78 " --> pdb=" O LYS J 38 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ASP J 76 " --> pdb=" O PRO J 40 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU J 74 " --> pdb=" O PRO J 42 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LYS J 72 " --> pdb=" O PRO J 44 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 42 through 47 removed outlier: 6.750A pdb=" N VAL K 35 " --> pdb=" O LEU K 43 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TRP K 45 " --> pdb=" O VAL K 33 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL K 33 " --> pdb=" O TRP K 45 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER K 47 " --> pdb=" O THR K 31 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR K 31 " --> pdb=" O SER K 47 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY K 18 " --> pdb=" O ILE K 80 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR K 82 " --> pdb=" O GLY K 18 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N VAL K 108 " --> pdb=" O ASN K 81 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL K 83 " --> pdb=" O VAL K 108 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER K 110 " --> pdb=" O VAL K 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 29 through 40 removed outlier: 5.665A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR L 95 " --> pdb=" O THR L 64 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 3 through 4 Processing sheet with id=AB8, first strand: chain 'P' and resid 49 through 51 removed outlier: 6.357A pdb=" N VAL P 20 " --> pdb=" O LEU P 37 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR P 39 " --> pdb=" O TYR P 18 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N TYR P 18 " --> pdb=" O TYR P 39 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA P 12 " --> pdb=" O ARG P 15 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Q' and resid 8 through 15 removed outlier: 14.453A pdb=" N GLU Q 8 " --> pdb=" O ARG Q 29 " (cutoff:3.500A) removed outlier: 11.583A pdb=" N ARG Q 29 " --> pdb=" O GLU Q 8 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE Q 10 " --> pdb=" O VAL Q 27 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N VAL Q 27 " --> pdb=" O ILE Q 10 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL Q 23 " --> pdb=" O VAL Q 14 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP Q 74 " --> pdb=" O LYS Q 46 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS Q 61 " --> pdb=" O VAL Q 77 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL Q 79 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LYS Q 59 " --> pdb=" O VAL Q 79 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 31 through 33 Processing sheet with id=AC2, first strand: chain 'W' and resid 4 through 8 removed outlier: 6.570A pdb=" N LYS W 4 " --> pdb=" O ILE W 40 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE W 42 " --> pdb=" O LYS W 4 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN W 6 " --> pdb=" O ILE W 42 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N LYS W 44 " --> pdb=" O GLN W 6 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL W 8 " --> pdb=" O LYS W 44 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN W 37 " --> pdb=" O HIS W 56 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'AC' and resid 167 through 171 removed outlier: 4.817A pdb=" N ILEAC 209 " --> pdb=" O VALAC 221 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'AC' and resid 57 through 61 Processing sheet with id=AC5, first strand: chain 'AC' and resid 91 through 93 removed outlier: 6.394A pdb=" N ILEAC 72 " --> pdb=" O TYRAC 91 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N GLYAC 93 " --> pdb=" O ILEAC 72 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VALAC 74 " --> pdb=" O GLYAC 93 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEUAC 73 " --> pdb=" O VALAC 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'AD' and resid 3 through 5 Processing sheet with id=AC7, first strand: chain 'AD' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'AD' and resid 103 through 107 removed outlier: 6.433A pdb=" N ILEAD 93 " --> pdb=" O ILEAD 83 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILEAD 83 " --> pdb=" O ILEAD 93 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEUAD 95 " --> pdb=" O ALAAD 81 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'AD' and resid 131 through 133 removed outlier: 5.713A pdb=" N ILEAD 166 " --> pdb=" O LYSAD 177 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYSAD 177 " --> pdb=" O ILEAD 166 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALAAD 168 " --> pdb=" O THRAD 175 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N METAD 183 " --> pdb=" O ILEAD 272 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'AE' and resid 3 through 15 removed outlier: 5.551A pdb=" N LYSAE 8 " --> pdb=" O GLUAE 28 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLUAE 28 " --> pdb=" O LYSAE 8 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLYAE 10 " --> pdb=" O VALAE 26 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYSAE 188 " --> pdb=" O VALAE 175 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VALAE 175 " --> pdb=" O LYSAE 188 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N THRAE 169 " --> pdb=" O GLYAE 110 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLYAE 110 " --> pdb=" O THRAE 169 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLNAE 171 " --> pdb=" O VALAE 108 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VALAE 108 " --> pdb=" O GLNAE 171 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N THRAE 111 " --> pdb=" O PHEAE 198 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N PHEAE 198 " --> pdb=" O THRAE 111 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'AE' and resid 80 through 84 removed outlier: 3.717A pdb=" N GLYAE 36 " --> pdb=" O ILEAE 49 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLYAE 51 " --> pdb=" O ILEAE 34 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILEAE 34 " --> pdb=" O GLYAE 51 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASNAE 32 " --> pdb=" O ILEAE 95 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'AE' and resid 117 through 118 Processing sheet with id=AD4, first strand: chain 'AF' and resid 2 through 6 Processing sheet with id=AD5, first strand: chain 'AF' and resid 123 through 126 removed outlier: 6.630A pdb=" N VALAF 153 " --> pdb=" O LYSAF 175 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEUAF 177 " --> pdb=" O VALAF 153 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILEAF 155 " --> pdb=" O LEUAF 177 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'AG' and resid 69 through 72 removed outlier: 3.608A pdb=" N GLYAG 89 " --> pdb=" O THRAG 71 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYSAG 36 " --> pdb=" O VALAG 160 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'AG' and resid 120 through 121 removed outlier: 5.604A pdb=" N ILEAG 120 " --> pdb=" O SERAG 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'AH' and resid 9 through 10 Processing sheet with id=AD9, first strand: chain 'AH' and resid 16 through 20 Processing sheet with id=AE1, first strand: chain 'AH' and resid 121 through 125 Processing sheet with id=AE2, first strand: chain 'AH' and resid 95 through 99 removed outlier: 4.569A pdb=" N GLNAH 112 " --> pdb=" O METAi 26 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SERAi 28 " --> pdb=" O GLNAH 112 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VALAH 116 " --> pdb=" O PHEAi 30 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'AI' and resid 18 through 20 Processing sheet with id=AE4, first strand: chain 'AI' and resid 76 through 81 removed outlier: 3.891A pdb=" N THRAI 130 " --> pdb=" O ASPAI 115 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASPAI 115 " --> pdb=" O THRAI 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'AJ' and resid 52 through 55 removed outlier: 6.487A pdb=" N ASPAJ 30 " --> pdb=" O VALAJ 108 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VALAJ 108 " --> pdb=" O ASPAJ 30 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'AK' and resid 6 through 15 Processing sheet with id=AE7, first strand: chain 'AK' and resid 100 through 102 removed outlier: 6.388A pdb=" N GLYAK 100 " --> pdb=" O GLUAK 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'AL' and resid 128 through 130 removed outlier: 6.298A pdb=" N TYRAL 22 " --> pdb=" O ILEAL 61 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILEAL 63 " --> pdb=" O TYRAL 22 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILEAL 24 " --> pdb=" O ILEAL 63 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRPAL 21 " --> pdb=" O ILEAL 144 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEUAL 146 " --> pdb=" O TRPAL 21 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VALAL 23 " --> pdb=" O LEUAL 146 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'AL' and resid 79 through 83 Processing sheet with id=AF1, first strand: chain 'AM' and resid 7 through 10 removed outlier: 5.370A pdb=" N LYSAM 17 " --> pdb=" O ILEAM 10 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLNAM 45 " --> pdb=" O LYSAM 17 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALAAM 19 " --> pdb=" O VALAM 43 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VALAM 43 " --> pdb=" O ALAAM 19 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N CYSAM 21 " --> pdb=" O ILEAM 41 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILEAM 41 " --> pdb=" O CYSAM 21 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYSAM 23 " --> pdb=" O ILEAM 39 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILEAM 39 " --> pdb=" O LYSAM 23 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYSAM 59 " --> pdb=" O LEUAM 87 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALAAM 83 " --> pdb=" O VALAM 63 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N CYSAM 84 " --> pdb=" O TYRAM 7 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N THRAM 9 " --> pdb=" O CYSAM 84 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILEAM 86 " --> pdb=" O THRAM 9 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'AM' and resid 76 through 79 removed outlier: 6.333A pdb=" N THRAR 57 " --> pdb=" O PHEAR 49 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHEAR 49 " --> pdb=" O THRAR 57 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEUAR 59 " --> pdb=" O ILEAR 47 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILEAR 63 " --> pdb=" O GLUAR 43 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N GLUAR 43 " --> pdb=" O ILEAR 63 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASNAR 36 " --> pdb=" O GLUAR 33 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ARGAR 26 " --> pdb=" O VALAR 85 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VALAR 85 " --> pdb=" O ARGAR 26 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VALAR 28 " --> pdb=" O VALAR 83 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VALAR 83 " --> pdb=" O VALAR 28 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N LYSAR 30 " --> pdb=" O GLUAR 81 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLUAR 81 " --> pdb=" O LYSAR 30 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'AM' and resid 102 through 103 removed outlier: 6.349A pdb=" N VALAM 102 " --> pdb=" O ILEAM 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'AN' and resid 74 through 76 removed outlier: 6.241A pdb=" N VALAN 75 " --> pdb=" O LEUAN 111 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'AN' and resid 89 through 90 removed outlier: 6.247A pdb=" N PHEAN 122 " --> pdb=" O GLNAN 143 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'AO' and resid 63 through 65 Processing sheet with id=AF7, first strand: chain 'AO' and resid 40 through 43 removed outlier: 6.855A pdb=" N TYRAO 74 " --> pdb=" O ASPAO 91 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TRPAO 93 " --> pdb=" O ILEAO 72 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILEAO 72 " --> pdb=" O TRPAO 93 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'AP' and resid 33 through 37 removed outlier: 6.142A pdb=" N METAP 110 " --> pdb=" O LEUAP 100 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'AQ' and resid 52 through 58 removed outlier: 5.738A pdb=" N THRAQ 53 " --> pdb=" O ASPAQ 47 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASPAQ 47 " --> pdb=" O THRAQ 53 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALAAQ 55 " --> pdb=" O VALAQ 45 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VALAQ 34 " --> pdb=" O ASPAQ 95 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'AT' and resid 10 through 14 removed outlier: 6.756A pdb=" N TYRAT 2 " --> pdb=" O ILEAT 41 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILEAT 41 " --> pdb=" O TYRAT 2 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEUAT 4 " --> pdb=" O LEUAT 39 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'AT' and resid 18 through 23 removed outlier: 3.978A pdb=" N GLUAT 18 " --> pdb=" O VALAT 98 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLUAT 65 " --> pdb=" O TYRAT 95 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEUAT 97 " --> pdb=" O TYRAT 63 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N TYRAT 63 " --> pdb=" O LEUAT 97 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASPAT 99 " --> pdb=" O CYSAT 61 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N CYSAT 61 " --> pdb=" O ASPAT 99 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILEAT 101 " --> pdb=" O ILEAT 59 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILEAT 59 " --> pdb=" O ILEAT 101 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'AT' and resid 72 through 77 Processing sheet with id=AG4, first strand: chain 'AU' and resid 8 through 14 removed outlier: 5.996A pdb=" N THRAU 8 " --> pdb=" O VALAU 112 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VALAU 112 " --> pdb=" O THRAU 8 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LYSAU 10 " --> pdb=" O VALAU 110 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VALAU 110 " --> pdb=" O LYSAU 10 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LYSAU 12 " --> pdb=" O ILEAU 108 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILEAU 108 " --> pdb=" O LYSAU 12 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASPAU 99 " --> pdb=" O ILEAU 90 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILEAU 90 " --> pdb=" O ASPAU 99 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEUAU 101 " --> pdb=" O LYSAU 88 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYSAU 88 " --> pdb=" O LEUAU 101 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASNAU 103 " --> pdb=" O ARGAU 86 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARGAU 86 " --> pdb=" O ASNAU 103 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASNAU 105 " --> pdb=" O GLYAU 84 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASPAU 113 " --> pdb=" O VALAU 76 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VALAU 76 " --> pdb=" O ASPAU 113 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'AV' and resid 7 through 10 removed outlier: 4.152A pdb=" N LYSAV 83 " --> pdb=" O VALAV 30 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SERAV 53 " --> pdb=" O TYRAV 88 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'AV' and resid 63 through 67 removed outlier: 6.199A pdb=" N LYSAV 64 " --> pdb=" O LYSAV 76 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYSAV 76 " --> pdb=" O LYSAV 64 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VALAV 66 " --> pdb=" O ILEAV 74 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'AW' and resid 65 through 66 Processing sheet with id=AG8, first strand: chain 'AW' and resid 42 through 47 Processing sheet with id=AG9, first strand: chain 'AW' and resid 81 through 85 Processing sheet with id=AH1, first strand: chain 'AX' and resid 6 through 11 removed outlier: 7.484A pdb=" N SERAX 8 " --> pdb=" O LYSAX 46 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYSAX 46 " --> pdb=" O SERAX 8 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N GLUAX 28 " --> pdb=" O TYRAX 89 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N ILEAX 91 " --> pdb=" O GLUAX 28 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N PHEAX 93 " --> pdb=" O PROAX 30 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VALAX 32 " --> pdb=" O PHEAX 93 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N GLUAX 95 " --> pdb=" O VALAX 32 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYRAX 34 " --> pdb=" O GLUAX 95 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILEAX 88 " --> pdb=" O GLUAX 81 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLUAX 81 " --> pdb=" O ILEAX 88 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N HISAX 90 " --> pdb=" O ALAAX 79 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALAAX 79 " --> pdb=" O HISAX 90 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASPAX 92 " --> pdb=" O LYSAX 77 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEUAX 7 " --> pdb=" O ASPAX 66 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'AX' and resid 143 through 146 Processing sheet with id=AH3, first strand: chain 'AX' and resid 123 through 124 removed outlier: 4.502A pdb=" N VALAX 179 " --> pdb=" O VALAX 156 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'AY' and resid 22 through 23 removed outlier: 6.623A pdb=" N ILEAY 59 " --> pdb=" O ILEAY 37 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'AY' and resid 30 through 31 Processing sheet with id=AH6, first strand: chain 'AZ' and resid 13 through 17 Processing sheet with id=AH7, first strand: chain 'AZ' and resid 20 through 23 Processing sheet with id=AH8, first strand: chain 'AZ' and resid 46 through 53 Processing sheet with id=AH9, first strand: chain 'Ab' and resid 75 through 79 Processing sheet with id=AI1, first strand: chain 'Ac' and resid 22 through 27 removed outlier: 7.542A pdb=" N LEUAc 11 " --> pdb=" O GLUAc 42 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLUAc 33 " --> pdb=" O LEUAc 45 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Ad' and resid 28 through 30 Processing sheet with id=AI3, first strand: chain 'Ae' and resid 25 through 30 removed outlier: 3.742A pdb=" N LYSAe 49 " --> pdb=" O CYSAe 44 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Ag' and resid 16 through 17 Processing sheet with id=AI5, first strand: chain 'Ah' and resid 2 through 4 removed outlier: 3.896A pdb=" N ARGAh 35 " --> pdb=" O LYSAh 2 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEUAh 23 " --> pdb=" O GLNAh 36 " (cutoff:3.500A) 2273 hydrogen bonds defined for protein. 6390 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3210 hydrogen bonds 5086 hydrogen bond angles 0 basepair planarities 1346 basepair parallelities 2669 stacking parallelities Total time for adding SS restraints: 246.42 Time building geometry restraints manager: 71.93 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: 15025 1.32 - 1.44: 70048 1.44 - 1.57: 65872 1.57 - 1.70: 9287 1.70 - 1.83: 292 Bond restraints: 160524 Sorted by residual: bond pdb=" CZ ARGAi 52 " pdb=" NH2 ARGAi 52 " ideal model delta sigma weight residual 1.330 1.271 0.059 1.30e-02 5.92e+03 2.06e+01 bond pdb=" CB LYSAi 36 " pdb=" CG LYSAi 36 " ideal model delta sigma weight residual 1.520 1.408 0.112 3.00e-02 1.11e+03 1.38e+01 bond pdb=" CG GLU Q 78 " pdb=" CD GLU Q 78 " ideal model delta sigma weight residual 1.516 1.425 0.091 2.50e-02 1.60e+03 1.31e+01 bond pdb=" CB GLUAR 33 " pdb=" CG GLUAR 33 " ideal model delta sigma weight residual 1.520 1.418 0.102 3.00e-02 1.11e+03 1.14e+01 bond pdb=" CG ARG D 69 " pdb=" CD ARG D 69 " ideal model delta sigma weight residual 1.520 1.420 0.100 3.00e-02 1.11e+03 1.11e+01 ... (remaining 160519 not shown) Histogram of bond angle deviations from ideal: 72.43 - 85.81: 105 85.81 - 99.19: 71 99.19 - 112.57: 114657 112.57 - 125.95: 106343 125.95 - 139.33: 17891 Bond angle restraints: 239067 Sorted by residual: angle pdb=" OP1 AAA1677 " pdb=" P AAA1677 " pdb=" OP2 AAA1677 " ideal model delta sigma weight residual 119.60 77.96 41.64 3.00e+00 1.11e-01 1.93e+02 angle pdb=" OP1 A A 721 " pdb=" P A A 721 " pdb=" OP2 A A 721 " ideal model delta sigma weight residual 119.60 78.29 41.31 3.00e+00 1.11e-01 1.90e+02 angle pdb=" OP1 AAA1967 " pdb=" P AAA1967 " pdb=" OP2 AAA1967 " ideal model delta sigma weight residual 119.60 79.01 40.59 3.00e+00 1.11e-01 1.83e+02 angle pdb=" OP1 G A1265 " pdb=" P G A1265 " pdb=" OP2 G A1265 " ideal model delta sigma weight residual 119.60 79.15 40.45 3.00e+00 1.11e-01 1.82e+02 angle pdb=" OP1 A A 999 " pdb=" P A A 999 " pdb=" OP2 A A 999 " ideal model delta sigma weight residual 119.60 79.50 40.10 3.00e+00 1.11e-01 1.79e+02 ... (remaining 239062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 89600 35.88 - 71.77: 10250 71.77 - 107.65: 1057 107.65 - 143.53: 32 143.53 - 179.42: 59 Dihedral angle restraints: 100998 sinusoidal: 83928 harmonic: 17070 Sorted by residual: dihedral pdb=" O4' C A 628 " pdb=" C1' C A 628 " pdb=" N1 C A 628 " pdb=" C2 C A 628 " ideal model delta sinusoidal sigma weight residual 200.00 23.62 176.38 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U X 55 " pdb=" C1' U X 55 " pdb=" N1 U X 55 " pdb=" C2 U X 55 " ideal model delta sinusoidal sigma weight residual 200.00 35.66 164.34 1 1.50e+01 4.44e-03 8.37e+01 dihedral pdb=" O4' U A1436 " pdb=" C1' U A1436 " pdb=" N1 U A1436 " pdb=" C2 U A1436 " ideal model delta sinusoidal sigma weight residual -160.00 -6.17 -153.83 1 1.50e+01 4.44e-03 8.10e+01 ... (remaining 100995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.424: 30046 0.424 - 0.849: 3 0.849 - 1.273: 1 1.273 - 1.698: 0 1.698 - 2.122: 47 Chirality restraints: 30097 Sorted by residual: chirality pdb=" P AAA1587 " pdb=" OP1 AAA1587 " pdb=" OP2 AAA1587 " pdb=" O5' AAA1587 " both_signs ideal model delta sigma weight residual True 2.41 0.29 2.12 2.00e-01 2.50e+01 1.13e+02 chirality pdb=" P AAA1520 " pdb=" OP1 AAA1520 " pdb=" OP2 AAA1520 " pdb=" O5' AAA1520 " both_signs ideal model delta sigma weight residual True 2.41 0.33 2.08 2.00e-01 2.50e+01 1.08e+02 chirality pdb=" P GAA 532 " pdb=" OP1 GAA 532 " pdb=" OP2 GAA 532 " pdb=" O5' GAA 532 " both_signs ideal model delta sigma weight residual True 2.41 0.34 2.07 2.00e-01 2.50e+01 1.08e+02 ... (remaining 30094 not shown) Planarity restraints: 13022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLUAi 31 " -0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" CD GLUAi 31 " 0.066 2.00e-02 2.50e+03 pdb=" OE1 GLUAi 31 " -0.023 2.00e-02 2.50e+03 pdb=" OE2 GLUAi 31 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 5 " 0.023 2.00e-02 2.50e+03 2.52e-02 1.27e+01 pdb=" CG TYR H 5 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR H 5 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR H 5 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR H 5 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR H 5 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR H 5 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 5 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 26 " 0.011 2.00e-02 2.50e+03 2.51e-02 1.26e+01 pdb=" CG TYR I 26 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR I 26 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR I 26 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR I 26 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR I 26 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR I 26 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR I 26 " -0.006 2.00e-02 2.50e+03 ... (remaining 13019 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 1825 2.59 - 3.17: 113791 3.17 - 3.75: 285830 3.75 - 4.32: 400100 4.32 - 4.90: 536328 Nonbonded interactions: 1337874 Sorted by model distance: nonbonded pdb=" P GAA2716 " pdb=" NH2 ARGAi 52 " model vdw 2.015 3.480 nonbonded pdb=" N CYS R 38 " pdb="ZN ZN R 101 " model vdw 2.042 2.310 nonbonded pdb=" NE2 GLNAG 66 " pdb=" O THRAG 93 " model vdw 2.063 2.520 nonbonded pdb=" OP1 GAA2716 " pdb=" NH2 ARGAi 52 " model vdw 2.084 2.520 nonbonded pdb=" O ILE M 17 " pdb=" OG1 THR M 20 " model vdw 2.091 2.440 ... (remaining 1337869 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=0.00 max=1.00 mean=0.99 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: 7.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.190 Extract box with map and model: 23.830 Check model and map are aligned: 1.620 Set scattering table: 1.090 Process input model: 564.030 Find NCS groups from input model: 3.160 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:9.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 611.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 160524 Z= 0.337 Angle : 0.857 41.637 239067 Z= 0.364 Chirality : 0.084 2.122 30097 Planarity : 0.004 0.102 13022 Dihedral : 22.487 179.417 90397 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.52 % Favored : 93.46 % Rotamer: Outliers : 0.04 % Allowed : 2.10 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.10), residues: 6239 helix: 0.74 (0.11), residues: 2140 sheet: -0.53 (0.14), residues: 1288 loop : -1.29 (0.11), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPAi 20 HIS 0.009 0.001 HISAP 16 PHE 0.054 0.002 PHEAi 30 TYR 0.061 0.002 TYR H 5 ARG 0.044 0.001 ARG S 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1204 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1202 time to evaluate : 6.748 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: C 29 TYR cc_start: 0.8527 (t80) cc_final: 0.8231 (t80) REVERT: C 42 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7787 (mm-30) REVERT: C 58 GLU cc_start: 0.7499 (pp20) cc_final: 0.7081 (pp20) REVERT: C 128 GLU cc_start: 0.8314 (tt0) cc_final: 0.7965 (mt-10) REVERT: C 184 ASN cc_start: 0.8262 (t0) cc_final: 0.8048 (t0) REVERT: D 140 ASP cc_start: 0.8824 (m-30) cc_final: 0.8077 (m-30) REVERT: E 69 ASN cc_start: 0.8425 (t0) cc_final: 0.7886 (t0) REVERT: F 13 SER cc_start: 0.8401 (t) cc_final: 0.7979 (p) REVERT: F 42 ILE cc_start: 0.8821 (mm) cc_final: 0.8597 (mp) REVERT: F 58 ARG cc_start: 0.7669 (mtp85) cc_final: 0.7211 (mtt90) REVERT: G 44 TYR cc_start: 0.8396 (m-10) cc_final: 0.7790 (m-10) REVERT: G 48 ASP cc_start: 0.7574 (m-30) cc_final: 0.7326 (m-30) REVERT: G 68 ASP cc_start: 0.8421 (m-30) cc_final: 0.8200 (m-30) REVERT: G 73 LEU cc_start: 0.8625 (mm) cc_final: 0.8311 (mm) REVERT: G 149 ASN cc_start: 0.8996 (t0) cc_final: 0.8645 (t0) REVERT: H 38 ASN cc_start: 0.8458 (t0) cc_final: 0.7857 (t0) REVERT: H 63 LEU cc_start: 0.9104 (mp) cc_final: 0.8844 (mm) REVERT: H 85 ARG cc_start: 0.8439 (ttp80) cc_final: 0.8019 (ttt-90) REVERT: H 117 GLU cc_start: 0.8346 (tt0) cc_final: 0.7840 (tt0) REVERT: I 26 TYR cc_start: 0.8434 (m-10) cc_final: 0.7780 (m-80) REVERT: I 33 ASN cc_start: 0.7690 (t0) cc_final: 0.7479 (p0) REVERT: I 34 ILE cc_start: 0.8638 (mm) cc_final: 0.8206 (mm) REVERT: I 49 ASN cc_start: 0.8964 (m-40) cc_final: 0.8654 (m110) REVERT: I 72 ASN cc_start: 0.8512 (t0) cc_final: 0.8220 (t0) REVERT: I 87 HIS cc_start: 0.9244 (t-90) cc_final: 0.8742 (t-90) REVERT: I 113 ASP cc_start: 0.8199 (t0) cc_final: 0.7629 (t0) REVERT: J 13 SER cc_start: 0.7928 (t) cc_final: 0.7504 (t) REVERT: J 67 GLU cc_start: 0.8398 (mp0) cc_final: 0.7421 (mp0) REVERT: K 109 LYS cc_start: 0.8338 (mtmt) cc_final: 0.8128 (mttt) REVERT: L 38 MET cc_start: 0.7729 (pmm) cc_final: 0.7314 (pmm) REVERT: L 70 ILE cc_start: 0.7805 (mt) cc_final: 0.7510 (pt) REVERT: L 108 ASN cc_start: 0.9016 (m110) cc_final: 0.8811 (m-40) REVERT: M 8 ASP cc_start: 0.7422 (p0) cc_final: 0.7147 (p0) REVERT: N 16 TYR cc_start: 0.6632 (t80) cc_final: 0.6358 (t80) REVERT: N 23 ARG cc_start: 0.6937 (mtp85) cc_final: 0.6455 (mtt90) REVERT: N 33 TYR cc_start: 0.8371 (t80) cc_final: 0.8122 (t80) REVERT: O 45 ASN cc_start: 0.8563 (m110) cc_final: 0.8349 (m-40) REVERT: P 24 ASN cc_start: 0.7909 (m-40) cc_final: 0.7609 (m-40) REVERT: P 44 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8164 (mm-30) REVERT: Q 19 SER cc_start: 0.8885 (t) cc_final: 0.8569 (p) REVERT: Q 25 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7839 (tm-30) REVERT: Q 49 ASP cc_start: 0.8370 (t0) cc_final: 0.8155 (t0) REVERT: R 58 GLU cc_start: 0.8225 (pm20) cc_final: 0.7581 (pm20) REVERT: S 16 TYR cc_start: 0.8652 (t80) cc_final: 0.8344 (t80) REVERT: S 32 LYS cc_start: 0.7659 (mtmt) cc_final: 0.7424 (mttm) REVERT: T 51 PHE cc_start: 0.9594 (t80) cc_final: 0.9299 (t80) REVERT: U 22 MET cc_start: 0.7586 (ptm) cc_final: 0.7065 (ttp) REVERT: V 13 SER cc_start: 0.9245 (m) cc_final: 0.8989 (p) REVERT: W 45 GLU cc_start: 0.8302 (tt0) cc_final: 0.7911 (tt0) REVERT: W 46 HIS cc_start: 0.6820 (m90) cc_final: 0.6438 (m90) REVERT: W 88 THR cc_start: 0.8678 (m) cc_final: 0.8341 (p) REVERT: W 90 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7913 (mm-30) REVERT: AE 149 THR cc_start: 0.8426 (m) cc_final: 0.8162 (p) REVERT: AF 127 GLU cc_start: 0.8281 (pm20) cc_final: 0.7781 (pm20) REVERT: AG 86 GLN cc_start: 0.8083 (mt0) cc_final: 0.7404 (mt0) REVERT: AG 126 ASP cc_start: 0.8681 (p0) cc_final: 0.8180 (p0) REVERT: AG 128 ASN cc_start: 0.8867 (m-40) cc_final: 0.8520 (m-40) REVERT: AG 145 ASP cc_start: 0.7876 (t70) cc_final: 0.7447 (t70) REVERT: AH 95 ARG cc_start: 0.7669 (mtm110) cc_final: 0.7395 (mtm110) REVERT: AH 155 GLU cc_start: 0.7478 (pp20) cc_final: 0.7028 (pp20) REVERT: AI 2 LYS cc_start: 0.8826 (ptpp) cc_final: 0.8556 (ptpp) REVERT: AN 72 TYR cc_start: 0.7818 (p90) cc_final: 0.7546 (p90) REVERT: AN 86 ASP cc_start: 0.7795 (m-30) cc_final: 0.7505 (m-30) REVERT: AO 116 GLU cc_start: 0.8286 (tp30) cc_final: 0.7700 (tp30) REVERT: AQ 1 MET cc_start: 0.6541 (ttp) cc_final: 0.5164 (mmt) REVERT: AQ 72 ASP cc_start: 0.8704 (m-30) cc_final: 0.8482 (m-30) REVERT: AQ 95 ASP cc_start: 0.8984 (t0) cc_final: 0.8706 (t0) REVERT: AQ 111 SER cc_start: 0.8916 (m) cc_final: 0.8308 (m) REVERT: AQ 115 PHE cc_start: 0.8521 (m-80) cc_final: 0.7173 (m-80) REVERT: AS 102 ASP cc_start: 0.7988 (t70) cc_final: 0.7372 (t0) REVERT: AW 9 ASP cc_start: 0.8466 (m-30) cc_final: 0.8054 (m-30) REVERT: AX 123 LEU cc_start: 0.6412 (mm) cc_final: 0.5733 (tm) REVERT: AZ 90 ASN cc_start: 0.9108 (m110) cc_final: 0.8897 (m-40) REVERT: Ac 1 MET cc_start: 0.3426 (mmm) cc_final: 0.3146 (mmt) REVERT: Ac 49 GLU cc_start: 0.8287 (mp0) cc_final: 0.7973 (pm20) REVERT: Ag 1 MET cc_start: 0.5129 (mmm) cc_final: 0.4553 (ptt) outliers start: 2 outliers final: 5 residues processed: 1203 average time/residue: 1.9355 time to fit residues: 3445.9251 Evaluate side-chains 970 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 965 time to evaluate : 6.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain AD residue 170 ASP Chi-restraints excluded: chain AO residue 58 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 905 optimal weight: 0.9990 chunk 812 optimal weight: 50.0000 chunk 450 optimal weight: 10.0000 chunk 277 optimal weight: 8.9990 chunk 548 optimal weight: 8.9990 chunk 434 optimal weight: 10.0000 chunk 840 optimal weight: 30.0000 chunk 325 optimal weight: 5.9990 chunk 510 optimal weight: 6.9990 chunk 625 optimal weight: 7.9990 chunk 973 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 ASN D 81 HIS F 40 ASN G 69 ASN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN I 37 ASN J 59 ASN K 30 ASN ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 50 ASN Q 28 GLN ** S 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 ASN W 46 HIS AD 136 ASN AE 168 GLN AH 99 GLN AM 110 ASN AN 51 GLN AO 94 ASN AQ 69 ASN AT 56 ASN ** AU 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AW 41 ASN AW 88 ASN AX 3 ASN ** Ac 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 28 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.158 160524 Z= 0.397 Angle : 0.945 41.116 239067 Z= 0.415 Chirality : 0.087 2.087 30097 Planarity : 0.005 0.051 13022 Dihedral : 23.098 179.744 78241 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.29 % Favored : 94.69 % Rotamer: Outliers : 3.24 % Allowed : 15.10 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.11), residues: 6239 helix: 1.12 (0.11), residues: 2136 sheet: -0.44 (0.14), residues: 1315 loop : -1.15 (0.12), residues: 2788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPAV 82 HIS 0.018 0.001 HIS W 30 PHE 0.024 0.002 PHEAi 30 TYR 0.032 0.002 TYRAc 58 ARG 0.018 0.001 ARG E 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1250 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1088 time to evaluate : 6.809 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: C 34 HIS cc_start: 0.7913 (OUTLIER) cc_final: 0.7395 (m-70) REVERT: C 36 ASP cc_start: 0.7976 (m-30) cc_final: 0.7368 (m-30) REVERT: C 111 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7771 (mpp80) REVERT: C 113 GLU cc_start: 0.8459 (mp0) cc_final: 0.7733 (pm20) REVERT: C 128 GLU cc_start: 0.8573 (tt0) cc_final: 0.8139 (mt-10) REVERT: C 184 ASN cc_start: 0.8374 (t0) cc_final: 0.8118 (t0) REVERT: D 140 ASP cc_start: 0.8883 (m-30) cc_final: 0.8076 (m-30) REVERT: E 69 ASN cc_start: 0.8451 (t0) cc_final: 0.7786 (t0) REVERT: E 130 ASN cc_start: 0.8346 (p0) cc_final: 0.8006 (p0) REVERT: F 13 SER cc_start: 0.8577 (t) cc_final: 0.8048 (p) REVERT: F 58 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7256 (mtt90) REVERT: G 44 TYR cc_start: 0.8398 (m-10) cc_final: 0.7815 (m-10) REVERT: G 48 ASP cc_start: 0.7514 (m-30) cc_final: 0.7273 (m-30) REVERT: G 73 LEU cc_start: 0.8614 (mm) cc_final: 0.8288 (mm) REVERT: G 117 MET cc_start: 0.6113 (mmt) cc_final: 0.5698 (mmt) REVERT: G 145 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.7940 (tpt) REVERT: H 63 LEU cc_start: 0.9048 (mp) cc_final: 0.8816 (mm) REVERT: H 71 ASN cc_start: 0.8513 (m110) cc_final: 0.8144 (m110) REVERT: H 85 ARG cc_start: 0.8430 (ttp80) cc_final: 0.7964 (ttt-90) REVERT: H 117 GLU cc_start: 0.8434 (tt0) cc_final: 0.7991 (tt0) REVERT: I 26 TYR cc_start: 0.8369 (m-80) cc_final: 0.8139 (m-80) REVERT: I 34 ILE cc_start: 0.8695 (mm) cc_final: 0.8311 (mm) REVERT: I 72 ASN cc_start: 0.8571 (t0) cc_final: 0.8299 (t0) REVERT: I 87 HIS cc_start: 0.9194 (t-90) cc_final: 0.8666 (t-90) REVERT: I 113 ASP cc_start: 0.8307 (t0) cc_final: 0.7549 (t0) REVERT: J 13 SER cc_start: 0.7940 (t) cc_final: 0.7715 (t) REVERT: J 41 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8064 (pp) REVERT: K 39 LYS cc_start: 0.8999 (tppp) cc_final: 0.8716 (tmmt) REVERT: K 95 GLU cc_start: 0.7512 (pp20) cc_final: 0.7173 (pp20) REVERT: K 99 ARG cc_start: 0.8419 (ttm-80) cc_final: 0.8191 (ttp-110) REVERT: L 38 MET cc_start: 0.7827 (pmm) cc_final: 0.7349 (pmm) REVERT: L 70 ILE cc_start: 0.7685 (mt) cc_final: 0.7449 (pt) REVERT: L 76 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8144 (mm-30) REVERT: L 82 ILE cc_start: 0.9099 (pt) cc_final: 0.8805 (pp) REVERT: N 23 ARG cc_start: 0.6862 (mtp85) cc_final: 0.6513 (mtt90) REVERT: O 45 ASN cc_start: 0.8484 (m110) cc_final: 0.8230 (m-40) REVERT: O 73 ASP cc_start: 0.7472 (t0) cc_final: 0.7184 (t0) REVERT: P 1 MET cc_start: 0.6619 (mpt) cc_final: 0.6355 (mpt) REVERT: P 24 ASN cc_start: 0.7966 (m-40) cc_final: 0.7483 (m-40) REVERT: P 44 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8263 (mm-30) REVERT: Q 19 SER cc_start: 0.8876 (t) cc_final: 0.8546 (p) REVERT: Q 25 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7583 (tm-30) REVERT: Q 49 ASP cc_start: 0.8125 (t0) cc_final: 0.7918 (t0) REVERT: R 42 LYS cc_start: 0.8897 (pttp) cc_final: 0.8640 (tptt) REVERT: R 57 THR cc_start: 0.8669 (t) cc_final: 0.8278 (t) REVERT: S 32 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7937 (mttm) REVERT: S 41 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7209 (pp) REVERT: S 79 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8759 (tp) REVERT: T 51 PHE cc_start: 0.9553 (t80) cc_final: 0.9227 (t80) REVERT: T 70 ASN cc_start: 0.8516 (m-40) cc_final: 0.8094 (m-40) REVERT: U 22 MET cc_start: 0.7451 (ptm) cc_final: 0.7001 (ttp) REVERT: U 54 ARG cc_start: 0.7469 (mmm160) cc_final: 0.7219 (mmm160) REVERT: V 13 SER cc_start: 0.9250 (m) cc_final: 0.8985 (p) REVERT: W 45 GLU cc_start: 0.8189 (tt0) cc_final: 0.7666 (tt0) REVERT: W 46 HIS cc_start: 0.6436 (m-70) cc_final: 0.6215 (m-70) REVERT: W 88 THR cc_start: 0.8699 (m) cc_final: 0.8360 (p) REVERT: W 90 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8046 (mm-30) REVERT: AF 127 GLU cc_start: 0.8263 (pm20) cc_final: 0.7793 (pm20) REVERT: AG 29 MET cc_start: 0.8598 (ppp) cc_final: 0.8364 (ppp) REVERT: AG 86 GLN cc_start: 0.7928 (mt0) cc_final: 0.7507 (mt0) REVERT: AG 128 ASN cc_start: 0.8890 (m-40) cc_final: 0.8568 (m-40) REVERT: AG 145 ASP cc_start: 0.8019 (t70) cc_final: 0.7555 (t70) REVERT: AH 27 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8027 (mm-30) REVERT: AH 95 ARG cc_start: 0.7691 (mtm110) cc_final: 0.7440 (mtm110) REVERT: AH 134 GLU cc_start: 0.7779 (mp0) cc_final: 0.7468 (mp0) REVERT: AH 155 GLU cc_start: 0.7539 (pp20) cc_final: 0.7128 (pp20) REVERT: AI 29 TYR cc_start: 0.8338 (t80) cc_final: 0.8066 (t80) REVERT: AM 105 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: AN 72 TYR cc_start: 0.7707 (p90) cc_final: 0.7114 (p90) REVERT: AO 116 GLU cc_start: 0.8242 (tp30) cc_final: 0.8037 (tp30) REVERT: AP 110 MET cc_start: 0.9063 (mmm) cc_final: 0.8780 (mmm) REVERT: AQ 1 MET cc_start: 0.6342 (ttp) cc_final: 0.4529 (mmt) REVERT: AQ 6 GLU cc_start: 0.7775 (pp20) cc_final: 0.7570 (pp20) REVERT: AQ 61 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8626 (mt-10) REVERT: AQ 95 ASP cc_start: 0.8916 (t0) cc_final: 0.8666 (t0) REVERT: AQ 111 SER cc_start: 0.8939 (m) cc_final: 0.8172 (m) REVERT: AS 102 ASP cc_start: 0.8124 (t70) cc_final: 0.7665 (t0) REVERT: AW 9 ASP cc_start: 0.8410 (m-30) cc_final: 0.7971 (m-30) REVERT: AW 21 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7899 (mtm110) REVERT: AW 33 ASN cc_start: 0.8172 (m-40) cc_final: 0.7947 (m-40) REVERT: AX 51 ASN cc_start: 0.8873 (m110) cc_final: 0.8625 (m110) REVERT: AX 105 TYR cc_start: 0.7973 (m-80) cc_final: 0.7547 (m-80) REVERT: AX 123 LEU cc_start: 0.6165 (mm) cc_final: 0.5451 (tm) REVERT: AZ 90 ASN cc_start: 0.9104 (m110) cc_final: 0.8895 (m-40) REVERT: Aa 59 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: Ac 1 MET cc_start: 0.3572 (mmm) cc_final: 0.3172 (mmt) REVERT: Ae 36 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7661 (mt-10) REVERT: Ag 1 MET cc_start: 0.5357 (mmm) cc_final: 0.4203 (ptt) REVERT: Ai 44 SER cc_start: 0.8847 (m) cc_final: 0.8577 (p) outliers start: 162 outliers final: 79 residues processed: 1133 average time/residue: 1.9317 time to fit residues: 3258.3465 Evaluate side-chains 1095 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1007 time to evaluate : 6.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 111 ARG Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 24 GLU Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 122 CYS Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain AD residue 170 ASP Chi-restraints excluded: chain AG residue 55 SER Chi-restraints excluded: chain AG residue 130 ASN Chi-restraints excluded: chain AG residue 162 THR Chi-restraints excluded: chain AI residue 3 VAL Chi-restraints excluded: chain AI residue 21 VAL Chi-restraints excluded: chain AL residue 134 SER Chi-restraints excluded: chain AM residue 14 THR Chi-restraints excluded: chain AM residue 105 GLU Chi-restraints excluded: chain AN residue 41 THR Chi-restraints excluded: chain AN residue 79 ASP Chi-restraints excluded: chain AN residue 136 ILE Chi-restraints excluded: chain AO residue 71 ASP Chi-restraints excluded: chain AO residue 123 SER Chi-restraints excluded: chain AP residue 35 SER Chi-restraints excluded: chain AQ residue 12 LEU Chi-restraints excluded: chain AQ residue 34 VAL Chi-restraints excluded: chain AQ residue 71 ASP Chi-restraints excluded: chain AR residue 51 ASN Chi-restraints excluded: chain AS residue 113 ILE Chi-restraints excluded: chain AU residue 60 SER Chi-restraints excluded: chain AU residue 73 MET Chi-restraints excluded: chain AU residue 82 ASP Chi-restraints excluded: chain AV residue 5 ASP Chi-restraints excluded: chain AW residue 21 ARG Chi-restraints excluded: chain AW residue 91 ILE Chi-restraints excluded: chain AW residue 97 ASN Chi-restraints excluded: chain AX residue 89 TYR Chi-restraints excluded: chain AZ residue 78 ASP Chi-restraints excluded: chain Aa residue 8 THR Chi-restraints excluded: chain Aa residue 17 LEU Chi-restraints excluded: chain Aa residue 18 GLU Chi-restraints excluded: chain Aa residue 35 VAL Chi-restraints excluded: chain Aa residue 59 GLU Chi-restraints excluded: chain Ab residue 38 ILE Chi-restraints excluded: chain Ab residue 101 MET Chi-restraints excluded: chain Ac residue 25 THR Chi-restraints excluded: chain Ac residue 55 HIS Chi-restraints excluded: chain Af residue 40 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 541 optimal weight: 7.9990 chunk 302 optimal weight: 0.7980 chunk 810 optimal weight: 7.9990 chunk 662 optimal weight: 7.9990 chunk 268 optimal weight: 9.9990 chunk 975 optimal weight: 5.9990 chunk 1053 optimal weight: 8.9990 chunk 868 optimal weight: 0.8980 chunk 967 optimal weight: 0.9990 chunk 332 optimal weight: 6.9990 chunk 782 optimal weight: 9.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN D 34 HIS ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 ASN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 ASN K 30 ASN ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 ASN AE 168 GLN ** AH 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 51 GLN AO 94 ASN AP 61 HIS AQ 91 ASN AT 56 ASN ** AU 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 41 ASN ** Ac 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 160524 Z= 0.230 Angle : 0.872 41.236 239067 Z= 0.372 Chirality : 0.085 2.107 30097 Planarity : 0.004 0.044 13022 Dihedral : 23.102 179.708 78236 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.90 % Allowed : 18.18 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.11), residues: 6239 helix: 1.37 (0.11), residues: 2146 sheet: -0.26 (0.14), residues: 1303 loop : -1.01 (0.12), residues: 2790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 132 HIS 0.014 0.001 HIS W 30 PHE 0.029 0.002 PHE F 74 TYR 0.028 0.002 TYR O 77 ARG 0.009 0.000 ARG E 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1299 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1104 time to evaluate : 6.812 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: C 42 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7509 (mm-30) REVERT: C 128 GLU cc_start: 0.8518 (tt0) cc_final: 0.8159 (mt-10) REVERT: C 173 GLU cc_start: 0.7687 (pm20) cc_final: 0.7448 (pm20) REVERT: C 184 ASN cc_start: 0.8447 (t0) cc_final: 0.8168 (t0) REVERT: D 28 ILE cc_start: 0.8527 (mm) cc_final: 0.8096 (tp) REVERT: D 140 ASP cc_start: 0.8881 (m-30) cc_final: 0.8117 (m-30) REVERT: E 69 ASN cc_start: 0.8408 (t0) cc_final: 0.7759 (t0) REVERT: E 130 ASN cc_start: 0.8365 (p0) cc_final: 0.8038 (p0) REVERT: F 58 ARG cc_start: 0.7791 (mtp85) cc_final: 0.7211 (mtt90) REVERT: F 78 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8723 (tt) REVERT: F 83 ASN cc_start: 0.7458 (m-40) cc_final: 0.7216 (m110) REVERT: G 44 TYR cc_start: 0.8473 (m-10) cc_final: 0.7998 (m-10) REVERT: G 48 ASP cc_start: 0.7584 (m-30) cc_final: 0.7289 (m-30) REVERT: G 73 LEU cc_start: 0.8673 (mm) cc_final: 0.8352 (mm) REVERT: H 63 LEU cc_start: 0.9076 (mp) cc_final: 0.8874 (mm) REVERT: H 71 ASN cc_start: 0.8629 (m110) cc_final: 0.8353 (m110) REVERT: H 85 ARG cc_start: 0.8442 (ttp80) cc_final: 0.8033 (ttt-90) REVERT: H 117 GLU cc_start: 0.8381 (tt0) cc_final: 0.7914 (tt0) REVERT: I 72 ASN cc_start: 0.8562 (t0) cc_final: 0.8311 (t0) REVERT: I 87 HIS cc_start: 0.9225 (t-90) cc_final: 0.8609 (t-90) REVERT: I 113 ASP cc_start: 0.8321 (t0) cc_final: 0.7427 (t0) REVERT: K 19 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8032 (mm-30) REVERT: K 39 LYS cc_start: 0.8991 (tppp) cc_final: 0.8645 (tmmt) REVERT: K 95 GLU cc_start: 0.7593 (pp20) cc_final: 0.7164 (pp20) REVERT: K 99 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.8291 (ttp-110) REVERT: K 101 ILE cc_start: 0.9146 (tt) cc_final: 0.8904 (tt) REVERT: L 70 ILE cc_start: 0.7675 (mt) cc_final: 0.7438 (pt) REVERT: L 82 ILE cc_start: 0.9019 (pt) cc_final: 0.8810 (pp) REVERT: M 74 VAL cc_start: 0.9361 (t) cc_final: 0.8922 (m) REVERT: N 23 ARG cc_start: 0.6972 (mtp85) cc_final: 0.6745 (mtt90) REVERT: O 6 GLN cc_start: 0.8852 (mt0) cc_final: 0.8620 (mt0) REVERT: O 45 ASN cc_start: 0.8417 (m110) cc_final: 0.8123 (m110) REVERT: O 73 ASP cc_start: 0.7637 (t0) cc_final: 0.7411 (t0) REVERT: P 24 ASN cc_start: 0.7873 (m-40) cc_final: 0.7411 (m110) REVERT: P 36 GLU cc_start: 0.8378 (mp0) cc_final: 0.8020 (mp0) REVERT: P 44 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8238 (tp30) REVERT: Q 25 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7735 (tm-30) REVERT: Q 49 ASP cc_start: 0.8078 (t0) cc_final: 0.7855 (t0) REVERT: Q 78 GLU cc_start: 0.8169 (tp30) cc_final: 0.7941 (tm-30) REVERT: R 42 LYS cc_start: 0.8809 (pttp) cc_final: 0.8608 (tptt) REVERT: R 57 THR cc_start: 0.8681 (t) cc_final: 0.8292 (t) REVERT: T 20 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6300 (ttm-80) REVERT: T 27 GLU cc_start: 0.8833 (tp30) cc_final: 0.8605 (mm-30) REVERT: T 51 PHE cc_start: 0.9493 (t80) cc_final: 0.9251 (t80) REVERT: T 59 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7734 (p0) REVERT: T 70 ASN cc_start: 0.8499 (m-40) cc_final: 0.8065 (m-40) REVERT: U 22 MET cc_start: 0.7237 (ptm) cc_final: 0.6839 (ttp) REVERT: U 54 ARG cc_start: 0.7581 (mmm160) cc_final: 0.7149 (mtm180) REVERT: V 13 SER cc_start: 0.9220 (m) cc_final: 0.8962 (p) REVERT: W 21 LEU cc_start: 0.9256 (mm) cc_final: 0.8805 (mm) REVERT: W 45 GLU cc_start: 0.8209 (tt0) cc_final: 0.7783 (tt0) REVERT: W 46 HIS cc_start: 0.6614 (m-70) cc_final: 0.6122 (m-70) REVERT: W 88 THR cc_start: 0.8685 (m) cc_final: 0.8351 (p) REVERT: W 90 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8139 (mm-30) REVERT: AD 200 GLU cc_start: 0.8377 (pm20) cc_final: 0.8161 (pm20) REVERT: AF 127 GLU cc_start: 0.8271 (pm20) cc_final: 0.7797 (pm20) REVERT: AF 205 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: AG 1 MET cc_start: 0.5025 (OUTLIER) cc_final: 0.4398 (ttt) REVERT: AG 18 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8549 (mp0) REVERT: AG 29 MET cc_start: 0.8551 (ppp) cc_final: 0.8169 (ppp) REVERT: AG 86 GLN cc_start: 0.7877 (mt0) cc_final: 0.7510 (mt0) REVERT: AG 128 ASN cc_start: 0.8847 (m-40) cc_final: 0.8515 (m-40) REVERT: AG 145 ASP cc_start: 0.8103 (t70) cc_final: 0.7609 (t70) REVERT: AH 1 MET cc_start: 0.3022 (OUTLIER) cc_final: 0.2735 (tmt) REVERT: AH 27 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7997 (mm-30) REVERT: AH 95 ARG cc_start: 0.7690 (mtm110) cc_final: 0.7457 (mtm110) REVERT: AH 155 GLU cc_start: 0.7514 (pp20) cc_final: 0.7111 (pp20) REVERT: AH 167 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8184 (pt0) REVERT: AM 105 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: AM 110 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.8166 (m-40) REVERT: AN 71 GLU cc_start: 0.7590 (pp20) cc_final: 0.7268 (pp20) REVERT: AO 71 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8360 (p0) REVERT: AP 110 MET cc_start: 0.9018 (mmm) cc_final: 0.8790 (mmm) REVERT: AQ 95 ASP cc_start: 0.8860 (t0) cc_final: 0.8621 (t0) REVERT: AQ 111 SER cc_start: 0.8937 (m) cc_final: 0.8725 (t) REVERT: AS 102 ASP cc_start: 0.7909 (t70) cc_final: 0.7678 (t0) REVERT: AW 9 ASP cc_start: 0.8328 (m-30) cc_final: 0.7887 (m-30) REVERT: AX 3 ASN cc_start: 0.8963 (t0) cc_final: 0.8698 (t0) REVERT: AX 51 ASN cc_start: 0.8848 (m110) cc_final: 0.8583 (m110) REVERT: AX 105 TYR cc_start: 0.8178 (m-80) cc_final: 0.7974 (m-80) REVERT: AX 123 LEU cc_start: 0.6063 (mm) cc_final: 0.5443 (tm) REVERT: AZ 90 ASN cc_start: 0.9071 (m110) cc_final: 0.8869 (m-40) REVERT: Aa 55 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8562 (mp) REVERT: Ac 24 LEU cc_start: 0.8832 (mt) cc_final: 0.8277 (mp) REVERT: Ac 48 VAL cc_start: 0.8348 (t) cc_final: 0.8053 (p) REVERT: Ae 11 GLU cc_start: 0.8198 (pt0) cc_final: 0.7182 (pt0) REVERT: Ae 31 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6761 (ptp-170) REVERT: Ae 34 LYS cc_start: 0.7806 (mmmt) cc_final: 0.7604 (mttm) REVERT: Ag 1 MET cc_start: 0.5222 (mmm) cc_final: 0.5011 (mmm) REVERT: Ah 1 MET cc_start: 0.6147 (pmm) cc_final: 0.5250 (pmm) REVERT: Ai 23 LYS cc_start: 0.8600 (mmmm) cc_final: 0.8294 (mmpt) outliers start: 195 outliers final: 86 residues processed: 1183 average time/residue: 1.8748 time to fit residues: 3330.2084 Evaluate side-chains 1109 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1010 time to evaluate : 6.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain I residue 49 ASN Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 24 GLU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 122 CYS Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 20 ARG Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain AD residue 182 GLU Chi-restraints excluded: chain AE residue 2 LEU Chi-restraints excluded: chain AF residue 205 GLU Chi-restraints excluded: chain AG residue 1 MET Chi-restraints excluded: chain AG residue 18 GLU Chi-restraints excluded: chain AG residue 28 ILE Chi-restraints excluded: chain AG residue 130 ASN Chi-restraints excluded: chain AG residue 162 THR Chi-restraints excluded: chain AH residue 1 MET Chi-restraints excluded: chain AH residue 167 GLU Chi-restraints excluded: chain AI residue 23 ASP Chi-restraints excluded: chain AL residue 134 SER Chi-restraints excluded: chain AM residue 105 GLU Chi-restraints excluded: chain AM residue 110 ASN Chi-restraints excluded: chain AM residue 117 LEU Chi-restraints excluded: chain AN residue 41 THR Chi-restraints excluded: chain AN residue 79 ASP Chi-restraints excluded: chain AO residue 71 ASP Chi-restraints excluded: chain AO residue 123 SER Chi-restraints excluded: chain AO residue 133 VAL Chi-restraints excluded: chain AP residue 35 SER Chi-restraints excluded: chain AQ residue 12 LEU Chi-restraints excluded: chain AQ residue 34 VAL Chi-restraints excluded: chain AQ residue 56 SER Chi-restraints excluded: chain AQ residue 71 ASP Chi-restraints excluded: chain AR residue 51 ASN Chi-restraints excluded: chain AR residue 108 MET Chi-restraints excluded: chain AR residue 114 LEU Chi-restraints excluded: chain AT residue 47 VAL Chi-restraints excluded: chain AU residue 60 SER Chi-restraints excluded: chain AU residue 72 ASP Chi-restraints excluded: chain AU residue 73 MET Chi-restraints excluded: chain AU residue 82 ASP Chi-restraints excluded: chain AV residue 5 ASP Chi-restraints excluded: chain AV residue 22 SER Chi-restraints excluded: chain AV residue 50 THR Chi-restraints excluded: chain AV residue 57 LEU Chi-restraints excluded: chain AW residue 37 VAL Chi-restraints excluded: chain AW residue 91 ILE Chi-restraints excluded: chain AX residue 89 TYR Chi-restraints excluded: chain AZ residue 59 SER Chi-restraints excluded: chain AZ residue 61 SER Chi-restraints excluded: chain AZ residue 78 ASP Chi-restraints excluded: chain Aa residue 8 THR Chi-restraints excluded: chain Aa residue 17 LEU Chi-restraints excluded: chain Aa residue 35 VAL Chi-restraints excluded: chain Aa residue 55 ILE Chi-restraints excluded: chain Ab residue 101 MET Chi-restraints excluded: chain Ac residue 25 THR Chi-restraints excluded: chain Ae residue 31 ARG Chi-restraints excluded: chain Ae residue 38 LEU Chi-restraints excluded: chain Ah residue 20 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 963 optimal weight: 5.9990 chunk 733 optimal weight: 2.9990 chunk 506 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 465 optimal weight: 7.9990 chunk 654 optimal weight: 10.0000 chunk 978 optimal weight: 20.0000 chunk 1036 optimal weight: 6.9990 chunk 511 optimal weight: 7.9990 chunk 927 optimal weight: 5.9990 chunk 279 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN C 179 HIS D 34 HIS ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 ASN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 ASN ** I 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 GLN K 30 ASN ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 ASN AD 155 GLN AE 168 GLN AH 112 GLN AN 51 GLN AQ 91 ASN AT 56 ASN ** AU 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 41 ASN AX 36 GLN AZ 48 ASN Ab 9 GLN ** Ac 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 160524 Z= 0.412 Angle : 0.943 41.102 239067 Z= 0.413 Chirality : 0.087 2.109 30097 Planarity : 0.005 0.067 13022 Dihedral : 23.119 179.873 78232 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.64 % Favored : 94.34 % Rotamer: Outliers : 4.91 % Allowed : 20.72 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.11), residues: 6239 helix: 1.35 (0.11), residues: 2139 sheet: -0.29 (0.14), residues: 1305 loop : -1.05 (0.12), residues: 2795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPAi 20 HIS 0.022 0.001 HIS W 30 PHE 0.038 0.002 PHE F 74 TYR 0.026 0.002 TYR N 33 ARG 0.010 0.001 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1284 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1039 time to evaluate : 6.752 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: C 150 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8312 (mt0) REVERT: C 184 ASN cc_start: 0.8624 (t0) cc_final: 0.8362 (t0) REVERT: D 28 ILE cc_start: 0.8690 (mm) cc_final: 0.8240 (tp) REVERT: D 34 HIS cc_start: 0.7903 (OUTLIER) cc_final: 0.6953 (p-80) REVERT: D 140 ASP cc_start: 0.8970 (m-30) cc_final: 0.8323 (m-30) REVERT: E 69 ASN cc_start: 0.8581 (t0) cc_final: 0.7966 (t0) REVERT: E 130 ASN cc_start: 0.8402 (p0) cc_final: 0.8065 (p0) REVERT: F 58 ARG cc_start: 0.7917 (mtp85) cc_final: 0.7369 (mtt90) REVERT: F 83 ASN cc_start: 0.7526 (m-40) cc_final: 0.7296 (m110) REVERT: G 44 TYR cc_start: 0.8506 (m-10) cc_final: 0.7909 (m-10) REVERT: G 48 ASP cc_start: 0.7611 (m-30) cc_final: 0.7328 (m-30) REVERT: G 73 LEU cc_start: 0.8615 (mm) cc_final: 0.8188 (mm) REVERT: H 43 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8677 (mm-30) REVERT: H 63 LEU cc_start: 0.9100 (mp) cc_final: 0.8852 (mm) REVERT: H 64 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9099 (mm) REVERT: H 71 ASN cc_start: 0.8644 (m110) cc_final: 0.8369 (m110) REVERT: H 85 ARG cc_start: 0.8400 (ttp80) cc_final: 0.7925 (ttt-90) REVERT: H 117 GLU cc_start: 0.8444 (tt0) cc_final: 0.7993 (tt0) REVERT: I 48 GLU cc_start: 0.8603 (pp20) cc_final: 0.8160 (pp20) REVERT: I 87 HIS cc_start: 0.9278 (t-90) cc_final: 0.8637 (t-90) REVERT: I 113 ASP cc_start: 0.8291 (t0) cc_final: 0.7388 (t0) REVERT: J 41 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8299 (pp) REVERT: K 19 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8148 (mm-30) REVERT: K 39 LYS cc_start: 0.9112 (tppp) cc_final: 0.8677 (tmmt) REVERT: K 82 TYR cc_start: 0.8095 (m-10) cc_final: 0.7884 (m-10) REVERT: K 95 GLU cc_start: 0.7524 (pp20) cc_final: 0.7108 (pp20) REVERT: L 70 ILE cc_start: 0.7687 (mt) cc_final: 0.7411 (pt) REVERT: M 74 VAL cc_start: 0.9295 (t) cc_final: 0.9046 (m) REVERT: O 45 ASN cc_start: 0.8466 (m110) cc_final: 0.8168 (m110) REVERT: O 73 ASP cc_start: 0.7734 (t0) cc_final: 0.7530 (t0) REVERT: P 24 ASN cc_start: 0.7930 (m-40) cc_final: 0.7602 (m110) REVERT: P 36 GLU cc_start: 0.8439 (mp0) cc_final: 0.8101 (mp0) REVERT: P 44 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8085 (tp30) REVERT: Q 25 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7733 (tm-30) REVERT: Q 49 ASP cc_start: 0.8107 (t0) cc_final: 0.7869 (t0) REVERT: R 48 ASP cc_start: 0.8206 (t0) cc_final: 0.7876 (t0) REVERT: R 57 THR cc_start: 0.8655 (t) cc_final: 0.8250 (t) REVERT: R 58 GLU cc_start: 0.7741 (pm20) cc_final: 0.7424 (pm20) REVERT: S 69 HIS cc_start: 0.8895 (m170) cc_final: 0.8664 (m-70) REVERT: S 79 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8810 (tp) REVERT: T 27 GLU cc_start: 0.8886 (tp30) cc_final: 0.8626 (mm-30) REVERT: T 51 PHE cc_start: 0.9505 (t80) cc_final: 0.9260 (t80) REVERT: T 59 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7848 (p0) REVERT: T 70 ASN cc_start: 0.8605 (m-40) cc_final: 0.8167 (m-40) REVERT: U 22 MET cc_start: 0.7094 (ptm) cc_final: 0.6654 (ttp) REVERT: U 54 ARG cc_start: 0.7580 (mmm160) cc_final: 0.7377 (mmm160) REVERT: V 13 SER cc_start: 0.9248 (m) cc_final: 0.8975 (p) REVERT: W 45 GLU cc_start: 0.8235 (tt0) cc_final: 0.7815 (tt0) REVERT: W 46 HIS cc_start: 0.6721 (m-70) cc_final: 0.5822 (m-70) REVERT: W 88 THR cc_start: 0.8598 (m) cc_final: 0.8248 (p) REVERT: W 90 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8077 (mm-30) REVERT: AE 168 GLN cc_start: 0.8624 (tt0) cc_final: 0.8420 (tt0) REVERT: AF 127 GLU cc_start: 0.8260 (pm20) cc_final: 0.7766 (pm20) REVERT: AG 1 MET cc_start: 0.5337 (OUTLIER) cc_final: 0.4616 (ttt) REVERT: AG 18 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8546 (mp0) REVERT: AG 29 MET cc_start: 0.8504 (ppp) cc_final: 0.8231 (ppp) REVERT: AG 62 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8272 (mp10) REVERT: AG 86 GLN cc_start: 0.8047 (mt0) cc_final: 0.7631 (mt0) REVERT: AG 117 PHE cc_start: 0.8347 (t80) cc_final: 0.8131 (t80) REVERT: AG 128 ASN cc_start: 0.8884 (m-40) cc_final: 0.8568 (m-40) REVERT: AG 145 ASP cc_start: 0.8131 (t70) cc_final: 0.7700 (t70) REVERT: AH 90 ASN cc_start: 0.8432 (t0) cc_final: 0.8197 (m-40) REVERT: AH 95 ARG cc_start: 0.7693 (mtm110) cc_final: 0.7423 (mtm110) REVERT: AH 155 GLU cc_start: 0.7521 (pp20) cc_final: 0.7123 (pp20) REVERT: AH 167 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8280 (pt0) REVERT: AI 29 TYR cc_start: 0.8115 (t80) cc_final: 0.7867 (t80) REVERT: AM 105 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: AN 71 GLU cc_start: 0.7814 (pp20) cc_final: 0.7574 (pp20) REVERT: AN 72 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.7100 (p90) REVERT: AQ 95 ASP cc_start: 0.8905 (t0) cc_final: 0.8658 (t0) REVERT: AS 102 ASP cc_start: 0.8080 (t70) cc_final: 0.7742 (t0) REVERT: AU 31 GLU cc_start: 0.8539 (tp30) cc_final: 0.8301 (mm-30) REVERT: AU 72 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8138 (p0) REVERT: AW 9 ASP cc_start: 0.8354 (m-30) cc_final: 0.7899 (m-30) REVERT: AW 57 ARG cc_start: 0.8522 (pmt170) cc_final: 0.7991 (pmt-80) REVERT: AX 51 ASN cc_start: 0.8885 (m110) cc_final: 0.8624 (m110) REVERT: AX 123 LEU cc_start: 0.6154 (mm) cc_final: 0.5477 (tm) REVERT: Aa 55 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8548 (mp) REVERT: Aa 59 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: Ac 24 LEU cc_start: 0.8934 (mt) cc_final: 0.8712 (mm) REVERT: Ac 48 VAL cc_start: 0.8402 (t) cc_final: 0.8108 (p) REVERT: Ae 31 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.6933 (ptp-170) REVERT: Ae 36 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7585 (mt-10) REVERT: Ag 1 MET cc_start: 0.5362 (mmm) cc_final: 0.4572 (mmt) outliers start: 245 outliers final: 136 residues processed: 1148 average time/residue: 1.8804 time to fit residues: 3266.3615 Evaluate side-chains 1137 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 986 time to evaluate : 6.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain I residue 49 ASN Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 24 GLU Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 122 CYS Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain AD residue 155 GLN Chi-restraints excluded: chain AD residue 182 GLU Chi-restraints excluded: chain AE residue 41 ASP Chi-restraints excluded: chain AE residue 53 VAL Chi-restraints excluded: chain AE residue 153 THR Chi-restraints excluded: chain AF residue 138 ASP Chi-restraints excluded: chain AG residue 1 MET Chi-restraints excluded: chain AG residue 18 GLU Chi-restraints excluded: chain AG residue 28 ILE Chi-restraints excluded: chain AG residue 41 VAL Chi-restraints excluded: chain AG residue 130 ASN Chi-restraints excluded: chain AG residue 162 THR Chi-restraints excluded: chain AH residue 3 ARG Chi-restraints excluded: chain AH residue 19 VAL Chi-restraints excluded: chain AH residue 167 GLU Chi-restraints excluded: chain AI residue 9 PHE Chi-restraints excluded: chain AI residue 23 ASP Chi-restraints excluded: chain AL residue 17 VAL Chi-restraints excluded: chain AL residue 134 SER Chi-restraints excluded: chain AM residue 14 THR Chi-restraints excluded: chain AM residue 105 GLU Chi-restraints excluded: chain AM residue 117 LEU Chi-restraints excluded: chain AN residue 17 VAL Chi-restraints excluded: chain AN residue 41 THR Chi-restraints excluded: chain AN residue 45 LEU Chi-restraints excluded: chain AN residue 72 TYR Chi-restraints excluded: chain AN residue 79 ASP Chi-restraints excluded: chain AN residue 136 ILE Chi-restraints excluded: chain AO residue 71 ASP Chi-restraints excluded: chain AO residue 80 GLU Chi-restraints excluded: chain AO residue 123 SER Chi-restraints excluded: chain AP residue 7 PHE Chi-restraints excluded: chain AP residue 35 SER Chi-restraints excluded: chain AP residue 118 LYS Chi-restraints excluded: chain AQ residue 12 LEU Chi-restraints excluded: chain AQ residue 34 VAL Chi-restraints excluded: chain AQ residue 56 SER Chi-restraints excluded: chain AQ residue 62 LYS Chi-restraints excluded: chain AQ residue 71 ASP Chi-restraints excluded: chain AQ residue 91 ASN Chi-restraints excluded: chain AR residue 51 ASN Chi-restraints excluded: chain AR residue 108 MET Chi-restraints excluded: chain AR residue 114 LEU Chi-restraints excluded: chain AS residue 72 THR Chi-restraints excluded: chain AT residue 33 LEU Chi-restraints excluded: chain AT residue 47 VAL Chi-restraints excluded: chain AU residue 14 LEU Chi-restraints excluded: chain AU residue 57 SER Chi-restraints excluded: chain AU residue 60 SER Chi-restraints excluded: chain AU residue 72 ASP Chi-restraints excluded: chain AU residue 73 MET Chi-restraints excluded: chain AU residue 82 ASP Chi-restraints excluded: chain AU residue 83 ASP Chi-restraints excluded: chain AV residue 5 ASP Chi-restraints excluded: chain AV residue 22 SER Chi-restraints excluded: chain AV residue 50 THR Chi-restraints excluded: chain AV residue 57 LEU Chi-restraints excluded: chain AV residue 72 TYR Chi-restraints excluded: chain AW residue 37 VAL Chi-restraints excluded: chain AW residue 81 LEU Chi-restraints excluded: chain AW residue 91 ILE Chi-restraints excluded: chain AW residue 97 ASN Chi-restraints excluded: chain AX residue 89 TYR Chi-restraints excluded: chain AZ residue 46 LEU Chi-restraints excluded: chain AZ residue 48 ASN Chi-restraints excluded: chain AZ residue 59 SER Chi-restraints excluded: chain AZ residue 61 SER Chi-restraints excluded: chain AZ residue 78 ASP Chi-restraints excluded: chain Aa residue 8 THR Chi-restraints excluded: chain Aa residue 17 LEU Chi-restraints excluded: chain Aa residue 35 VAL Chi-restraints excluded: chain Aa residue 55 ILE Chi-restraints excluded: chain Aa residue 59 GLU Chi-restraints excluded: chain Ab residue 77 VAL Chi-restraints excluded: chain Ac residue 25 THR Chi-restraints excluded: chain Ac residue 28 THR Chi-restraints excluded: chain Ac residue 55 HIS Chi-restraints excluded: chain Ad residue 56 LEU Chi-restraints excluded: chain Ae residue 27 THR Chi-restraints excluded: chain Ae residue 31 ARG Chi-restraints excluded: chain Ae residue 38 LEU Chi-restraints excluded: chain Af residue 4 THR Chi-restraints excluded: chain Af residue 22 MET Chi-restraints excluded: chain Af residue 44 VAL Chi-restraints excluded: chain Ag residue 7 THR Chi-restraints excluded: chain Ah residue 20 LYS Chi-restraints excluded: chain Ah residue 28 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 862 optimal weight: 2.9990 chunk 588 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 771 optimal weight: 10.0000 chunk 427 optimal weight: 10.0000 chunk 884 optimal weight: 0.6980 chunk 716 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 529 optimal weight: 10.0000 chunk 930 optimal weight: 0.8980 chunk 261 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN D 34 HIS ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 ASN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 ASN K 30 ASN ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 GLN W 9 ASN AH 99 GLN AM 90 ASN AN 51 GLN AO 94 ASN AQ 91 ASN AT 56 ASN ** AU 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 41 ASN ** Ac 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 160524 Z= 0.208 Angle : 0.875 41.273 239067 Z= 0.375 Chirality : 0.085 2.106 30097 Planarity : 0.004 0.047 13022 Dihedral : 23.136 179.901 78230 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.86 % Favored : 95.13 % Rotamer: Outliers : 4.08 % Allowed : 23.45 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.11), residues: 6239 helix: 1.52 (0.12), residues: 2135 sheet: -0.21 (0.14), residues: 1310 loop : -0.95 (0.12), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 132 HIS 0.017 0.001 HIS D 34 PHE 0.026 0.001 PHE F 74 TYR 0.037 0.002 TYR O 77 ARG 0.010 0.000 ARG T 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1061 time to evaluate : 6.737 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: C 150 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8326 (mt0) REVERT: D 28 ILE cc_start: 0.8682 (mm) cc_final: 0.8275 (tp) REVERT: D 34 HIS cc_start: 0.7650 (OUTLIER) cc_final: 0.6349 (p-80) REVERT: D 140 ASP cc_start: 0.8919 (m-30) cc_final: 0.8161 (m-30) REVERT: E 69 ASN cc_start: 0.8547 (t0) cc_final: 0.7909 (t0) REVERT: E 130 ASN cc_start: 0.8382 (p0) cc_final: 0.8013 (p0) REVERT: F 83 ASN cc_start: 0.7495 (m-40) cc_final: 0.7234 (m110) REVERT: G 44 TYR cc_start: 0.8478 (m-10) cc_final: 0.7872 (m-10) REVERT: G 48 ASP cc_start: 0.7634 (m-30) cc_final: 0.7331 (m-30) REVERT: G 73 LEU cc_start: 0.8646 (mm) cc_final: 0.8268 (mm) REVERT: G 117 MET cc_start: 0.6287 (mmt) cc_final: 0.6049 (mmt) REVERT: G 127 ASN cc_start: 0.8888 (t0) cc_final: 0.8661 (t0) REVERT: H 63 LEU cc_start: 0.9086 (mp) cc_final: 0.8878 (mm) REVERT: H 64 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9057 (mm) REVERT: H 71 ASN cc_start: 0.8553 (m110) cc_final: 0.8099 (m110) REVERT: H 85 ARG cc_start: 0.8411 (ttp80) cc_final: 0.7969 (ttt-90) REVERT: H 117 GLU cc_start: 0.8445 (tt0) cc_final: 0.8041 (tt0) REVERT: I 26 TYR cc_start: 0.8493 (m-80) cc_final: 0.8062 (m-80) REVERT: I 48 GLU cc_start: 0.8626 (pp20) cc_final: 0.8165 (pp20) REVERT: I 70 TYR cc_start: 0.7593 (t80) cc_final: 0.7169 (t80) REVERT: I 87 HIS cc_start: 0.9274 (t-90) cc_final: 0.9074 (t70) REVERT: I 113 ASP cc_start: 0.8345 (t0) cc_final: 0.7383 (t0) REVERT: J 41 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8301 (pp) REVERT: K 19 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8086 (mm-30) REVERT: K 39 LYS cc_start: 0.9050 (tppp) cc_final: 0.8629 (tmmt) REVERT: K 95 GLU cc_start: 0.7345 (pp20) cc_final: 0.7135 (pp20) REVERT: L 70 ILE cc_start: 0.7756 (mt) cc_final: 0.7456 (pt) REVERT: M 1 MET cc_start: 0.2648 (tmm) cc_final: 0.1396 (tpp) REVERT: M 11 ASN cc_start: 0.7725 (m110) cc_final: 0.7419 (p0) REVERT: M 74 VAL cc_start: 0.9279 (t) cc_final: 0.9033 (m) REVERT: O 21 THR cc_start: 0.8976 (p) cc_final: 0.8713 (t) REVERT: O 45 ASN cc_start: 0.8406 (m110) cc_final: 0.8059 (m110) REVERT: O 70 GLN cc_start: 0.8662 (tt0) cc_final: 0.8305 (tm-30) REVERT: O 73 ASP cc_start: 0.7662 (t0) cc_final: 0.7389 (t0) REVERT: P 24 ASN cc_start: 0.7832 (m-40) cc_final: 0.7469 (m110) REVERT: P 36 GLU cc_start: 0.8397 (mp0) cc_final: 0.8042 (mp0) REVERT: P 44 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8064 (tp30) REVERT: Q 25 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7661 (tm-30) REVERT: Q 49 ASP cc_start: 0.8050 (t0) cc_final: 0.7821 (t0) REVERT: R 57 THR cc_start: 0.8592 (t) cc_final: 0.8207 (t) REVERT: R 95 LYS cc_start: 0.7764 (mmmt) cc_final: 0.7268 (ptmm) REVERT: S 69 HIS cc_start: 0.8900 (m170) cc_final: 0.8684 (m-70) REVERT: T 21 ASN cc_start: 0.7619 (m-40) cc_final: 0.7398 (m110) REVERT: T 49 GLU cc_start: 0.8483 (mp0) cc_final: 0.8274 (mp0) REVERT: T 59 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7858 (p0) REVERT: U 22 MET cc_start: 0.6934 (ptm) cc_final: 0.6532 (ttp) REVERT: U 54 ARG cc_start: 0.7575 (mmm160) cc_final: 0.7370 (mmm160) REVERT: V 13 SER cc_start: 0.9221 (m) cc_final: 0.8967 (p) REVERT: W 4 LYS cc_start: 0.7598 (ttpt) cc_final: 0.6755 (tmmt) REVERT: W 21 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8945 (mm) REVERT: W 45 GLU cc_start: 0.8084 (tt0) cc_final: 0.7662 (tt0) REVERT: W 46 HIS cc_start: 0.6628 (OUTLIER) cc_final: 0.5535 (m-70) REVERT: W 88 THR cc_start: 0.8590 (m) cc_final: 0.8226 (p) REVERT: W 90 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8081 (mm-30) REVERT: AF 127 GLU cc_start: 0.8255 (pm20) cc_final: 0.7795 (pm20) REVERT: AG 1 MET cc_start: 0.5328 (OUTLIER) cc_final: 0.4639 (ttt) REVERT: AG 18 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8503 (mp0) REVERT: AG 29 MET cc_start: 0.8488 (ppp) cc_final: 0.8211 (ppp) REVERT: AG 40 SER cc_start: 0.8375 (p) cc_final: 0.8018 (m) REVERT: AG 86 GLN cc_start: 0.7885 (mt0) cc_final: 0.7414 (mt0) REVERT: AG 128 ASN cc_start: 0.8830 (m-40) cc_final: 0.8539 (m-40) REVERT: AG 145 ASP cc_start: 0.8119 (t70) cc_final: 0.7642 (t70) REVERT: AH 90 ASN cc_start: 0.8392 (t0) cc_final: 0.8162 (m-40) REVERT: AH 95 ARG cc_start: 0.7682 (mtm110) cc_final: 0.7440 (mtm110) REVERT: AH 155 GLU cc_start: 0.7424 (pp20) cc_final: 0.7042 (pp20) REVERT: AH 167 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8167 (pt0) REVERT: AI 29 TYR cc_start: 0.8074 (t80) cc_final: 0.7700 (t80) REVERT: AM 105 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: AN 45 LEU cc_start: 0.4184 (OUTLIER) cc_final: 0.3815 (pp) REVERT: AN 71 GLU cc_start: 0.7861 (pp20) cc_final: 0.7554 (pp20) REVERT: AQ 1 MET cc_start: 0.4317 (ttp) cc_final: 0.2702 (mmt) REVERT: AQ 95 ASP cc_start: 0.8854 (t0) cc_final: 0.8608 (t0) REVERT: AT 36 ASN cc_start: 0.8471 (t160) cc_final: 0.8269 (t160) REVERT: AU 31 GLU cc_start: 0.8517 (tp30) cc_final: 0.8287 (mm-30) REVERT: AU 72 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.8033 (p0) REVERT: AV 1 MET cc_start: 0.7739 (mtp) cc_final: 0.7538 (mtp) REVERT: AW 9 ASP cc_start: 0.8308 (m-30) cc_final: 0.7858 (m-30) REVERT: AW 19 ARG cc_start: 0.7817 (tpp80) cc_final: 0.7313 (ttm-80) REVERT: AW 57 ARG cc_start: 0.8561 (pmt170) cc_final: 0.8271 (pmt-80) REVERT: AX 51 ASN cc_start: 0.8851 (m110) cc_final: 0.8597 (m110) REVERT: AX 105 TYR cc_start: 0.7754 (m-80) cc_final: 0.7462 (m-80) REVERT: AX 123 LEU cc_start: 0.5999 (mm) cc_final: 0.5381 (tm) REVERT: AZ 13 MET cc_start: 0.8652 (ttp) cc_final: 0.8186 (ptm) REVERT: Aa 55 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8848 (mp) REVERT: Ab 69 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8720 (mt) REVERT: Ac 24 LEU cc_start: 0.8879 (mt) cc_final: 0.8676 (mm) REVERT: Ac 48 VAL cc_start: 0.8393 (t) cc_final: 0.8116 (p) REVERT: Ad 46 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8585 (mtpt) REVERT: Ae 36 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7416 (mt-10) REVERT: Ag 1 MET cc_start: 0.5432 (mmm) cc_final: 0.4466 (mmt) REVERT: Ai 23 LYS cc_start: 0.8579 (mmmm) cc_final: 0.8370 (mmmt) REVERT: Ai 24 ILE cc_start: 0.9173 (mt) cc_final: 0.8840 (mp) outliers start: 204 outliers final: 112 residues processed: 1156 average time/residue: 1.8706 time to fit residues: 3269.2399 Evaluate side-chains 1126 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 998 time to evaluate : 6.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 24 GLU Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain R residue 40 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 46 HIS Chi-restraints excluded: chain AD residue 170 ASP Chi-restraints excluded: chain AD residue 182 GLU Chi-restraints excluded: chain AE residue 2 LEU Chi-restraints excluded: chain AE residue 153 THR Chi-restraints excluded: chain AF residue 138 ASP Chi-restraints excluded: chain AG residue 1 MET Chi-restraints excluded: chain AG residue 18 GLU Chi-restraints excluded: chain AG residue 130 ASN Chi-restraints excluded: chain AG residue 155 LEU Chi-restraints excluded: chain AG residue 162 THR Chi-restraints excluded: chain AH residue 3 ARG Chi-restraints excluded: chain AH residue 167 GLU Chi-restraints excluded: chain AI residue 9 PHE Chi-restraints excluded: chain AL residue 59 ASN Chi-restraints excluded: chain AL residue 132 SER Chi-restraints excluded: chain AL residue 134 SER Chi-restraints excluded: chain AM residue 29 LYS Chi-restraints excluded: chain AM residue 105 GLU Chi-restraints excluded: chain AM residue 117 LEU Chi-restraints excluded: chain AN residue 17 VAL Chi-restraints excluded: chain AN residue 41 THR Chi-restraints excluded: chain AN residue 45 LEU Chi-restraints excluded: chain AN residue 79 ASP Chi-restraints excluded: chain AO residue 123 SER Chi-restraints excluded: chain AP residue 35 SER Chi-restraints excluded: chain AP residue 118 LYS Chi-restraints excluded: chain AQ residue 12 LEU Chi-restraints excluded: chain AQ residue 34 VAL Chi-restraints excluded: chain AQ residue 62 LYS Chi-restraints excluded: chain AQ residue 71 ASP Chi-restraints excluded: chain AQ residue 91 ASN Chi-restraints excluded: chain AR residue 51 ASN Chi-restraints excluded: chain AR residue 108 MET Chi-restraints excluded: chain AR residue 114 LEU Chi-restraints excluded: chain AS residue 72 THR Chi-restraints excluded: chain AS residue 113 ILE Chi-restraints excluded: chain AT residue 47 VAL Chi-restraints excluded: chain AU residue 14 LEU Chi-restraints excluded: chain AU residue 57 SER Chi-restraints excluded: chain AU residue 60 SER Chi-restraints excluded: chain AU residue 72 ASP Chi-restraints excluded: chain AU residue 73 MET Chi-restraints excluded: chain AU residue 82 ASP Chi-restraints excluded: chain AU residue 83 ASP Chi-restraints excluded: chain AV residue 5 ASP Chi-restraints excluded: chain AV residue 50 THR Chi-restraints excluded: chain AV residue 57 LEU Chi-restraints excluded: chain AW residue 37 VAL Chi-restraints excluded: chain AW residue 91 ILE Chi-restraints excluded: chain AW residue 97 ASN Chi-restraints excluded: chain AX residue 89 TYR Chi-restraints excluded: chain AX residue 139 LEU Chi-restraints excluded: chain AZ residue 59 SER Chi-restraints excluded: chain Aa residue 8 THR Chi-restraints excluded: chain Aa residue 35 VAL Chi-restraints excluded: chain Aa residue 55 ILE Chi-restraints excluded: chain Ab residue 38 ILE Chi-restraints excluded: chain Ab residue 69 LEU Chi-restraints excluded: chain Ab residue 101 MET Chi-restraints excluded: chain Ac residue 25 THR Chi-restraints excluded: chain Ac residue 28 THR Chi-restraints excluded: chain Ac residue 55 HIS Chi-restraints excluded: chain Ad residue 46 LYS Chi-restraints excluded: chain Ae residue 27 THR Chi-restraints excluded: chain Ae residue 38 LEU Chi-restraints excluded: chain Af residue 22 MET Chi-restraints excluded: chain Ah residue 20 LYS Chi-restraints excluded: chain Ai residue 41 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 348 optimal weight: 0.9980 chunk 933 optimal weight: 5.9990 chunk 204 optimal weight: 9.9990 chunk 608 optimal weight: 8.9990 chunk 255 optimal weight: 7.9990 chunk 1037 optimal weight: 3.9990 chunk 861 optimal weight: 10.0000 chunk 480 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 343 optimal weight: 0.6980 chunk 544 optimal weight: 10.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN C 184 ASN D 34 HIS ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 ASN G 123 ASN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 ASN K 30 ASN K 65 GLN ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 ASN AD 145 ASN AE 168 GLN AN 51 GLN AO 94 ASN AQ 91 ASN AT 56 ASN ** AU 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AW 41 ASN AW 69 ASN Ab 46 GLN ** Ae 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 42 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 160524 Z= 0.279 Angle : 0.891 41.128 239067 Z= 0.383 Chirality : 0.085 2.109 30097 Planarity : 0.004 0.046 13022 Dihedral : 23.103 179.681 78230 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.13 % Favored : 94.85 % Rotamer: Outliers : 4.57 % Allowed : 24.17 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.11), residues: 6239 helix: 1.51 (0.12), residues: 2136 sheet: -0.22 (0.14), residues: 1311 loop : -0.96 (0.12), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 132 HIS 0.013 0.001 HIS D 34 PHE 0.022 0.001 PHE U 52 TYR 0.037 0.002 TYR O 77 ARG 0.009 0.000 ARG N 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1257 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1029 time to evaluate : 6.747 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: C 42 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7439 (mm-30) REVERT: C 128 GLU cc_start: 0.8621 (tt0) cc_final: 0.8305 (mt-10) REVERT: D 28 ILE cc_start: 0.8725 (mm) cc_final: 0.8320 (tp) REVERT: D 34 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.6520 (p-80) REVERT: D 140 ASP cc_start: 0.8947 (m-30) cc_final: 0.8231 (m-30) REVERT: E 69 ASN cc_start: 0.8576 (t0) cc_final: 0.7961 (t0) REVERT: E 130 ASN cc_start: 0.8387 (p0) cc_final: 0.8024 (p0) REVERT: F 83 ASN cc_start: 0.7501 (m-40) cc_final: 0.7213 (m110) REVERT: G 48 ASP cc_start: 0.7624 (m-30) cc_final: 0.7318 (m-30) REVERT: G 73 LEU cc_start: 0.8670 (mm) cc_final: 0.8270 (mm) REVERT: G 127 ASN cc_start: 0.8920 (t0) cc_final: 0.8683 (t0) REVERT: H 63 LEU cc_start: 0.9076 (mp) cc_final: 0.8854 (mm) REVERT: H 64 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9050 (mm) REVERT: H 71 ASN cc_start: 0.8585 (m110) cc_final: 0.7085 (m110) REVERT: H 85 ARG cc_start: 0.8424 (ttp80) cc_final: 0.7970 (ttt-90) REVERT: H 117 GLU cc_start: 0.8464 (tt0) cc_final: 0.7965 (tt0) REVERT: I 26 TYR cc_start: 0.8509 (m-80) cc_final: 0.8041 (m-80) REVERT: I 48 GLU cc_start: 0.8614 (pp20) cc_final: 0.8175 (pp20) REVERT: I 70 TYR cc_start: 0.7516 (t80) cc_final: 0.7110 (t80) REVERT: I 113 ASP cc_start: 0.8347 (t0) cc_final: 0.7391 (t0) REVERT: J 41 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8365 (pp) REVERT: K 39 LYS cc_start: 0.9091 (tppp) cc_final: 0.8647 (tmmt) REVERT: K 95 GLU cc_start: 0.7335 (pp20) cc_final: 0.7094 (pp20) REVERT: L 70 ILE cc_start: 0.7723 (mt) cc_final: 0.7412 (pt) REVERT: M 1 MET cc_start: 0.2480 (tmm) cc_final: 0.2249 (tpp) REVERT: M 9 LEU cc_start: 0.9053 (mt) cc_final: 0.8805 (mm) REVERT: M 74 VAL cc_start: 0.9277 (t) cc_final: 0.9024 (m) REVERT: O 21 THR cc_start: 0.8988 (p) cc_final: 0.8739 (t) REVERT: O 45 ASN cc_start: 0.8444 (m110) cc_final: 0.8116 (m110) REVERT: O 70 GLN cc_start: 0.8588 (tt0) cc_final: 0.8376 (tm-30) REVERT: P 24 ASN cc_start: 0.7992 (m-40) cc_final: 0.7577 (m110) REVERT: P 36 GLU cc_start: 0.8390 (mp0) cc_final: 0.8009 (mp0) REVERT: P 44 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8042 (tp30) REVERT: Q 25 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7702 (tm-30) REVERT: Q 49 ASP cc_start: 0.8072 (t0) cc_final: 0.7814 (t0) REVERT: R 57 THR cc_start: 0.8541 (t) cc_final: 0.8161 (t) REVERT: R 95 LYS cc_start: 0.7892 (mmmt) cc_final: 0.7327 (ptmm) REVERT: S 69 HIS cc_start: 0.8936 (m170) cc_final: 0.8708 (m-70) REVERT: T 21 ASN cc_start: 0.7641 (m-40) cc_final: 0.7410 (m110) REVERT: T 59 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7824 (p0) REVERT: U 22 MET cc_start: 0.6917 (ptm) cc_final: 0.6539 (ttp) REVERT: U 54 ARG cc_start: 0.7591 (mmm160) cc_final: 0.7370 (mmm160) REVERT: V 13 SER cc_start: 0.9225 (m) cc_final: 0.8965 (p) REVERT: W 4 LYS cc_start: 0.7396 (ttpt) cc_final: 0.6692 (tmmt) REVERT: W 21 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8823 (mm) REVERT: W 45 GLU cc_start: 0.8050 (tt0) cc_final: 0.7603 (tt0) REVERT: W 46 HIS cc_start: 0.6563 (OUTLIER) cc_final: 0.5424 (m-70) REVERT: W 88 THR cc_start: 0.8573 (m) cc_final: 0.8225 (p) REVERT: W 90 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8153 (mm-30) REVERT: AD 227 MET cc_start: 0.8723 (mmt) cc_final: 0.8226 (mmt) REVERT: AF 127 GLU cc_start: 0.8276 (pm20) cc_final: 0.7801 (pm20) REVERT: AG 1 MET cc_start: 0.5318 (OUTLIER) cc_final: 0.4624 (ttt) REVERT: AG 18 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: AG 29 MET cc_start: 0.8413 (ppp) cc_final: 0.8099 (ppp) REVERT: AG 40 SER cc_start: 0.8377 (p) cc_final: 0.8029 (m) REVERT: AG 62 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8304 (mp10) REVERT: AG 86 GLN cc_start: 0.7889 (mt0) cc_final: 0.7414 (mt0) REVERT: AG 128 ASN cc_start: 0.8821 (m-40) cc_final: 0.8576 (m-40) REVERT: AG 145 ASP cc_start: 0.8143 (t70) cc_final: 0.7628 (t70) REVERT: AH 27 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7598 (mp0) REVERT: AH 90 ASN cc_start: 0.8408 (t0) cc_final: 0.8181 (m-40) REVERT: AH 95 ARG cc_start: 0.7687 (mtm110) cc_final: 0.7447 (mtm110) REVERT: AH 155 GLU cc_start: 0.7416 (pp20) cc_final: 0.7032 (pp20) REVERT: AH 167 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8186 (pt0) REVERT: AI 29 TYR cc_start: 0.8107 (t80) cc_final: 0.7756 (t80) REVERT: AM 105 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7907 (mp0) REVERT: AN 45 LEU cc_start: 0.4030 (OUTLIER) cc_final: 0.3619 (pp) REVERT: AN 71 GLU cc_start: 0.7886 (pp20) cc_final: 0.7526 (pp20) REVERT: AN 72 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.6607 (p90) REVERT: AO 130 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7905 (tpp) REVERT: AQ 1 MET cc_start: 0.4238 (ttp) cc_final: 0.2682 (mmt) REVERT: AQ 95 ASP cc_start: 0.8855 (t0) cc_final: 0.8625 (t0) REVERT: AR 93 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.7813 (mmp80) REVERT: AU 31 GLU cc_start: 0.8543 (tp30) cc_final: 0.8321 (mm-30) REVERT: AU 63 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8099 (mpp) REVERT: AV 1 MET cc_start: 0.7642 (mtp) cc_final: 0.7434 (mtp) REVERT: AW 9 ASP cc_start: 0.8293 (m-30) cc_final: 0.7844 (m-30) REVERT: AW 57 ARG cc_start: 0.8533 (pmt170) cc_final: 0.8127 (pmt170) REVERT: AX 51 ASN cc_start: 0.8862 (m110) cc_final: 0.8613 (m110) REVERT: AX 105 TYR cc_start: 0.7923 (m-80) cc_final: 0.7692 (m-80) REVERT: AX 123 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5442 (tm) REVERT: AZ 7 ILE cc_start: 0.9224 (mm) cc_final: 0.8870 (mm) REVERT: AZ 13 MET cc_start: 0.8688 (ttp) cc_final: 0.8035 (ptm) REVERT: Aa 55 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8587 (mp) REVERT: Aa 59 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7887 (mp0) REVERT: Ac 48 VAL cc_start: 0.8347 (t) cc_final: 0.7983 (p) REVERT: Ac 49 GLU cc_start: 0.8420 (mp0) cc_final: 0.8113 (pm20) REVERT: Ag 1 MET cc_start: 0.5630 (mmm) cc_final: 0.4579 (mmt) REVERT: Ai 24 ILE cc_start: 0.9147 (mt) cc_final: 0.8816 (mp) outliers start: 228 outliers final: 143 residues processed: 1139 average time/residue: 1.8372 time to fit residues: 3165.0092 Evaluate side-chains 1152 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 992 time to evaluate : 6.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain I residue 49 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 24 GLU Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 108 ASN Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain R residue 40 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 46 HIS Chi-restraints excluded: chain AD residue 134 LEU Chi-restraints excluded: chain AD residue 182 GLU Chi-restraints excluded: chain AE residue 2 LEU Chi-restraints excluded: chain AE residue 41 ASP Chi-restraints excluded: chain AE residue 153 THR Chi-restraints excluded: chain AF residue 138 ASP Chi-restraints excluded: chain AG residue 1 MET Chi-restraints excluded: chain AG residue 18 GLU Chi-restraints excluded: chain AG residue 28 ILE Chi-restraints excluded: chain AG residue 41 VAL Chi-restraints excluded: chain AG residue 130 ASN Chi-restraints excluded: chain AG residue 155 LEU Chi-restraints excluded: chain AG residue 162 THR Chi-restraints excluded: chain AH residue 3 ARG Chi-restraints excluded: chain AH residue 19 VAL Chi-restraints excluded: chain AH residue 167 GLU Chi-restraints excluded: chain AI residue 9 PHE Chi-restraints excluded: chain AI residue 37 VAL Chi-restraints excluded: chain AL residue 59 ASN Chi-restraints excluded: chain AL residue 132 SER Chi-restraints excluded: chain AL residue 134 SER Chi-restraints excluded: chain AM residue 29 LYS Chi-restraints excluded: chain AM residue 105 GLU Chi-restraints excluded: chain AM residue 117 LEU Chi-restraints excluded: chain AN residue 17 VAL Chi-restraints excluded: chain AN residue 41 THR Chi-restraints excluded: chain AN residue 45 LEU Chi-restraints excluded: chain AN residue 72 TYR Chi-restraints excluded: chain AN residue 79 ASP Chi-restraints excluded: chain AO residue 80 GLU Chi-restraints excluded: chain AO residue 123 SER Chi-restraints excluded: chain AO residue 130 MET Chi-restraints excluded: chain AP residue 7 PHE Chi-restraints excluded: chain AP residue 35 SER Chi-restraints excluded: chain AP residue 118 LYS Chi-restraints excluded: chain AQ residue 12 LEU Chi-restraints excluded: chain AQ residue 34 VAL Chi-restraints excluded: chain AQ residue 62 LYS Chi-restraints excluded: chain AQ residue 71 ASP Chi-restraints excluded: chain AQ residue 91 ASN Chi-restraints excluded: chain AR residue 51 ASN Chi-restraints excluded: chain AR residue 93 ARG Chi-restraints excluded: chain AR residue 108 MET Chi-restraints excluded: chain AS residue 71 ASP Chi-restraints excluded: chain AS residue 72 THR Chi-restraints excluded: chain AS residue 113 ILE Chi-restraints excluded: chain AT residue 47 VAL Chi-restraints excluded: chain AU residue 14 LEU Chi-restraints excluded: chain AU residue 57 SER Chi-restraints excluded: chain AU residue 60 SER Chi-restraints excluded: chain AU residue 63 MET Chi-restraints excluded: chain AU residue 73 MET Chi-restraints excluded: chain AU residue 82 ASP Chi-restraints excluded: chain AU residue 83 ASP Chi-restraints excluded: chain AV residue 5 ASP Chi-restraints excluded: chain AV residue 22 SER Chi-restraints excluded: chain AV residue 50 THR Chi-restraints excluded: chain AV residue 57 LEU Chi-restraints excluded: chain AV residue 72 TYR Chi-restraints excluded: chain AW residue 37 VAL Chi-restraints excluded: chain AW residue 91 ILE Chi-restraints excluded: chain AW residue 97 ASN Chi-restraints excluded: chain AX residue 89 TYR Chi-restraints excluded: chain AX residue 123 LEU Chi-restraints excluded: chain AX residue 139 LEU Chi-restraints excluded: chain AZ residue 59 SER Chi-restraints excluded: chain AZ residue 78 ASP Chi-restraints excluded: chain Aa residue 8 THR Chi-restraints excluded: chain Aa residue 17 LEU Chi-restraints excluded: chain Aa residue 35 VAL Chi-restraints excluded: chain Aa residue 55 ILE Chi-restraints excluded: chain Ab residue 12 LYS Chi-restraints excluded: chain Ab residue 38 ILE Chi-restraints excluded: chain Ab residue 77 VAL Chi-restraints excluded: chain Ac residue 25 THR Chi-restraints excluded: chain Ac residue 28 THR Chi-restraints excluded: chain Ac residue 55 HIS Chi-restraints excluded: chain Ad residue 56 LEU Chi-restraints excluded: chain Ae residue 27 THR Chi-restraints excluded: chain Ae residue 38 LEU Chi-restraints excluded: chain Af residue 4 THR Chi-restraints excluded: chain Af residue 10 VAL Chi-restraints excluded: chain Af residue 22 MET Chi-restraints excluded: chain Af residue 44 VAL Chi-restraints excluded: chain Af residue 45 SER Chi-restraints excluded: chain Ah residue 20 LYS Chi-restraints excluded: chain Ah residue 28 ASP Chi-restraints excluded: chain Ai residue 41 CYS Chi-restraints excluded: chain Ai residue 42 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 999 optimal weight: 0.0870 chunk 116 optimal weight: 20.0000 chunk 590 optimal weight: 7.9990 chunk 757 optimal weight: 0.7980 chunk 586 optimal weight: 7.9990 chunk 873 optimal weight: 0.9990 chunk 579 optimal weight: 8.9990 chunk 1033 optimal weight: 10.0000 chunk 646 optimal weight: 10.0000 chunk 629 optimal weight: 10.0000 chunk 477 optimal weight: 10.0000 overall best weight: 3.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN D 34 HIS ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 ASN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 ASN I 37 ASN K 30 ASN K 65 GLN ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 24 ASN R 43 HIS ** T 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 ASN W 9 ASN AM 90 ASN AN 51 GLN AO 94 ASN AQ 91 ASN AT 36 ASN AT 56 ASN ** AU 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 33 ASN AW 41 ASN AW 69 ASN ** Ae 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 160524 Z= 0.258 Angle : 0.888 41.211 239067 Z= 0.381 Chirality : 0.085 2.112 30097 Planarity : 0.004 0.062 13022 Dihedral : 23.102 179.447 78230 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.10 % Favored : 94.89 % Rotamer: Outliers : 4.45 % Allowed : 25.07 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.11), residues: 6239 helix: 1.49 (0.11), residues: 2140 sheet: -0.18 (0.14), residues: 1302 loop : -0.95 (0.12), residues: 2797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 132 HIS 0.014 0.001 HIS D 34 PHE 0.030 0.001 PHEAG 117 TYR 0.033 0.002 TYR C 133 ARG 0.013 0.000 ARG E 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1032 time to evaluate : 6.798 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: D 28 ILE cc_start: 0.8760 (mm) cc_final: 0.8361 (tp) REVERT: D 140 ASP cc_start: 0.8936 (m-30) cc_final: 0.8217 (m-30) REVERT: E 69 ASN cc_start: 0.8532 (t0) cc_final: 0.7944 (t0) REVERT: E 130 ASN cc_start: 0.8381 (p0) cc_final: 0.8020 (p0) REVERT: F 41 PHE cc_start: 0.8610 (t80) cc_final: 0.8200 (t80) REVERT: F 42 ILE cc_start: 0.8459 (mp) cc_final: 0.8247 (mm) REVERT: F 71 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8284 (mp) REVERT: F 83 ASN cc_start: 0.7491 (m-40) cc_final: 0.7157 (m110) REVERT: G 44 TYR cc_start: 0.8456 (m-10) cc_final: 0.8036 (m-10) REVERT: G 48 ASP cc_start: 0.7570 (m-30) cc_final: 0.7232 (m-30) REVERT: G 73 LEU cc_start: 0.8671 (mm) cc_final: 0.8271 (mm) REVERT: G 127 ASN cc_start: 0.8927 (t0) cc_final: 0.8664 (t0) REVERT: H 63 LEU cc_start: 0.9061 (mp) cc_final: 0.8845 (mm) REVERT: H 64 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9034 (mm) REVERT: H 71 ASN cc_start: 0.8697 (m-40) cc_final: 0.8166 (m110) REVERT: H 85 ARG cc_start: 0.8419 (ttp80) cc_final: 0.7968 (ttt-90) REVERT: H 117 GLU cc_start: 0.8459 (tt0) cc_final: 0.8034 (tt0) REVERT: I 26 TYR cc_start: 0.8501 (m-80) cc_final: 0.8115 (m-80) REVERT: I 48 GLU cc_start: 0.8621 (pp20) cc_final: 0.8245 (pp20) REVERT: I 70 TYR cc_start: 0.7535 (t80) cc_final: 0.7065 (t80) REVERT: I 113 ASP cc_start: 0.8334 (t0) cc_final: 0.7357 (t0) REVERT: J 41 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8377 (pp) REVERT: K 39 LYS cc_start: 0.9098 (tppp) cc_final: 0.8667 (tmmt) REVERT: L 70 ILE cc_start: 0.7717 (mt) cc_final: 0.7402 (pt) REVERT: M 8 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7228 (p0) REVERT: M 74 VAL cc_start: 0.9285 (t) cc_final: 0.9031 (m) REVERT: N 6 MET cc_start: 0.4324 (mmt) cc_final: 0.4002 (mmp) REVERT: O 21 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8762 (t) REVERT: O 45 ASN cc_start: 0.8418 (m110) cc_final: 0.8066 (m110) REVERT: O 70 GLN cc_start: 0.8533 (tt0) cc_final: 0.8329 (tm-30) REVERT: O 73 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7225 (t0) REVERT: P 21 VAL cc_start: 0.9394 (OUTLIER) cc_final: 0.9139 (m) REVERT: P 24 ASN cc_start: 0.8041 (m110) cc_final: 0.7602 (m110) REVERT: P 36 GLU cc_start: 0.8392 (mp0) cc_final: 0.8001 (mp0) REVERT: P 44 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8058 (tp30) REVERT: Q 25 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7736 (tm-30) REVERT: Q 49 ASP cc_start: 0.8063 (t0) cc_final: 0.7792 (t0) REVERT: R 57 THR cc_start: 0.8487 (t) cc_final: 0.8141 (t) REVERT: R 95 LYS cc_start: 0.7937 (mmmt) cc_final: 0.7351 (ptmm) REVERT: S 69 HIS cc_start: 0.8909 (m170) cc_final: 0.8669 (m-70) REVERT: T 21 ASN cc_start: 0.7575 (m-40) cc_final: 0.7345 (m110) REVERT: T 59 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7820 (p0) REVERT: U 22 MET cc_start: 0.6849 (ptm) cc_final: 0.6470 (ttp) REVERT: U 54 ARG cc_start: 0.7631 (mmm160) cc_final: 0.7256 (mtm180) REVERT: V 13 SER cc_start: 0.9222 (m) cc_final: 0.8961 (p) REVERT: W 1 MET cc_start: 0.7228 (ppp) cc_final: 0.6919 (ttp) REVERT: W 4 LYS cc_start: 0.7382 (ttpt) cc_final: 0.6691 (tmmt) REVERT: W 45 GLU cc_start: 0.8036 (tt0) cc_final: 0.7637 (tt0) REVERT: W 46 HIS cc_start: 0.6532 (OUTLIER) cc_final: 0.5448 (m-70) REVERT: W 88 THR cc_start: 0.8570 (m) cc_final: 0.8220 (p) REVERT: W 90 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8160 (mm-30) REVERT: AF 127 GLU cc_start: 0.8272 (pm20) cc_final: 0.7811 (pm20) REVERT: AF 144 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8897 (tmmm) REVERT: AG 1 MET cc_start: 0.5291 (OUTLIER) cc_final: 0.4597 (ttt) REVERT: AG 18 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8503 (mp0) REVERT: AG 29 MET cc_start: 0.8374 (ppp) cc_final: 0.8075 (ppp) REVERT: AG 40 SER cc_start: 0.8389 (p) cc_final: 0.8042 (m) REVERT: AG 62 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8274 (mp10) REVERT: AG 86 GLN cc_start: 0.7863 (mt0) cc_final: 0.7397 (mt0) REVERT: AG 128 ASN cc_start: 0.8803 (m-40) cc_final: 0.8548 (m-40) REVERT: AG 145 ASP cc_start: 0.8119 (t70) cc_final: 0.7612 (t70) REVERT: AH 27 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7628 (mp0) REVERT: AH 30 ARG cc_start: 0.7869 (ttm110) cc_final: 0.7620 (ttm110) REVERT: AH 95 ARG cc_start: 0.7680 (mtm110) cc_final: 0.7477 (mtm110) REVERT: AH 155 GLU cc_start: 0.7408 (pp20) cc_final: 0.7029 (pp20) REVERT: AI 29 TYR cc_start: 0.8111 (t80) cc_final: 0.7727 (t80) REVERT: AM 4 MET cc_start: 0.8851 (ttt) cc_final: 0.8626 (ttt) REVERT: AM 105 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: AN 45 LEU cc_start: 0.4040 (OUTLIER) cc_final: 0.3628 (pp) REVERT: AN 71 GLU cc_start: 0.7928 (pp20) cc_final: 0.7590 (pp20) REVERT: AN 72 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.6614 (p90) REVERT: AO 130 MET cc_start: 0.8229 (ttp) cc_final: 0.8007 (tpp) REVERT: AQ 1 MET cc_start: 0.4422 (ttp) cc_final: 0.2731 (mmm) REVERT: AQ 95 ASP cc_start: 0.8863 (t0) cc_final: 0.8632 (t0) REVERT: AR 93 ARG cc_start: 0.9295 (OUTLIER) cc_final: 0.7801 (mmp80) REVERT: AU 31 GLU cc_start: 0.8540 (tp30) cc_final: 0.8274 (mm-30) REVERT: AU 63 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8115 (mpp) REVERT: AV 1 MET cc_start: 0.7503 (mtp) cc_final: 0.7256 (mtp) REVERT: AW 9 ASP cc_start: 0.8290 (m-30) cc_final: 0.7869 (m-30) REVERT: AW 19 ARG cc_start: 0.8032 (tpp80) cc_final: 0.7370 (tpp80) REVERT: AW 33 ASN cc_start: 0.8556 (t0) cc_final: 0.8322 (t160) REVERT: AW 57 ARG cc_start: 0.8534 (pmt170) cc_final: 0.8066 (pmt170) REVERT: AX 51 ASN cc_start: 0.8858 (m110) cc_final: 0.8616 (m110) REVERT: AX 123 LEU cc_start: 0.6173 (OUTLIER) cc_final: 0.5527 (tm) REVERT: AZ 6 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8366 (mp0) REVERT: AZ 13 MET cc_start: 0.8657 (ttp) cc_final: 0.8007 (ptm) REVERT: Aa 55 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8764 (mp) REVERT: Ac 1 MET cc_start: 0.4049 (mmt) cc_final: 0.3787 (mmt) REVERT: Ac 48 VAL cc_start: 0.8341 (t) cc_final: 0.7989 (p) REVERT: Ac 49 GLU cc_start: 0.8346 (mp0) cc_final: 0.8086 (pm20) REVERT: Ae 36 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7344 (mt-10) REVERT: Ag 1 MET cc_start: 0.5553 (mmm) cc_final: 0.4586 (mmt) REVERT: Ah 1 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7794 (pmm) REVERT: Ai 24 ILE cc_start: 0.9203 (mt) cc_final: 0.8878 (mp) outliers start: 222 outliers final: 133 residues processed: 1138 average time/residue: 1.8315 time to fit residues: 3164.5911 Evaluate side-chains 1151 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 998 time to evaluate : 6.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain I residue 49 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 24 GLU Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 11 ASN Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain R residue 40 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 38 MET Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 46 HIS Chi-restraints excluded: chain AD residue 134 LEU Chi-restraints excluded: chain AD residue 182 GLU Chi-restraints excluded: chain AE residue 2 LEU Chi-restraints excluded: chain AE residue 40 VAL Chi-restraints excluded: chain AE residue 41 ASP Chi-restraints excluded: chain AE residue 153 THR Chi-restraints excluded: chain AF residue 138 ASP Chi-restraints excluded: chain AF residue 144 LYS Chi-restraints excluded: chain AG residue 1 MET Chi-restraints excluded: chain AG residue 18 GLU Chi-restraints excluded: chain AG residue 28 ILE Chi-restraints excluded: chain AG residue 41 VAL Chi-restraints excluded: chain AG residue 130 ASN Chi-restraints excluded: chain AG residue 155 LEU Chi-restraints excluded: chain AG residue 162 THR Chi-restraints excluded: chain AH residue 3 ARG Chi-restraints excluded: chain AH residue 19 VAL Chi-restraints excluded: chain AI residue 23 ASP Chi-restraints excluded: chain AI residue 37 VAL Chi-restraints excluded: chain AL residue 59 ASN Chi-restraints excluded: chain AL residue 132 SER Chi-restraints excluded: chain AL residue 134 SER Chi-restraints excluded: chain AM residue 14 THR Chi-restraints excluded: chain AM residue 29 LYS Chi-restraints excluded: chain AM residue 47 ILE Chi-restraints excluded: chain AM residue 105 GLU Chi-restraints excluded: chain AM residue 117 LEU Chi-restraints excluded: chain AN residue 17 VAL Chi-restraints excluded: chain AN residue 41 THR Chi-restraints excluded: chain AN residue 45 LEU Chi-restraints excluded: chain AN residue 72 TYR Chi-restraints excluded: chain AN residue 79 ASP Chi-restraints excluded: chain AO residue 2 LEU Chi-restraints excluded: chain AO residue 80 GLU Chi-restraints excluded: chain AO residue 123 SER Chi-restraints excluded: chain AP residue 7 PHE Chi-restraints excluded: chain AP residue 35 SER Chi-restraints excluded: chain AP residue 118 LYS Chi-restraints excluded: chain AQ residue 12 LEU Chi-restraints excluded: chain AQ residue 34 VAL Chi-restraints excluded: chain AQ residue 62 LYS Chi-restraints excluded: chain AQ residue 71 ASP Chi-restraints excluded: chain AQ residue 91 ASN Chi-restraints excluded: chain AR residue 37 GLU Chi-restraints excluded: chain AR residue 51 ASN Chi-restraints excluded: chain AR residue 93 ARG Chi-restraints excluded: chain AR residue 108 MET Chi-restraints excluded: chain AS residue 72 THR Chi-restraints excluded: chain AT residue 47 VAL Chi-restraints excluded: chain AU residue 14 LEU Chi-restraints excluded: chain AU residue 57 SER Chi-restraints excluded: chain AU residue 60 SER Chi-restraints excluded: chain AU residue 63 MET Chi-restraints excluded: chain AU residue 73 MET Chi-restraints excluded: chain AU residue 82 ASP Chi-restraints excluded: chain AU residue 83 ASP Chi-restraints excluded: chain AV residue 5 ASP Chi-restraints excluded: chain AV residue 22 SER Chi-restraints excluded: chain AV residue 50 THR Chi-restraints excluded: chain AV residue 57 LEU Chi-restraints excluded: chain AV residue 72 TYR Chi-restraints excluded: chain AW residue 37 VAL Chi-restraints excluded: chain AW residue 91 ILE Chi-restraints excluded: chain AW residue 97 ASN Chi-restraints excluded: chain AX residue 89 TYR Chi-restraints excluded: chain AX residue 123 LEU Chi-restraints excluded: chain AX residue 139 LEU Chi-restraints excluded: chain AZ residue 59 SER Chi-restraints excluded: chain AZ residue 78 ASP Chi-restraints excluded: chain Aa residue 8 THR Chi-restraints excluded: chain Aa residue 35 VAL Chi-restraints excluded: chain Aa residue 55 ILE Chi-restraints excluded: chain Ab residue 38 ILE Chi-restraints excluded: chain Ab residue 77 VAL Chi-restraints excluded: chain Ac residue 25 THR Chi-restraints excluded: chain Ac residue 28 THR Chi-restraints excluded: chain Ac residue 55 HIS Chi-restraints excluded: chain Ae residue 27 THR Chi-restraints excluded: chain Ae residue 38 LEU Chi-restraints excluded: chain Af residue 22 MET Chi-restraints excluded: chain Af residue 44 VAL Chi-restraints excluded: chain Af residue 45 SER Chi-restraints excluded: chain Ah residue 1 MET Chi-restraints excluded: chain Ah residue 20 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 639 optimal weight: 7.9990 chunk 412 optimal weight: 20.0000 chunk 617 optimal weight: 8.9990 chunk 311 optimal weight: 0.7980 chunk 203 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 656 optimal weight: 10.0000 chunk 703 optimal weight: 1.9990 chunk 510 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 812 optimal weight: 40.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN D 34 HIS ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 ASN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 ASN K 30 ASN ** K 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 GLN R 43 HIS ** T 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 ASN W 9 ASN AE 168 GLN AH 112 GLN ** AM 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 94 ASN AQ 91 ASN AT 36 ASN AT 56 ASN ** AU 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 41 ASN AW 69 ASN AX 60 ASN ** Ae 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 160524 Z= 0.281 Angle : 0.896 41.182 239067 Z= 0.385 Chirality : 0.085 2.111 30097 Planarity : 0.004 0.046 13022 Dihedral : 23.093 179.467 78230 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.15 % Favored : 94.84 % Rotamer: Outliers : 4.39 % Allowed : 25.77 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.11), residues: 6239 helix: 1.46 (0.11), residues: 2141 sheet: -0.21 (0.14), residues: 1297 loop : -0.95 (0.12), residues: 2801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 132 HIS 0.014 0.001 HIS D 34 PHE 0.021 0.001 PHE U 52 TYR 0.036 0.002 TYR C 133 ARG 0.010 0.000 ARGAX 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1239 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1020 time to evaluate : 6.624 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: D 28 ILE cc_start: 0.8795 (mm) cc_final: 0.8403 (tp) REVERT: D 140 ASP cc_start: 0.8922 (m-30) cc_final: 0.8133 (m-30) REVERT: E 69 ASN cc_start: 0.8537 (t0) cc_final: 0.8007 (t0) REVERT: E 130 ASN cc_start: 0.8370 (p0) cc_final: 0.7997 (p0) REVERT: F 41 PHE cc_start: 0.8611 (t80) cc_final: 0.8159 (t80) REVERT: F 83 ASN cc_start: 0.7470 (m-40) cc_final: 0.7180 (m110) REVERT: G 44 TYR cc_start: 0.8417 (m-10) cc_final: 0.7979 (m-10) REVERT: G 48 ASP cc_start: 0.7629 (m-30) cc_final: 0.7306 (m-30) REVERT: G 73 LEU cc_start: 0.8678 (mm) cc_final: 0.8251 (mm) REVERT: G 127 ASN cc_start: 0.8965 (t0) cc_final: 0.8717 (t0) REVERT: G 145 MET cc_start: 0.8645 (tpt) cc_final: 0.8313 (tpp) REVERT: H 10 MET cc_start: 0.9059 (ptm) cc_final: 0.8809 (ttp) REVERT: H 63 LEU cc_start: 0.9067 (mp) cc_final: 0.8863 (mm) REVERT: H 71 ASN cc_start: 0.8651 (m-40) cc_final: 0.8161 (m110) REVERT: H 85 ARG cc_start: 0.8424 (ttp80) cc_final: 0.7971 (ttt-90) REVERT: H 117 GLU cc_start: 0.8471 (tt0) cc_final: 0.8042 (tt0) REVERT: I 48 GLU cc_start: 0.8611 (pp20) cc_final: 0.8244 (pp20) REVERT: I 70 TYR cc_start: 0.7497 (t80) cc_final: 0.7080 (t80) REVERT: I 113 ASP cc_start: 0.8321 (t0) cc_final: 0.7327 (t0) REVERT: J 41 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8387 (pp) REVERT: J 65 GLN cc_start: 0.8532 (mt0) cc_final: 0.8222 (mt0) REVERT: K 39 LYS cc_start: 0.9128 (tppp) cc_final: 0.8683 (tmmt) REVERT: L 70 ILE cc_start: 0.7675 (mt) cc_final: 0.7383 (pt) REVERT: M 32 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8527 (mt-10) REVERT: M 74 VAL cc_start: 0.9285 (t) cc_final: 0.9032 (m) REVERT: M 82 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6931 (ttt) REVERT: N 6 MET cc_start: 0.4330 (mmt) cc_final: 0.4002 (mmp) REVERT: N 31 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7321 (ptm160) REVERT: O 21 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8788 (t) REVERT: O 45 ASN cc_start: 0.8440 (m110) cc_final: 0.8085 (m110) REVERT: O 73 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7036 (t0) REVERT: P 21 VAL cc_start: 0.9386 (OUTLIER) cc_final: 0.9138 (m) REVERT: P 24 ASN cc_start: 0.7979 (m110) cc_final: 0.7550 (m110) REVERT: P 36 GLU cc_start: 0.8421 (mp0) cc_final: 0.8024 (mp0) REVERT: P 44 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8044 (tp30) REVERT: Q 25 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7743 (tm-30) REVERT: Q 49 ASP cc_start: 0.8057 (t0) cc_final: 0.7788 (t0) REVERT: R 57 THR cc_start: 0.8461 (t) cc_final: 0.8124 (t) REVERT: S 69 HIS cc_start: 0.8808 (m170) cc_final: 0.8570 (m-70) REVERT: T 21 ASN cc_start: 0.7560 (m-40) cc_final: 0.7329 (m110) REVERT: T 59 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7819 (p0) REVERT: U 22 MET cc_start: 0.6793 (ptm) cc_final: 0.6461 (ttp) REVERT: V 13 SER cc_start: 0.9224 (m) cc_final: 0.8963 (p) REVERT: W 1 MET cc_start: 0.7213 (ppp) cc_final: 0.6936 (ttp) REVERT: W 4 LYS cc_start: 0.7345 (ttpt) cc_final: 0.6636 (tmmt) REVERT: W 45 GLU cc_start: 0.8031 (tt0) cc_final: 0.7619 (tt0) REVERT: W 46 HIS cc_start: 0.6485 (OUTLIER) cc_final: 0.5452 (m-70) REVERT: W 90 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8172 (mm-30) REVERT: AD 227 MET cc_start: 0.8846 (mmt) cc_final: 0.8592 (mmm) REVERT: AF 127 GLU cc_start: 0.8273 (pm20) cc_final: 0.7797 (pm20) REVERT: AG 1 MET cc_start: 0.5287 (OUTLIER) cc_final: 0.4592 (ttt) REVERT: AG 29 MET cc_start: 0.8306 (ppp) cc_final: 0.7984 (ppp) REVERT: AG 40 SER cc_start: 0.8431 (p) cc_final: 0.8052 (m) REVERT: AG 86 GLN cc_start: 0.7854 (mt0) cc_final: 0.7385 (mt0) REVERT: AG 128 ASN cc_start: 0.8807 (m-40) cc_final: 0.8587 (m-40) REVERT: AG 145 ASP cc_start: 0.8108 (t70) cc_final: 0.7583 (t70) REVERT: AH 95 ARG cc_start: 0.7703 (mtm110) cc_final: 0.7475 (mtm110) REVERT: AH 155 GLU cc_start: 0.7408 (pp20) cc_final: 0.7031 (pp20) REVERT: AI 29 TYR cc_start: 0.8132 (t80) cc_final: 0.7775 (t80) REVERT: AM 105 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: AM 107 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8013 (mmm160) REVERT: AN 45 LEU cc_start: 0.4103 (OUTLIER) cc_final: 0.3689 (pp) REVERT: AN 71 GLU cc_start: 0.7966 (pp20) cc_final: 0.7648 (pp20) REVERT: AO 130 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.8052 (tpp) REVERT: AP 32 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: AQ 1 MET cc_start: 0.4421 (ttp) cc_final: 0.2775 (mmm) REVERT: AR 93 ARG cc_start: 0.9295 (OUTLIER) cc_final: 0.7797 (mmp80) REVERT: AU 31 GLU cc_start: 0.8538 (tp30) cc_final: 0.8276 (mm-30) REVERT: AU 63 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8126 (mpp) REVERT: AV 1 MET cc_start: 0.7449 (mtp) cc_final: 0.7244 (mtp) REVERT: AW 9 ASP cc_start: 0.8306 (m-30) cc_final: 0.7889 (m-30) REVERT: AW 57 ARG cc_start: 0.8536 (pmt170) cc_final: 0.8054 (pmt170) REVERT: AX 51 ASN cc_start: 0.8861 (m110) cc_final: 0.8619 (m110) REVERT: AZ 6 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8371 (mp0) REVERT: AZ 7 ILE cc_start: 0.9210 (mm) cc_final: 0.8921 (mm) REVERT: AZ 13 MET cc_start: 0.8710 (ttp) cc_final: 0.8182 (ptm) REVERT: Aa 55 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8586 (mp) REVERT: Ac 48 VAL cc_start: 0.8285 (t) cc_final: 0.7952 (p) REVERT: Ae 36 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7384 (mt-10) REVERT: Ag 1 MET cc_start: 0.5585 (mmm) cc_final: 0.4774 (mmm) REVERT: Ai 24 ILE cc_start: 0.9187 (mt) cc_final: 0.8950 (mp) outliers start: 219 outliers final: 146 residues processed: 1125 average time/residue: 1.8352 time to fit residues: 3121.2558 Evaluate side-chains 1157 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 993 time to evaluate : 6.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain I residue 49 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 24 GLU Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain Q residue 21 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain R residue 40 SER Chi-restraints excluded: chain R residue 43 HIS Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 46 HIS Chi-restraints excluded: chain AD residue 134 LEU Chi-restraints excluded: chain AD residue 147 GLU Chi-restraints excluded: chain AD residue 182 GLU Chi-restraints excluded: chain AD residue 205 ILE Chi-restraints excluded: chain AE residue 2 LEU Chi-restraints excluded: chain AE residue 40 VAL Chi-restraints excluded: chain AE residue 41 ASP Chi-restraints excluded: chain AE residue 53 VAL Chi-restraints excluded: chain AE residue 153 THR Chi-restraints excluded: chain AF residue 138 ASP Chi-restraints excluded: chain AG residue 1 MET Chi-restraints excluded: chain AG residue 28 ILE Chi-restraints excluded: chain AG residue 41 VAL Chi-restraints excluded: chain AG residue 130 ASN Chi-restraints excluded: chain AG residue 155 LEU Chi-restraints excluded: chain AG residue 162 THR Chi-restraints excluded: chain AH residue 19 VAL Chi-restraints excluded: chain AI residue 23 ASP Chi-restraints excluded: chain AI residue 37 VAL Chi-restraints excluded: chain AL residue 59 ASN Chi-restraints excluded: chain AL residue 132 SER Chi-restraints excluded: chain AL residue 134 SER Chi-restraints excluded: chain AM residue 14 THR Chi-restraints excluded: chain AM residue 29 LYS Chi-restraints excluded: chain AM residue 47 ILE Chi-restraints excluded: chain AM residue 80 ASP Chi-restraints excluded: chain AM residue 105 GLU Chi-restraints excluded: chain AM residue 107 ARG Chi-restraints excluded: chain AM residue 117 LEU Chi-restraints excluded: chain AN residue 17 VAL Chi-restraints excluded: chain AN residue 41 THR Chi-restraints excluded: chain AN residue 45 LEU Chi-restraints excluded: chain AO residue 2 LEU Chi-restraints excluded: chain AO residue 80 GLU Chi-restraints excluded: chain AO residue 123 SER Chi-restraints excluded: chain AO residue 130 MET Chi-restraints excluded: chain AP residue 7 PHE Chi-restraints excluded: chain AP residue 32 GLU Chi-restraints excluded: chain AP residue 35 SER Chi-restraints excluded: chain AP residue 118 LYS Chi-restraints excluded: chain AQ residue 12 LEU Chi-restraints excluded: chain AQ residue 34 VAL Chi-restraints excluded: chain AQ residue 62 LYS Chi-restraints excluded: chain AQ residue 71 ASP Chi-restraints excluded: chain AQ residue 91 ASN Chi-restraints excluded: chain AR residue 25 VAL Chi-restraints excluded: chain AR residue 51 ASN Chi-restraints excluded: chain AR residue 93 ARG Chi-restraints excluded: chain AR residue 108 MET Chi-restraints excluded: chain AS residue 71 ASP Chi-restraints excluded: chain AS residue 72 THR Chi-restraints excluded: chain AT residue 47 VAL Chi-restraints excluded: chain AU residue 14 LEU Chi-restraints excluded: chain AU residue 57 SER Chi-restraints excluded: chain AU residue 60 SER Chi-restraints excluded: chain AU residue 63 MET Chi-restraints excluded: chain AU residue 73 MET Chi-restraints excluded: chain AU residue 82 ASP Chi-restraints excluded: chain AU residue 83 ASP Chi-restraints excluded: chain AV residue 5 ASP Chi-restraints excluded: chain AV residue 22 SER Chi-restraints excluded: chain AV residue 50 THR Chi-restraints excluded: chain AV residue 57 LEU Chi-restraints excluded: chain AV residue 72 TYR Chi-restraints excluded: chain AW residue 37 VAL Chi-restraints excluded: chain AW residue 97 ASN Chi-restraints excluded: chain AX residue 89 TYR Chi-restraints excluded: chain AX residue 139 LEU Chi-restraints excluded: chain AX residue 162 VAL Chi-restraints excluded: chain AZ residue 59 SER Chi-restraints excluded: chain AZ residue 78 ASP Chi-restraints excluded: chain Aa residue 35 VAL Chi-restraints excluded: chain Aa residue 55 ILE Chi-restraints excluded: chain Ab residue 12 LYS Chi-restraints excluded: chain Ab residue 38 ILE Chi-restraints excluded: chain Ab residue 43 ILE Chi-restraints excluded: chain Ab residue 77 VAL Chi-restraints excluded: chain Ac residue 28 THR Chi-restraints excluded: chain Ac residue 55 HIS Chi-restraints excluded: chain Ae residue 27 THR Chi-restraints excluded: chain Ae residue 38 LEU Chi-restraints excluded: chain Ae residue 51 THR Chi-restraints excluded: chain Af residue 10 VAL Chi-restraints excluded: chain Af residue 22 MET Chi-restraints excluded: chain Af residue 44 VAL Chi-restraints excluded: chain Af residue 45 SER Chi-restraints excluded: chain Ah residue 20 LYS Chi-restraints excluded: chain Ah residue 28 ASP Chi-restraints excluded: chain Ai residue 25 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 939 optimal weight: 0.7980 chunk 989 optimal weight: 3.9990 chunk 903 optimal weight: 0.9980 chunk 962 optimal weight: 10.0000 chunk 579 optimal weight: 8.9990 chunk 419 optimal weight: 20.0000 chunk 756 optimal weight: 0.9980 chunk 295 optimal weight: 5.9990 chunk 870 optimal weight: 10.0000 chunk 910 optimal weight: 9.9990 chunk 959 optimal weight: 0.8980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN D 34 HIS ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 ASN G 123 ASN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 ASN I 107 ASN I 132 GLN K 30 ASN K 65 GLN ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 13 GLN T 37 ASN W 9 ASN AD 155 GLN AE 168 GLN AM 90 ASN ** AM 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 94 ASN AQ 91 ASN AT 36 ASN AT 56 ASN ** AU 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 33 ASN AW 41 ASN AW 69 ASN ** Ae 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 160524 Z= 0.156 Angle : 0.866 41.447 239067 Z= 0.368 Chirality : 0.084 2.115 30097 Planarity : 0.004 0.070 13022 Dihedral : 23.106 179.896 78230 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.02 % Allowed : 27.47 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.11), residues: 6239 helix: 1.51 (0.12), residues: 2140 sheet: -0.09 (0.14), residues: 1283 loop : -0.84 (0.12), residues: 2816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 132 HIS 0.030 0.001 HIS D 34 PHE 0.024 0.001 PHE U 52 TYR 0.038 0.002 TYR C 133 ARG 0.014 0.000 ARGAH 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1069 time to evaluate : 6.599 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: D 28 ILE cc_start: 0.8778 (mm) cc_final: 0.8401 (tp) REVERT: D 70 GLN cc_start: 0.8676 (tt0) cc_final: 0.8435 (mt0) REVERT: D 140 ASP cc_start: 0.8757 (m-30) cc_final: 0.7988 (m-30) REVERT: E 69 ASN cc_start: 0.8558 (t0) cc_final: 0.8032 (t0) REVERT: E 130 ASN cc_start: 0.8393 (p0) cc_final: 0.8027 (p0) REVERT: F 83 ASN cc_start: 0.7407 (m-40) cc_final: 0.7139 (m110) REVERT: G 44 TYR cc_start: 0.8434 (m-10) cc_final: 0.8004 (m-10) REVERT: G 48 ASP cc_start: 0.7703 (m-30) cc_final: 0.7384 (m-30) REVERT: G 73 LEU cc_start: 0.8679 (mm) cc_final: 0.8277 (mm) REVERT: G 145 MET cc_start: 0.8612 (tpt) cc_final: 0.8275 (tpp) REVERT: H 10 MET cc_start: 0.9018 (ptm) cc_final: 0.8764 (ttp) REVERT: H 71 ASN cc_start: 0.8713 (m-40) cc_final: 0.8223 (m110) REVERT: H 85 ARG cc_start: 0.8408 (ttp80) cc_final: 0.7976 (ttt-90) REVERT: H 117 GLU cc_start: 0.8444 (tt0) cc_final: 0.8003 (tt0) REVERT: I 48 GLU cc_start: 0.8633 (pp20) cc_final: 0.8250 (pp20) REVERT: I 70 TYR cc_start: 0.7424 (t80) cc_final: 0.6925 (t80) REVERT: I 113 ASP cc_start: 0.8260 (t0) cc_final: 0.7210 (t0) REVERT: J 65 GLN cc_start: 0.8521 (mt0) cc_final: 0.8224 (mt0) REVERT: K 39 LYS cc_start: 0.9092 (tppp) cc_final: 0.8659 (tmmt) REVERT: K 77 ASP cc_start: 0.8140 (m-30) cc_final: 0.7859 (m-30) REVERT: L 70 ILE cc_start: 0.7730 (mt) cc_final: 0.7371 (pt) REVERT: M 32 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8509 (mt-10) REVERT: M 74 VAL cc_start: 0.9282 (t) cc_final: 0.9027 (m) REVERT: M 82 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7059 (ttt) REVERT: N 6 MET cc_start: 0.4325 (mmt) cc_final: 0.4029 (mmp) REVERT: O 6 GLN cc_start: 0.8873 (mt0) cc_final: 0.8525 (mt0) REVERT: O 45 ASN cc_start: 0.8308 (m110) cc_final: 0.8005 (m110) REVERT: O 73 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6758 (t0) REVERT: P 21 VAL cc_start: 0.9377 (OUTLIER) cc_final: 0.9154 (m) REVERT: P 36 GLU cc_start: 0.8410 (mp0) cc_final: 0.8006 (mp0) REVERT: P 44 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8055 (tp30) REVERT: Q 25 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7654 (tm-30) REVERT: Q 49 ASP cc_start: 0.7971 (t0) cc_final: 0.7678 (t0) REVERT: R 42 LYS cc_start: 0.8755 (tppt) cc_final: 0.8463 (tmmm) REVERT: R 48 ASP cc_start: 0.8188 (t0) cc_final: 0.7837 (t0) REVERT: R 57 THR cc_start: 0.8465 (t) cc_final: 0.8100 (t) REVERT: R 58 GLU cc_start: 0.7935 (pm20) cc_final: 0.7694 (pm20) REVERT: R 95 LYS cc_start: 0.7743 (mmmt) cc_final: 0.7309 (mttp) REVERT: S 36 ARG cc_start: 0.8219 (mtp-110) cc_final: 0.7968 (ptp-110) REVERT: S 39 THR cc_start: 0.7627 (OUTLIER) cc_final: 0.7231 (t) REVERT: T 59 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7752 (p0) REVERT: U 22 MET cc_start: 0.6771 (ptm) cc_final: 0.6438 (ttp) REVERT: V 13 SER cc_start: 0.9200 (m) cc_final: 0.8953 (p) REVERT: W 1 MET cc_start: 0.7128 (ppp) cc_final: 0.6803 (ttp) REVERT: W 4 LYS cc_start: 0.7313 (ttpt) cc_final: 0.6623 (tmmt) REVERT: W 36 ASP cc_start: 0.7451 (m-30) cc_final: 0.6858 (m-30) REVERT: W 45 GLU cc_start: 0.7978 (tt0) cc_final: 0.7567 (tt0) REVERT: W 46 HIS cc_start: 0.6358 (OUTLIER) cc_final: 0.5227 (m-70) REVERT: W 90 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8151 (mm-30) REVERT: AD 227 MET cc_start: 0.8847 (mmt) cc_final: 0.8371 (mmt) REVERT: AF 127 GLU cc_start: 0.8239 (pm20) cc_final: 0.7800 (pm20) REVERT: AG 1 MET cc_start: 0.5278 (OUTLIER) cc_final: 0.4904 (tmm) REVERT: AG 29 MET cc_start: 0.8285 (ppp) cc_final: 0.7996 (ppp) REVERT: AG 40 SER cc_start: 0.8401 (p) cc_final: 0.8083 (m) REVERT: AG 86 GLN cc_start: 0.7799 (mt0) cc_final: 0.7348 (mt0) REVERT: AG 87 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7605 (mm-30) REVERT: AG 145 ASP cc_start: 0.8020 (t70) cc_final: 0.7477 (t70) REVERT: AH 95 ARG cc_start: 0.7669 (mtm110) cc_final: 0.7456 (mtm110) REVERT: AH 155 GLU cc_start: 0.7425 (pp20) cc_final: 0.7028 (pp20) REVERT: AI 4 ILE cc_start: 0.7821 (mm) cc_final: 0.7619 (mp) REVERT: AI 29 TYR cc_start: 0.8054 (t80) cc_final: 0.7688 (t80) REVERT: AN 45 LEU cc_start: 0.4120 (OUTLIER) cc_final: 0.3789 (pp) REVERT: AN 71 GLU cc_start: 0.7925 (pp20) cc_final: 0.7537 (pp20) REVERT: AN 72 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.6582 (p90) REVERT: AN 98 ASN cc_start: 0.9394 (t160) cc_final: 0.9138 (t160) REVERT: AP 32 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: AQ 1 MET cc_start: 0.4402 (ttp) cc_final: 0.3855 (ttm) REVERT: AQ 6 GLU cc_start: 0.7670 (pp20) cc_final: 0.7469 (pp20) REVERT: AS 102 ASP cc_start: 0.7879 (t0) cc_final: 0.7458 (t0) REVERT: AU 31 GLU cc_start: 0.8513 (tp30) cc_final: 0.8240 (mm-30) REVERT: AU 63 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8120 (mpp) REVERT: AV 1 MET cc_start: 0.7201 (mtp) cc_final: 0.6995 (mtp) REVERT: AV 11 MET cc_start: 0.8616 (mtp) cc_final: 0.8337 (mtp) REVERT: AW 9 ASP cc_start: 0.8255 (m-30) cc_final: 0.7838 (m-30) REVERT: AW 57 ARG cc_start: 0.8547 (pmt170) cc_final: 0.8118 (pmt170) REVERT: AX 51 ASN cc_start: 0.8821 (m110) cc_final: 0.8603 (m110) REVERT: AX 123 LEU cc_start: 0.6309 (mm) cc_final: 0.5804 (tm) REVERT: AZ 6 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8271 (mt-10) REVERT: AZ 13 MET cc_start: 0.8601 (ttp) cc_final: 0.8273 (ptm) REVERT: Aa 55 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8686 (mp) REVERT: Ac 48 VAL cc_start: 0.8220 (t) cc_final: 0.7941 (p) REVERT: Ae 36 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7372 (mt-10) REVERT: Ag 1 MET cc_start: 0.5536 (mmm) cc_final: 0.4798 (mmm) REVERT: Ai 24 ILE cc_start: 0.9162 (mt) cc_final: 0.8925 (mp) outliers start: 151 outliers final: 90 residues processed: 1141 average time/residue: 1.8855 time to fit residues: 3261.3901 Evaluate side-chains 1113 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1010 time to evaluate : 6.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 24 GLU Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain Q residue 21 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 46 HIS Chi-restraints excluded: chain AD residue 155 GLN Chi-restraints excluded: chain AD residue 205 ILE Chi-restraints excluded: chain AE residue 2 LEU Chi-restraints excluded: chain AE residue 153 THR Chi-restraints excluded: chain AF residue 138 ASP Chi-restraints excluded: chain AG residue 1 MET Chi-restraints excluded: chain AG residue 28 ILE Chi-restraints excluded: chain AG residue 41 VAL Chi-restraints excluded: chain AG residue 130 ASN Chi-restraints excluded: chain AG residue 155 LEU Chi-restraints excluded: chain AH residue 19 VAL Chi-restraints excluded: chain AI residue 37 VAL Chi-restraints excluded: chain AL residue 59 ASN Chi-restraints excluded: chain AL residue 132 SER Chi-restraints excluded: chain AN residue 17 VAL Chi-restraints excluded: chain AN residue 41 THR Chi-restraints excluded: chain AN residue 45 LEU Chi-restraints excluded: chain AN residue 72 TYR Chi-restraints excluded: chain AP residue 7 PHE Chi-restraints excluded: chain AP residue 32 GLU Chi-restraints excluded: chain AP residue 35 SER Chi-restraints excluded: chain AP residue 118 LYS Chi-restraints excluded: chain AQ residue 62 LYS Chi-restraints excluded: chain AQ residue 71 ASP Chi-restraints excluded: chain AQ residue 91 ASN Chi-restraints excluded: chain AR residue 37 GLU Chi-restraints excluded: chain AR residue 51 ASN Chi-restraints excluded: chain AR residue 108 MET Chi-restraints excluded: chain AS residue 103 VAL Chi-restraints excluded: chain AS residue 113 ILE Chi-restraints excluded: chain AT residue 25 ILE Chi-restraints excluded: chain AT residue 47 VAL Chi-restraints excluded: chain AU residue 14 LEU Chi-restraints excluded: chain AU residue 57 SER Chi-restraints excluded: chain AU residue 60 SER Chi-restraints excluded: chain AU residue 63 MET Chi-restraints excluded: chain AU residue 73 MET Chi-restraints excluded: chain AU residue 82 ASP Chi-restraints excluded: chain AU residue 83 ASP Chi-restraints excluded: chain AV residue 50 THR Chi-restraints excluded: chain AV residue 66 VAL Chi-restraints excluded: chain AV residue 72 TYR Chi-restraints excluded: chain AW residue 37 VAL Chi-restraints excluded: chain AX residue 89 TYR Chi-restraints excluded: chain AZ residue 59 SER Chi-restraints excluded: chain Aa residue 35 VAL Chi-restraints excluded: chain Aa residue 55 ILE Chi-restraints excluded: chain Ab residue 12 LYS Chi-restraints excluded: chain Ab residue 77 VAL Chi-restraints excluded: chain Ac residue 55 HIS Chi-restraints excluded: chain Af residue 10 VAL Chi-restraints excluded: chain Af residue 22 MET Chi-restraints excluded: chain Ah residue 28 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 632 optimal weight: 7.9990 chunk 1018 optimal weight: 0.2980 chunk 621 optimal weight: 9.9990 chunk 483 optimal weight: 8.9990 chunk 707 optimal weight: 10.0000 chunk 1067 optimal weight: 9.9990 chunk 982 optimal weight: 1.9990 chunk 850 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 656 optimal weight: 10.0000 chunk 521 optimal weight: 9.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN D 34 HIS ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 ASN I 37 ASN ** J 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 GLN T 37 ASN W 9 ASN AD 155 GLN ** AM 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 94 ASN AQ 91 ASN AT 36 ASN AT 56 ASN ** AU 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 41 ASN AW 69 ASN ** AW 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 9 GLN Ac 10 ASN ** Ae 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 160524 Z= 0.298 Angle : 0.901 41.098 239067 Z= 0.388 Chirality : 0.085 2.116 30097 Planarity : 0.004 0.065 13022 Dihedral : 23.046 179.882 78230 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.03 % Favored : 94.95 % Rotamer: Outliers : 2.80 % Allowed : 28.33 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.11), residues: 6239 helix: 1.44 (0.12), residues: 2142 sheet: -0.16 (0.14), residues: 1287 loop : -0.89 (0.12), residues: 2810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAV 82 HIS 0.012 0.001 HIS D 34 PHE 0.021 0.002 PHEAc 74 TYR 0.095 0.002 TYR H 5 ARG 0.015 0.001 ARGAG 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1158 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1018 time to evaluate : 6.863 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: D 28 ILE cc_start: 0.8862 (mm) cc_final: 0.8481 (tp) REVERT: D 70 GLN cc_start: 0.8703 (tt0) cc_final: 0.8471 (mt0) REVERT: D 140 ASP cc_start: 0.8810 (m-30) cc_final: 0.8016 (m-30) REVERT: E 69 ASN cc_start: 0.8584 (t0) cc_final: 0.8055 (t0) REVERT: E 130 ASN cc_start: 0.8396 (p0) cc_final: 0.8045 (p0) REVERT: F 83 ASN cc_start: 0.7433 (m-40) cc_final: 0.7168 (m110) REVERT: G 44 TYR cc_start: 0.8439 (m-10) cc_final: 0.8005 (m-10) REVERT: G 48 ASP cc_start: 0.7675 (m-30) cc_final: 0.7361 (m-30) REVERT: G 50 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8535 (mm) REVERT: G 73 LEU cc_start: 0.8650 (mm) cc_final: 0.8248 (mm) REVERT: G 117 MET cc_start: 0.6614 (mmt) cc_final: 0.6044 (mmt) REVERT: G 145 MET cc_start: 0.8654 (tpt) cc_final: 0.8324 (tpp) REVERT: H 10 MET cc_start: 0.9031 (ptm) cc_final: 0.8755 (ttp) REVERT: H 71 ASN cc_start: 0.8769 (m-40) cc_final: 0.8205 (m110) REVERT: H 85 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8043 (ttt-90) REVERT: H 117 GLU cc_start: 0.8474 (tt0) cc_final: 0.8037 (tt0) REVERT: I 48 GLU cc_start: 0.8546 (pp20) cc_final: 0.8234 (pp20) REVERT: I 70 TYR cc_start: 0.7434 (t80) cc_final: 0.7031 (t80) REVERT: I 113 ASP cc_start: 0.8275 (t0) cc_final: 0.7288 (t0) REVERT: J 65 GLN cc_start: 0.8518 (mt0) cc_final: 0.8191 (mt0) REVERT: K 39 LYS cc_start: 0.9165 (tppp) cc_final: 0.8720 (tmmt) REVERT: L 70 ILE cc_start: 0.7719 (mt) cc_final: 0.7405 (pt) REVERT: M 32 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8534 (mt-10) REVERT: M 74 VAL cc_start: 0.9288 (t) cc_final: 0.9035 (m) REVERT: M 82 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.7027 (ttt) REVERT: N 6 MET cc_start: 0.4387 (mmt) cc_final: 0.4111 (mmp) REVERT: O 45 ASN cc_start: 0.8408 (m110) cc_final: 0.8041 (m110) REVERT: O 73 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.6897 (t0) REVERT: P 21 VAL cc_start: 0.9387 (OUTLIER) cc_final: 0.9164 (m) REVERT: P 36 GLU cc_start: 0.8465 (mp0) cc_final: 0.8055 (mp0) REVERT: P 44 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8054 (tp30) REVERT: Q 25 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7657 (tm-30) REVERT: Q 49 ASP cc_start: 0.8051 (t0) cc_final: 0.7783 (t0) REVERT: R 42 LYS cc_start: 0.8582 (tppt) cc_final: 0.8227 (tmmm) REVERT: R 48 ASP cc_start: 0.8305 (t0) cc_final: 0.7960 (t0) REVERT: R 57 THR cc_start: 0.8493 (t) cc_final: 0.8117 (t) REVERT: R 58 GLU cc_start: 0.8003 (pm20) cc_final: 0.7716 (pm20) REVERT: R 95 LYS cc_start: 0.7797 (mmmt) cc_final: 0.7344 (mttp) REVERT: T 21 ASN cc_start: 0.7568 (m-40) cc_final: 0.7340 (m110) REVERT: T 59 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7798 (p0) REVERT: U 22 MET cc_start: 0.6769 (ptm) cc_final: 0.6481 (ttp) REVERT: V 13 SER cc_start: 0.9222 (m) cc_final: 0.8960 (p) REVERT: W 1 MET cc_start: 0.7337 (ppp) cc_final: 0.6897 (ttp) REVERT: W 4 LYS cc_start: 0.7335 (ttpt) cc_final: 0.6643 (tmmt) REVERT: W 45 GLU cc_start: 0.8024 (tt0) cc_final: 0.7596 (tt0) REVERT: W 46 HIS cc_start: 0.6505 (OUTLIER) cc_final: 0.5454 (m-70) REVERT: W 90 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8177 (mm-30) REVERT: AD 227 MET cc_start: 0.8860 (mmt) cc_final: 0.8577 (mmm) REVERT: AF 127 GLU cc_start: 0.8254 (pm20) cc_final: 0.7786 (pm20) REVERT: AG 1 MET cc_start: 0.5264 (OUTLIER) cc_final: 0.4890 (tmm) REVERT: AG 29 MET cc_start: 0.8329 (ppp) cc_final: 0.8003 (ppp) REVERT: AG 40 SER cc_start: 0.8401 (p) cc_final: 0.8086 (m) REVERT: AG 86 GLN cc_start: 0.7824 (mt0) cc_final: 0.7364 (mt0) REVERT: AG 145 ASP cc_start: 0.8033 (t70) cc_final: 0.7491 (t70) REVERT: AH 95 ARG cc_start: 0.7674 (mtm110) cc_final: 0.7450 (mtm110) REVERT: AH 147 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7944 (tm-30) REVERT: AH 155 GLU cc_start: 0.7435 (pp20) cc_final: 0.7041 (pp20) REVERT: AI 29 TYR cc_start: 0.8119 (t80) cc_final: 0.7764 (t80) REVERT: AM 105 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: AN 45 LEU cc_start: 0.4179 (OUTLIER) cc_final: 0.3769 (pp) REVERT: AN 71 GLU cc_start: 0.8006 (pp20) cc_final: 0.7708 (pp20) REVERT: AQ 1 MET cc_start: 0.4536 (ttp) cc_final: 0.3947 (ttm) REVERT: AQ 6 GLU cc_start: 0.7648 (pp20) cc_final: 0.7445 (pp20) REVERT: AU 31 GLU cc_start: 0.8518 (tp30) cc_final: 0.8249 (mm-30) REVERT: AU 63 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8098 (mpp) REVERT: AW 9 ASP cc_start: 0.8273 (m-30) cc_final: 0.7851 (m-30) REVERT: AW 57 ARG cc_start: 0.8554 (pmt170) cc_final: 0.8075 (pmt170) REVERT: AX 51 ASN cc_start: 0.8862 (m110) cc_final: 0.8622 (m110) REVERT: AX 105 TYR cc_start: 0.7728 (m-80) cc_final: 0.7519 (m-80) REVERT: AX 123 LEU cc_start: 0.6359 (mm) cc_final: 0.5795 (tm) REVERT: AZ 6 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8354 (mp0) REVERT: AZ 7 ILE cc_start: 0.9258 (mm) cc_final: 0.8989 (mm) REVERT: AZ 13 MET cc_start: 0.8690 (ttp) cc_final: 0.8187 (ptm) REVERT: Aa 55 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8640 (mp) REVERT: Ab 101 MET cc_start: 0.5956 (OUTLIER) cc_final: 0.5724 (mpt) REVERT: Ac 1 MET cc_start: 0.4198 (mmt) cc_final: 0.3351 (mmm) REVERT: Ac 48 VAL cc_start: 0.8194 (t) cc_final: 0.7921 (p) REVERT: Ae 36 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7349 (mt-10) REVERT: Ai 40 GLU cc_start: 0.7262 (tp30) cc_final: 0.7046 (tp30) outliers start: 140 outliers final: 98 residues processed: 1083 average time/residue: 1.8706 time to fit residues: 3064.8940 Evaluate side-chains 1110 residues out of total 5544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 999 time to evaluate : 6.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 24 GLU Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 77 HIS Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain Q residue 21 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 46 HIS Chi-restraints excluded: chain AD residue 134 LEU Chi-restraints excluded: chain AD residue 205 ILE Chi-restraints excluded: chain AE residue 2 LEU Chi-restraints excluded: chain AE residue 40 VAL Chi-restraints excluded: chain AE residue 153 THR Chi-restraints excluded: chain AF residue 138 ASP Chi-restraints excluded: chain AG residue 1 MET Chi-restraints excluded: chain AG residue 27 SER Chi-restraints excluded: chain AG residue 28 ILE Chi-restraints excluded: chain AG residue 41 VAL Chi-restraints excluded: chain AG residue 130 ASN Chi-restraints excluded: chain AG residue 155 LEU Chi-restraints excluded: chain AH residue 19 VAL Chi-restraints excluded: chain AI residue 37 VAL Chi-restraints excluded: chain AL residue 59 ASN Chi-restraints excluded: chain AL residue 132 SER Chi-restraints excluded: chain AM residue 80 ASP Chi-restraints excluded: chain AM residue 105 GLU Chi-restraints excluded: chain AN residue 17 VAL Chi-restraints excluded: chain AN residue 41 THR Chi-restraints excluded: chain AN residue 45 LEU Chi-restraints excluded: chain AP residue 7 PHE Chi-restraints excluded: chain AP residue 35 SER Chi-restraints excluded: chain AP residue 118 LYS Chi-restraints excluded: chain AQ residue 62 LYS Chi-restraints excluded: chain AQ residue 71 ASP Chi-restraints excluded: chain AQ residue 91 ASN Chi-restraints excluded: chain AR residue 37 GLU Chi-restraints excluded: chain AR residue 108 MET Chi-restraints excluded: chain AS residue 72 THR Chi-restraints excluded: chain AS residue 103 VAL Chi-restraints excluded: chain AS residue 113 ILE Chi-restraints excluded: chain AT residue 47 VAL Chi-restraints excluded: chain AU residue 14 LEU Chi-restraints excluded: chain AU residue 57 SER Chi-restraints excluded: chain AU residue 60 SER Chi-restraints excluded: chain AU residue 63 MET Chi-restraints excluded: chain AU residue 73 MET Chi-restraints excluded: chain AU residue 82 ASP Chi-restraints excluded: chain AU residue 83 ASP Chi-restraints excluded: chain AV residue 22 SER Chi-restraints excluded: chain AV residue 50 THR Chi-restraints excluded: chain AV residue 57 LEU Chi-restraints excluded: chain AV residue 66 VAL Chi-restraints excluded: chain AV residue 72 TYR Chi-restraints excluded: chain AW residue 37 VAL Chi-restraints excluded: chain AX residue 89 TYR Chi-restraints excluded: chain AX residue 162 VAL Chi-restraints excluded: chain AZ residue 59 SER Chi-restraints excluded: chain Aa residue 17 LEU Chi-restraints excluded: chain Aa residue 35 VAL Chi-restraints excluded: chain Aa residue 55 ILE Chi-restraints excluded: chain Ab residue 12 LYS Chi-restraints excluded: chain Ab residue 77 VAL Chi-restraints excluded: chain Ab residue 101 MET Chi-restraints excluded: chain Ac residue 55 HIS Chi-restraints excluded: chain Ae residue 38 LEU Chi-restraints excluded: chain Af residue 10 VAL Chi-restraints excluded: chain Ah residue 28 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 675 optimal weight: 20.0000 chunk 905 optimal weight: 0.7980 chunk 260 optimal weight: 10.0000 chunk 784 optimal weight: 10.0000 chunk 125 optimal weight: 30.0000 chunk 236 optimal weight: 0.0370 chunk 851 optimal weight: 1.9990 chunk 356 optimal weight: 4.9990 chunk 874 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN D 34 HIS ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 ASN I 37 ASN J 31 GLN ** K 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 ASN W 9 ASN AH 99 GLN AM 45 GLN AM 90 ASN AO 94 ASN AQ 91 ASN AT 36 ASN AT 56 ASN ** AU 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 33 ASN AW 41 ASN AW 69 ASN Ac 10 ASN ** Ae 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.089974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.058690 restraints weight = 402260.611| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.36 r_work: 0.2869 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 160524 Z= 0.167 Angle : 0.870 41.395 239067 Z= 0.370 Chirality : 0.084 2.114 30097 Planarity : 0.004 0.064 13022 Dihedral : 23.080 179.841 78230 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.40 % Allowed : 28.87 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.11), residues: 6239 helix: 1.52 (0.12), residues: 2133 sheet: -0.06 (0.14), residues: 1278 loop : -0.81 (0.12), residues: 2828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 132 HIS 0.007 0.001 HIS W 30 PHE 0.032 0.001 PHEAG 117 TYR 0.080 0.002 TYR H 5 ARG 0.015 0.000 ARGAG 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 46889.14 seconds wall clock time: 815 minutes 27.86 seconds (48927.86 seconds total)