Starting phenix.real_space_refine on Thu Feb 22 06:32:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7f_33663/02_2024/7y7f_33663_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7f_33663/02_2024/7y7f_33663.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7f_33663/02_2024/7y7f_33663_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7f_33663/02_2024/7y7f_33663_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7f_33663/02_2024/7y7f_33663_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7f_33663/02_2024/7y7f_33663.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7f_33663/02_2024/7y7f_33663.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7f_33663/02_2024/7y7f_33663_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7f_33663/02_2024/7y7f_33663_updated.pdb" } resolution = 2.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 P 4556 5.49 5 Mg 259 5.21 5 S 150 5.16 5 C 71109 2.51 5 N 26434 2.21 5 O 39421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 44": "OE1" <-> "OE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B ASP 192": "OD1" <-> "OD2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "E ASP 41": "OD1" <-> "OD2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 41": "OD1" <-> "OD2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 15": "OD1" <-> "OD2" Residue "G PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 33": "OD1" <-> "OD2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "H ASP 9": "OD1" <-> "OD2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H ASP 90": "OD1" <-> "OD2" Residue "H ASP 113": "OD1" <-> "OD2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 42": "OE1" <-> "OE2" Residue "I GLU 92": "OE1" <-> "OE2" Residue "I ARG 95": "NH1" <-> "NH2" Residue "I GLU 97": "OE1" <-> "OE2" Residue "I ASP 107": "OD1" <-> "OD2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "I ARG 124": "NH1" <-> "NH2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 18": "OD1" <-> "OD2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "L ARG 14": "NH1" <-> "NH2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L ASP 103": "OD1" <-> "OD2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M ASP 42": "OD1" <-> "OD2" Residue "M ASP 58": "OD1" <-> "OD2" Residue "M GLU 59": "OE1" <-> "OE2" Residue "M TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "N ARG 65": "NH1" <-> "NH2" Residue "N GLU 92": "OE1" <-> "OE2" Residue "P TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 77": "OE1" <-> "OE2" Residue "Q ASP 15": "OD1" <-> "OD2" Residue "Q GLU 18": "OE1" <-> "OE2" Residue "Q ASP 48": "OD1" <-> "OD2" Residue "Q GLU 49": "OE1" <-> "OE2" Residue "Q ASP 57": "OD1" <-> "OD2" Residue "Q GLU 63": "OE1" <-> "OE2" Residue "R PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 72": "OD1" <-> "OD2" Residue "S ARG 3": "NH1" <-> "NH2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "U GLU 36": "OE1" <-> "OE2" Residue "U PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 66": "NH1" <-> "NH2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ASP 72": "OD1" <-> "OD2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c GLU 82": "OE1" <-> "OE2" Residue "c TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 98": "OD1" <-> "OD2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c GLU 180": "OE1" <-> "OE2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "c ASP 187": "OD1" <-> "OD2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "c ASP 229": "OD1" <-> "OD2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d GLU 28": "OE1" <-> "OE2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d GLU 64": "OE1" <-> "OE2" Residue "d GLU 74": "OE1" <-> "OE2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d ASP 108": "OD1" <-> "OD2" Residue "d GLU 168": "OE1" <-> "OE2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d GLU 183": "OE1" <-> "OE2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e GLU 144": "OE1" <-> "OE2" Residue "e GLU 155": "OE1" <-> "OE2" Residue "e PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "e PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f ARG 102": "NH1" <-> "NH2" Residue "f ARG 110": "NH1" <-> "NH2" Residue "f ARG 112": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "f GLU 134": "OE1" <-> "OE2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g GLU 124": "OE1" <-> "OE2" Residue "g ASP 147": "OD1" <-> "OD2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "h TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i ASP 14": "OD1" <-> "OD2" Residue "i GLU 31": "OE1" <-> "OE2" Residue "i ARG 37": "NH1" <-> "NH2" Residue "i GLU 43": "OE1" <-> "OE2" Residue "i PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 91": "OE1" <-> "OE2" Residue "i ARG 96": "NH1" <-> "NH2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "i ASP 141": "OD1" <-> "OD2" Residue "j ASP 73": "OD1" <-> "OD2" Residue "j GLU 92": "OE1" <-> "OE2" Residue "k GLU 10": "OE1" <-> "OE2" Residue "k ARG 21": "NH1" <-> "NH2" Residue "k ARG 33": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k ARG 47": "NH1" <-> "NH2" Residue "k GLU 51": "OE1" <-> "OE2" Residue "k ARG 60": "NH1" <-> "NH2" Residue "k PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 76": "OE1" <-> "OE2" Residue "k ARG 78": "NH1" <-> "NH2" Residue "k GLU 115": "OE1" <-> "OE2" Residue "k ARG 123": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "l ARG 10": "NH1" <-> "NH2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ARG 40": "NH1" <-> "NH2" Residue "l ARG 44": "NH1" <-> "NH2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l ASP 106": "OD1" <-> "OD2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "m ARG 12": "NH1" <-> "NH2" Residue "m ARG 17": "NH1" <-> "NH2" Residue "m ARG 22": "NH1" <-> "NH2" Residue "m GLU 43": "OE1" <-> "OE2" Residue "m ARG 46": "NH1" <-> "NH2" Residue "m GLU 49": "OE1" <-> "OE2" Residue "m ARG 63": "NH1" <-> "NH2" Residue "m ARG 64": "NH1" <-> "NH2" Residue "m ARG 69": "NH1" <-> "NH2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m ASP 72": "OD1" <-> "OD2" Residue "m ARG 96": "NH1" <-> "NH2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "n ARG 10": "NH1" <-> "NH2" Residue "n ARG 16": "NH1" <-> "NH2" Residue "n ARG 25": "NH1" <-> "NH2" Residue "n GLU 46": "OE1" <-> "OE2" Residue "n ARG 81": "NH1" <-> "NH2" Residue "n GLU 84": "OE1" <-> "OE2" Residue "n ASP 93": "OD1" <-> "OD2" Residue "n ARG 94": "NH1" <-> "NH2" Residue "n ARG 102": "NH1" <-> "NH2" Residue "n ARG 111": "NH1" <-> "NH2" Residue "n GLU 112": "OE1" <-> "OE2" Residue "o GLU 11": "OE1" <-> "OE2" Residue "o ASP 16": "OD1" <-> "OD2" Residue "o ARG 21": "NH1" <-> "NH2" Residue "o ARG 39": "NH1" <-> "NH2" Residue "o ASP 82": "OD1" <-> "OD2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "o ARG 101": "NH1" <-> "NH2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "p ARG 3": "NH1" <-> "NH2" Residue "p ARG 6": "NH1" <-> "NH2" Residue "p ARG 13": "NH1" <-> "NH2" Residue "p ARG 33": "NH1" <-> "NH2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p GLU 89": "OE1" <-> "OE2" Residue "p ASP 91": "OD1" <-> "OD2" Residue "q TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q GLU 23": "OE1" <-> "OE2" Residue "q ARG 68": "NH1" <-> "NH2" Residue "q GLU 70": "OE1" <-> "OE2" Residue "q ARG 79": "NH1" <-> "NH2" Residue "q ARG 84": "NH1" <-> "NH2" Residue "r GLU 2": "OE1" <-> "OE2" Residue "r ASP 77": "OD1" <-> "OD2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r ARG 88": "NH1" <-> "NH2" Residue "r ARG 95": "NH1" <-> "NH2" Residue "r ARG 110": "NH1" <-> "NH2" Residue "s GLU 52": "OE1" <-> "OE2" Residue "s GLU 54": "OE1" <-> "OE2" Residue "s GLU 56": "OE1" <-> "OE2" Residue "s ARG 73": "NH1" <-> "NH2" Residue "t ARG 6": "NH1" <-> "NH2" Residue "t ARG 7": "NH1" <-> "NH2" Residue "t ASP 18": "OD1" <-> "OD2" Residue "t GLU 62": "OE1" <-> "OE2" Residue "t ASP 81": "OD1" <-> "OD2" Residue "t ARG 82": "NH1" <-> "NH2" Residue "t ARG 86": "NH1" <-> "NH2" Residue "t ARG 94": "NH1" <-> "NH2" Residue "u PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 90": "OD1" <-> "OD2" Residue "v PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 3": "NH1" <-> "NH2" Residue "w ARG 11": "NH1" <-> "NH2" Residue "w ARG 37": "NH1" <-> "NH2" Residue "w GLU 43": "OE1" <-> "OE2" Residue "w ARG 50": "NH1" <-> "NH2" Residue "w ARG 57": "NH1" <-> "NH2" Residue "w ARG 74": "NH1" <-> "NH2" Residue "x GLU 17": "OE1" <-> "OE2" Residue "x ARG 29": "NH1" <-> "NH2" Residue "x ARG 47": "NH1" <-> "NH2" Residue "x ARG 52": "NH1" <-> "NH2" Residue "y ARG 11": "NH1" <-> "NH2" Residue "y ARG 30": "NH1" <-> "NH2" Residue "y ASP 40": "OD1" <-> "OD2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "y GLU 58": "OE1" <-> "OE2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "z ASP 46": "OD1" <-> "OD2" Residue "z ARG 52": "NH1" <-> "NH2" Residue "0 GLU 7": "OE1" <-> "OE2" Residue "0 TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 35": "OE1" <-> "OE2" Residue "0 ARG 44": "NH1" <-> "NH2" Residue "0 GLU 51": "OE1" <-> "OE2" Residue "1 ARG 3": "NH1" <-> "NH2" Residue "1 ARG 12": "NH1" <-> "NH2" Residue "1 ARG 14": "NH1" <-> "NH2" Residue "1 ARG 21": "NH1" <-> "NH2" Residue "1 ARG 33": "NH1" <-> "NH2" Residue "1 ARG 41": "NH1" <-> "NH2" Residue "2 ARG 13": "NH1" <-> "NH2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 ARG 40": "NH1" <-> "NH2" Residue "2 TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "3 GLU 30": "OE1" <-> "OE2" Residue "4 TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 11": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 141929 Number of models: 1 Model: "" Number of chains: 63 Chain: "A" Number of atoms: 32634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1520, 32634 Classifications: {'RNA': 1520} Modifications used: {'rna2p': 1, 'rna2p_pur': 122, 'rna2p_pyr': 82, 'rna3p': 10, 'rna3p_pur': 741, 'rna3p_pyr': 564} Link IDs: {'rna2p': 205, 'rna3p': 1314} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 839 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "G" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1203 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'IAS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "S" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 668 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "a" Number of atoms: 59130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2753, 59130 Classifications: {'RNA': 2753} Modifications used: {'rna2p': 7, 'rna2p_pur': 267, 'rna2p_pyr': 142, 'rna3p': 17, 'rna3p_pur': 1318, 'rna3p_pyr': 1002} Link IDs: {'rna2p': 415, 'rna3p': 2337} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "b" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "h" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "i" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "j" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "k" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "l" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Unusual residues: {'MS6': 1} Classifications: {'peptide': 135, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126, None: 2} Not linked: pdbres="4D4 l 81 " pdbres="MS6 l 82 " Not linked: pdbres="MS6 l 82 " pdbres="GLY l 83 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "n" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "o" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "p" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "r" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "s" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "t" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "u" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "v" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 628 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "x" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "y" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "0" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "2" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "3" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "4" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 480 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 1 Chain: "X" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 279 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 10} Chain: "Z" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1645 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p': 4, 'rna3p_pur': 34, 'rna3p_pyr': 30} Link IDs: {'rna2p': 8, 'rna3p': 68} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "V" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1612 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p': 3, 'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p': 8, 'rna3p_pur': 31, 'rna3p_pyr': 27} Link IDs: {'rna2p': 9, 'rna3p': 65} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Unusual residues: {' MG': 63} Classifications: {'undetermined': 63} Link IDs: {None: 62} Chain: "a" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 185 Unusual residues: {' MG': 185} Classifications: {'undetermined': 185} Link IDs: {None: 184} Chain: "b" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' MG': 2, 'MAN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 56.51, per 1000 atoms: 0.40 Number of scatterers: 141929 At special positions: 0 Unit cell: (251.035, 237.779, 247.721, 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) S 150 16.00 P 4556 15.00 Mg 259 11.99 O 39421 8.00 N 26434 7.00 C 71109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 59.07 Conformation dependent library (CDL) restraints added in 7.7 seconds 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10270 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 169 helices and 68 sheets defined 38.8% alpha, 18.7% beta 1580 base pairs and 2444 stacking pairs defined. Time for finding SS restraints: 74.18 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.898A pdb=" N MET B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 64 Proline residue: B 48 - end of helix removed outlier: 3.764A pdb=" N LYS B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 removed outlier: 4.203A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 124 removed outlier: 3.519A pdb=" N VAL B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 148 removed outlier: 6.262A pdb=" N ALA B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 206 through 227 Processing helix chain 'C' and resid 6 through 12 removed outlier: 3.877A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 48 Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.605A pdb=" N VAL C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 112 through 127 removed outlier: 3.513A pdb=" N ARG C 127 " --> pdb=" O GLN C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.815A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.784A pdb=" N LYS D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 83 removed outlier: 5.208A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.771A pdb=" N ARG D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 110 through 121 removed outlier: 3.639A pdb=" N LYS D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.572A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 3.664A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.801A pdb=" N LEU D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N SER D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 192' Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.972A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.972A pdb=" N MET E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 147 removed outlier: 3.694A pdb=" N MET E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 15 through 33 Proline residue: F 19 - end of helix removed outlier: 3.619A pdb=" N GLU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 82 removed outlier: 5.605A pdb=" N ASP F 82 " --> pdb=" O PHE F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 55 removed outlier: 3.547A pdb=" N ALA G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 removed outlier: 3.886A pdb=" N ALA G 61 " --> pdb=" O SER G 57 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 112 removed outlier: 3.607A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLY G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 Processing helix chain 'G' and resid 132 through 149 removed outlier: 3.633A pdb=" N ASN G 148 " --> pdb=" O MET G 144 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS G 149 " --> pdb=" O ALA G 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 21 Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 112 through 120 Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 41 through 56 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 91 Processing helix chain 'I' and resid 92 through 102 removed outlier: 5.062A pdb=" N SER I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLU I 97 " --> pdb=" O SER I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 33 removed outlier: 3.661A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 removed outlier: 3.546A pdb=" N ARG J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 51 removed outlier: 4.564A pdb=" N GLY K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 4.013A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 54 through 59' Processing helix chain 'K' and resid 60 through 75 Processing helix chain 'K' and resid 92 through 104 removed outlier: 4.261A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY K 104 " --> pdb=" O LEU K 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 11 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 113 through 118 removed outlier: 3.668A pdb=" N TYR L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.984A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 removed outlier: 3.695A pdb=" N SER M 30 " --> pdb=" O GLY M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 64 removed outlier: 4.157A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N VAL M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 21 removed outlier: 3.518A pdb=" N LYS N 7 " --> pdb=" O LYS N 3 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE N 21 " --> pdb=" O ALA N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 33 Processing helix chain 'N' and resid 37 through 51 removed outlier: 4.058A pdb=" N ARG N 41 " --> pdb=" O SER N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 91 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 44 removed outlier: 4.342A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.890A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 80 removed outlier: 3.935A pdb=" N LYS P 80 " --> pdb=" O LYS P 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 17 Processing helix chain 'R' and resid 25 through 34 removed outlier: 4.527A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N THR R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 48 through 66 Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 70 through 76 removed outlier: 4.581A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA S 75 " --> pdb=" O LEU S 71 " (cutoff:3.500A) Proline residue: S 76 - end of helix No H-bonds generated for 'chain 'S' and resid 70 through 76' Processing helix chain 'T' and resid 4 through 41 Processing helix chain 'T' and resid 44 through 65 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 removed outlier: 3.680A pdb=" N ALA T 87 " --> pdb=" O ILE T 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 27 Processing helix chain 'U' and resid 28 through 37 removed outlier: 4.868A pdb=" N PHE U 37 " --> pdb=" O ARG U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 69 removed outlier: 5.103A pdb=" N ARG U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 15 removed outlier: 5.051A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 4.057A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N GLU c 35 " --> pdb=" O ALA c 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 30 through 35' Processing helix chain 'c' and resid 131 through 136 removed outlier: 3.698A pdb=" N ILE c 135 " --> pdb=" O PRO c 131 " (cutoff:3.500A) Proline residue: c 136 - end of helix No H-bonds generated for 'chain 'c' and resid 131 through 136' Processing helix chain 'c' and resid 207 through 215 removed outlier: 3.684A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY c 215 " --> pdb=" O ALA c 211 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 4.054A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASN c 226 " --> pdb=" O GLY c 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 221 through 226' Processing helix chain 'c' and resid 260 through 268 removed outlier: 3.568A pdb=" N ASP c 264 " --> pdb=" O ASN c 260 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 260 through 268' Processing helix chain 'c' and resid 197 through 202 removed outlier: 4.422A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 61 removed outlier: 6.075A pdb=" N THR d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 72 Processing helix chain 'd' and resid 98 through 103 removed outlier: 4.306A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP d 103 " --> pdb=" O GLU d 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 98 through 103' Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'd' and resid 39 through 44 Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 40 removed outlier: 3.572A pdb=" N ALA e 39 " --> pdb=" O TYR e 35 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 116 removed outlier: 3.512A pdb=" N ASP e 116 " --> pdb=" O LEU e 112 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 142 removed outlier: 3.523A pdb=" N LEU e 134 " --> pdb=" O LYS e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 163 removed outlier: 3.512A pdb=" N ARG e 162 " --> pdb=" O PHE e 158 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 removed outlier: 3.587A pdb=" N PHE e 183 " --> pdb=" O SER e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'f' and resid 2 through 21 removed outlier: 4.976A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 47 removed outlier: 3.646A pdb=" N ASP f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS f 47 " --> pdb=" O ALA f 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 42 through 47' Processing helix chain 'f' and resid 48 through 62 Processing helix chain 'f' and resid 93 through 111 removed outlier: 4.523A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 Processing helix chain 'f' and resid 134 through 139 removed outlier: 4.026A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) Proline residue: f 139 - end of helix Processing helix chain 'g' and resid 2 through 8 removed outlier: 3.913A pdb=" N ALA g 7 " --> pdb=" O ARG g 3 " (cutoff:3.500A) Proline residue: g 8 - end of helix Processing helix chain 'g' and resid 60 through 81 removed outlier: 5.353A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL g 79 " --> pdb=" O MET g 75 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR g 80 " --> pdb=" O VAL g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 4.330A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG g 153 " --> pdb=" O ARG g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 28 Processing helix chain 'h' and resid 29 through 34 Processing helix chain 'i' and resid 24 through 38 removed outlier: 3.878A pdb=" N GLU i 31 " --> pdb=" O ARG i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 88 through 96 Processing helix chain 'i' and resid 97 through 110 removed outlier: 4.405A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET i 108 " --> pdb=" O ALA i 104 " (cutoff:3.500A) Proline residue: i 110 - end of helix Processing helix chain 'i' and resid 112 through 122 removed outlier: 4.092A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 104 through 109 removed outlier: 4.590A pdb=" N ARG j 108 " --> pdb=" O THR j 104 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N SER j 109 " --> pdb=" O ARG j 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 104 through 109' Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'k' and resid 37 through 42 removed outlier: 3.652A pdb=" N ARG k 41 " --> pdb=" O GLY k 37 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N SER k 42 " --> pdb=" O GLN k 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 37 through 42' Processing helix chain 'k' and resid 56 through 62 removed outlier: 3.645A pdb=" N LEU k 61 " --> pdb=" O LEU k 57 " (cutoff:3.500A) Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 4.180A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR k 74 " --> pdb=" O LYS k 70 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 68 through 75' Processing helix chain 'k' and resid 78 through 85 removed outlier: 3.873A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL k 85 " --> pdb=" O ASP k 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 78 through 85' Processing helix chain 'k' and resid 91 through 99 Processing helix chain 'k' and resid 128 through 139 Processing helix chain 'l' and resid 42 through 58 Processing helix chain 'l' and resid 109 through 125 removed outlier: 3.681A pdb=" N ALA l 122 " --> pdb=" O LYS l 118 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) Proline residue: l 125 - end of helix Processing helix chain 'm' and resid 13 through 32 Processing helix chain 'm' and resid 38 through 58 removed outlier: 4.343A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 3.506A pdb=" N LYS m 56 " --> pdb=" O ILE m 52 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASP m 58 " --> pdb=" O LEU m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 4.436A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 5.090A pdb=" N GLY m 84 " --> pdb=" O PHE m 80 " (cutoff:3.500A) Proline residue: m 85 - end of helix Processing helix chain 'n' and resid 2 through 22 removed outlier: 4.442A pdb=" N ALA n 6 " --> pdb=" O ASP n 2 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 5.423A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LYS n 63 " --> pdb=" O ALA n 59 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 86 Processing helix chain 'n' and resid 101 through 114 removed outlier: 3.629A pdb=" N GLY n 114 " --> pdb=" O ALA n 110 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 13 removed outlier: 3.759A pdb=" N GLU o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET o 13 " --> pdb=" O GLU o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.651A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N THR o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 97 through 104' Processing helix chain 'p' and resid 6 through 22 removed outlier: 3.952A pdb=" N LYS p 22 " --> pdb=" O LEU p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.844A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 32 through 37 removed outlier: 3.914A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 73 removed outlier: 3.791A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 87 Processing helix chain 'p' and resid 91 through 102 Processing helix chain 'p' and resid 103 through 118 Processing helix chain 'r' and resid 13 through 25 removed outlier: 3.731A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG r 25 " --> pdb=" O ALA r 21 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 39 Processing helix chain 'r' and resid 41 through 61 removed outlier: 3.609A pdb=" N VAL r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 65 through 70 removed outlier: 3.901A pdb=" N LEU r 69 " --> pdb=" O ASP r 65 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LYS r 70 " --> pdb=" O ILE r 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 65 through 70' Processing helix chain 's' and resid 3 through 11 removed outlier: 4.382A pdb=" N LEU s 11 " --> pdb=" O LEU s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 17 through 27 Processing helix chain 's' and resid 39 through 51 Processing helix chain 't' and resid 66 through 71 removed outlier: 3.906A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA t 71 " --> pdb=" O VAL t 67 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 66 through 71' Processing helix chain 'u' and resid 13 through 24 removed outlier: 3.572A pdb=" N ALA u 23 " --> pdb=" O ARG u 19 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN u 24 " --> pdb=" O LEU u 20 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 53 removed outlier: 4.100A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 4.670A pdb=" N SER u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU u 59 " --> pdb=" O GLU u 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 54 through 59' Processing helix chain 'w' and resid 52 through 63 Processing helix chain 'w' and resid 64 through 75 Processing helix chain 'x' and resid 2 through 10 removed outlier: 4.323A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N SER x 10 " --> pdb=" O LEU x 6 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 35 removed outlier: 3.559A pdb=" N GLY x 35 " --> pdb=" O GLN x 31 " (cutoff:3.500A) Processing helix chain 'x' and resid 40 through 62 removed outlier: 4.190A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY x 62 " --> pdb=" O ASN x 58 " (cutoff:3.500A) Processing helix chain 'y' and resid 17 through 28 Processing helix chain 'y' and resid 41 through 52 Processing helix chain 'z' and resid 9 through 19 removed outlier: 4.640A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 24 removed outlier: 4.402A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 25 through 38 Processing helix chain '2' and resid 7 through 14 removed outlier: 3.935A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 37 through 46 Proline residue: 2 46 - end of helix Processing helix chain '2' and resid 51 through 63 removed outlier: 4.684A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU 2 57 " --> pdb=" O GLY 2 53 " (cutoff:3.500A) Proline residue: 2 63 - end of helix Processing helix chain '4' and resid 41 through 46 Processing helix chain '4' and resid 55 through 65 removed outlier: 3.818A pdb=" N ASN 4 65 " --> pdb=" O ASN 4 61 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 15 through 18 removed outlier: 6.134A pdb=" N HIS B 15 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N HIS B 39 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 89 through 93 removed outlier: 3.568A pdb=" N ALA B 185 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 53 through 59 Processing sheet with id= 4, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.552A pdb=" N GLY C 148 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY C 194 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 141 through 145 removed outlier: 3.912A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N MET D 178 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 12 through 16 removed outlier: 6.722A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 84 through 88 removed outlier: 3.561A pdb=" N GLY E 87 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA E 99 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 32 through 40 Processing sheet with id= 9, first strand: chain 'F' and resid 38 through 42 removed outlier: 5.467A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU F 5 " --> pdb=" O MET F 90 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 43 through 47 removed outlier: 3.856A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 57 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 72 through 79 removed outlier: 6.715A pdb=" N THR G 72 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 23 through 29 removed outlier: 6.112A pdb=" N ALA H 23 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER H 29 " --> pdb=" O PRO H 57 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.554A pdb=" N SER H 74 " --> pdb=" O ALA H 130 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'I' and resid 5 through 11 Processing sheet with id= 15, first strand: chain 'I' and resid 26 through 30 Processing sheet with id= 16, first strand: chain 'J' and resid 39 through 42 removed outlier: 4.467A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 44 through 52 Processing sheet with id= 18, first strand: chain 'K' and resid 30 through 35 Processing sheet with id= 19, first strand: chain 'L' and resid 29 through 32 removed outlier: 5.098A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ARG L 94 " --> pdb=" O GLY L 85 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'L' and resid 36 through 41 removed outlier: 5.086A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'P' and resid 4 through 10 removed outlier: 3.668A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'Q' and resid 7 through 11 removed outlier: 6.834A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'Q' and resid 19 through 30 No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 'Q' and resid 56 through 59 removed outlier: 8.321A pdb=" N GLY Q 56 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA Q 82 " --> pdb=" O GLY Q 56 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'S' and resid 30 through 33 removed outlier: 4.587A pdb=" N LEU S 47 " --> pdb=" O VAL S 62 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'c' and resid 2 through 6 removed outlier: 6.006A pdb=" N VAL c 16 " --> pdb=" O CYS c 6 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'c' and resid 80 through 83 removed outlier: 3.607A pdb=" N ARG c 80 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'c' and resid 138 through 142 removed outlier: 4.255A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'c' and resid 90 through 96 removed outlier: 5.358A pdb=" N ASN c 90 " --> pdb=" O ALA c 106 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU c 100 " --> pdb=" O TYR c 96 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'd' and resid 3 through 9 removed outlier: 4.348A pdb=" N SER d 199 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'd' and resid 10 through 16 removed outlier: 3.703A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'd' and resid 79 through 84 removed outlier: 5.959A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'e' and resid 1 through 6 removed outlier: 4.287A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'e' and resid 117 through 120 removed outlier: 5.573A pdb=" N ARG e 117 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'f' and resid 65 through 69 removed outlier: 5.159A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'g' and resid 16 through 19 Processing sheet with id= 37, first strand: chain 'g' and resid 41 through 45 removed outlier: 5.093A pdb=" N THR g 51 " --> pdb=" O LYS g 44 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'g' and resid 82 through 89 removed outlier: 5.919A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'g' and resid 94 through 98 removed outlier: 3.997A pdb=" N VAL g 113 " --> pdb=" O LEU g 105 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'h' and resid 17 through 21 removed outlier: 4.401A pdb=" N ASP h 17 " --> pdb=" O LEU h 5 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU h 5 " --> pdb=" O ASP h 17 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN h 2 " --> pdb=" O ALA h 39 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'i' and resid 52 through 57 removed outlier: 4.942A pdb=" N ASP i 19 " --> pdb=" O LEU i 140 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.641A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'j' and resid 18 through 21 removed outlier: 4.231A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASN j 82 " --> pdb=" O MET j 7 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'l' and resid 37 through 40 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain 'l' and resid 62 through 65 removed outlier: 3.610A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU l 33 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS l 100 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'l' and resid 30 through 36 removed outlier: 7.999A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'm' and resid 33 through 37 removed outlier: 5.607A pdb=" N MET m 110 " --> pdb=" O CYS m 100 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'n' and resid 49 through 53 removed outlier: 3.722A pdb=" N VAL n 49 " --> pdb=" O VAL n 39 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE n 35 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'o' and resid 49 through 53 removed outlier: 3.746A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG o 53 " --> pdb=" O HIS o 56 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR o 60 " --> pdb=" O ILE o 48 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER o 83 " --> pdb=" O LYS o 29 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'o' and resid 57 through 64 removed outlier: 7.650A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'q' and resid 11 through 15 removed outlier: 3.545A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU q 46 " --> pdb=" O ASN q 43 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'q' and resid 18 through 23 removed outlier: 4.292A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 54, first strand: chain 'q' and resid 65 through 68 Processing sheet with id= 55, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.160A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'r' and resid 2 through 8 removed outlier: 4.705A pdb=" N THR r 100 " --> pdb=" O GLY r 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS r 73 " --> pdb=" O VAL r 106 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 's' and resid 28 through 33 removed outlier: 6.694A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 't' and resid 83 through 86 Processing sheet with id= 59, first strand: chain 'u' and resid 69 through 72 removed outlier: 3.515A pdb=" N GLU u 7 " --> pdb=" O GLU u 41 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA u 39 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'v' and resid 51 through 54 removed outlier: 4.248A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'v' and resid 65 through 71 Processing sheet with id= 62, first strand: chain 'w' and resid 12 through 19 removed outlier: 4.436A pdb=" N ASN w 23 " --> pdb=" O SER w 19 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.381A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'z' and resid 29 through 32 removed outlier: 4.273A pdb=" N GLU z 36 " --> pdb=" O ASP z 31 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain '0' and resid 19 through 25 removed outlier: 6.019A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE 0 48 " --> pdb=" O SER 0 14 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain '2' and resid 22 through 25 removed outlier: 5.674A pdb=" N PHE 2 22 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '3' and resid 14 through 19 Processing sheet with id= 68, first strand: chain '4' and resid 11 through 16 removed outlier: 4.291A pdb=" N ASN 4 20 " --> pdb=" O CYS 4 16 " (cutoff:3.500A) 1870 hydrogen bonds defined for protein. 5526 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3978 hydrogen bonds 6238 hydrogen bond angles 0 basepair planarities 1580 basepair parallelities 2444 stacking parallelities Total time for adding SS restraints: 237.13 Time building geometry restraints manager: 64.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 12457 1.29 - 1.43: 69272 1.43 - 1.57: 62892 1.57 - 1.70: 9112 1.70 - 1.84: 264 Bond restraints: 153997 Sorted by residual: bond pdb=" C5 5MU Z 55 " pdb=" C6 5MU Z 55 " ideal model delta sigma weight residual 1.155 1.443 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C5 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.155 1.440 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C5 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.155 1.438 -0.283 2.00e-02 2.50e+03 2.00e+02 bond pdb=" C5 5MU V 53 " pdb=" C6 5MU V 53 " ideal model delta sigma weight residual 1.155 1.434 -0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C MS6 l 82 " pdb=" S MS6 l 82 " ideal model delta sigma weight residual 1.829 1.567 0.262 2.00e-02 2.50e+03 1.71e+02 ... (remaining 153992 not shown) Histogram of bond angle deviations from ideal: 97.54 - 106.41: 27610 106.41 - 115.28: 102113 115.28 - 124.15: 80399 124.15 - 133.01: 20259 133.01 - 141.88: 81 Bond angle restraints: 230462 Sorted by residual: angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C8 2MA a2503 " ideal model delta sigma weight residual 106.32 141.88 -35.56 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C1' G7M a2069 " pdb=" N9 G7M a2069 " pdb=" C8 G7M a2069 " ideal model delta sigma weight residual 94.96 126.54 -31.58 3.00e+00 1.11e-01 1.11e+02 angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C8 G7M A 527 " ideal model delta sigma weight residual 94.96 124.52 -29.56 3.00e+00 1.11e-01 9.71e+01 angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C4 2MA a2503 " ideal model delta sigma weight residual 138.88 110.66 28.22 3.00e+00 1.11e-01 8.85e+01 angle pdb=" C1' 1MA V 9 " pdb=" N9 1MA V 9 " pdb=" C8 1MA V 9 " ideal model delta sigma weight residual 100.68 128.77 -28.09 3.00e+00 1.11e-01 8.77e+01 ... (remaining 230457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 87449 35.55 - 71.11: 9847 71.11 - 106.66: 1213 106.66 - 142.22: 19 142.22 - 177.77: 11 Dihedral angle restraints: 98539 sinusoidal: 82618 harmonic: 15921 Sorted by residual: dihedral pdb=" CA ASP g 47 " pdb=" C ASP g 47 " pdb=" N ASN g 48 " pdb=" CA ASN g 48 " ideal model delta harmonic sigma weight residual -180.00 -110.91 -69.09 0 5.00e+00 4.00e-02 1.91e+02 dihedral pdb=" CA HIS 2 31 " pdb=" C HIS 2 31 " pdb=" N ILE 2 32 " pdb=" CA ILE 2 32 " ideal model delta harmonic sigma weight residual -180.00 -131.83 -48.17 0 5.00e+00 4.00e-02 9.28e+01 dihedral pdb=" O4' C V 73 " pdb=" C1' C V 73 " pdb=" N1 C V 73 " pdb=" C2 C V 73 " ideal model delta sinusoidal sigma weight residual -160.00 8.37 -168.37 1 1.50e+01 4.44e-03 8.45e+01 ... (remaining 98536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 25962 0.077 - 0.153: 3065 0.153 - 0.230: 244 0.230 - 0.306: 30 0.306 - 0.383: 3 Chirality restraints: 29304 Sorted by residual: chirality pdb=" C1* PSU A 516 " pdb=" O4* PSU A 516 " pdb=" C2* PSU A 516 " pdb=" C5 PSU A 516 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C1* PSU a2580 " pdb=" O4* PSU a2580 " pdb=" C2* PSU a2580 " pdb=" C5 PSU a2580 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C1' A a 980 " pdb=" O4' A a 980 " pdb=" C2' A a 980 " pdb=" N9 A a 980 " both_signs ideal model delta sigma weight residual False 2.46 2.13 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 29301 not shown) Planarity restraints: 12266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.068 2.00e-02 2.50e+03 6.07e-01 8.29e+03 pdb=" C4' 2MG A1516 " -0.429 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " -0.611 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " 0.604 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " 0.661 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " 0.156 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " -1.011 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " -0.228 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " 0.925 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " -0.064 2.00e-02 2.50e+03 6.05e-01 8.22e+03 pdb=" C4' 2MG A1207 " -0.448 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " -0.659 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " 0.640 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " 0.184 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " -0.971 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " -0.210 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " 0.931 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " -0.065 2.00e-02 2.50e+03 6.00e-01 8.11e+03 pdb=" C4' 5MC A1407 " -0.442 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " -0.621 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " 0.599 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " 0.650 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " 0.174 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " -0.984 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " -0.222 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " 0.911 2.00e-02 2.50e+03 ... (remaining 12263 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 578 2.44 - 3.06: 84236 3.06 - 3.67: 259411 3.67 - 4.29: 417377 4.29 - 4.90: 556404 Nonbonded interactions: 1318006 Sorted by model distance: nonbonded pdb=" O6 G A1222 " pdb="MG MG A1604 " model vdw 1.827 2.170 nonbonded pdb=" OP1 A a 751 " pdb="MG MG a6019 " model vdw 1.840 2.170 nonbonded pdb=" OP1 G a1026 " pdb="MG MG a6120 " model vdw 1.846 2.170 nonbonded pdb=" OP2 C a2611 " pdb="MG MG a6061 " model vdw 1.857 2.170 nonbonded pdb=" OP1 C a 787 " pdb="MG MG a6125 " model vdw 1.865 2.170 ... (remaining 1318001 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 36.280 Check model and map are aligned: 1.610 Set scattering table: 1.040 Process input model: 535.010 Find NCS groups from input model: 2.790 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:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 603.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.012 0.288 153997 Z= 0.702 Angle : 0.799 35.565 230462 Z= 0.411 Chirality : 0.050 0.383 29304 Planarity : 0.025 0.607 12266 Dihedral : 22.497 177.773 88269 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.22 % Favored : 95.69 % Rotamer: Outliers : 0.04 % Allowed : 0.35 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.11), residues: 5480 helix: 1.02 (0.12), residues: 1807 sheet: -0.41 (0.15), residues: 1104 loop : -0.77 (0.11), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 23 HIS 0.024 0.002 HIS c 53 PHE 0.058 0.003 PHE J 49 TYR 0.025 0.002 TYR r 38 ARG 0.024 0.001 ARG t 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1047 time to evaluate : 6.268 Fit side-chains REVERT: B 8 ASP cc_start: 0.3105 (p0) cc_final: 0.1946 (t70) REVERT: B 27 MET cc_start: 0.3962 (mmt) cc_final: 0.3190 (tpt) REVERT: B 73 LYS cc_start: 0.4206 (mtmm) cc_final: 0.3816 (mtpp) REVERT: B 151 ILE cc_start: 0.4985 (pt) cc_final: 0.4440 (pp) REVERT: B 154 MET cc_start: 0.3597 (tpp) cc_final: 0.3371 (mmt) REVERT: B 173 ILE cc_start: 0.5111 (mt) cc_final: 0.4678 (mm) REVERT: B 174 LYS cc_start: 0.4016 (tptp) cc_final: 0.3281 (tptm) REVERT: B 179 LEU cc_start: 0.4513 (mt) cc_final: 0.4211 (mt) REVERT: C 28 GLU cc_start: 0.6322 (pm20) cc_final: 0.6074 (pm20) REVERT: C 41 GLN cc_start: 0.6758 (tt0) cc_final: 0.6147 (tt0) REVERT: C 49 LYS cc_start: 0.6332 (mtpp) cc_final: 0.5837 (mmmt) REVERT: C 58 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6587 (mt-10) REVERT: C 86 LYS cc_start: 0.6677 (mtmm) cc_final: 0.6288 (ttpp) REVERT: C 110 GLU cc_start: 0.5923 (mp0) cc_final: 0.5577 (mm-30) REVERT: C 132 ARG cc_start: 0.5552 (mtp180) cc_final: 0.5027 (ttm170) REVERT: C 142 MET cc_start: 0.7102 (mmm) cc_final: 0.6709 (mmp) REVERT: C 207 ILE cc_start: 0.4766 (mp) cc_final: 0.4171 (tt) REVERT: D 8 LYS cc_start: 0.5678 (mmtp) cc_final: 0.5011 (mmtp) REVERT: D 45 LYS cc_start: 0.5425 (mtmm) cc_final: 0.4716 (mptm) REVERT: D 70 ARG cc_start: 0.7203 (tpp80) cc_final: 0.6948 (tpp80) REVERT: D 71 GLN cc_start: 0.7669 (tt0) cc_final: 0.7283 (mt0) REVERT: D 83 LYS cc_start: 0.6123 (mmtp) cc_final: 0.5459 (mttt) REVERT: D 124 MET cc_start: 0.5894 (ptp) cc_final: 0.5501 (ptt) REVERT: D 128 ARG cc_start: 0.4970 (ttm110) cc_final: 0.4457 (ttp80) REVERT: D 204 TYR cc_start: 0.7384 (m-80) cc_final: 0.7081 (m-80) REVERT: E 14 LYS cc_start: 0.8210 (ttmm) cc_final: 0.7974 (ttmm) REVERT: E 26 LYS cc_start: 0.7569 (ttmt) cc_final: 0.7274 (ttpt) REVERT: E 45 ARG cc_start: 0.7170 (mtp85) cc_final: 0.6571 (mtm180) REVERT: E 48 PHE cc_start: 0.8217 (p90) cc_final: 0.7327 (p90) REVERT: E 54 ARG cc_start: 0.6477 (mmt90) cc_final: 0.6240 (mmt90) REVERT: E 55 GLU cc_start: 0.6544 (mt-10) cc_final: 0.6243 (mt-10) REVERT: E 70 ASN cc_start: 0.6954 (m-40) cc_final: 0.6733 (m-40) REVERT: E 134 ILE cc_start: 0.7766 (mt) cc_final: 0.7508 (mt) REVERT: E 146 ASN cc_start: 0.6447 (m-40) cc_final: 0.6157 (m110) REVERT: E 157 ARG cc_start: 0.7175 (mtp180) cc_final: 0.6971 (mtm180) REVERT: F 8 PHE cc_start: 0.7582 (p90) cc_final: 0.7213 (p90) REVERT: F 55 HIS cc_start: 0.7079 (m-70) cc_final: 0.6827 (m170) REVERT: F 56 LYS cc_start: 0.6755 (mttp) cc_final: 0.6427 (mmmm) REVERT: F 90 MET cc_start: 0.6615 (mtp) cc_final: 0.6117 (mtm) REVERT: F 92 THR cc_start: 0.6190 (m) cc_final: 0.5958 (p) REVERT: G 18 PHE cc_start: 0.6604 (m-80) cc_final: 0.6391 (m-80) REVERT: G 41 SER cc_start: 0.7608 (m) cc_final: 0.7390 (m) REVERT: G 58 GLU cc_start: 0.4636 (mp0) cc_final: 0.4370 (mt-10) REVERT: G 63 GLU cc_start: 0.6114 (mm-30) cc_final: 0.5707 (mm-30) REVERT: G 74 GLU cc_start: 0.5976 (pt0) cc_final: 0.5692 (pm20) REVERT: G 78 ARG cc_start: 0.4271 (tpp-160) cc_final: 0.3409 (tmt170) REVERT: G 106 GLU cc_start: 0.7234 (tt0) cc_final: 0.6595 (mm-30) REVERT: G 118 LEU cc_start: 0.7439 (tp) cc_final: 0.7233 (mt) REVERT: G 125 SER cc_start: 0.6804 (t) cc_final: 0.6268 (m) REVERT: G 146 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6867 (tm-30) REVERT: H 18 GLN cc_start: 0.7915 (mm110) cc_final: 0.7527 (mm-40) REVERT: H 21 ASN cc_start: 0.7721 (m110) cc_final: 0.7447 (m110) REVERT: H 89 LYS cc_start: 0.6615 (tmmt) cc_final: 0.6070 (ptmt) REVERT: I 21 ILE cc_start: 0.6567 (mt) cc_final: 0.6335 (mm) REVERT: I 32 GLN cc_start: 0.6904 (mm-40) cc_final: 0.6684 (mm-40) REVERT: I 57 MET cc_start: 0.6178 (mtp) cc_final: 0.5200 (tpp) REVERT: I 95 ARG cc_start: 0.6492 (ttm-80) cc_final: 0.6116 (ttm110) REVERT: I 107 ASP cc_start: 0.7544 (t0) cc_final: 0.7299 (t0) REVERT: J 66 GLU cc_start: 0.7264 (pt0) cc_final: 0.6953 (pt0) REVERT: J 68 ARG cc_start: 0.7863 (mtt180) cc_final: 0.7479 (mtt180) REVERT: J 88 MET cc_start: 0.3660 (mmp) cc_final: 0.3253 (mmt) REVERT: K 37 ARG cc_start: 0.6546 (mmm-85) cc_final: 0.5738 (mtp180) REVERT: K 56 ARG cc_start: 0.7012 (mtp-110) cc_final: 0.6686 (mmm-85) REVERT: K 68 GLU cc_start: 0.6625 (mt-10) cc_final: 0.6424 (mt-10) REVERT: K 69 ARG cc_start: 0.6438 (mtp180) cc_final: 0.5902 (mtp-110) REVERT: K 83 GLU cc_start: 0.6155 (mt-10) cc_final: 0.5884 (mt-10) REVERT: K 85 MET cc_start: 0.7394 (mmm) cc_final: 0.6938 (mtm) REVERT: K 98 ARG cc_start: 0.6547 (mtt90) cc_final: 0.6316 (mtt-85) REVERT: K 106 ARG cc_start: 0.5241 (ttp-110) cc_final: 0.4397 (ptp-170) REVERT: L 20 ASN cc_start: 0.7424 (m-40) cc_final: 0.7154 (m110) REVERT: L 30 LYS cc_start: 0.7975 (mmtt) cc_final: 0.7751 (mmtm) REVERT: L 40 THR cc_start: 0.7904 (p) cc_final: 0.7592 (t) REVERT: L 62 GLU cc_start: 0.7274 (tt0) cc_final: 0.7006 (tt0) REVERT: L 120 LYS cc_start: 0.7219 (mttm) cc_final: 0.6943 (mttp) REVERT: M 72 GLU cc_start: 0.6231 (pt0) cc_final: 0.5372 (mp0) REVERT: M 79 ARG cc_start: 0.6528 (ttt-90) cc_final: 0.6307 (ttt180) REVERT: M 86 TYR cc_start: 0.6927 (t80) cc_final: 0.6633 (t80) REVERT: N 12 LYS cc_start: 0.7409 (tttt) cc_final: 0.6917 (tttt) REVERT: N 16 LEU cc_start: 0.7319 (mt) cc_final: 0.7039 (mt) REVERT: N 21 PHE cc_start: 0.6438 (t80) cc_final: 0.6065 (t80) REVERT: N 41 ARG cc_start: 0.5681 (mtm-85) cc_final: 0.5084 (ttm110) REVERT: N 47 LYS cc_start: 0.6232 (tptp) cc_final: 0.5323 (mptt) REVERT: N 90 ARG cc_start: 0.7302 (mtm-85) cc_final: 0.6990 (mtm110) REVERT: O 10 LYS cc_start: 0.6628 (mtpp) cc_final: 0.6026 (mptt) REVERT: O 47 LYS cc_start: 0.7065 (mttp) cc_final: 0.6815 (mtmm) REVERT: O 57 LEU cc_start: 0.8325 (mm) cc_final: 0.7843 (mt) REVERT: O 58 ARG cc_start: 0.7460 (ttm170) cc_final: 0.7079 (ttm170) REVERT: O 62 GLN cc_start: 0.6928 (tt0) cc_final: 0.6422 (mm110) REVERT: O 68 ASP cc_start: 0.7226 (m-30) cc_final: 0.6714 (m-30) REVERT: O 69 TYR cc_start: 0.8293 (t80) cc_final: 0.7922 (t80) REVERT: O 72 ARG cc_start: 0.6556 (ttm110) cc_final: 0.5959 (ttp80) REVERT: P 3 THR cc_start: 0.7372 (p) cc_final: 0.6974 (m) REVERT: P 32 PHE cc_start: 0.7849 (p90) cc_final: 0.7403 (p90) REVERT: P 35 ARG cc_start: 0.7249 (ttt-90) cc_final: 0.7001 (ttt-90) REVERT: P 51 ARG cc_start: 0.5928 (ptp-170) cc_final: 0.5242 (mtp-110) REVERT: P 63 GLN cc_start: 0.5508 (OUTLIER) cc_final: 0.4665 (mm110) REVERT: P 71 VAL cc_start: 0.7274 (p) cc_final: 0.7024 (m) REVERT: Q 11 ARG cc_start: 0.5926 (mtp-110) cc_final: 0.5464 (mtp-110) REVERT: Q 44 LEU cc_start: 0.7964 (mt) cc_final: 0.7610 (mt) REVERT: Q 75 LEU cc_start: 0.6809 (tp) cc_final: 0.6579 (tt) REVERT: R 42 SER cc_start: 0.7677 (m) cc_final: 0.7413 (p) REVERT: R 54 GLN cc_start: 0.7167 (pt0) cc_final: 0.6844 (pt0) REVERT: R 57 ARG cc_start: 0.7047 (ttm110) cc_final: 0.6448 (mtp180) REVERT: R 73 ARG cc_start: 0.5282 (ttp-110) cc_final: 0.4828 (tmt-80) REVERT: S 47 LEU cc_start: 0.6751 (mt) cc_final: 0.6520 (mt) REVERT: T 13 GLN cc_start: 0.6690 (tt0) cc_final: 0.6466 (tt0) REVERT: T 18 ARG cc_start: 0.7199 (ttp80) cc_final: 0.6991 (tmm160) REVERT: T 20 HIS cc_start: 0.6735 (t-90) cc_final: 0.6408 (t70) REVERT: T 21 ASN cc_start: 0.7396 (m-40) cc_final: 0.7111 (m-40) REVERT: T 24 ARG cc_start: 0.6518 (mmm160) cc_final: 0.6166 (mmt90) REVERT: T 28 MET cc_start: 0.6916 (ttp) cc_final: 0.6517 (tmm) REVERT: T 29 ARG cc_start: 0.6785 (mtm-85) cc_final: 0.6373 (mtp180) REVERT: T 54 MET cc_start: 0.6523 (tmm) cc_final: 0.6162 (tmm) REVERT: U 34 ARG cc_start: 0.5806 (ttp80) cc_final: 0.5407 (ttt-90) REVERT: U 38 TYR cc_start: 0.8225 (t80) cc_final: 0.7982 (t80) REVERT: U 39 GLU cc_start: 0.6507 (mm-30) cc_final: 0.6229 (tp30) REVERT: U 40 LYS cc_start: 0.6626 (mtpt) cc_final: 0.6404 (mtpt) REVERT: U 47 ARG cc_start: 0.5956 (ttp-110) cc_final: 0.5651 (mtm110) REVERT: c 35 GLU cc_start: 0.7197 (pt0) cc_final: 0.6893 (pm20) REVERT: c 108 LYS cc_start: 0.7993 (tttt) cc_final: 0.7678 (ttpm) REVERT: c 117 GLN cc_start: 0.7347 (tt0) cc_final: 0.6982 (tt0) REVERT: c 185 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6923 (mt-10) REVERT: c 269 ARG cc_start: 0.6610 (ttt90) cc_final: 0.6400 (ttp80) REVERT: d 30 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6946 (mt-10) REVERT: d 43 ASP cc_start: 0.6834 (m-30) cc_final: 0.6627 (m-30) REVERT: d 100 LEU cc_start: 0.7506 (tt) cc_final: 0.7190 (tp) REVERT: d 184 ARG cc_start: 0.6742 (mtm-85) cc_final: 0.6353 (mtm180) REVERT: d 200 ASP cc_start: 0.7434 (m-30) cc_final: 0.7213 (m-30) REVERT: e 18 THR cc_start: 0.7437 (t) cc_final: 0.7089 (m) REVERT: e 111 GLU cc_start: 0.7522 (tp30) cc_final: 0.7211 (tp30) REVERT: e 141 MET cc_start: 0.6682 (mtp) cc_final: 0.6442 (mtm) REVERT: e 150 THR cc_start: 0.7322 (p) cc_final: 0.6868 (m) REVERT: e 166 LYS cc_start: 0.6436 (mttp) cc_final: 0.5936 (mmtp) REVERT: e 170 ARG cc_start: 0.6847 (mmt90) cc_final: 0.6616 (mpt-90) REVERT: e 193 VAL cc_start: 0.7307 (t) cc_final: 0.7072 (t) REVERT: e 199 MET cc_start: 0.6310 (ttm) cc_final: 0.6013 (ttm) REVERT: f 3 LYS cc_start: 0.5662 (ttpt) cc_final: 0.4826 (mmmt) REVERT: f 17 MET cc_start: 0.5839 (mmm) cc_final: 0.5545 (mmt) REVERT: f 26 MET cc_start: 0.7432 (mmm) cc_final: 0.6092 (mmm) REVERT: f 47 LYS cc_start: 0.4232 (mppt) cc_final: 0.3988 (mmmm) REVERT: f 48 LYS cc_start: 0.5648 (mmmt) cc_final: 0.5119 (ttpt) REVERT: f 51 ASP cc_start: 0.6273 (m-30) cc_final: 0.5870 (m-30) REVERT: f 72 LYS cc_start: 0.6543 (ptmt) cc_final: 0.6307 (ptmm) REVERT: f 98 GLU cc_start: 0.6907 (mp0) cc_final: 0.6657 (mt-10) REVERT: f 101 GLU cc_start: 0.6821 (tt0) cc_final: 0.6520 (tm-30) REVERT: f 103 LEU cc_start: 0.6806 (tp) cc_final: 0.6387 (tm) REVERT: f 120 LYS cc_start: 0.6746 (ptpp) cc_final: 0.6458 (pptt) REVERT: f 130 MET cc_start: 0.6951 (ptm) cc_final: 0.6723 (ptm) REVERT: f 134 GLU cc_start: 0.6074 (mt-10) cc_final: 0.5822 (mt-10) REVERT: f 148 ARG cc_start: 0.5698 (mtp-110) cc_final: 0.4711 (ttp80) REVERT: f 167 ARG cc_start: 0.6554 (ttm110) cc_final: 0.5948 (ttm110) REVERT: g 69 ARG cc_start: 0.8143 (tmt170) cc_final: 0.7623 (tpt90) REVERT: g 74 SER cc_start: 0.7028 (m) cc_final: 0.6748 (t) REVERT: g 94 TYR cc_start: 0.7517 (m-10) cc_final: 0.7195 (m-10) REVERT: g 99 LYS cc_start: 0.5546 (tppp) cc_final: 0.4916 (pttt) REVERT: g 113 VAL cc_start: 0.6540 (p) cc_final: 0.6293 (m) REVERT: g 153 ARG cc_start: 0.6811 (mtt-85) cc_final: 0.6452 (mtt-85) REVERT: i 1 MET cc_start: 0.4994 (mtt) cc_final: 0.4759 (mpp) REVERT: i 34 ARG cc_start: 0.7715 (ttt-90) cc_final: 0.7471 (ttt-90) REVERT: i 85 LYS cc_start: 0.8189 (mttm) cc_final: 0.7874 (mmtm) REVERT: i 91 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7288 (mt-10) REVERT: i 95 ARG cc_start: 0.7024 (ttp-110) cc_final: 0.6641 (ttt90) REVERT: i 102 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7694 (mt-10) REVERT: i 118 MET cc_start: 0.8194 (mtt) cc_final: 0.7853 (mtt) REVERT: i 129 GLU cc_start: 0.6496 (mm-30) cc_final: 0.6213 (mt-10) REVERT: j 18 ARG cc_start: 0.7797 (mmm-85) cc_final: 0.7381 (mtp85) REVERT: j 29 HIS cc_start: 0.7524 (m-70) cc_final: 0.7141 (m170) REVERT: j 47 ILE cc_start: 0.7527 (pt) cc_final: 0.7149 (pp) REVERT: j 54 LYS cc_start: 0.7445 (tttt) cc_final: 0.7224 (tttt) REVERT: j 71 ARG cc_start: 0.7951 (mmt90) cc_final: 0.7681 (mmt90) REVERT: j 73 ASP cc_start: 0.7917 (p0) cc_final: 0.7516 (p0) REVERT: j 100 PHE cc_start: 0.8016 (m-80) cc_final: 0.7661 (m-80) REVERT: j 105 ARG cc_start: 0.6556 (mtp85) cc_final: 0.6085 (mtm-85) REVERT: j 111 LYS cc_start: 0.6731 (ptmt) cc_final: 0.6194 (ttpt) REVERT: k 76 GLU cc_start: 0.7809 (pt0) cc_final: 0.7253 (pt0) REVERT: k 92 LEU cc_start: 0.7109 (tp) cc_final: 0.6755 (tp) REVERT: k 129 LYS cc_start: 0.6779 (mtpp) cc_final: 0.6479 (mptt) REVERT: k 132 ARG cc_start: 0.7138 (ttt90) cc_final: 0.6936 (ttm-80) REVERT: l 6 ARG cc_start: 0.6862 (ptt90) cc_final: 0.6135 (ptm-80) REVERT: l 31 PHE cc_start: 0.8008 (m-80) cc_final: 0.7569 (m-10) REVERT: l 58 LYS cc_start: 0.7402 (mttm) cc_final: 0.7138 (mttt) REVERT: l 118 LYS cc_start: 0.7832 (ttpp) cc_final: 0.7390 (tttm) REVERT: l 127 LYS cc_start: 0.7431 (mtpp) cc_final: 0.7120 (mmmm) REVERT: l 136 MET cc_start: 0.5843 (ptp) cc_final: 0.5461 (ptp) REVERT: m 89 SER cc_start: 0.6844 (p) cc_final: 0.6493 (m) REVERT: n 13 ARG cc_start: 0.6683 (ttm-80) cc_final: 0.6441 (ttp80) REVERT: n 16 ARG cc_start: 0.6920 (mmp80) cc_final: 0.6587 (mmt-90) REVERT: n 17 LYS cc_start: 0.7904 (tptt) cc_final: 0.7585 (tptp) REVERT: n 46 GLU cc_start: 0.6277 (mm-30) cc_final: 0.5757 (mt-10) REVERT: n 108 ASP cc_start: 0.7205 (m-30) cc_final: 0.6958 (m-30) REVERT: o 6 LYS cc_start: 0.7020 (mtmm) cc_final: 0.6550 (mtmm) REVERT: o 7 GLN cc_start: 0.7028 (tm-30) cc_final: 0.6475 (tp40) REVERT: o 9 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6917 (mt-10) REVERT: o 38 LYS cc_start: 0.7218 (ptmt) cc_final: 0.6944 (ptmm) REVERT: o 68 GLU cc_start: 0.6104 (mm-30) cc_final: 0.5873 (mm-30) REVERT: o 88 ARG cc_start: 0.7783 (ttt-90) cc_final: 0.7358 (ttt-90) REVERT: o 89 ARG cc_start: 0.7107 (mtm-85) cc_final: 0.6543 (mtp-110) REVERT: o 111 LYS cc_start: 0.7050 (ttpp) cc_final: 0.6691 (ttpt) REVERT: o 112 GLU cc_start: 0.7269 (tt0) cc_final: 0.7042 (tt0) REVERT: o 113 ARG cc_start: 0.7225 (ttp-110) cc_final: 0.6810 (ttp80) REVERT: p 59 GLN cc_start: 0.8227 (mt0) cc_final: 0.7773 (tt0) REVERT: p 84 LYS cc_start: 0.7351 (tttm) cc_final: 0.6867 (tppt) REVERT: q 6 GLN cc_start: 0.7321 (mt0) cc_final: 0.6974 (mm-40) REVERT: q 40 MET cc_start: 0.7732 (ttm) cc_final: 0.7217 (ttm) REVERT: q 48 LYS cc_start: 0.7342 (mtpt) cc_final: 0.7077 (mttp) REVERT: q 84 ARG cc_start: 0.7534 (ttp-110) cc_final: 0.7329 (ttp-170) REVERT: r 31 GLN cc_start: 0.7005 (mt0) cc_final: 0.6766 (mt0) REVERT: r 77 ASP cc_start: 0.7798 (m-30) cc_final: 0.7511 (m-30) REVERT: s 27 SER cc_start: 0.7219 (m) cc_final: 0.6481 (p) REVERT: s 33 LYS cc_start: 0.7562 (tttm) cc_final: 0.7308 (tmtt) REVERT: s 73 ARG cc_start: 0.4614 (ttm110) cc_final: 0.4361 (ttm-80) REVERT: t 18 ASP cc_start: 0.7097 (m-30) cc_final: 0.6768 (m-30) REVERT: t 22 ARG cc_start: 0.6514 (mtp180) cc_final: 0.6164 (mtm180) REVERT: t 46 GLN cc_start: 0.6975 (tp-100) cc_final: 0.5996 (tt0) REVERT: t 91 LYS cc_start: 0.6386 (mmtt) cc_final: 0.5673 (mptt) REVERT: u 5 ASN cc_start: 0.7310 (m-40) cc_final: 0.7035 (m-40) REVERT: u 38 LEU cc_start: 0.7987 (tp) cc_final: 0.7632 (tt) REVERT: u 50 MET cc_start: 0.7427 (ttm) cc_final: 0.6950 (ttm) REVERT: u 76 ASP cc_start: 0.6760 (t70) cc_final: 0.6513 (t70) REVERT: u 85 LYS cc_start: 0.7887 (mtpp) cc_final: 0.7348 (mtmt) REVERT: u 90 ASP cc_start: 0.8013 (m-30) cc_final: 0.7426 (m-30) REVERT: v 3 HIS cc_start: 0.5399 (m170) cc_final: 0.5188 (m-70) REVERT: v 5 LYS cc_start: 0.6190 (mtpt) cc_final: 0.5713 (mtpt) REVERT: v 17 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7151 (tp30) REVERT: v 68 LYS cc_start: 0.7695 (tttp) cc_final: 0.7378 (tptm) REVERT: v 83 GLU cc_start: 0.7081 (pt0) cc_final: 0.6779 (pt0) REVERT: x 13 GLU cc_start: 0.5437 (pm20) cc_final: 0.5155 (mm-30) REVERT: x 23 ARG cc_start: 0.7210 (mtt90) cc_final: 0.6499 (ttp-110) REVERT: x 45 GLN cc_start: 0.6895 (mt0) cc_final: 0.6678 (mt0) REVERT: x 58 ASN cc_start: 0.6754 (t0) cc_final: 0.6193 (t0) REVERT: y 6 LYS cc_start: 0.7547 (mmtp) cc_final: 0.6968 (tppt) REVERT: y 56 LYS cc_start: 0.7720 (ttpt) cc_final: 0.7071 (tttt) REVERT: z 12 LYS cc_start: 0.8295 (mptt) cc_final: 0.8091 (tptt) REVERT: 0 25 LYS cc_start: 0.7935 (ttmt) cc_final: 0.7684 (ttpt) REVERT: 2 15 LYS cc_start: 0.7950 (mmtt) cc_final: 0.7402 (mttt) REVERT: 2 16 LYS cc_start: 0.7819 (tttt) cc_final: 0.7595 (tttm) REVERT: 3 34 LYS cc_start: 0.7958 (ptmt) cc_final: 0.7684 (pttt) REVERT: 4 26 SER cc_start: 0.6889 (p) cc_final: 0.6675 (t) outliers start: 2 outliers final: 0 residues processed: 1049 average time/residue: 2.3471 time to fit residues: 3426.3894 Evaluate side-chains 862 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 861 time to evaluate : 6.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 63 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 835 optimal weight: 3.9990 chunk 750 optimal weight: 3.9990 chunk 416 optimal weight: 7.9990 chunk 256 optimal weight: 8.9990 chunk 506 optimal weight: 4.9990 chunk 400 optimal weight: 10.0000 chunk 775 optimal weight: 8.9990 chunk 300 optimal weight: 2.9990 chunk 471 optimal weight: 30.0000 chunk 577 optimal weight: 0.9990 chunk 899 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN C 100 GLN C 139 GLN C 190 HIS D 54 GLN D 74 ASN D 85 ASN E 19 ASN F 3 HIS G 97 ASN G 142 HIS I 37 GLN J 20 GLN K 109 ASN O 37 ASN O 40 GLN P 29 ASN P 63 GLN R 74 HIS d 32 ASN f 27 GLN f 81 GLN g 73 ASN g 88 GLN g 104 ASN j 93 GLN k 54 GLN l 3 GLN n 38 GLN p 71 GLN q 86 GLN ** u 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 75 GLN 1 29 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 153997 Z= 0.195 Angle : 0.706 16.532 230462 Z= 0.386 Chirality : 0.037 0.375 29304 Planarity : 0.007 0.139 12266 Dihedral : 23.051 179.594 77234 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.41 % Favored : 96.51 % Rotamer: Outliers : 1.84 % Allowed : 8.31 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.25 (0.11), residues: 5480 helix: 1.43 (0.12), residues: 1863 sheet: -0.11 (0.15), residues: 1082 loop : -0.62 (0.12), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 201 HIS 0.007 0.001 HIS L 77 PHE 0.017 0.002 PHE H 45 TYR 0.018 0.002 TYR p 32 ARG 0.007 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 986 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 902 time to evaluate : 6.294 Fit side-chains REVERT: B 8 ASP cc_start: 0.3342 (p0) cc_final: 0.2195 (t70) REVERT: B 173 ILE cc_start: 0.5123 (mt) cc_final: 0.4686 (mm) REVERT: B 174 LYS cc_start: 0.3822 (tptp) cc_final: 0.3136 (tptm) REVERT: C 28 GLU cc_start: 0.6290 (pm20) cc_final: 0.5923 (pm20) REVERT: C 41 GLN cc_start: 0.6795 (tt0) cc_final: 0.6257 (tt0) REVERT: C 49 LYS cc_start: 0.6372 (mtpp) cc_final: 0.5939 (mmmt) REVERT: C 58 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6654 (mt-10) REVERT: C 86 LYS cc_start: 0.6657 (mtmm) cc_final: 0.6228 (ttpp) REVERT: C 110 GLU cc_start: 0.5796 (mp0) cc_final: 0.5530 (mm-30) REVERT: C 132 ARG cc_start: 0.5715 (mtp180) cc_final: 0.5157 (ttm170) REVERT: C 142 MET cc_start: 0.7246 (mmm) cc_final: 0.6979 (mmp) REVERT: C 154 SER cc_start: 0.8399 (OUTLIER) cc_final: 0.8132 (m) REVERT: D 8 LYS cc_start: 0.5666 (mmtp) cc_final: 0.5028 (mmtp) REVERT: D 45 LYS cc_start: 0.5483 (mtmm) cc_final: 0.4728 (mptm) REVERT: D 71 GLN cc_start: 0.7637 (tt0) cc_final: 0.7396 (tt0) REVERT: D 83 LYS cc_start: 0.6441 (mmtp) cc_final: 0.5706 (mttt) REVERT: D 128 ARG cc_start: 0.5087 (ttm110) cc_final: 0.4502 (ttp80) REVERT: D 159 LEU cc_start: 0.5131 (tt) cc_final: 0.4769 (mt) REVERT: D 204 TYR cc_start: 0.7475 (m-80) cc_final: 0.7199 (m-80) REVERT: E 14 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7900 (ttmm) REVERT: E 26 LYS cc_start: 0.7625 (ttmt) cc_final: 0.7332 (ttpt) REVERT: E 45 ARG cc_start: 0.7256 (mtp85) cc_final: 0.6520 (mtm180) REVERT: E 48 PHE cc_start: 0.8183 (p90) cc_final: 0.7463 (p90) REVERT: E 70 ASN cc_start: 0.6485 (m-40) cc_final: 0.6221 (m-40) REVERT: E 134 ILE cc_start: 0.7722 (mt) cc_final: 0.7493 (mt) REVERT: E 146 ASN cc_start: 0.6604 (m-40) cc_final: 0.6301 (m110) REVERT: F 8 PHE cc_start: 0.7593 (p90) cc_final: 0.7220 (p90) REVERT: F 55 HIS cc_start: 0.7019 (m-70) cc_final: 0.6765 (m170) REVERT: F 56 LYS cc_start: 0.6885 (mttp) cc_final: 0.6488 (mmtm) REVERT: F 79 ARG cc_start: 0.6281 (ttm-80) cc_final: 0.5002 (ttp-110) REVERT: F 90 MET cc_start: 0.6608 (mtp) cc_final: 0.6050 (mtm) REVERT: F 92 THR cc_start: 0.6527 (m) cc_final: 0.6127 (p) REVERT: G 11 LYS cc_start: 0.6103 (mtpp) cc_final: 0.5507 (pttm) REVERT: G 41 SER cc_start: 0.7534 (m) cc_final: 0.7305 (m) REVERT: G 58 GLU cc_start: 0.4541 (mp0) cc_final: 0.4154 (mt-10) REVERT: G 63 GLU cc_start: 0.6002 (mm-30) cc_final: 0.5600 (mm-30) REVERT: G 74 GLU cc_start: 0.6142 (pt0) cc_final: 0.5894 (pt0) REVERT: G 106 GLU cc_start: 0.7260 (tt0) cc_final: 0.6670 (mm-30) REVERT: G 118 LEU cc_start: 0.7320 (tp) cc_final: 0.6577 (mm) REVERT: G 123 GLU cc_start: 0.6473 (tp30) cc_final: 0.6107 (mm-30) REVERT: H 18 GLN cc_start: 0.7941 (mm110) cc_final: 0.7511 (mm-40) REVERT: H 21 ASN cc_start: 0.7740 (m110) cc_final: 0.7423 (m110) REVERT: I 36 GLU cc_start: 0.6273 (mm-30) cc_final: 0.5841 (mm-30) REVERT: I 57 MET cc_start: 0.6235 (mtp) cc_final: 0.5193 (tpp) REVERT: I 72 ILE cc_start: 0.6954 (mt) cc_final: 0.6744 (mp) REVERT: I 119 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6852 (mtm-85) REVERT: J 66 GLU cc_start: 0.7406 (pt0) cc_final: 0.7130 (pt0) REVERT: J 88 MET cc_start: 0.3438 (mmp) cc_final: 0.3157 (mmt) REVERT: K 37 ARG cc_start: 0.6430 (mmm-85) cc_final: 0.5763 (mtp180) REVERT: K 56 ARG cc_start: 0.6963 (mtp-110) cc_final: 0.6727 (mtm-85) REVERT: K 68 GLU cc_start: 0.6614 (mt-10) cc_final: 0.6327 (mt-10) REVERT: K 69 ARG cc_start: 0.6385 (mtp180) cc_final: 0.5669 (mtp-110) REVERT: K 85 MET cc_start: 0.7345 (mmm) cc_final: 0.6942 (mtm) REVERT: K 98 ARG cc_start: 0.6490 (mtt90) cc_final: 0.6290 (mtt-85) REVERT: K 106 ARG cc_start: 0.5435 (ttp-110) cc_final: 0.4581 (ptp-170) REVERT: L 30 LYS cc_start: 0.7938 (mmtt) cc_final: 0.7610 (mmtm) REVERT: L 62 GLU cc_start: 0.7266 (tt0) cc_final: 0.7028 (tt0) REVERT: M 7 ILE cc_start: 0.7282 (pt) cc_final: 0.6848 (pp) REVERT: M 45 ILE cc_start: 0.7153 (mm) cc_final: 0.6720 (mm) REVERT: M 72 GLU cc_start: 0.6126 (pt0) cc_final: 0.5389 (mp0) REVERT: M 79 ARG cc_start: 0.6475 (ttt-90) cc_final: 0.5921 (tmt170) REVERT: M 86 TYR cc_start: 0.6926 (t80) cc_final: 0.6596 (t80) REVERT: N 16 LEU cc_start: 0.7223 (mt) cc_final: 0.6958 (mt) REVERT: N 21 PHE cc_start: 0.6425 (t80) cc_final: 0.6031 (t80) REVERT: N 41 ARG cc_start: 0.5698 (mtm-85) cc_final: 0.5025 (ttm110) REVERT: N 47 LYS cc_start: 0.5801 (tptp) cc_final: 0.5111 (mptt) REVERT: N 51 LEU cc_start: 0.6003 (OUTLIER) cc_final: 0.5407 (mt) REVERT: N 90 ARG cc_start: 0.7151 (mtm-85) cc_final: 0.6947 (mtm110) REVERT: O 10 LYS cc_start: 0.6684 (mtpp) cc_final: 0.5925 (mptt) REVERT: O 26 GLU cc_start: 0.6699 (mp0) cc_final: 0.6412 (mp0) REVERT: O 57 LEU cc_start: 0.8317 (mm) cc_final: 0.7811 (mt) REVERT: O 62 GLN cc_start: 0.6998 (tt0) cc_final: 0.6560 (mm110) REVERT: O 68 ASP cc_start: 0.7165 (m-30) cc_final: 0.6659 (m-30) REVERT: O 69 TYR cc_start: 0.8298 (t80) cc_final: 0.8017 (t80) REVERT: O 72 ARG cc_start: 0.6583 (ttm110) cc_final: 0.6373 (ttp-110) REVERT: O 78 TYR cc_start: 0.6542 (t80) cc_final: 0.5973 (t80) REVERT: P 32 PHE cc_start: 0.7898 (p90) cc_final: 0.7411 (p90) REVERT: P 35 ARG cc_start: 0.7237 (ttt-90) cc_final: 0.6985 (ttt-90) REVERT: P 71 VAL cc_start: 0.7292 (p) cc_final: 0.7080 (m) REVERT: Q 11 ARG cc_start: 0.6059 (mtp-110) cc_final: 0.5496 (mtp180) REVERT: Q 44 LEU cc_start: 0.7928 (mt) cc_final: 0.7600 (mt) REVERT: Q 75 LEU cc_start: 0.6581 (tp) cc_final: 0.6362 (tt) REVERT: R 42 SER cc_start: 0.7605 (m) cc_final: 0.7352 (p) REVERT: R 57 ARG cc_start: 0.6974 (ttm110) cc_final: 0.6383 (mtp180) REVERT: R 73 ARG cc_start: 0.5511 (ttp-110) cc_final: 0.5001 (ptm-80) REVERT: S 56 GLN cc_start: 0.6358 (OUTLIER) cc_final: 0.6135 (pt0) REVERT: T 13 GLN cc_start: 0.6844 (tt0) cc_final: 0.6563 (tt0) REVERT: T 18 ARG cc_start: 0.7405 (ttp80) cc_final: 0.7099 (ttp80) REVERT: T 20 HIS cc_start: 0.6675 (t-90) cc_final: 0.6451 (t-90) REVERT: T 24 ARG cc_start: 0.6508 (mmm160) cc_final: 0.6064 (mmt90) REVERT: T 28 MET cc_start: 0.6913 (ttp) cc_final: 0.6567 (tmm) REVERT: T 29 ARG cc_start: 0.6826 (mtm-85) cc_final: 0.6198 (mtm-85) REVERT: T 54 MET cc_start: 0.6781 (tmm) cc_final: 0.6293 (tmm) REVERT: U 38 TYR cc_start: 0.8196 (t80) cc_final: 0.7898 (t80) REVERT: U 40 LYS cc_start: 0.6847 (mtpt) cc_final: 0.6546 (mtpt) REVERT: c 97 LYS cc_start: 0.7182 (ttmm) cc_final: 0.6815 (mmtt) REVERT: c 108 LYS cc_start: 0.8012 (tttt) cc_final: 0.7795 (ttpm) REVERT: c 117 GLN cc_start: 0.7169 (tt0) cc_final: 0.6943 (tt0) REVERT: c 185 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6805 (mt-10) REVERT: c 187 ASP cc_start: 0.7290 (m-30) cc_final: 0.7078 (m-30) REVERT: d 128 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7241 (mmp-170) REVERT: e 18 THR cc_start: 0.7345 (t) cc_final: 0.6828 (m) REVERT: e 111 GLU cc_start: 0.7388 (tp30) cc_final: 0.6936 (tp30) REVERT: e 132 LYS cc_start: 0.7082 (pttp) cc_final: 0.6845 (pttt) REVERT: e 166 LYS cc_start: 0.6624 (mttp) cc_final: 0.5994 (mmtp) REVERT: e 193 VAL cc_start: 0.7370 (t) cc_final: 0.7065 (t) REVERT: e 197 GLU cc_start: 0.6227 (pt0) cc_final: 0.5816 (pt0) REVERT: f 3 LYS cc_start: 0.5629 (ttpt) cc_final: 0.4825 (mmmt) REVERT: f 17 MET cc_start: 0.5858 (mmm) cc_final: 0.5545 (mmm) REVERT: f 48 LYS cc_start: 0.5849 (mmmt) cc_final: 0.5400 (ttpp) REVERT: f 51 ASP cc_start: 0.6323 (m-30) cc_final: 0.5435 (OUTLIER) REVERT: f 98 GLU cc_start: 0.6829 (mp0) cc_final: 0.6399 (mt-10) REVERT: f 101 GLU cc_start: 0.6682 (tt0) cc_final: 0.6402 (tm-30) REVERT: f 103 LEU cc_start: 0.6898 (tp) cc_final: 0.6449 (tm) REVERT: f 120 LYS cc_start: 0.6682 (ptpp) cc_final: 0.6387 (pptt) REVERT: f 134 GLU cc_start: 0.5971 (mt-10) cc_final: 0.5701 (mt-10) REVERT: f 148 ARG cc_start: 0.5773 (mtp-110) cc_final: 0.5083 (ptm-80) REVERT: f 167 ARG cc_start: 0.6506 (ttm110) cc_final: 0.5990 (ttm110) REVERT: g 69 ARG cc_start: 0.8064 (tmt170) cc_final: 0.7790 (tpt90) REVERT: g 74 SER cc_start: 0.6864 (m) cc_final: 0.6627 (t) REVERT: g 94 TYR cc_start: 0.7503 (m-10) cc_final: 0.7235 (m-10) REVERT: g 99 LYS cc_start: 0.5539 (tppp) cc_final: 0.4848 (pttt) REVERT: g 113 VAL cc_start: 0.6493 (p) cc_final: 0.6142 (m) REVERT: g 153 ARG cc_start: 0.6688 (mtt-85) cc_final: 0.6371 (mtt-85) REVERT: i 91 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7247 (mt-10) REVERT: i 95 ARG cc_start: 0.6934 (ttp-110) cc_final: 0.6378 (ttt90) REVERT: i 102 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7643 (mt-10) REVERT: j 18 ARG cc_start: 0.7831 (mmm-85) cc_final: 0.7522 (mtp85) REVERT: j 29 HIS cc_start: 0.7433 (m-70) cc_final: 0.7085 (m170) REVERT: j 54 LYS cc_start: 0.7430 (tttt) cc_final: 0.7204 (tttt) REVERT: j 73 ASP cc_start: 0.7946 (p0) cc_final: 0.7588 (p0) REVERT: j 117 SER cc_start: 0.7044 (p) cc_final: 0.6677 (m) REVERT: k 55 MET cc_start: 0.8557 (tpp) cc_final: 0.8216 (tpp) REVERT: k 76 GLU cc_start: 0.7873 (pt0) cc_final: 0.7649 (pt0) REVERT: k 84 LYS cc_start: 0.7452 (ptpt) cc_final: 0.6943 (ptmt) REVERT: k 129 LYS cc_start: 0.6715 (mtpp) cc_final: 0.6391 (mptt) REVERT: l 6 ARG cc_start: 0.7004 (ptt90) cc_final: 0.6678 (ptm-80) REVERT: l 58 LYS cc_start: 0.7377 (mttm) cc_final: 0.7108 (mttt) REVERT: l 90 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7398 (mm-30) REVERT: l 110 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6619 (tt0) REVERT: l 112 LEU cc_start: 0.7211 (tp) cc_final: 0.7005 (tp) REVERT: l 118 LYS cc_start: 0.7817 (ttpp) cc_final: 0.7422 (tttm) REVERT: l 127 LYS cc_start: 0.7456 (mtpp) cc_final: 0.6973 (mtpp) REVERT: m 89 SER cc_start: 0.6938 (p) cc_final: 0.6605 (m) REVERT: n 16 ARG cc_start: 0.6895 (mmp80) cc_final: 0.6552 (mmt-90) REVERT: n 46 GLU cc_start: 0.6516 (mm-30) cc_final: 0.5818 (mt-10) REVERT: n 62 LEU cc_start: 0.7071 (mt) cc_final: 0.6868 (mt) REVERT: n 108 ASP cc_start: 0.7219 (m-30) cc_final: 0.6966 (m-30) REVERT: o 6 LYS cc_start: 0.6948 (mtmm) cc_final: 0.6394 (mtmm) REVERT: o 7 GLN cc_start: 0.7158 (tm-30) cc_final: 0.6494 (tp40) REVERT: o 37 LYS cc_start: 0.5869 (ptpt) cc_final: 0.5462 (ptpp) REVERT: o 38 LYS cc_start: 0.7227 (ptmt) cc_final: 0.6990 (ptmm) REVERT: o 68 GLU cc_start: 0.6123 (mm-30) cc_final: 0.5827 (mm-30) REVERT: o 87 LYS cc_start: 0.7793 (mmtt) cc_final: 0.7184 (mmtp) REVERT: o 89 ARG cc_start: 0.7042 (mtm-85) cc_final: 0.6523 (mtp-110) REVERT: o 111 LYS cc_start: 0.7035 (ttpp) cc_final: 0.6653 (ttpt) REVERT: o 112 GLU cc_start: 0.7163 (tt0) cc_final: 0.6905 (tt0) REVERT: p 11 ARG cc_start: 0.8011 (ttp-110) cc_final: 0.7682 (ttp-110) REVERT: p 13 ARG cc_start: 0.7577 (mtp85) cc_final: 0.7222 (mtt-85) REVERT: p 59 GLN cc_start: 0.8149 (mt0) cc_final: 0.7814 (tt0) REVERT: p 84 LYS cc_start: 0.7567 (tttm) cc_final: 0.6938 (tppt) REVERT: q 18 GLN cc_start: 0.7028 (mt0) cc_final: 0.6824 (mt0) REVERT: q 40 MET cc_start: 0.7730 (ttm) cc_final: 0.7314 (ttm) REVERT: r 31 GLN cc_start: 0.6895 (mt0) cc_final: 0.6683 (mt0) REVERT: r 77 ASP cc_start: 0.7988 (m-30) cc_final: 0.7666 (m-30) REVERT: s 73 ARG cc_start: 0.4716 (ttm110) cc_final: 0.4424 (ttm110) REVERT: t 18 ASP cc_start: 0.7011 (m-30) cc_final: 0.6700 (m-30) REVERT: t 46 GLN cc_start: 0.6943 (tp-100) cc_final: 0.6631 (tp40) REVERT: t 91 LYS cc_start: 0.6224 (mmtt) cc_final: 0.5451 (mptt) REVERT: u 5 ASN cc_start: 0.7437 (m-40) cc_final: 0.7086 (m-40) REVERT: u 12 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6387 (mp10) REVERT: u 43 ASP cc_start: 0.7008 (t70) cc_final: 0.6778 (t0) REVERT: u 50 MET cc_start: 0.7366 (ttm) cc_final: 0.6910 (ttm) REVERT: u 76 ASP cc_start: 0.6691 (t70) cc_final: 0.6490 (t70) REVERT: u 85 LYS cc_start: 0.7791 (mtpp) cc_final: 0.7318 (mtmt) REVERT: u 90 ASP cc_start: 0.8038 (m-30) cc_final: 0.7499 (m-30) REVERT: v 5 LYS cc_start: 0.6287 (mtpt) cc_final: 0.5889 (mtpt) REVERT: v 17 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7149 (tp30) REVERT: v 25 ARG cc_start: 0.7453 (mmt-90) cc_final: 0.7017 (mmt180) REVERT: v 68 LYS cc_start: 0.7638 (tttp) cc_final: 0.7424 (tttm) REVERT: v 83 GLU cc_start: 0.7025 (pt0) cc_final: 0.6709 (pt0) REVERT: x 5 GLU cc_start: 0.6033 (mm-30) cc_final: 0.5492 (mp0) REVERT: x 13 GLU cc_start: 0.5537 (pm20) cc_final: 0.5263 (mm-30) REVERT: x 23 ARG cc_start: 0.7233 (mtt90) cc_final: 0.6502 (ttp-110) REVERT: x 45 GLN cc_start: 0.6996 (mt0) cc_final: 0.6763 (mt0) REVERT: y 6 LYS cc_start: 0.7688 (mmtp) cc_final: 0.7046 (tppt) REVERT: y 19 LYS cc_start: 0.7030 (mttm) cc_final: 0.6744 (mtpt) REVERT: y 56 LYS cc_start: 0.7654 (ttpt) cc_final: 0.7047 (tttt) REVERT: 0 10 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7412 (tttt) REVERT: 0 28 ARG cc_start: 0.6243 (mpp80) cc_final: 0.6001 (mpt90) REVERT: 0 35 GLU cc_start: 0.6905 (tt0) cc_final: 0.6635 (tm-30) REVERT: 1 41 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6711 (mtp180) REVERT: 2 15 LYS cc_start: 0.7865 (mmtt) cc_final: 0.7367 (mttt) REVERT: 2 59 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7654 (mt) REVERT: 3 9 LYS cc_start: 0.7966 (mttp) cc_final: 0.7757 (mttm) REVERT: 3 34 LYS cc_start: 0.7970 (ptmt) cc_final: 0.7669 (pttt) outliers start: 84 outliers final: 36 residues processed: 939 average time/residue: 2.3712 time to fit residues: 3097.3781 Evaluate side-chains 900 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 855 time to evaluate : 5.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 119 ARG Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain S residue 56 GLN Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 202 ILE Chi-restraints excluded: chain f residue 73 SER Chi-restraints excluded: chain f residue 111 ILE Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 161 LYS Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain m residue 36 THR Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain u residue 8 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 1 residue 41 ARG Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 4 residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 499 optimal weight: 10.0000 chunk 279 optimal weight: 9.9990 chunk 748 optimal weight: 8.9990 chunk 612 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 900 optimal weight: 10.0000 chunk 972 optimal weight: 8.9990 chunk 802 optimal weight: 0.0980 chunk 893 optimal weight: 0.9980 chunk 307 optimal weight: 2.9990 chunk 722 optimal weight: 0.6980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 GLN C 139 GLN C 190 HIS D 54 GLN F 3 HIS G 142 HIS P 29 ASN Q 47 HIS R 54 GLN T 21 ASN d 32 ASN g 22 GLN g 73 ASN g 88 GLN g 116 GLN j 89 ASN j 93 GLN l 22 GLN n 38 GLN p 71 GLN q 6 GLN q 86 GLN u 75 GLN 1 29 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 153997 Z= 0.137 Angle : 0.622 14.318 230462 Z= 0.352 Chirality : 0.034 0.386 29304 Planarity : 0.007 0.130 12266 Dihedral : 22.920 178.470 77231 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.36 % Favored : 96.57 % Rotamer: Outliers : 1.73 % Allowed : 11.10 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.59 (0.11), residues: 5480 helix: 1.79 (0.12), residues: 1861 sheet: 0.01 (0.15), residues: 1099 loop : -0.45 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 201 HIS 0.006 0.001 HIS L 77 PHE 0.017 0.001 PHE B 90 TYR 0.014 0.001 TYR C 42 ARG 0.009 0.000 ARG R 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 897 time to evaluate : 6.257 Fit side-chains revert: symmetry clash REVERT: B 8 ASP cc_start: 0.3118 (p0) cc_final: 0.2039 (t70) REVERT: B 27 MET cc_start: 0.3589 (tpp) cc_final: 0.2835 (tpt) REVERT: B 173 ILE cc_start: 0.5078 (mt) cc_final: 0.4654 (mm) REVERT: B 174 LYS cc_start: 0.3771 (tptp) cc_final: 0.3130 (tptm) REVERT: C 28 GLU cc_start: 0.6239 (pm20) cc_final: 0.5812 (pm20) REVERT: C 41 GLN cc_start: 0.6748 (tt0) cc_final: 0.6227 (tt0) REVERT: C 49 LYS cc_start: 0.6126 (mtpp) cc_final: 0.5709 (mmmm) REVERT: C 58 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6686 (mt-10) REVERT: C 86 LYS cc_start: 0.6657 (mtmm) cc_final: 0.6229 (ttpp) REVERT: C 110 GLU cc_start: 0.5774 (mp0) cc_final: 0.5222 (mm-30) REVERT: C 129 MET cc_start: 0.5718 (mmm) cc_final: 0.5334 (mtp) REVERT: C 132 ARG cc_start: 0.5721 (mtp180) cc_final: 0.5176 (ttm170) REVERT: C 142 MET cc_start: 0.7180 (mmm) cc_final: 0.6952 (mmp) REVERT: D 8 LYS cc_start: 0.5651 (mmtp) cc_final: 0.4978 (mmtp) REVERT: D 45 LYS cc_start: 0.5578 (mtmm) cc_final: 0.4849 (mmtp) REVERT: D 83 LYS cc_start: 0.6479 (mmtp) cc_final: 0.5749 (mttt) REVERT: D 128 ARG cc_start: 0.5038 (ttm110) cc_final: 0.4459 (ttp80) REVERT: D 159 LEU cc_start: 0.5119 (tt) cc_final: 0.4705 (mt) REVERT: D 204 TYR cc_start: 0.7442 (m-80) cc_final: 0.7202 (m-80) REVERT: E 14 LYS cc_start: 0.8123 (ttmm) cc_final: 0.7908 (ttmm) REVERT: E 26 LYS cc_start: 0.7644 (ttmt) cc_final: 0.7327 (ttpt) REVERT: E 45 ARG cc_start: 0.7131 (mtp85) cc_final: 0.6454 (mtm180) REVERT: E 48 PHE cc_start: 0.8172 (p90) cc_final: 0.7878 (p90) REVERT: E 70 ASN cc_start: 0.6579 (m-40) cc_final: 0.6340 (m-40) REVERT: E 146 ASN cc_start: 0.6550 (m-40) cc_final: 0.6246 (m-40) REVERT: F 8 PHE cc_start: 0.7590 (p90) cc_final: 0.7209 (p90) REVERT: F 55 HIS cc_start: 0.6999 (m-70) cc_final: 0.6709 (m-70) REVERT: F 56 LYS cc_start: 0.6928 (mttp) cc_final: 0.6562 (mmmm) REVERT: F 92 THR cc_start: 0.6624 (m) cc_final: 0.6041 (p) REVERT: G 41 SER cc_start: 0.7431 (m) cc_final: 0.7198 (m) REVERT: G 58 GLU cc_start: 0.4555 (mp0) cc_final: 0.4098 (mt-10) REVERT: G 63 GLU cc_start: 0.5945 (mm-30) cc_final: 0.5510 (mm-30) REVERT: G 74 GLU cc_start: 0.6096 (pt0) cc_final: 0.5868 (pt0) REVERT: G 78 ARG cc_start: 0.4201 (tpp-160) cc_final: 0.3991 (ttm-80) REVERT: G 106 GLU cc_start: 0.7210 (tt0) cc_final: 0.6587 (mm-30) REVERT: G 118 LEU cc_start: 0.7275 (tp) cc_final: 0.6574 (mm) REVERT: G 123 GLU cc_start: 0.6505 (tp30) cc_final: 0.6081 (mm-30) REVERT: H 18 GLN cc_start: 0.7963 (mm110) cc_final: 0.7493 (mm110) REVERT: H 21 ASN cc_start: 0.7696 (m110) cc_final: 0.7344 (m110) REVERT: I 21 ILE cc_start: 0.6687 (mt) cc_final: 0.6384 (mm) REVERT: I 36 GLU cc_start: 0.6273 (mm-30) cc_final: 0.5843 (mm-30) REVERT: I 57 MET cc_start: 0.6255 (mtp) cc_final: 0.5217 (tpp) REVERT: I 72 ILE cc_start: 0.7002 (mt) cc_final: 0.6765 (mp) REVERT: I 97 GLU cc_start: 0.5154 (pm20) cc_final: 0.4898 (mm-30) REVERT: J 16 ARG cc_start: 0.5930 (mtm-85) cc_final: 0.5607 (mtp-110) REVERT: J 66 GLU cc_start: 0.7399 (pt0) cc_final: 0.7129 (pt0) REVERT: J 71 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7911 (tt) REVERT: J 88 MET cc_start: 0.3147 (mmp) cc_final: 0.2881 (mmt) REVERT: K 37 ARG cc_start: 0.6381 (mmm-85) cc_final: 0.5527 (mtp180) REVERT: K 56 ARG cc_start: 0.6912 (mtp-110) cc_final: 0.6683 (mtm-85) REVERT: K 69 ARG cc_start: 0.6321 (mtp180) cc_final: 0.5845 (mtp-110) REVERT: K 98 ARG cc_start: 0.6498 (mtt90) cc_final: 0.6155 (mtt-85) REVERT: K 106 ARG cc_start: 0.5332 (ttp-110) cc_final: 0.4558 (ptp-170) REVERT: L 20 ASN cc_start: 0.7507 (m-40) cc_final: 0.7176 (m110) REVERT: L 30 LYS cc_start: 0.7883 (mmtt) cc_final: 0.7648 (mmtm) REVERT: L 62 GLU cc_start: 0.7273 (tt0) cc_final: 0.7035 (tt0) REVERT: M 7 ILE cc_start: 0.7280 (pt) cc_final: 0.6910 (pp) REVERT: M 72 GLU cc_start: 0.6128 (pt0) cc_final: 0.5413 (mp0) REVERT: M 79 ARG cc_start: 0.6446 (ttt-90) cc_final: 0.5901 (tmt170) REVERT: M 86 TYR cc_start: 0.6984 (t80) cc_final: 0.6644 (t80) REVERT: N 16 LEU cc_start: 0.7240 (mt) cc_final: 0.6980 (mt) REVERT: N 21 PHE cc_start: 0.6427 (t80) cc_final: 0.6007 (t80) REVERT: N 23 LYS cc_start: 0.6452 (tttt) cc_final: 0.5966 (ttmm) REVERT: N 41 ARG cc_start: 0.5716 (mtm-85) cc_final: 0.4974 (ttm110) REVERT: N 47 LYS cc_start: 0.5682 (tptp) cc_final: 0.5077 (mptt) REVERT: N 51 LEU cc_start: 0.5890 (OUTLIER) cc_final: 0.4989 (mt) REVERT: O 10 LYS cc_start: 0.6694 (mtpp) cc_final: 0.6063 (mptt) REVERT: O 26 GLU cc_start: 0.6707 (mp0) cc_final: 0.6416 (mp0) REVERT: O 57 LEU cc_start: 0.8271 (mm) cc_final: 0.7778 (mt) REVERT: O 62 GLN cc_start: 0.6991 (tt0) cc_final: 0.6562 (mm110) REVERT: O 68 ASP cc_start: 0.7124 (m-30) cc_final: 0.6587 (m-30) REVERT: O 69 TYR cc_start: 0.8325 (t80) cc_final: 0.8056 (t80) REVERT: O 82 ILE cc_start: 0.6862 (pt) cc_final: 0.6175 (mm) REVERT: P 32 PHE cc_start: 0.7865 (p90) cc_final: 0.7424 (p90) REVERT: P 35 ARG cc_start: 0.7210 (ttt-90) cc_final: 0.6954 (ttt-90) REVERT: P 71 VAL cc_start: 0.7266 (p) cc_final: 0.7048 (m) REVERT: Q 11 ARG cc_start: 0.6100 (mtp-110) cc_final: 0.5621 (mtt180) REVERT: Q 44 LEU cc_start: 0.7862 (mt) cc_final: 0.7552 (mt) REVERT: Q 75 LEU cc_start: 0.6564 (tp) cc_final: 0.6363 (tt) REVERT: R 42 SER cc_start: 0.7615 (m) cc_final: 0.7338 (p) REVERT: R 57 ARG cc_start: 0.6940 (ttm110) cc_final: 0.6416 (mtp180) REVERT: R 73 ARG cc_start: 0.5517 (ttp-110) cc_final: 0.4890 (ptm-80) REVERT: S 47 LEU cc_start: 0.6719 (mt) cc_final: 0.6165 (mt) REVERT: S 56 GLN cc_start: 0.6341 (pt0) cc_final: 0.6129 (pt0) REVERT: T 24 ARG cc_start: 0.6607 (mmm160) cc_final: 0.6163 (mmt90) REVERT: T 29 ARG cc_start: 0.6821 (mtm-85) cc_final: 0.6151 (mtm-85) REVERT: T 54 MET cc_start: 0.6717 (tmm) cc_final: 0.6208 (tmm) REVERT: T 79 LEU cc_start: 0.7125 (mt) cc_final: 0.6835 (mp) REVERT: U 38 TYR cc_start: 0.8154 (t80) cc_final: 0.7892 (t80) REVERT: U 40 LYS cc_start: 0.6879 (mtpt) cc_final: 0.6548 (mtpt) REVERT: c 97 LYS cc_start: 0.7113 (ttmm) cc_final: 0.6822 (mmtt) REVERT: c 117 GLN cc_start: 0.7208 (tt0) cc_final: 0.6982 (tt0) REVERT: c 185 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6840 (mt-10) REVERT: c 187 ASP cc_start: 0.7251 (m-30) cc_final: 0.7044 (m-30) REVERT: d 128 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7007 (mmp-170) REVERT: d 200 ASP cc_start: 0.7415 (m-30) cc_final: 0.7182 (m-30) REVERT: e 132 LYS cc_start: 0.7104 (pttp) cc_final: 0.6884 (pttt) REVERT: e 166 LYS cc_start: 0.6642 (mttp) cc_final: 0.6033 (mmtp) REVERT: f 17 MET cc_start: 0.5767 (mmm) cc_final: 0.5442 (mmm) REVERT: f 48 LYS cc_start: 0.5787 (mmmt) cc_final: 0.5325 (ttpp) REVERT: f 83 TYR cc_start: 0.5921 (m-10) cc_final: 0.5109 (t80) REVERT: f 98 GLU cc_start: 0.6868 (mp0) cc_final: 0.6382 (mt-10) REVERT: f 101 GLU cc_start: 0.6729 (tt0) cc_final: 0.6433 (tm-30) REVERT: f 103 LEU cc_start: 0.6928 (tp) cc_final: 0.6458 (tm) REVERT: f 120 LYS cc_start: 0.6718 (ptpp) cc_final: 0.6407 (pptt) REVERT: f 134 GLU cc_start: 0.6004 (mt-10) cc_final: 0.5747 (mt-10) REVERT: f 148 ARG cc_start: 0.5730 (mtp-110) cc_final: 0.5122 (ptm-80) REVERT: f 167 ARG cc_start: 0.6495 (ttm110) cc_final: 0.5584 (ttp-170) REVERT: g 44 LYS cc_start: 0.3829 (tppt) cc_final: 0.3064 (mmtp) REVERT: g 69 ARG cc_start: 0.7919 (tmt170) cc_final: 0.7676 (tpt90) REVERT: g 74 SER cc_start: 0.6856 (m) cc_final: 0.6631 (t) REVERT: g 94 TYR cc_start: 0.7423 (m-10) cc_final: 0.7142 (m-10) REVERT: g 99 LYS cc_start: 0.5683 (tppp) cc_final: 0.4958 (pttt) REVERT: g 153 ARG cc_start: 0.6655 (mtt-85) cc_final: 0.6427 (mtt-85) REVERT: i 91 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7286 (mt-10) REVERT: i 95 ARG cc_start: 0.6938 (ttp-110) cc_final: 0.6303 (ttt90) REVERT: i 102 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7605 (mt-10) REVERT: j 18 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7546 (mtp85) REVERT: j 29 HIS cc_start: 0.7349 (m-70) cc_final: 0.6965 (m-70) REVERT: j 47 ILE cc_start: 0.7613 (pt) cc_final: 0.7227 (pp) REVERT: j 54 LYS cc_start: 0.7403 (tttt) cc_final: 0.7168 (tttt) REVERT: j 73 ASP cc_start: 0.7901 (p0) cc_final: 0.7672 (p0) REVERT: j 100 PHE cc_start: 0.7951 (m-80) cc_final: 0.7678 (m-80) REVERT: j 117 SER cc_start: 0.7098 (p) cc_final: 0.6766 (m) REVERT: k 55 MET cc_start: 0.8587 (tpp) cc_final: 0.8323 (tpp) REVERT: k 76 GLU cc_start: 0.7857 (pt0) cc_final: 0.7629 (pt0) REVERT: k 84 LYS cc_start: 0.7410 (ptpt) cc_final: 0.6883 (ptmt) REVERT: k 129 LYS cc_start: 0.6630 (mtpp) cc_final: 0.6350 (mptt) REVERT: l 6 ARG cc_start: 0.7046 (ptt90) cc_final: 0.6720 (ptm-80) REVERT: l 30 SER cc_start: 0.8174 (m) cc_final: 0.7778 (p) REVERT: l 58 LYS cc_start: 0.7315 (mttm) cc_final: 0.7055 (mttt) REVERT: l 90 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7366 (mm-30) REVERT: l 112 LEU cc_start: 0.7243 (tp) cc_final: 0.6925 (tp) REVERT: l 118 LYS cc_start: 0.7823 (ttpp) cc_final: 0.7431 (tttm) REVERT: l 126 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7339 (mt) REVERT: l 127 LYS cc_start: 0.7437 (mtpp) cc_final: 0.6841 (mtpp) REVERT: m 89 SER cc_start: 0.6917 (p) cc_final: 0.6621 (m) REVERT: m 114 GLU cc_start: 0.7935 (pt0) cc_final: 0.7703 (pt0) REVERT: n 16 ARG cc_start: 0.6881 (mmp80) cc_final: 0.6521 (mmt-90) REVERT: n 46 GLU cc_start: 0.6414 (mm-30) cc_final: 0.5686 (mt-10) REVERT: n 62 LEU cc_start: 0.7066 (mt) cc_final: 0.6859 (mt) REVERT: n 108 ASP cc_start: 0.7196 (m-30) cc_final: 0.6944 (m-30) REVERT: o 6 LYS cc_start: 0.7052 (mtmm) cc_final: 0.6485 (mtmm) REVERT: o 7 GLN cc_start: 0.7167 (tm-30) cc_final: 0.6472 (tp40) REVERT: o 9 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7257 (mt-10) REVERT: o 37 LYS cc_start: 0.5764 (ptpt) cc_final: 0.5358 (ptpp) REVERT: o 38 LYS cc_start: 0.7216 (ptmt) cc_final: 0.7001 (ptmm) REVERT: o 68 GLU cc_start: 0.6031 (mm-30) cc_final: 0.5827 (mm-30) REVERT: o 82 ASP cc_start: 0.7531 (t70) cc_final: 0.7174 (t70) REVERT: o 87 LYS cc_start: 0.7821 (mmtt) cc_final: 0.7165 (mmtp) REVERT: o 89 ARG cc_start: 0.7008 (mtm-85) cc_final: 0.6501 (mtp-110) REVERT: o 111 LYS cc_start: 0.7042 (ttpp) cc_final: 0.6711 (ttpt) REVERT: o 112 GLU cc_start: 0.7119 (tt0) cc_final: 0.6747 (tt0) REVERT: o 114 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6236 (mt) REVERT: p 13 ARG cc_start: 0.7510 (mtp85) cc_final: 0.7128 (mtt-85) REVERT: p 59 GLN cc_start: 0.8101 (mt0) cc_final: 0.7847 (tt0) REVERT: p 84 LYS cc_start: 0.7515 (tttm) cc_final: 0.6871 (tppt) REVERT: r 31 GLN cc_start: 0.6754 (mt0) cc_final: 0.6338 (mt0) REVERT: r 77 ASP cc_start: 0.8065 (m-30) cc_final: 0.7716 (m-30) REVERT: s 33 LYS cc_start: 0.7698 (tttm) cc_final: 0.7389 (tmtt) REVERT: s 73 ARG cc_start: 0.4854 (ttm110) cc_final: 0.4621 (ttm110) REVERT: t 46 GLN cc_start: 0.6900 (tp-100) cc_final: 0.6558 (tp40) REVERT: t 91 LYS cc_start: 0.6115 (mmtt) cc_final: 0.5355 (mptt) REVERT: t 94 ARG cc_start: 0.8265 (mtm180) cc_final: 0.7972 (mtm180) REVERT: u 5 ASN cc_start: 0.7437 (m-40) cc_final: 0.7060 (m-40) REVERT: u 50 MET cc_start: 0.7463 (ttm) cc_final: 0.6971 (ttm) REVERT: u 76 ASP cc_start: 0.6674 (t70) cc_final: 0.6453 (t70) REVERT: u 85 LYS cc_start: 0.7737 (mtpp) cc_final: 0.7283 (mtmt) REVERT: u 90 ASP cc_start: 0.7991 (m-30) cc_final: 0.7508 (m-30) REVERT: v 5 LYS cc_start: 0.6304 (mtpt) cc_final: 0.5946 (mtpt) REVERT: v 17 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7148 (tp30) REVERT: v 25 ARG cc_start: 0.7352 (mmt-90) cc_final: 0.6961 (mmt180) REVERT: v 44 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7660 (ptpp) REVERT: v 68 LYS cc_start: 0.7630 (tttp) cc_final: 0.7412 (tttm) REVERT: v 83 GLU cc_start: 0.7014 (pt0) cc_final: 0.6645 (pt0) REVERT: x 5 GLU cc_start: 0.5858 (mm-30) cc_final: 0.5443 (mp0) REVERT: x 13 GLU cc_start: 0.5459 (pm20) cc_final: 0.5180 (mm-30) REVERT: x 23 ARG cc_start: 0.7139 (mtt90) cc_final: 0.6433 (ttp-110) REVERT: x 45 GLN cc_start: 0.7064 (mt0) cc_final: 0.6844 (mt0) REVERT: y 6 LYS cc_start: 0.7697 (mmtp) cc_final: 0.7062 (tppt) REVERT: y 19 LYS cc_start: 0.7030 (mttm) cc_final: 0.6750 (mtpt) REVERT: y 25 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8333 (tm) REVERT: y 56 LYS cc_start: 0.7602 (ttpt) cc_final: 0.7035 (tttm) REVERT: 0 10 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7425 (tttt) REVERT: 0 35 GLU cc_start: 0.6908 (tt0) cc_final: 0.6639 (tm-30) REVERT: 1 1 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6358 (mmm) REVERT: 1 41 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7117 (mpp-170) REVERT: 2 15 LYS cc_start: 0.7845 (mmtt) cc_final: 0.7361 (mttt) REVERT: 2 52 LYS cc_start: 0.6831 (ttpt) cc_final: 0.6617 (ttpt) REVERT: 2 59 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7715 (mt) REVERT: 3 9 LYS cc_start: 0.7936 (mttp) cc_final: 0.7716 (mttm) REVERT: 3 34 LYS cc_start: 0.7892 (ptmt) cc_final: 0.7565 (ptmt) outliers start: 79 outliers final: 31 residues processed: 939 average time/residue: 2.3663 time to fit residues: 3102.1629 Evaluate side-chains 896 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 854 time to evaluate : 6.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain f residue 73 SER Chi-restraints excluded: chain f residue 111 ILE Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain u residue 8 VAL Chi-restraints excluded: chain v residue 44 LYS Chi-restraints excluded: chain y residue 25 LEU Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 41 ARG Chi-restraints excluded: chain 2 residue 59 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 889 optimal weight: 9.9990 chunk 677 optimal weight: 1.9990 chunk 467 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 429 optimal weight: 10.0000 chunk 604 optimal weight: 10.0000 chunk 903 optimal weight: 8.9990 chunk 956 optimal weight: 9.9990 chunk 472 optimal weight: 40.0000 chunk 856 optimal weight: 9.9990 chunk 257 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 GLN C 139 GLN C 190 HIS D 54 GLN D 71 GLN E 12 GLN F 3 HIS G 142 HIS H 18 GLN I 75 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 ASN ** Q 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN T 21 ASN T 82 GLN d 32 ASN f 81 GLN g 88 GLN g 104 ASN g 116 GLN i 67 ASN ** j 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 93 GLN n 38 GLN p 71 GLN q 6 GLN q 86 GLN u 12 GLN u 51 GLN u 75 GLN 0 26 ASN 1 29 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 153997 Z= 0.382 Angle : 0.905 21.366 230462 Z= 0.471 Chirality : 0.046 0.374 29304 Planarity : 0.009 0.152 12266 Dihedral : 23.202 178.606 77231 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.25 % Favored : 95.64 % Rotamer: Outliers : 2.97 % Allowed : 12.55 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 5480 helix: 1.08 (0.12), residues: 1874 sheet: -0.30 (0.15), residues: 1065 loop : -0.74 (0.11), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP c 248 HIS 0.011 0.002 HIS J 56 PHE 0.027 0.003 PHE H 45 TYR 0.028 0.003 TYR p 32 ARG 0.013 0.001 ARG p 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 872 time to evaluate : 6.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 ASP cc_start: 0.3509 (p0) cc_final: 0.2231 (t70) REVERT: B 21 ARG cc_start: 0.4037 (ttm-80) cc_final: 0.3760 (ttt180) REVERT: B 27 MET cc_start: 0.3663 (tpp) cc_final: 0.2952 (tpt) REVERT: B 151 ILE cc_start: 0.4921 (pt) cc_final: 0.4682 (pp) REVERT: B 154 MET cc_start: 0.4239 (OUTLIER) cc_final: 0.3981 (mmt) REVERT: B 174 LYS cc_start: 0.4010 (tptp) cc_final: 0.3242 (tptm) REVERT: C 41 GLN cc_start: 0.6816 (tt0) cc_final: 0.6251 (tt0) REVERT: C 49 LYS cc_start: 0.6339 (mtpp) cc_final: 0.6008 (mmmm) REVERT: C 58 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6749 (mt-10) REVERT: C 86 LYS cc_start: 0.6745 (mtmm) cc_final: 0.6117 (ttpp) REVERT: C 132 ARG cc_start: 0.6064 (mtp180) cc_final: 0.5332 (ttm170) REVERT: D 8 LYS cc_start: 0.6145 (mmtp) cc_final: 0.5376 (mmtp) REVERT: D 45 LYS cc_start: 0.5732 (mtmm) cc_final: 0.5039 (mmtp) REVERT: D 128 ARG cc_start: 0.5127 (ttm110) cc_final: 0.4449 (ttp80) REVERT: D 130 VAL cc_start: 0.6984 (OUTLIER) cc_final: 0.6776 (t) REVERT: E 26 LYS cc_start: 0.7636 (ttmt) cc_final: 0.7380 (ttpp) REVERT: E 45 ARG cc_start: 0.7193 (mtp85) cc_final: 0.6589 (mtm180) REVERT: E 93 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7312 (mtp180) REVERT: E 146 ASN cc_start: 0.6681 (m-40) cc_final: 0.6416 (m110) REVERT: E 152 MET cc_start: 0.6412 (OUTLIER) cc_final: 0.6132 (mpp) REVERT: F 8 PHE cc_start: 0.7578 (p90) cc_final: 0.7302 (p90) REVERT: F 55 HIS cc_start: 0.6944 (m-70) cc_final: 0.6701 (m170) REVERT: F 79 ARG cc_start: 0.6285 (ttm-80) cc_final: 0.5175 (ttp-110) REVERT: G 4 ARG cc_start: 0.6086 (mtt90) cc_final: 0.5770 (mtm180) REVERT: G 41 SER cc_start: 0.7640 (m) cc_final: 0.7424 (m) REVERT: G 63 GLU cc_start: 0.5987 (mm-30) cc_final: 0.5638 (mm-30) REVERT: G 76 LYS cc_start: 0.6066 (mmtt) cc_final: 0.5482 (mmmt) REVERT: G 80 VAL cc_start: -0.0324 (OUTLIER) cc_final: -0.0563 (m) REVERT: G 106 GLU cc_start: 0.7346 (tt0) cc_final: 0.6785 (mm-30) REVERT: G 136 LYS cc_start: 0.7135 (ttmm) cc_final: 0.6099 (mptp) REVERT: H 18 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7503 (mm110) REVERT: H 21 ASN cc_start: 0.7806 (m110) cc_final: 0.7479 (m110) REVERT: I 72 ILE cc_start: 0.6908 (mt) cc_final: 0.6683 (mp) REVERT: I 97 GLU cc_start: 0.5533 (pm20) cc_final: 0.5288 (mm-30) REVERT: J 66 GLU cc_start: 0.7509 (pt0) cc_final: 0.7276 (pt0) REVERT: J 88 MET cc_start: 0.3806 (mmp) cc_final: 0.3476 (mmt) REVERT: K 37 ARG cc_start: 0.6502 (mmm-85) cc_final: 0.5673 (mpp80) REVERT: K 56 ARG cc_start: 0.6952 (mtp-110) cc_final: 0.6652 (mmm-85) REVERT: K 98 ARG cc_start: 0.6608 (mtt90) cc_final: 0.6315 (mtt-85) REVERT: K 106 ARG cc_start: 0.5396 (ttp-110) cc_final: 0.4585 (ptp-170) REVERT: L 20 ASN cc_start: 0.7670 (m-40) cc_final: 0.7414 (m110) REVERT: L 62 GLU cc_start: 0.7291 (tt0) cc_final: 0.6896 (tt0) REVERT: L 76 GLU cc_start: 0.5450 (tp30) cc_final: 0.5234 (mm-30) REVERT: M 75 MET cc_start: 0.6000 (mtp) cc_final: 0.5271 (tmm) REVERT: M 79 ARG cc_start: 0.6343 (ttt-90) cc_final: 0.5878 (tmt170) REVERT: N 21 PHE cc_start: 0.6559 (t80) cc_final: 0.6122 (t80) REVERT: N 30 ILE cc_start: 0.6745 (OUTLIER) cc_final: 0.6526 (mt) REVERT: N 41 ARG cc_start: 0.5533 (mtm-85) cc_final: 0.5143 (mtp180) REVERT: N 47 LYS cc_start: 0.5681 (tptp) cc_final: 0.5109 (mptt) REVERT: O 10 LYS cc_start: 0.6818 (mtpp) cc_final: 0.6123 (mptt) REVERT: O 26 GLU cc_start: 0.6788 (mp0) cc_final: 0.6469 (mp0) REVERT: O 62 GLN cc_start: 0.7167 (tt0) cc_final: 0.6620 (mm110) REVERT: O 69 TYR cc_start: 0.8341 (t80) cc_final: 0.8063 (t80) REVERT: P 35 ARG cc_start: 0.7163 (ttt-90) cc_final: 0.6887 (ttt-90) REVERT: P 71 VAL cc_start: 0.7198 (p) cc_final: 0.6923 (m) REVERT: Q 11 ARG cc_start: 0.6102 (mtp-110) cc_final: 0.5620 (mtt180) REVERT: Q 44 LEU cc_start: 0.7796 (mt) cc_final: 0.7516 (mt) REVERT: Q 75 LEU cc_start: 0.6691 (tp) cc_final: 0.6465 (tt) REVERT: R 42 SER cc_start: 0.7865 (m) cc_final: 0.7346 (p) REVERT: R 73 ARG cc_start: 0.5532 (ttp-110) cc_final: 0.4975 (ptm-80) REVERT: T 21 ASN cc_start: 0.7262 (m-40) cc_final: 0.7058 (m-40) REVERT: T 24 ARG cc_start: 0.6480 (mmm160) cc_final: 0.6179 (mmm-85) REVERT: T 29 ARG cc_start: 0.6881 (mtm-85) cc_final: 0.6096 (mtm-85) REVERT: T 49 LYS cc_start: 0.6581 (OUTLIER) cc_final: 0.6262 (tptp) REVERT: T 54 MET cc_start: 0.6668 (tmm) cc_final: 0.6200 (tmm) REVERT: c 97 LYS cc_start: 0.7369 (ttmm) cc_final: 0.6976 (mmtt) REVERT: c 108 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7548 (ttpm) REVERT: d 128 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7250 (mmp-170) REVERT: e 123 LYS cc_start: 0.6068 (tttm) cc_final: 0.5599 (mmtm) REVERT: e 132 LYS cc_start: 0.7075 (pttp) cc_final: 0.6852 (pttt) REVERT: e 166 LYS cc_start: 0.6636 (mttp) cc_final: 0.5994 (mmtp) REVERT: e 197 GLU cc_start: 0.6246 (pt0) cc_final: 0.5896 (pt0) REVERT: f 48 LYS cc_start: 0.5957 (mmmt) cc_final: 0.5327 (ttpt) REVERT: f 51 ASP cc_start: 0.6364 (m-30) cc_final: 0.6140 (m-30) REVERT: f 98 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6391 (mt-10) REVERT: f 101 GLU cc_start: 0.6790 (tt0) cc_final: 0.6506 (tm-30) REVERT: f 103 LEU cc_start: 0.6994 (tp) cc_final: 0.6476 (tm) REVERT: f 120 LYS cc_start: 0.6916 (ptpp) cc_final: 0.6589 (pptt) REVERT: f 134 GLU cc_start: 0.5919 (mt-10) cc_final: 0.5638 (mt-10) REVERT: f 142 ASP cc_start: 0.4654 (t0) cc_final: 0.4398 (t0) REVERT: f 147 ASP cc_start: 0.4003 (p0) cc_final: 0.3615 (t0) REVERT: f 148 ARG cc_start: 0.5977 (mtp-110) cc_final: 0.5334 (ptm-80) REVERT: f 167 ARG cc_start: 0.6477 (ttm110) cc_final: 0.5631 (ttp-170) REVERT: f 177 PHE cc_start: 0.6890 (m-80) cc_final: 0.6528 (m-80) REVERT: g 69 ARG cc_start: 0.8047 (tmt170) cc_final: 0.7726 (tpt90) REVERT: g 74 SER cc_start: 0.6652 (m) cc_final: 0.6321 (t) REVERT: g 94 TYR cc_start: 0.7433 (m-10) cc_final: 0.7161 (m-10) REVERT: g 99 LYS cc_start: 0.5572 (tppp) cc_final: 0.4788 (ptpt) REVERT: g 112 PRO cc_start: 0.6076 (Cg_endo) cc_final: 0.5674 (Cg_exo) REVERT: g 153 ARG cc_start: 0.6616 (mtt-85) cc_final: 0.6258 (mtt-85) REVERT: i 91 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7248 (mt-10) REVERT: i 95 ARG cc_start: 0.6918 (ttp-110) cc_final: 0.6400 (ttp80) REVERT: i 102 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7549 (mt-10) REVERT: j 17 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6753 (mmt90) REVERT: j 18 ARG cc_start: 0.7783 (mmm-85) cc_final: 0.7546 (mtp85) REVERT: j 20 MET cc_start: 0.8147 (ttp) cc_final: 0.7938 (ttm) REVERT: j 45 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6391 (pm20) REVERT: j 73 ASP cc_start: 0.7934 (p0) cc_final: 0.7480 (p0) REVERT: j 117 SER cc_start: 0.7100 (p) cc_final: 0.6758 (m) REVERT: k 84 LYS cc_start: 0.7349 (ptpt) cc_final: 0.6839 (ptmt) REVERT: k 129 LYS cc_start: 0.6861 (mtpp) cc_final: 0.6435 (mmtm) REVERT: l 58 LYS cc_start: 0.7347 (mttm) cc_final: 0.7095 (mtpt) REVERT: l 105 MET cc_start: 0.7980 (ttm) cc_final: 0.7745 (ttm) REVERT: l 110 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6692 (tt0) REVERT: l 118 LYS cc_start: 0.7784 (ttpp) cc_final: 0.7396 (tttm) REVERT: l 127 LYS cc_start: 0.7466 (mtpp) cc_final: 0.7034 (mtpp) REVERT: m 78 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7498 (tmtp) REVERT: m 89 SER cc_start: 0.6887 (p) cc_final: 0.6579 (m) REVERT: m 114 GLU cc_start: 0.7848 (pt0) cc_final: 0.7547 (pt0) REVERT: n 30 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7782 (ppt90) REVERT: n 46 GLU cc_start: 0.6537 (mm-30) cc_final: 0.5836 (mt-10) REVERT: n 62 LEU cc_start: 0.6994 (mt) cc_final: 0.6772 (mt) REVERT: n 108 ASP cc_start: 0.7288 (m-30) cc_final: 0.7027 (m-30) REVERT: o 6 LYS cc_start: 0.6884 (mtmm) cc_final: 0.6544 (mttp) REVERT: o 7 GLN cc_start: 0.7054 (tm-30) cc_final: 0.6395 (tp40) REVERT: o 37 LYS cc_start: 0.5900 (OUTLIER) cc_final: 0.5182 (pttt) REVERT: o 38 LYS cc_start: 0.7164 (ptmt) cc_final: 0.6922 (ptmm) REVERT: o 82 ASP cc_start: 0.7562 (t70) cc_final: 0.7159 (t70) REVERT: o 87 LYS cc_start: 0.7844 (mmtt) cc_final: 0.7107 (mmtp) REVERT: o 89 ARG cc_start: 0.6947 (mtm-85) cc_final: 0.6228 (mtt-85) REVERT: o 111 LYS cc_start: 0.7131 (ttpp) cc_final: 0.6735 (ttpt) REVERT: o 112 GLU cc_start: 0.7161 (tt0) cc_final: 0.6798 (tt0) REVERT: p 59 GLN cc_start: 0.8172 (mt0) cc_final: 0.7927 (tt0) REVERT: p 84 LYS cc_start: 0.7646 (tttm) cc_final: 0.6943 (tppt) REVERT: q 18 GLN cc_start: 0.6846 (mt0) cc_final: 0.6610 (mt0) REVERT: q 46 GLU cc_start: 0.5517 (OUTLIER) cc_final: 0.5009 (tt0) REVERT: q 48 LYS cc_start: 0.7505 (mtpt) cc_final: 0.7161 (mttp) REVERT: r 77 ASP cc_start: 0.8109 (m-30) cc_final: 0.7814 (m-30) REVERT: t 46 GLN cc_start: 0.6926 (tp-100) cc_final: 0.5984 (tt0) REVERT: t 91 LYS cc_start: 0.5837 (mmtt) cc_final: 0.5102 (mptt) REVERT: u 50 MET cc_start: 0.7422 (ttm) cc_final: 0.6837 (ttm) REVERT: u 76 ASP cc_start: 0.6631 (t70) cc_final: 0.6316 (t70) REVERT: u 85 LYS cc_start: 0.7736 (mtpp) cc_final: 0.7228 (mtmt) REVERT: u 90 ASP cc_start: 0.8010 (m-30) cc_final: 0.7364 (m-30) REVERT: v 17 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7200 (tp30) REVERT: v 25 ARG cc_start: 0.7296 (mmt-90) cc_final: 0.6913 (mmt180) REVERT: v 44 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7671 (ptpp) REVERT: x 23 ARG cc_start: 0.7108 (mtt90) cc_final: 0.6433 (ttp-110) REVERT: x 48 ARG cc_start: 0.7029 (mmt90) cc_final: 0.6657 (mmm-85) REVERT: y 6 LYS cc_start: 0.7687 (mmtp) cc_final: 0.7045 (mptt) REVERT: y 37 GLU cc_start: 0.6478 (tp30) cc_final: 0.6231 (mt-10) REVERT: y 56 LYS cc_start: 0.7739 (ttpt) cc_final: 0.7069 (tttm) REVERT: 0 10 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7705 (ttpt) REVERT: 0 35 GLU cc_start: 0.6920 (tt0) cc_final: 0.6617 (tm-30) REVERT: 1 41 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7088 (mpp-170) REVERT: 2 15 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7371 (mtpt) REVERT: 2 59 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7635 (mt) REVERT: 3 9 LYS cc_start: 0.7937 (mttp) cc_final: 0.7670 (mttm) REVERT: 3 34 LYS cc_start: 0.7934 (ptmt) cc_final: 0.7676 (pttt) outliers start: 136 outliers final: 71 residues processed: 947 average time/residue: 2.3442 time to fit residues: 3097.0191 Evaluate side-chains 933 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 842 time to evaluate : 6.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 ARG Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 49 LYS Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain c residue 108 LYS Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 202 ILE Chi-restraints excluded: chain e residue 154 ASP Chi-restraints excluded: chain e residue 193 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 111 ILE Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 161 LYS Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain j residue 17 ARG Chi-restraints excluded: chain j residue 45 GLU Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 111 GLU Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain m residue 36 THR Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 78 LYS Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 65 THR Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain o residue 37 LYS Chi-restraints excluded: chain q residue 46 GLU Chi-restraints excluded: chain s residue 26 LYS Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 65 ILE Chi-restraints excluded: chain u residue 8 VAL Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain v residue 44 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 1 residue 41 ARG Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 4 residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 796 optimal weight: 20.0000 chunk 543 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 712 optimal weight: 7.9990 chunk 394 optimal weight: 10.0000 chunk 816 optimal weight: 1.9990 chunk 661 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 488 optimal weight: 30.0000 chunk 858 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 overall best weight: 4.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 GLN C 139 GLN D 54 GLN D 74 ASN F 3 HIS G 97 ASN G 142 HIS K 38 GLN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 GLN P 29 ASN Q 47 HIS R 54 GLN c 117 GLN d 32 ASN f 81 GLN g 88 GLN g 116 GLN i 67 ASN ** j 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 93 GLN n 38 GLN p 71 GLN q 6 GLN q 86 GLN u 12 GLN u 51 GLN u 75 GLN 1 29 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 153997 Z= 0.240 Angle : 0.739 15.914 230462 Z= 0.403 Chirality : 0.039 0.370 29304 Planarity : 0.008 0.143 12266 Dihedral : 23.080 179.745 77231 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 2.80 % Allowed : 14.08 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 5480 helix: 1.31 (0.12), residues: 1871 sheet: -0.29 (0.15), residues: 1080 loop : -0.69 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 201 HIS 0.008 0.001 HIS u 44 PHE 0.019 0.002 PHE U 12 TYR 0.024 0.002 TYR p 32 ARG 0.008 0.001 ARG p 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 845 time to evaluate : 6.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 ASP cc_start: 0.3546 (p0) cc_final: 0.2287 (t70) REVERT: B 14 VAL cc_start: 0.3456 (m) cc_final: 0.3242 (m) REVERT: B 45 LYS cc_start: 0.3099 (tptt) cc_final: 0.2783 (mmmt) REVERT: B 151 ILE cc_start: 0.4838 (pt) cc_final: 0.4607 (pp) REVERT: B 154 MET cc_start: 0.4192 (OUTLIER) cc_final: 0.3986 (mmt) REVERT: B 174 LYS cc_start: 0.3875 (tptp) cc_final: 0.3139 (tptm) REVERT: C 41 GLN cc_start: 0.6741 (tt0) cc_final: 0.6172 (tt0) REVERT: C 49 LYS cc_start: 0.6259 (mtpp) cc_final: 0.5823 (mttp) REVERT: C 58 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6860 (mt-10) REVERT: C 86 LYS cc_start: 0.6816 (mtmm) cc_final: 0.6292 (ttpp) REVERT: C 132 ARG cc_start: 0.6001 (mtp180) cc_final: 0.5278 (ttm170) REVERT: D 8 LYS cc_start: 0.6119 (mmtp) cc_final: 0.5336 (mmtp) REVERT: D 45 LYS cc_start: 0.5739 (mtmm) cc_final: 0.5050 (mmtp) REVERT: D 128 ARG cc_start: 0.5146 (ttm110) cc_final: 0.4484 (ttp80) REVERT: D 159 LEU cc_start: 0.5178 (tt) cc_final: 0.4786 (mt) REVERT: E 26 LYS cc_start: 0.7649 (ttmt) cc_final: 0.7392 (ttpp) REVERT: E 45 ARG cc_start: 0.7139 (mtp85) cc_final: 0.6514 (mtm180) REVERT: E 70 ASN cc_start: 0.6882 (m-40) cc_final: 0.6660 (m-40) REVERT: E 71 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7400 (mtm) REVERT: E 93 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7241 (mtp180) REVERT: E 146 ASN cc_start: 0.6638 (m-40) cc_final: 0.6381 (m110) REVERT: F 8 PHE cc_start: 0.7609 (p90) cc_final: 0.7213 (p90) REVERT: F 55 HIS cc_start: 0.6938 (m-70) cc_final: 0.6655 (m170) REVERT: F 56 LYS cc_start: 0.6950 (mttp) cc_final: 0.6660 (mmtm) REVERT: F 96 VAL cc_start: 0.5504 (OUTLIER) cc_final: 0.5259 (t) REVERT: G 4 ARG cc_start: 0.6026 (mtt90) cc_final: 0.5799 (mtm180) REVERT: G 41 SER cc_start: 0.7588 (m) cc_final: 0.7346 (m) REVERT: G 63 GLU cc_start: 0.6009 (mm-30) cc_final: 0.5670 (mm-30) REVERT: G 76 LYS cc_start: 0.6043 (mmtt) cc_final: 0.5450 (mmmt) REVERT: G 80 VAL cc_start: -0.0579 (OUTLIER) cc_final: -0.0866 (m) REVERT: G 106 GLU cc_start: 0.7266 (tt0) cc_final: 0.6697 (mm-30) REVERT: G 136 LYS cc_start: 0.7095 (ttmm) cc_final: 0.6068 (mptp) REVERT: H 18 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7591 (mm-40) REVERT: H 21 ASN cc_start: 0.7741 (m110) cc_final: 0.7391 (m110) REVERT: I 57 MET cc_start: 0.6135 (mtt) cc_final: 0.5227 (tpp) REVERT: I 72 ILE cc_start: 0.6905 (mt) cc_final: 0.6677 (mp) REVERT: I 97 GLU cc_start: 0.5458 (pm20) cc_final: 0.5117 (mm-30) REVERT: J 66 GLU cc_start: 0.7490 (pt0) cc_final: 0.7245 (pt0) REVERT: J 71 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7934 (tt) REVERT: J 88 MET cc_start: 0.3609 (mmp) cc_final: 0.3333 (mmt) REVERT: K 37 ARG cc_start: 0.6469 (mmm-85) cc_final: 0.5902 (mtp180) REVERT: K 56 ARG cc_start: 0.6895 (mtp-110) cc_final: 0.6634 (mmm-85) REVERT: K 98 ARG cc_start: 0.6594 (mtt90) cc_final: 0.6250 (mtt-85) REVERT: K 106 ARG cc_start: 0.5526 (ttp-110) cc_final: 0.4740 (ptp-170) REVERT: L 20 ASN cc_start: 0.7590 (m-40) cc_final: 0.7364 (m110) REVERT: L 62 GLU cc_start: 0.7308 (tt0) cc_final: 0.6910 (tt0) REVERT: L 76 GLU cc_start: 0.5399 (tp30) cc_final: 0.5188 (mm-30) REVERT: M 75 MET cc_start: 0.5959 (mtp) cc_final: 0.5157 (tmm) REVERT: M 79 ARG cc_start: 0.6420 (ttt-90) cc_final: 0.5961 (tmt170) REVERT: N 41 ARG cc_start: 0.5514 (mtm-85) cc_final: 0.4838 (mtp180) REVERT: N 47 LYS cc_start: 0.5677 (tptp) cc_final: 0.5165 (mptt) REVERT: O 10 LYS cc_start: 0.6833 (mtpp) cc_final: 0.6148 (mptt) REVERT: O 26 GLU cc_start: 0.6823 (mp0) cc_final: 0.6492 (mp0) REVERT: O 62 GLN cc_start: 0.7206 (tt0) cc_final: 0.6673 (mm110) REVERT: O 69 TYR cc_start: 0.8318 (t80) cc_final: 0.8058 (t80) REVERT: P 35 ARG cc_start: 0.7146 (ttt-90) cc_final: 0.6906 (ttt-90) REVERT: P 71 VAL cc_start: 0.7311 (p) cc_final: 0.7075 (m) REVERT: Q 11 ARG cc_start: 0.6177 (mtp-110) cc_final: 0.5672 (mtt180) REVERT: Q 44 LEU cc_start: 0.7880 (mt) cc_final: 0.7613 (mt) REVERT: Q 75 LEU cc_start: 0.6795 (tp) cc_final: 0.6587 (tt) REVERT: R 50 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6296 (tttt) REVERT: R 73 ARG cc_start: 0.5482 (ttp-110) cc_final: 0.4957 (ptm-80) REVERT: T 24 ARG cc_start: 0.6589 (mmm160) cc_final: 0.6245 (mmm-85) REVERT: T 29 ARG cc_start: 0.6906 (mtm-85) cc_final: 0.6337 (mtt180) REVERT: T 49 LYS cc_start: 0.6528 (OUTLIER) cc_final: 0.6251 (tptp) REVERT: c 97 LYS cc_start: 0.7209 (ttmm) cc_final: 0.6854 (mmtt) REVERT: c 187 ASP cc_start: 0.7331 (m-30) cc_final: 0.7073 (m-30) REVERT: d 128 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7225 (mmp-170) REVERT: e 123 LYS cc_start: 0.6048 (tttm) cc_final: 0.5733 (mptt) REVERT: e 132 LYS cc_start: 0.7133 (pttp) cc_final: 0.6682 (ptmt) REVERT: e 166 LYS cc_start: 0.6698 (mttp) cc_final: 0.6070 (mmtp) REVERT: f 48 LYS cc_start: 0.5955 (mmmt) cc_final: 0.5302 (ttpt) REVERT: f 51 ASP cc_start: 0.6348 (m-30) cc_final: 0.6090 (m-30) REVERT: f 83 TYR cc_start: 0.5964 (m-10) cc_final: 0.5138 (t80) REVERT: f 98 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6306 (mt-10) REVERT: f 101 GLU cc_start: 0.6784 (tt0) cc_final: 0.6530 (tm-30) REVERT: f 103 LEU cc_start: 0.6981 (tp) cc_final: 0.6491 (tm) REVERT: f 112 ARG cc_start: 0.5413 (mmm-85) cc_final: 0.4501 (mmm-85) REVERT: f 120 LYS cc_start: 0.6977 (ptpp) cc_final: 0.6583 (pptt) REVERT: f 134 GLU cc_start: 0.5928 (mt-10) cc_final: 0.5639 (mt-10) REVERT: f 142 ASP cc_start: 0.4622 (t0) cc_final: 0.4376 (t0) REVERT: f 147 ASP cc_start: 0.3641 (p0) cc_final: 0.3425 (t0) REVERT: f 148 ARG cc_start: 0.5879 (mtp-110) cc_final: 0.5236 (ptm-80) REVERT: f 167 ARG cc_start: 0.6535 (ttm110) cc_final: 0.5642 (ttp-170) REVERT: f 177 PHE cc_start: 0.6809 (m-80) cc_final: 0.6500 (m-80) REVERT: g 69 ARG cc_start: 0.8010 (tmt170) cc_final: 0.7724 (tpt90) REVERT: g 74 SER cc_start: 0.6587 (m) cc_final: 0.6287 (t) REVERT: g 94 TYR cc_start: 0.7363 (m-10) cc_final: 0.7044 (m-10) REVERT: g 99 LYS cc_start: 0.5598 (tppp) cc_final: 0.5164 (tmtm) REVERT: g 112 PRO cc_start: 0.6103 (Cg_endo) cc_final: 0.5717 (Cg_exo) REVERT: g 153 ARG cc_start: 0.6544 (mtt-85) cc_final: 0.6221 (mtt-85) REVERT: i 1 MET cc_start: 0.5549 (OUTLIER) cc_final: 0.5135 (mpp) REVERT: i 91 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7227 (mt-10) REVERT: i 95 ARG cc_start: 0.6943 (ttp-110) cc_final: 0.6442 (ttp80) REVERT: i 102 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7521 (mt-10) REVERT: j 18 ARG cc_start: 0.7786 (mmm-85) cc_final: 0.7557 (mtp85) REVERT: j 45 GLU cc_start: 0.6572 (pm20) cc_final: 0.6315 (pm20) REVERT: j 73 ASP cc_start: 0.7917 (p0) cc_final: 0.7513 (p0) REVERT: j 117 SER cc_start: 0.7125 (p) cc_final: 0.6785 (m) REVERT: k 84 LYS cc_start: 0.7287 (ptpt) cc_final: 0.6697 (ptmt) REVERT: k 129 LYS cc_start: 0.6781 (mtpp) cc_final: 0.6426 (mptt) REVERT: l 58 LYS cc_start: 0.7362 (mttm) cc_final: 0.7115 (mtpt) REVERT: l 110 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6601 (tt0) REVERT: l 118 LYS cc_start: 0.7779 (ttpp) cc_final: 0.7400 (tttm) REVERT: l 127 LYS cc_start: 0.7468 (mtpp) cc_final: 0.6976 (mtpp) REVERT: m 89 SER cc_start: 0.6871 (p) cc_final: 0.6571 (m) REVERT: m 114 GLU cc_start: 0.7853 (pt0) cc_final: 0.7587 (pt0) REVERT: n 16 ARG cc_start: 0.7060 (mmp80) cc_final: 0.6621 (mmt-90) REVERT: n 30 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7976 (ppt90) REVERT: n 36 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.6114 (m-80) REVERT: n 46 GLU cc_start: 0.6521 (mm-30) cc_final: 0.5845 (mt-10) REVERT: n 62 LEU cc_start: 0.7015 (mt) cc_final: 0.6802 (mt) REVERT: n 108 ASP cc_start: 0.7292 (m-30) cc_final: 0.7051 (m-30) REVERT: o 6 LYS cc_start: 0.6981 (mtmm) cc_final: 0.6503 (mtmm) REVERT: o 7 GLN cc_start: 0.7069 (tm-30) cc_final: 0.6483 (tp40) REVERT: o 38 LYS cc_start: 0.7149 (ptmt) cc_final: 0.6916 (ptmm) REVERT: o 82 ASP cc_start: 0.7517 (t70) cc_final: 0.7079 (t70) REVERT: o 89 ARG cc_start: 0.7024 (mtm-85) cc_final: 0.6298 (mtt-85) REVERT: o 111 LYS cc_start: 0.7084 (ttpp) cc_final: 0.6747 (ttpt) REVERT: o 112 GLU cc_start: 0.7050 (tt0) cc_final: 0.6791 (tt0) REVERT: p 59 GLN cc_start: 0.8127 (mt0) cc_final: 0.7893 (tt0) REVERT: p 84 LYS cc_start: 0.7637 (tttm) cc_final: 0.6936 (tppt) REVERT: q 46 GLU cc_start: 0.5489 (OUTLIER) cc_final: 0.4972 (tt0) REVERT: q 48 LYS cc_start: 0.7489 (mtpt) cc_final: 0.7152 (mttp) REVERT: r 77 ASP cc_start: 0.8103 (m-30) cc_final: 0.7806 (m-30) REVERT: s 1 MET cc_start: 0.4073 (tpt) cc_final: 0.3738 (tpt) REVERT: t 46 GLN cc_start: 0.6897 (tp-100) cc_final: 0.5957 (tt0) REVERT: t 61 LYS cc_start: 0.6926 (ptpt) cc_final: 0.6671 (ptpp) REVERT: t 91 LYS cc_start: 0.5824 (mmtt) cc_final: 0.5110 (mptt) REVERT: u 50 MET cc_start: 0.7420 (ttm) cc_final: 0.6855 (ttm) REVERT: u 76 ASP cc_start: 0.6507 (t70) cc_final: 0.6281 (t70) REVERT: u 85 LYS cc_start: 0.7677 (mtpp) cc_final: 0.7181 (mtmt) REVERT: u 90 ASP cc_start: 0.8024 (m-30) cc_final: 0.7403 (m-30) REVERT: v 5 LYS cc_start: 0.6375 (mtpt) cc_final: 0.5916 (mtpt) REVERT: v 17 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7223 (tp30) REVERT: v 25 ARG cc_start: 0.7321 (mmt-90) cc_final: 0.6942 (mmt180) REVERT: v 44 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7628 (ptpp) REVERT: x 5 GLU cc_start: 0.5828 (mm-30) cc_final: 0.5310 (mp0) REVERT: x 23 ARG cc_start: 0.7142 (mtt90) cc_final: 0.6484 (ttp-110) REVERT: y 6 LYS cc_start: 0.7684 (mmtp) cc_final: 0.7163 (tppt) REVERT: y 19 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.6885 (ttpt) REVERT: y 56 LYS cc_start: 0.7684 (ttpt) cc_final: 0.7056 (tttt) REVERT: 0 10 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7520 (tttt) REVERT: 0 35 GLU cc_start: 0.6906 (tt0) cc_final: 0.6627 (tm-30) REVERT: 1 1 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6169 (mtm) REVERT: 1 41 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7051 (mpp-170) REVERT: 2 15 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7398 (mttt) REVERT: 2 59 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7616 (mt) REVERT: 3 9 LYS cc_start: 0.7947 (mttp) cc_final: 0.7678 (mttm) REVERT: 3 34 LYS cc_start: 0.7934 (ptmt) cc_final: 0.7685 (pttt) REVERT: 4 66 ILE cc_start: 0.3438 (OUTLIER) cc_final: 0.3227 (tt) outliers start: 128 outliers final: 69 residues processed: 916 average time/residue: 2.3026 time to fit residues: 2959.7116 Evaluate side-chains 919 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 829 time to evaluate : 5.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 ARG Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 49 LYS Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain U residue 44 GLU Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 202 ILE Chi-restraints excluded: chain e residue 193 VAL Chi-restraints excluded: chain f residue 73 SER Chi-restraints excluded: chain f residue 111 ILE Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 136 GLN Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain m residue 36 THR Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 36 TYR Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain n residue 80 GLU Chi-restraints excluded: chain q residue 46 GLU Chi-restraints excluded: chain s residue 24 MET Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain u residue 8 VAL Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain v residue 44 LYS Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 41 ARG Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 321 optimal weight: 10.0000 chunk 861 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 chunk 561 optimal weight: 10.0000 chunk 236 optimal weight: 4.9990 chunk 957 optimal weight: 5.9990 chunk 795 optimal weight: 7.9990 chunk 443 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 316 optimal weight: 30.0000 chunk 502 optimal weight: 10.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 GLN C 139 GLN D 54 GLN E 12 GLN E 78 ASN F 3 HIS G 142 HIS J 56 HIS ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 ASN Q 47 HIS R 54 GLN d 32 ASN f 81 GLN g 88 GLN g 116 GLN i 67 ASN ** j 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 93 GLN n 38 GLN p 71 GLN q 6 GLN q 86 GLN u 12 GLN ** u 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 75 GLN 1 29 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 153997 Z= 0.331 Angle : 0.840 19.531 230462 Z= 0.445 Chirality : 0.044 0.380 29304 Planarity : 0.008 0.149 12266 Dihedral : 23.182 179.067 77231 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.53 % Favored : 95.38 % Rotamer: Outliers : 3.43 % Allowed : 14.64 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.17 (0.11), residues: 5480 helix: 1.03 (0.12), residues: 1867 sheet: -0.36 (0.15), residues: 1088 loop : -0.80 (0.12), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP c 248 HIS 0.009 0.002 HIS u 44 PHE 0.027 0.003 PHE q 53 TYR 0.026 0.003 TYR p 32 ARG 0.009 0.001 ARG p 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 845 time to evaluate : 6.330 Fit side-chains revert: symmetry clash REVERT: B 8 ASP cc_start: 0.3524 (p0) cc_final: 0.2238 (t70) REVERT: B 14 VAL cc_start: 0.3518 (m) cc_final: 0.3250 (m) REVERT: B 35 ARG cc_start: 0.3273 (ttm110) cc_final: 0.2958 (mtt90) REVERT: B 78 GLU cc_start: 0.3562 (OUTLIER) cc_final: 0.3232 (tt0) REVERT: B 113 ARG cc_start: 0.3921 (tpt-90) cc_final: 0.3258 (tpt170) REVERT: B 137 ARG cc_start: 0.2675 (mtp85) cc_final: 0.1941 (mtp85) REVERT: B 151 ILE cc_start: 0.4837 (pt) cc_final: 0.4606 (pp) REVERT: B 174 LYS cc_start: 0.3914 (tptp) cc_final: 0.3089 (tptm) REVERT: C 41 GLN cc_start: 0.6757 (tt0) cc_final: 0.6190 (tt0) REVERT: C 49 LYS cc_start: 0.6371 (mtpp) cc_final: 0.5992 (mmmm) REVERT: C 132 ARG cc_start: 0.6115 (mtp180) cc_final: 0.5462 (ttm170) REVERT: D 8 LYS cc_start: 0.6187 (mmtp) cc_final: 0.5339 (mmtp) REVERT: D 45 LYS cc_start: 0.5815 (mtmm) cc_final: 0.5115 (mmtp) REVERT: D 128 ARG cc_start: 0.5128 (ttm110) cc_final: 0.4432 (ttp80) REVERT: D 159 LEU cc_start: 0.5119 (tt) cc_final: 0.4767 (mt) REVERT: E 26 LYS cc_start: 0.7714 (ttmt) cc_final: 0.7448 (ttpp) REVERT: E 45 ARG cc_start: 0.7137 (mtp85) cc_final: 0.6597 (mtm180) REVERT: E 93 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7274 (mtp180) REVERT: E 146 ASN cc_start: 0.6650 (m-40) cc_final: 0.6392 (m110) REVERT: F 8 PHE cc_start: 0.7595 (p90) cc_final: 0.7322 (p90) REVERT: F 55 HIS cc_start: 0.6898 (m-70) cc_final: 0.6637 (m170) REVERT: G 4 ARG cc_start: 0.6078 (mtt90) cc_final: 0.5830 (mtm180) REVERT: G 41 SER cc_start: 0.7667 (m) cc_final: 0.7428 (m) REVERT: G 63 GLU cc_start: 0.6129 (mm-30) cc_final: 0.5724 (mm-30) REVERT: G 76 LYS cc_start: 0.6074 (mmtt) cc_final: 0.5482 (mmmt) REVERT: G 80 VAL cc_start: -0.0975 (OUTLIER) cc_final: -0.1233 (m) REVERT: G 106 GLU cc_start: 0.7313 (tt0) cc_final: 0.6771 (mm-30) REVERT: G 118 LEU cc_start: 0.7275 (tp) cc_final: 0.6767 (mt) REVERT: G 136 LYS cc_start: 0.7103 (ttmm) cc_final: 0.6076 (mptp) REVERT: H 18 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7665 (mm-40) REVERT: H 21 ASN cc_start: 0.7789 (m110) cc_final: 0.7445 (m110) REVERT: I 72 ILE cc_start: 0.6921 (mt) cc_final: 0.6696 (mp) REVERT: I 97 GLU cc_start: 0.5564 (pm20) cc_final: 0.5320 (mm-30) REVERT: J 66 GLU cc_start: 0.7486 (pt0) cc_final: 0.7237 (pt0) REVERT: J 71 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7981 (tt) REVERT: J 88 MET cc_start: 0.3813 (mmp) cc_final: 0.3484 (mmt) REVERT: J 99 GLN cc_start: 0.5937 (mt0) cc_final: 0.5577 (tt0) REVERT: K 56 ARG cc_start: 0.6969 (mtp-110) cc_final: 0.6736 (mmm-85) REVERT: K 98 ARG cc_start: 0.6616 (mtt90) cc_final: 0.6305 (mtt-85) REVERT: K 106 ARG cc_start: 0.5398 (ttp-110) cc_final: 0.4515 (ptp-170) REVERT: L 62 GLU cc_start: 0.7359 (tt0) cc_final: 0.6914 (tt0) REVERT: L 76 GLU cc_start: 0.5397 (tp30) cc_final: 0.5156 (mm-30) REVERT: M 75 MET cc_start: 0.6020 (mtp) cc_final: 0.5214 (tmm) REVERT: M 79 ARG cc_start: 0.6368 (ttt-90) cc_final: 0.5925 (tmt170) REVERT: N 12 LYS cc_start: 0.7299 (tttt) cc_final: 0.7068 (ttmt) REVERT: N 21 PHE cc_start: 0.6636 (t80) cc_final: 0.6275 (t80) REVERT: N 30 ILE cc_start: 0.6668 (OUTLIER) cc_final: 0.6438 (mt) REVERT: N 41 ARG cc_start: 0.5425 (mtm-85) cc_final: 0.5009 (mtp180) REVERT: N 47 LYS cc_start: 0.5721 (tptp) cc_final: 0.5207 (mptt) REVERT: O 10 LYS cc_start: 0.6786 (mtpp) cc_final: 0.6202 (mptt) REVERT: O 26 GLU cc_start: 0.6782 (mp0) cc_final: 0.6468 (mp0) REVERT: O 57 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7852 (mp) REVERT: O 62 GLN cc_start: 0.7219 (tt0) cc_final: 0.6667 (mm110) REVERT: P 35 ARG cc_start: 0.7154 (ttt-90) cc_final: 0.6927 (ttt-90) REVERT: P 71 VAL cc_start: 0.7217 (p) cc_final: 0.6950 (m) REVERT: Q 11 ARG cc_start: 0.6287 (mtp-110) cc_final: 0.5697 (mtt180) REVERT: Q 44 LEU cc_start: 0.7821 (mt) cc_final: 0.7532 (mt) REVERT: R 50 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6479 (tttt) REVERT: R 73 ARG cc_start: 0.5503 (ttp-110) cc_final: 0.4969 (ptm-80) REVERT: T 24 ARG cc_start: 0.6552 (mmm160) cc_final: 0.6234 (mmm-85) REVERT: T 29 ARG cc_start: 0.7065 (mtm-85) cc_final: 0.6439 (mtt180) REVERT: T 49 LYS cc_start: 0.6539 (OUTLIER) cc_final: 0.6242 (tptp) REVERT: c 97 LYS cc_start: 0.7273 (ttmm) cc_final: 0.6896 (mmtt) REVERT: c 187 ASP cc_start: 0.7308 (m-30) cc_final: 0.7023 (m-30) REVERT: d 128 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7205 (mmp-170) REVERT: e 123 LYS cc_start: 0.6000 (tttm) cc_final: 0.5709 (mptt) REVERT: e 166 LYS cc_start: 0.6694 (mttp) cc_final: 0.6038 (mmtp) REVERT: f 48 LYS cc_start: 0.5934 (mmmt) cc_final: 0.5301 (ttpt) REVERT: f 51 ASP cc_start: 0.6334 (m-30) cc_final: 0.6101 (m-30) REVERT: f 98 GLU cc_start: 0.6709 (mt-10) cc_final: 0.6254 (mt-10) REVERT: f 101 GLU cc_start: 0.6766 (tt0) cc_final: 0.6471 (tm-30) REVERT: f 103 LEU cc_start: 0.6935 (tp) cc_final: 0.6417 (tm) REVERT: f 112 ARG cc_start: 0.5334 (mmm-85) cc_final: 0.4408 (mmm-85) REVERT: f 120 LYS cc_start: 0.6994 (ptpp) cc_final: 0.6592 (pptt) REVERT: f 134 GLU cc_start: 0.5888 (mt-10) cc_final: 0.5616 (mt-10) REVERT: f 147 ASP cc_start: 0.4051 (p0) cc_final: 0.3735 (t0) REVERT: f 148 ARG cc_start: 0.6013 (mtp-110) cc_final: 0.5283 (ptm-80) REVERT: f 167 ARG cc_start: 0.6602 (ttm110) cc_final: 0.5713 (ttp-170) REVERT: f 177 PHE cc_start: 0.6932 (m-80) cc_final: 0.6617 (m-80) REVERT: g 69 ARG cc_start: 0.8018 (tmt170) cc_final: 0.7732 (tpt90) REVERT: g 74 SER cc_start: 0.6467 (m) cc_final: 0.6201 (t) REVERT: g 94 TYR cc_start: 0.7312 (m-10) cc_final: 0.7018 (m-10) REVERT: g 99 LYS cc_start: 0.5609 (tppp) cc_final: 0.5225 (tmtm) REVERT: g 112 PRO cc_start: 0.6154 (Cg_endo) cc_final: 0.5777 (Cg_exo) REVERT: g 153 ARG cc_start: 0.6629 (mtt-85) cc_final: 0.6233 (mtt-85) REVERT: i 91 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7258 (mt-10) REVERT: i 95 ARG cc_start: 0.6919 (ttp-110) cc_final: 0.6436 (ttp80) REVERT: j 18 ARG cc_start: 0.7749 (mmm-85) cc_final: 0.7528 (mtp85) REVERT: j 20 MET cc_start: 0.8154 (ttp) cc_final: 0.7924 (ttm) REVERT: j 45 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.6296 (pm20) REVERT: j 73 ASP cc_start: 0.7897 (p0) cc_final: 0.7500 (p0) REVERT: j 117 SER cc_start: 0.7100 (p) cc_final: 0.6762 (m) REVERT: k 84 LYS cc_start: 0.7238 (ptpt) cc_final: 0.6626 (ptmt) REVERT: k 129 LYS cc_start: 0.6900 (mtpp) cc_final: 0.6523 (mptt) REVERT: l 58 LYS cc_start: 0.7387 (mttm) cc_final: 0.7129 (mtpt) REVERT: l 110 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6648 (tt0) REVERT: l 118 LYS cc_start: 0.7754 (ttpp) cc_final: 0.7378 (tttm) REVERT: l 127 LYS cc_start: 0.7445 (mtpp) cc_final: 0.6961 (mtpp) REVERT: m 89 SER cc_start: 0.6877 (p) cc_final: 0.6563 (m) REVERT: m 114 GLU cc_start: 0.7854 (pt0) cc_final: 0.7554 (pt0) REVERT: n 30 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7870 (ppt90) REVERT: n 46 GLU cc_start: 0.6531 (mm-30) cc_final: 0.5872 (mt-10) REVERT: n 80 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6157 (tt0) REVERT: n 108 ASP cc_start: 0.7334 (m-30) cc_final: 0.7057 (m-30) REVERT: o 6 LYS cc_start: 0.6926 (mtmm) cc_final: 0.6433 (mtmm) REVERT: o 7 GLN cc_start: 0.6887 (tm-30) cc_final: 0.6332 (tp40) REVERT: o 38 LYS cc_start: 0.7152 (ptmt) cc_final: 0.6869 (ptmm) REVERT: o 82 ASP cc_start: 0.7510 (t70) cc_final: 0.7078 (t70) REVERT: o 89 ARG cc_start: 0.7071 (mtm-85) cc_final: 0.6348 (mtt-85) REVERT: o 111 LYS cc_start: 0.7277 (ttpp) cc_final: 0.6852 (ttpt) REVERT: o 112 GLU cc_start: 0.6979 (tt0) cc_final: 0.6712 (tt0) REVERT: p 13 ARG cc_start: 0.7581 (mtp85) cc_final: 0.7321 (mtt180) REVERT: p 59 GLN cc_start: 0.8149 (mt0) cc_final: 0.7926 (tt0) REVERT: p 84 LYS cc_start: 0.7676 (tttm) cc_final: 0.6946 (tppt) REVERT: q 46 GLU cc_start: 0.5503 (OUTLIER) cc_final: 0.4976 (tt0) REVERT: q 48 LYS cc_start: 0.7508 (mtpt) cc_final: 0.7189 (mttp) REVERT: r 77 ASP cc_start: 0.8121 (m-30) cc_final: 0.7832 (m-30) REVERT: s 1 MET cc_start: 0.4079 (tpt) cc_final: 0.3743 (tpt) REVERT: t 46 GLN cc_start: 0.6908 (tp-100) cc_final: 0.5975 (tt0) REVERT: t 91 LYS cc_start: 0.5803 (mmtt) cc_final: 0.5025 (mptt) REVERT: u 50 MET cc_start: 0.7389 (ttm) cc_final: 0.6833 (ttm) REVERT: u 76 ASP cc_start: 0.6639 (t70) cc_final: 0.6387 (t70) REVERT: u 85 LYS cc_start: 0.7632 (mtpp) cc_final: 0.7131 (mtmt) REVERT: u 90 ASP cc_start: 0.8023 (m-30) cc_final: 0.7380 (m-30) REVERT: v 17 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7169 (tp30) REVERT: v 25 ARG cc_start: 0.7289 (mmt-90) cc_final: 0.6930 (mmt180) REVERT: v 44 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7620 (ptpp) REVERT: x 5 GLU cc_start: 0.5807 (mm-30) cc_final: 0.5587 (mp0) REVERT: x 23 ARG cc_start: 0.7163 (mtt90) cc_final: 0.6474 (ttp-110) REVERT: y 6 LYS cc_start: 0.7747 (mmtp) cc_final: 0.7183 (tppt) REVERT: y 19 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6768 (ttpt) REVERT: y 56 LYS cc_start: 0.7614 (ttpt) cc_final: 0.7057 (tttt) REVERT: 0 10 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7696 (ttpt) REVERT: 0 27 LYS cc_start: 0.7406 (mttp) cc_final: 0.7178 (mmtm) REVERT: 0 35 GLU cc_start: 0.6935 (tt0) cc_final: 0.6634 (tm-30) REVERT: 1 1 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6305 (mtm) REVERT: 1 41 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7049 (mpp-170) REVERT: 2 15 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7411 (mttt) REVERT: 2 59 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7628 (mt) REVERT: 3 9 LYS cc_start: 0.7954 (mttp) cc_final: 0.7671 (mttm) REVERT: 3 19 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7822 (mtm180) outliers start: 157 outliers final: 87 residues processed: 935 average time/residue: 2.3206 time to fit residues: 3040.9799 Evaluate side-chains 931 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 823 time to evaluate : 6.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 ARG Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 49 LYS Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 202 ILE Chi-restraints excluded: chain e residue 154 ASP Chi-restraints excluded: chain e residue 193 VAL Chi-restraints excluded: chain f residue 73 SER Chi-restraints excluded: chain f residue 111 ILE Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 161 LYS Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 136 GLN Chi-restraints excluded: chain j residue 45 GLU Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain m residue 36 THR Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain n residue 76 LYS Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain n residue 80 GLU Chi-restraints excluded: chain q residue 46 GLU Chi-restraints excluded: chain s residue 24 MET Chi-restraints excluded: chain s residue 26 LYS Chi-restraints excluded: chain s residue 55 VAL Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 65 ILE Chi-restraints excluded: chain u residue 8 VAL Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain v residue 44 LYS Chi-restraints excluded: chain v residue 83 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 41 ARG Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain 4 residue 1 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 923 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 545 optimal weight: 10.0000 chunk 699 optimal weight: 6.9990 chunk 541 optimal weight: 10.0000 chunk 806 optimal weight: 7.9990 chunk 534 optimal weight: 10.0000 chunk 954 optimal weight: 3.9990 chunk 597 optimal weight: 10.0000 chunk 581 optimal weight: 10.0000 chunk 440 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 100 GLN C 139 GLN D 54 GLN D 74 ASN D 126 ASN E 12 GLN E 78 ASN F 3 HIS G 97 ASN G 142 HIS ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS R 54 GLN T 20 HIS d 32 ASN f 81 GLN g 116 GLN i 67 ASN ** j 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 93 GLN n 38 GLN p 71 GLN q 6 GLN q 86 GLN u 12 GLN u 51 GLN u 75 GLN 1 29 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 153997 Z= 0.336 Angle : 0.842 19.136 230462 Z= 0.446 Chirality : 0.044 0.376 29304 Planarity : 0.008 0.149 12266 Dihedral : 23.206 179.022 77231 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.58 % Rotamer: Outliers : 3.72 % Allowed : 15.04 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.28 (0.11), residues: 5480 helix: 0.94 (0.12), residues: 1853 sheet: -0.43 (0.15), residues: 1089 loop : -0.87 (0.11), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 201 HIS 0.010 0.002 HIS u 44 PHE 0.026 0.003 PHE F 80 TYR 0.027 0.003 TYR p 32 ARG 0.009 0.001 ARG p 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 853 time to evaluate : 6.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 ASP cc_start: 0.3548 (p0) cc_final: 0.2310 (t70) REVERT: B 14 VAL cc_start: 0.3475 (m) cc_final: 0.3096 (m) REVERT: B 151 ILE cc_start: 0.4888 (pt) cc_final: 0.4649 (pp) REVERT: B 174 LYS cc_start: 0.3852 (tptp) cc_final: 0.2964 (tptm) REVERT: C 41 GLN cc_start: 0.6776 (tt0) cc_final: 0.6206 (tt0) REVERT: C 100 GLN cc_start: 0.6153 (tt0) cc_final: 0.5919 (tt0) REVERT: C 132 ARG cc_start: 0.6002 (mtp180) cc_final: 0.5357 (ttm170) REVERT: C 147 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7566 (mtpp) REVERT: D 8 LYS cc_start: 0.6167 (mmtp) cc_final: 0.5297 (mmtp) REVERT: D 45 LYS cc_start: 0.5889 (mtmm) cc_final: 0.5151 (mmtp) REVERT: D 128 ARG cc_start: 0.5041 (ttm110) cc_final: 0.4369 (ttp80) REVERT: D 159 LEU cc_start: 0.5065 (tt) cc_final: 0.4701 (mt) REVERT: E 45 ARG cc_start: 0.7088 (mtp85) cc_final: 0.6647 (mtm180) REVERT: E 65 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5617 (tm-30) REVERT: E 93 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7282 (mtp180) REVERT: E 146 ASN cc_start: 0.6640 (m-40) cc_final: 0.6384 (m110) REVERT: F 8 PHE cc_start: 0.7589 (p90) cc_final: 0.7178 (p90) REVERT: F 55 HIS cc_start: 0.6935 (m-70) cc_final: 0.6670 (m170) REVERT: G 41 SER cc_start: 0.7723 (m) cc_final: 0.7497 (m) REVERT: G 63 GLU cc_start: 0.6165 (mm-30) cc_final: 0.5793 (mm-30) REVERT: G 76 LYS cc_start: 0.6073 (mmtt) cc_final: 0.5482 (mmmt) REVERT: G 80 VAL cc_start: -0.0793 (OUTLIER) cc_final: -0.1367 (t) REVERT: G 106 GLU cc_start: 0.7323 (tt0) cc_final: 0.6778 (mm-30) REVERT: G 118 LEU cc_start: 0.7298 (tp) cc_final: 0.6783 (mt) REVERT: H 18 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7673 (mm-40) REVERT: H 21 ASN cc_start: 0.7794 (m110) cc_final: 0.7473 (m110) REVERT: H 31 LYS cc_start: 0.7187 (ttpt) cc_final: 0.6809 (tmmm) REVERT: H 96 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6700 (ttm) REVERT: I 36 GLU cc_start: 0.6033 (mm-30) cc_final: 0.5631 (mm-30) REVERT: I 72 ILE cc_start: 0.6963 (mt) cc_final: 0.6712 (mp) REVERT: I 97 GLU cc_start: 0.5460 (pm20) cc_final: 0.5227 (mm-30) REVERT: J 66 GLU cc_start: 0.7484 (pt0) cc_final: 0.7273 (pt0) REVERT: J 71 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7948 (tt) REVERT: J 88 MET cc_start: 0.3808 (mmp) cc_final: 0.3518 (mmt) REVERT: J 99 GLN cc_start: 0.5940 (mt0) cc_final: 0.5551 (tt0) REVERT: K 56 ARG cc_start: 0.6859 (mtp-110) cc_final: 0.6430 (mtp85) REVERT: K 98 ARG cc_start: 0.6628 (mtt90) cc_final: 0.6275 (mtt-85) REVERT: K 106 ARG cc_start: 0.5488 (ttp-110) cc_final: 0.4914 (tpt-90) REVERT: L 62 GLU cc_start: 0.7366 (tt0) cc_final: 0.6905 (tt0) REVERT: L 76 GLU cc_start: 0.5488 (tp30) cc_final: 0.5247 (mm-30) REVERT: M 75 MET cc_start: 0.5965 (mtp) cc_final: 0.5202 (tmm) REVERT: N 30 ILE cc_start: 0.6641 (OUTLIER) cc_final: 0.6409 (mt) REVERT: N 41 ARG cc_start: 0.5472 (mtm-85) cc_final: 0.5000 (mtp180) REVERT: N 47 LYS cc_start: 0.5706 (tptp) cc_final: 0.5216 (mptt) REVERT: O 10 LYS cc_start: 0.6837 (mtpp) cc_final: 0.6210 (mptt) REVERT: O 26 GLU cc_start: 0.6778 (mp0) cc_final: 0.6458 (mp0) REVERT: O 57 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7839 (mp) REVERT: O 62 GLN cc_start: 0.7193 (tt0) cc_final: 0.6620 (mm110) REVERT: P 35 ARG cc_start: 0.7178 (ttt-90) cc_final: 0.6955 (ttt-90) REVERT: P 71 VAL cc_start: 0.7248 (p) cc_final: 0.6988 (m) REVERT: Q 11 ARG cc_start: 0.6236 (mtp-110) cc_final: 0.5706 (mtt180) REVERT: Q 26 GLU cc_start: 0.6071 (OUTLIER) cc_final: 0.5672 (mm-30) REVERT: Q 27 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6296 (mtp-110) REVERT: Q 44 LEU cc_start: 0.7708 (mt) cc_final: 0.7477 (mt) REVERT: R 50 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6517 (tttt) REVERT: R 73 ARG cc_start: 0.5431 (ttp-110) cc_final: 0.4956 (ptm-80) REVERT: T 24 ARG cc_start: 0.6538 (mmm160) cc_final: 0.6227 (mmm-85) REVERT: T 29 ARG cc_start: 0.7096 (mtm-85) cc_final: 0.6521 (mtt180) REVERT: T 49 LYS cc_start: 0.6538 (OUTLIER) cc_final: 0.6305 (tptp) REVERT: T 54 MET cc_start: 0.6658 (tmm) cc_final: 0.6312 (tmm) REVERT: U 44 GLU cc_start: 0.6237 (pp20) cc_final: 0.5880 (pp20) REVERT: c 97 LYS cc_start: 0.7291 (ttmm) cc_final: 0.6908 (mmtt) REVERT: c 108 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7563 (ttpm) REVERT: c 187 ASP cc_start: 0.7313 (m-30) cc_final: 0.7041 (m-30) REVERT: d 128 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7233 (mmp-170) REVERT: d 172 VAL cc_start: 0.8412 (OUTLIER) cc_final: 0.7961 (t) REVERT: e 123 LYS cc_start: 0.5884 (tttm) cc_final: 0.5639 (mptt) REVERT: e 166 LYS cc_start: 0.6684 (mttp) cc_final: 0.6036 (mmtp) REVERT: f 17 MET cc_start: 0.5697 (mmm) cc_final: 0.5470 (mmt) REVERT: f 48 LYS cc_start: 0.5861 (mmmt) cc_final: 0.5246 (ttpt) REVERT: f 51 ASP cc_start: 0.6240 (m-30) cc_final: 0.5997 (m-30) REVERT: f 98 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6289 (mt-10) REVERT: f 101 GLU cc_start: 0.6750 (tt0) cc_final: 0.6467 (tm-30) REVERT: f 103 LEU cc_start: 0.6930 (tp) cc_final: 0.6413 (tm) REVERT: f 112 ARG cc_start: 0.5192 (mmm-85) cc_final: 0.4317 (mmm-85) REVERT: f 120 LYS cc_start: 0.7020 (ptpp) cc_final: 0.6599 (pptt) REVERT: f 134 GLU cc_start: 0.5962 (mt-10) cc_final: 0.5578 (mt-10) REVERT: f 147 ASP cc_start: 0.4065 (p0) cc_final: 0.3725 (t0) REVERT: f 148 ARG cc_start: 0.5860 (mtp-110) cc_final: 0.5211 (ptm-80) REVERT: f 167 ARG cc_start: 0.6550 (ttm110) cc_final: 0.5762 (ttp-170) REVERT: f 177 PHE cc_start: 0.6922 (m-80) cc_final: 0.6641 (m-80) REVERT: g 3 ARG cc_start: 0.5577 (OUTLIER) cc_final: 0.5003 (mtm-85) REVERT: g 36 THR cc_start: 0.6805 (OUTLIER) cc_final: 0.6471 (t) REVERT: g 69 ARG cc_start: 0.7993 (tmt170) cc_final: 0.7703 (tpt90) REVERT: g 74 SER cc_start: 0.6509 (m) cc_final: 0.6239 (t) REVERT: g 94 TYR cc_start: 0.7219 (m-10) cc_final: 0.6932 (m-10) REVERT: g 99 LYS cc_start: 0.5535 (tppp) cc_final: 0.4719 (pttt) REVERT: g 112 PRO cc_start: 0.6130 (Cg_endo) cc_final: 0.5761 (Cg_exo) REVERT: g 153 ARG cc_start: 0.6499 (mtt-85) cc_final: 0.6184 (mtt-85) REVERT: i 95 ARG cc_start: 0.6976 (ttp-110) cc_final: 0.6342 (ttm-80) REVERT: j 17 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6766 (mmt90) REVERT: j 18 ARG cc_start: 0.7729 (mmm-85) cc_final: 0.7518 (mtp85) REVERT: j 20 MET cc_start: 0.8149 (ttp) cc_final: 0.7927 (ttm) REVERT: j 45 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6309 (pm20) REVERT: j 73 ASP cc_start: 0.7929 (p0) cc_final: 0.7537 (p0) REVERT: j 117 SER cc_start: 0.7077 (p) cc_final: 0.6733 (m) REVERT: k 84 LYS cc_start: 0.7257 (ptpt) cc_final: 0.6648 (pttt) REVERT: k 129 LYS cc_start: 0.6770 (mtpp) cc_final: 0.6393 (mptt) REVERT: l 6 ARG cc_start: 0.7176 (ptt90) cc_final: 0.6097 (ptm-80) REVERT: l 58 LYS cc_start: 0.7429 (mttm) cc_final: 0.7162 (mtpt) REVERT: l 110 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6616 (tt0) REVERT: l 118 LYS cc_start: 0.7710 (ttpp) cc_final: 0.7399 (tttm) REVERT: l 127 LYS cc_start: 0.7430 (mtpp) cc_final: 0.6992 (mtpp) REVERT: m 78 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7145 (tmtp) REVERT: m 89 SER cc_start: 0.6888 (p) cc_final: 0.6568 (m) REVERT: m 114 GLU cc_start: 0.7851 (pt0) cc_final: 0.7552 (pt0) REVERT: n 30 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7877 (ppt90) REVERT: n 36 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.6192 (m-80) REVERT: n 46 GLU cc_start: 0.6526 (mm-30) cc_final: 0.5871 (mt-10) REVERT: n 80 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6237 (tt0) REVERT: n 108 ASP cc_start: 0.7335 (m-30) cc_final: 0.7058 (m-30) REVERT: o 6 LYS cc_start: 0.7003 (mtmm) cc_final: 0.6496 (mtmm) REVERT: o 7 GLN cc_start: 0.6925 (tm-30) cc_final: 0.6431 (tp40) REVERT: o 37 LYS cc_start: 0.5869 (OUTLIER) cc_final: 0.5498 (ptpp) REVERT: o 38 LYS cc_start: 0.7168 (ptmt) cc_final: 0.6801 (ptpp) REVERT: o 82 ASP cc_start: 0.7521 (t70) cc_final: 0.7077 (t70) REVERT: o 89 ARG cc_start: 0.7053 (mtm-85) cc_final: 0.6357 (mtt-85) REVERT: o 111 LYS cc_start: 0.7307 (ttpp) cc_final: 0.6886 (ttpt) REVERT: o 112 GLU cc_start: 0.7067 (tt0) cc_final: 0.6801 (tt0) REVERT: p 13 ARG cc_start: 0.7583 (mtp85) cc_final: 0.7311 (mtt180) REVERT: p 59 GLN cc_start: 0.8149 (mt0) cc_final: 0.7927 (tt0) REVERT: p 84 LYS cc_start: 0.7672 (tttm) cc_final: 0.6947 (tppt) REVERT: q 46 GLU cc_start: 0.5502 (OUTLIER) cc_final: 0.4985 (tt0) REVERT: q 48 LYS cc_start: 0.7498 (mtpt) cc_final: 0.7179 (mttp) REVERT: r 77 ASP cc_start: 0.8122 (m-30) cc_final: 0.7847 (m-30) REVERT: r 78 GLU cc_start: 0.7571 (pt0) cc_final: 0.7321 (mt-10) REVERT: s 1 MET cc_start: 0.4004 (tpt) cc_final: 0.3670 (tpt) REVERT: t 46 GLN cc_start: 0.6899 (tp-100) cc_final: 0.6647 (tp40) REVERT: t 91 LYS cc_start: 0.5831 (mmtt) cc_final: 0.5104 (mptt) REVERT: u 50 MET cc_start: 0.7425 (ttm) cc_final: 0.6854 (ttm) REVERT: u 85 LYS cc_start: 0.7590 (mtpp) cc_final: 0.7007 (mtmt) REVERT: u 90 ASP cc_start: 0.8020 (m-30) cc_final: 0.7379 (m-30) REVERT: v 17 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7131 (tp30) REVERT: v 25 ARG cc_start: 0.7270 (mmt-90) cc_final: 0.6918 (mmt180) REVERT: v 44 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7592 (ptpp) REVERT: x 23 ARG cc_start: 0.7138 (mtt90) cc_final: 0.6471 (ttp-110) REVERT: x 48 ARG cc_start: 0.6997 (mmt90) cc_final: 0.6608 (mmm-85) REVERT: y 6 LYS cc_start: 0.7709 (mmtp) cc_final: 0.7142 (tppt) REVERT: y 19 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6889 (ttpt) REVERT: y 56 LYS cc_start: 0.7708 (ttpt) cc_final: 0.7180 (tttm) REVERT: z 53 LYS cc_start: 0.7406 (tptm) cc_final: 0.7178 (tmtt) REVERT: 0 10 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7692 (ttpt) REVERT: 0 35 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6633 (tm-30) REVERT: 1 1 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.6289 (mtm) REVERT: 1 41 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7089 (mpp-170) REVERT: 2 15 LYS cc_start: 0.7950 (mmtt) cc_final: 0.7416 (mttt) REVERT: 2 52 LYS cc_start: 0.6969 (ttpt) cc_final: 0.6750 (ttpt) REVERT: 2 59 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7616 (mt) REVERT: 3 9 LYS cc_start: 0.7952 (mttp) cc_final: 0.7665 (mttm) REVERT: 3 19 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7821 (mtm180) outliers start: 170 outliers final: 91 residues processed: 954 average time/residue: 2.2904 time to fit residues: 3061.2283 Evaluate side-chains 958 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 833 time to evaluate : 6.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 ARG Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 49 LYS Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain c residue 108 LYS Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 202 ILE Chi-restraints excluded: chain e residue 154 ASP Chi-restraints excluded: chain e residue 193 VAL Chi-restraints excluded: chain e residue 196 VAL Chi-restraints excluded: chain f residue 111 ILE Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 161 LYS Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 136 GLN Chi-restraints excluded: chain j residue 17 ARG Chi-restraints excluded: chain j residue 45 GLU Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain m residue 36 THR Chi-restraints excluded: chain m residue 78 LYS Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 36 TYR Chi-restraints excluded: chain n residue 65 THR Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain n residue 76 LYS Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain n residue 80 GLU Chi-restraints excluded: chain n residue 115 LEU Chi-restraints excluded: chain o residue 37 LYS Chi-restraints excluded: chain q residue 46 GLU Chi-restraints excluded: chain q residue 71 LYS Chi-restraints excluded: chain s residue 24 MET Chi-restraints excluded: chain s residue 26 LYS Chi-restraints excluded: chain s residue 55 VAL Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain t residue 19 LYS Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 65 ILE Chi-restraints excluded: chain u residue 8 VAL Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain v residue 44 LYS Chi-restraints excluded: chain v residue 83 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 41 ARG Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain 4 residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 590 optimal weight: 10.0000 chunk 381 optimal weight: 3.9990 chunk 569 optimal weight: 10.0000 chunk 287 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 184 optimal weight: 9.9990 chunk 606 optimal weight: 10.0000 chunk 650 optimal weight: 10.0000 chunk 471 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 750 optimal weight: 4.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN D 54 GLN E 12 GLN F 3 HIS G 142 HIS ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS R 54 GLN T 20 HIS d 32 ASN f 81 GLN g 116 GLN i 67 ASN ** j 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 93 GLN n 38 GLN o 66 ASN q 6 GLN q 86 GLN u 12 GLN u 51 GLN u 75 GLN 1 29 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 153997 Z= 0.313 Angle : 0.821 18.437 230462 Z= 0.437 Chirality : 0.043 0.373 29304 Planarity : 0.008 0.148 12266 Dihedral : 23.189 179.125 77231 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.49 % Rotamer: Outliers : 3.26 % Allowed : 16.44 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.25 (0.11), residues: 5480 helix: 0.98 (0.12), residues: 1857 sheet: -0.40 (0.15), residues: 1076 loop : -0.87 (0.11), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 201 HIS 0.009 0.002 HIS u 44 PHE 0.023 0.003 PHE G 18 TYR 0.027 0.003 TYR p 32 ARG 0.009 0.001 ARG g 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 844 time to evaluate : 6.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 ASP cc_start: 0.3534 (p0) cc_final: 0.2298 (t70) REVERT: B 14 VAL cc_start: 0.3433 (m) cc_final: 0.3210 (m) REVERT: B 41 ILE cc_start: 0.4152 (mm) cc_final: 0.3230 (tp) REVERT: B 151 ILE cc_start: 0.4815 (pt) cc_final: 0.4590 (pp) REVERT: B 174 LYS cc_start: 0.3878 (tptp) cc_final: 0.2961 (tptm) REVERT: C 41 GLN cc_start: 0.6767 (tt0) cc_final: 0.6196 (tt0) REVERT: C 100 GLN cc_start: 0.6117 (tt0) cc_final: 0.5826 (tt0) REVERT: C 132 ARG cc_start: 0.5964 (mtp180) cc_final: 0.5332 (ttm170) REVERT: C 147 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7472 (mtpp) REVERT: D 8 LYS cc_start: 0.6148 (mmtp) cc_final: 0.5275 (mmtp) REVERT: D 45 LYS cc_start: 0.5894 (mtmm) cc_final: 0.5150 (mmtp) REVERT: D 128 ARG cc_start: 0.5119 (ttm110) cc_final: 0.4445 (ttp80) REVERT: D 159 LEU cc_start: 0.5246 (tt) cc_final: 0.4866 (mt) REVERT: E 45 ARG cc_start: 0.7137 (mtp85) cc_final: 0.6680 (mtm180) REVERT: E 65 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5607 (tm-30) REVERT: E 93 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7262 (mtp180) REVERT: E 146 ASN cc_start: 0.6633 (m-40) cc_final: 0.6377 (m110) REVERT: F 8 PHE cc_start: 0.7587 (p90) cc_final: 0.7302 (p90) REVERT: F 55 HIS cc_start: 0.6950 (m-70) cc_final: 0.6680 (m170) REVERT: G 41 SER cc_start: 0.7687 (m) cc_final: 0.7457 (m) REVERT: G 63 GLU cc_start: 0.6148 (mm-30) cc_final: 0.5782 (mm-30) REVERT: G 76 LYS cc_start: 0.6050 (mmtt) cc_final: 0.5475 (mmmt) REVERT: G 80 VAL cc_start: -0.0929 (OUTLIER) cc_final: -0.1646 (t) REVERT: G 106 GLU cc_start: 0.7299 (tt0) cc_final: 0.6756 (mm-30) REVERT: G 118 LEU cc_start: 0.7297 (tp) cc_final: 0.6785 (mt) REVERT: G 136 LYS cc_start: 0.7102 (ttmm) cc_final: 0.6078 (mptp) REVERT: H 18 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7636 (mm-40) REVERT: H 21 ASN cc_start: 0.7746 (m110) cc_final: 0.7424 (m110) REVERT: H 96 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6701 (ttm) REVERT: I 72 ILE cc_start: 0.6931 (mt) cc_final: 0.6691 (mp) REVERT: I 97 GLU cc_start: 0.5474 (pm20) cc_final: 0.5235 (mm-30) REVERT: J 66 GLU cc_start: 0.7507 (pt0) cc_final: 0.7255 (pt0) REVERT: J 71 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7956 (tt) REVERT: J 88 MET cc_start: 0.3813 (mmp) cc_final: 0.3534 (mmt) REVERT: J 99 GLN cc_start: 0.5983 (mt0) cc_final: 0.5587 (tt0) REVERT: K 56 ARG cc_start: 0.6879 (mtp-110) cc_final: 0.6444 (mtp85) REVERT: K 98 ARG cc_start: 0.6622 (mtt90) cc_final: 0.6267 (mtt-85) REVERT: K 106 ARG cc_start: 0.5524 (ttp-110) cc_final: 0.4875 (tpt-90) REVERT: L 19 SER cc_start: 0.6759 (p) cc_final: 0.6201 (m) REVERT: L 62 GLU cc_start: 0.7361 (tt0) cc_final: 0.6895 (tt0) REVERT: L 76 GLU cc_start: 0.5542 (tp30) cc_final: 0.5321 (mm-30) REVERT: M 75 MET cc_start: 0.5978 (mtp) cc_final: 0.5193 (tmm) REVERT: N 30 ILE cc_start: 0.6637 (OUTLIER) cc_final: 0.6403 (mt) REVERT: N 41 ARG cc_start: 0.5478 (mtm-85) cc_final: 0.5000 (mtp180) REVERT: N 47 LYS cc_start: 0.5746 (tptp) cc_final: 0.5239 (mptt) REVERT: O 10 LYS cc_start: 0.6831 (mtpp) cc_final: 0.6218 (mptt) REVERT: O 26 GLU cc_start: 0.6819 (mp0) cc_final: 0.6496 (mp0) REVERT: O 57 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7844 (mp) REVERT: O 62 GLN cc_start: 0.7229 (tt0) cc_final: 0.6667 (mm110) REVERT: P 35 ARG cc_start: 0.7160 (ttt-90) cc_final: 0.6936 (ttt-90) REVERT: P 71 VAL cc_start: 0.7261 (p) cc_final: 0.7005 (m) REVERT: Q 11 ARG cc_start: 0.6323 (mtp-110) cc_final: 0.5736 (mtt180) REVERT: Q 27 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6285 (mtp-110) REVERT: Q 44 LEU cc_start: 0.7679 (mt) cc_final: 0.7453 (mt) REVERT: R 29 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6759 (mp) REVERT: R 50 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6419 (tttt) REVERT: T 24 ARG cc_start: 0.6536 (mmm160) cc_final: 0.6222 (mmm-85) REVERT: T 29 ARG cc_start: 0.6993 (mtm-85) cc_final: 0.6407 (mtt180) REVERT: T 49 LYS cc_start: 0.6596 (OUTLIER) cc_final: 0.6326 (tptp) REVERT: T 54 MET cc_start: 0.6513 (tmm) cc_final: 0.6218 (tmm) REVERT: U 44 GLU cc_start: 0.6180 (pp20) cc_final: 0.5820 (pp20) REVERT: c 97 LYS cc_start: 0.7248 (ttmm) cc_final: 0.6876 (mmtt) REVERT: c 108 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7562 (ttpm) REVERT: c 187 ASP cc_start: 0.7317 (m-30) cc_final: 0.7033 (m-30) REVERT: d 128 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7238 (mmp-170) REVERT: e 123 LYS cc_start: 0.5992 (tttm) cc_final: 0.5725 (mptt) REVERT: e 166 LYS cc_start: 0.6700 (mttp) cc_final: 0.6006 (mmtp) REVERT: f 48 LYS cc_start: 0.5844 (mmmt) cc_final: 0.5226 (ttpt) REVERT: f 51 ASP cc_start: 0.6277 (m-30) cc_final: 0.6038 (m-30) REVERT: f 98 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6240 (mt-10) REVERT: f 101 GLU cc_start: 0.6770 (tt0) cc_final: 0.6483 (tm-30) REVERT: f 112 ARG cc_start: 0.5234 (mmm-85) cc_final: 0.4404 (mmm-85) REVERT: f 120 LYS cc_start: 0.7073 (ptpp) cc_final: 0.6644 (pptt) REVERT: f 134 GLU cc_start: 0.5884 (mt-10) cc_final: 0.5493 (mt-10) REVERT: f 147 ASP cc_start: 0.3735 (p0) cc_final: 0.3532 (t0) REVERT: f 167 ARG cc_start: 0.6533 (ttm110) cc_final: 0.5728 (ttp-170) REVERT: f 177 PHE cc_start: 0.6963 (m-80) cc_final: 0.6702 (m-80) REVERT: g 36 THR cc_start: 0.6770 (OUTLIER) cc_final: 0.6453 (t) REVERT: g 69 ARG cc_start: 0.7992 (tmt170) cc_final: 0.7711 (tpt90) REVERT: g 74 SER cc_start: 0.6586 (m) cc_final: 0.6287 (t) REVERT: g 94 TYR cc_start: 0.7231 (m-10) cc_final: 0.6940 (m-10) REVERT: g 99 LYS cc_start: 0.5520 (tppp) cc_final: 0.4710 (pttt) REVERT: g 112 PRO cc_start: 0.6188 (Cg_endo) cc_final: 0.5827 (Cg_exo) REVERT: i 1 MET cc_start: 0.5337 (mtt) cc_final: 0.5096 (mtt) REVERT: i 95 ARG cc_start: 0.6959 (ttp-110) cc_final: 0.6580 (ttp80) REVERT: j 17 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6761 (mmt90) REVERT: j 18 ARG cc_start: 0.7729 (mmm-85) cc_final: 0.7515 (mtp85) REVERT: j 20 MET cc_start: 0.8147 (ttp) cc_final: 0.7926 (ttm) REVERT: j 45 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6309 (pm20) REVERT: j 73 ASP cc_start: 0.7924 (p0) cc_final: 0.7516 (p0) REVERT: j 117 SER cc_start: 0.7089 (p) cc_final: 0.6749 (m) REVERT: k 84 LYS cc_start: 0.7231 (ptpt) cc_final: 0.6607 (pttt) REVERT: k 129 LYS cc_start: 0.6841 (mtpp) cc_final: 0.6446 (mptt) REVERT: l 6 ARG cc_start: 0.7183 (ptt90) cc_final: 0.6201 (ptm-80) REVERT: l 58 LYS cc_start: 0.7384 (mttm) cc_final: 0.7123 (mtpt) REVERT: l 110 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6591 (tt0) REVERT: l 118 LYS cc_start: 0.7711 (ttpp) cc_final: 0.7407 (tttm) REVERT: l 127 LYS cc_start: 0.7428 (mtpp) cc_final: 0.6997 (mtpp) REVERT: m 78 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7134 (tmtp) REVERT: m 89 SER cc_start: 0.6899 (p) cc_final: 0.6575 (m) REVERT: m 114 GLU cc_start: 0.7862 (pt0) cc_final: 0.7568 (pt0) REVERT: n 30 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7869 (ppt90) REVERT: n 36 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.6187 (m-80) REVERT: n 46 GLU cc_start: 0.6514 (mm-30) cc_final: 0.5840 (mt-10) REVERT: n 80 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6264 (tt0) REVERT: n 92 PHE cc_start: 0.8095 (t80) cc_final: 0.7823 (t80) REVERT: n 108 ASP cc_start: 0.7346 (m-30) cc_final: 0.7089 (m-30) REVERT: o 6 LYS cc_start: 0.7002 (mtmm) cc_final: 0.6509 (mtmm) REVERT: o 7 GLN cc_start: 0.6873 (tm-30) cc_final: 0.6388 (tp40) REVERT: o 38 LYS cc_start: 0.7159 (ptmt) cc_final: 0.6864 (ptmm) REVERT: o 82 ASP cc_start: 0.7473 (t70) cc_final: 0.7033 (t70) REVERT: o 89 ARG cc_start: 0.7062 (mtm-85) cc_final: 0.6368 (mtt-85) REVERT: o 111 LYS cc_start: 0.7313 (ttpp) cc_final: 0.6892 (ttpt) REVERT: o 112 GLU cc_start: 0.7066 (tt0) cc_final: 0.6809 (tt0) REVERT: p 13 ARG cc_start: 0.7574 (mtp85) cc_final: 0.7297 (mtt180) REVERT: p 59 GLN cc_start: 0.8142 (mt0) cc_final: 0.7938 (tt0) REVERT: p 84 LYS cc_start: 0.7676 (tttm) cc_final: 0.6957 (tppt) REVERT: q 46 GLU cc_start: 0.5525 (OUTLIER) cc_final: 0.4994 (tt0) REVERT: q 48 LYS cc_start: 0.7468 (mtpt) cc_final: 0.7148 (mttp) REVERT: r 77 ASP cc_start: 0.8121 (m-30) cc_final: 0.7835 (m-30) REVERT: s 1 MET cc_start: 0.3937 (tpt) cc_final: 0.3607 (tpt) REVERT: t 46 GLN cc_start: 0.6895 (tp-100) cc_final: 0.6638 (tp40) REVERT: t 91 LYS cc_start: 0.5812 (mmtt) cc_final: 0.5081 (mptt) REVERT: u 50 MET cc_start: 0.7389 (ttm) cc_final: 0.6861 (ttm) REVERT: u 85 LYS cc_start: 0.7571 (mtpp) cc_final: 0.7054 (mtmt) REVERT: u 90 ASP cc_start: 0.8035 (m-30) cc_final: 0.7384 (m-30) REVERT: v 17 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7190 (tp30) REVERT: v 25 ARG cc_start: 0.7285 (mmt-90) cc_final: 0.6935 (mmt180) REVERT: v 44 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7593 (ptpp) REVERT: x 5 GLU cc_start: 0.5920 (mm-30) cc_final: 0.5506 (mp0) REVERT: x 23 ARG cc_start: 0.7131 (mtt90) cc_final: 0.6460 (ttp-110) REVERT: y 6 LYS cc_start: 0.7688 (mmtp) cc_final: 0.7118 (mptt) REVERT: y 19 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6886 (ttpt) REVERT: y 37 GLU cc_start: 0.6633 (tt0) cc_final: 0.6172 (mt-10) REVERT: y 56 LYS cc_start: 0.7703 (ttpt) cc_final: 0.7154 (tttm) REVERT: z 53 LYS cc_start: 0.7422 (tptm) cc_final: 0.7201 (tmtt) REVERT: 0 10 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7657 (ttpt) REVERT: 0 35 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6610 (tm-30) REVERT: 1 1 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6270 (mtm) REVERT: 1 41 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6983 (mpp-170) REVERT: 2 15 LYS cc_start: 0.7941 (mmtt) cc_final: 0.7409 (mttt) REVERT: 2 59 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7611 (mt) REVERT: 3 9 LYS cc_start: 0.7962 (mttp) cc_final: 0.7682 (mttm) REVERT: 3 19 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7807 (mtm180) outliers start: 149 outliers final: 93 residues processed: 940 average time/residue: 2.2752 time to fit residues: 3005.3561 Evaluate side-chains 955 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 831 time to evaluate : 6.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 ARG Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain G residue 4 ARG Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 49 LYS Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain c residue 108 LYS Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 202 ILE Chi-restraints excluded: chain e residue 154 ASP Chi-restraints excluded: chain e residue 193 VAL Chi-restraints excluded: chain e residue 196 VAL Chi-restraints excluded: chain f residue 111 ILE Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 161 LYS Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 24 ILE Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 136 GLN Chi-restraints excluded: chain j residue 17 ARG Chi-restraints excluded: chain j residue 45 GLU Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain m residue 36 THR Chi-restraints excluded: chain m residue 78 LYS Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 36 TYR Chi-restraints excluded: chain n residue 65 THR Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain n residue 76 LYS Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain n residue 80 GLU Chi-restraints excluded: chain n residue 115 LEU Chi-restraints excluded: chain q residue 46 GLU Chi-restraints excluded: chain q residue 71 LYS Chi-restraints excluded: chain s residue 24 MET Chi-restraints excluded: chain s residue 26 LYS Chi-restraints excluded: chain s residue 55 VAL Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 65 ILE Chi-restraints excluded: chain u residue 8 VAL Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain v residue 44 LYS Chi-restraints excluded: chain v residue 83 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 41 ARG Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain 3 residue 34 LYS Chi-restraints excluded: chain 4 residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 868 optimal weight: 0.8980 chunk 914 optimal weight: 0.6980 chunk 834 optimal weight: 1.9990 chunk 889 optimal weight: 9.9990 chunk 913 optimal weight: 5.9990 chunk 535 optimal weight: 30.0000 chunk 387 optimal weight: 10.0000 chunk 698 optimal weight: 8.9990 chunk 272 optimal weight: 4.9990 chunk 803 optimal weight: 3.9990 chunk 840 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN D 54 GLN D 74 ASN E 12 GLN F 3 HIS G 142 HIS ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS R 54 GLN T 20 HIS T 52 ASN T 82 GLN d 32 ASN f 81 GLN g 116 GLN i 67 ASN ** j 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 93 GLN n 38 GLN q 6 GLN q 66 HIS q 86 GLN u 12 GLN ** u 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 75 GLN 1 29 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 153997 Z= 0.139 Angle : 0.664 14.236 230462 Z= 0.374 Chirality : 0.037 0.422 29304 Planarity : 0.007 0.129 12266 Dihedral : 23.080 178.896 77231 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.41 % Favored : 96.51 % Rotamer: Outliers : 2.03 % Allowed : 17.92 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.11), residues: 5480 helix: 1.45 (0.12), residues: 1859 sheet: -0.27 (0.15), residues: 1074 loop : -0.71 (0.12), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 201 HIS 0.008 0.001 HIS F 11 PHE 0.027 0.002 PHE G 18 TYR 0.017 0.002 TYR C 42 ARG 0.009 0.001 ARG t 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 859 time to evaluate : 6.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 ASP cc_start: 0.3495 (p0) cc_final: 0.2249 (t70) REVERT: B 14 VAL cc_start: 0.3429 (m) cc_final: 0.3137 (m) REVERT: B 70 VAL cc_start: 0.4970 (OUTLIER) cc_final: 0.4495 (t) REVERT: B 103 ASN cc_start: 0.6517 (t0) cc_final: 0.6032 (t0) REVERT: B 151 ILE cc_start: 0.4790 (pt) cc_final: 0.4584 (pp) REVERT: B 174 LYS cc_start: 0.3850 (tptp) cc_final: 0.3023 (tptm) REVERT: C 41 GLN cc_start: 0.6733 (tt0) cc_final: 0.6127 (tt0) REVERT: C 129 MET cc_start: 0.5851 (mmm) cc_final: 0.5059 (ttm) REVERT: C 132 ARG cc_start: 0.5972 (mtp180) cc_final: 0.5296 (ttm170) REVERT: C 147 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7434 (mtpp) REVERT: D 8 LYS cc_start: 0.6078 (mmtp) cc_final: 0.5340 (mmtp) REVERT: D 35 GLU cc_start: 0.5409 (pm20) cc_final: 0.4610 (mm-30) REVERT: D 45 LYS cc_start: 0.5905 (mtmm) cc_final: 0.5160 (mmtp) REVERT: D 70 ARG cc_start: 0.7299 (tpp80) cc_final: 0.7078 (tpp80) REVERT: D 128 ARG cc_start: 0.5035 (ttm110) cc_final: 0.4386 (ttp80) REVERT: D 159 LEU cc_start: 0.5247 (tt) cc_final: 0.4831 (mt) REVERT: E 45 ARG cc_start: 0.7068 (mtp85) cc_final: 0.6626 (mtm180) REVERT: E 71 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7326 (mtm) REVERT: E 93 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7160 (mtp180) REVERT: E 146 ASN cc_start: 0.6596 (m-40) cc_final: 0.6339 (m110) REVERT: F 8 PHE cc_start: 0.7576 (p90) cc_final: 0.7097 (p90) REVERT: F 55 HIS cc_start: 0.6898 (m-70) cc_final: 0.6633 (m170) REVERT: G 25 LYS cc_start: 0.6937 (tppt) cc_final: 0.6695 (tptt) REVERT: G 41 SER cc_start: 0.7540 (m) cc_final: 0.7241 (m) REVERT: G 63 GLU cc_start: 0.6132 (mm-30) cc_final: 0.5762 (mm-30) REVERT: G 76 LYS cc_start: 0.5901 (mmtt) cc_final: 0.5414 (mmmt) REVERT: G 106 GLU cc_start: 0.7223 (tt0) cc_final: 0.6635 (mm-30) REVERT: G 118 LEU cc_start: 0.7248 (tp) cc_final: 0.6766 (mt) REVERT: G 136 LYS cc_start: 0.7097 (ttmm) cc_final: 0.6070 (mptp) REVERT: H 18 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7615 (mm-40) REVERT: H 21 ASN cc_start: 0.7694 (m110) cc_final: 0.7351 (m110) REVERT: H 31 LYS cc_start: 0.7069 (ttpt) cc_final: 0.6668 (tmmm) REVERT: H 96 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6620 (ttm) REVERT: I 57 MET cc_start: 0.6259 (mtt) cc_final: 0.5173 (tpp) REVERT: I 72 ILE cc_start: 0.6974 (mt) cc_final: 0.6735 (mp) REVERT: I 97 GLU cc_start: 0.5486 (pm20) cc_final: 0.5157 (mm-30) REVERT: J 66 GLU cc_start: 0.7490 (pt0) cc_final: 0.7240 (pt0) REVERT: J 88 MET cc_start: 0.3474 (mmp) cc_final: 0.3263 (mmt) REVERT: K 56 ARG cc_start: 0.6849 (mtp-110) cc_final: 0.6625 (mmm-85) REVERT: K 98 ARG cc_start: 0.6605 (mtt90) cc_final: 0.6371 (mtt-85) REVERT: K 106 ARG cc_start: 0.5490 (ttp-110) cc_final: 0.4859 (tpt-90) REVERT: L 19 SER cc_start: 0.6706 (p) cc_final: 0.6464 (t) REVERT: L 62 GLU cc_start: 0.7381 (tt0) cc_final: 0.6928 (tt0) REVERT: M 28 THR cc_start: 0.6533 (m) cc_final: 0.6012 (m) REVERT: M 75 MET cc_start: 0.5939 (mtp) cc_final: 0.5165 (tmm) REVERT: N 41 ARG cc_start: 0.5368 (mtm-85) cc_final: 0.4893 (mtp180) REVERT: N 47 LYS cc_start: 0.5650 (tptp) cc_final: 0.5215 (mptt) REVERT: O 10 LYS cc_start: 0.6822 (mtpp) cc_final: 0.6202 (mptt) REVERT: O 26 GLU cc_start: 0.6784 (mp0) cc_final: 0.6457 (mp0) REVERT: O 62 GLN cc_start: 0.7181 (tt0) cc_final: 0.6632 (mm110) REVERT: O 68 ASP cc_start: 0.7165 (m-30) cc_final: 0.6899 (m-30) REVERT: Q 11 ARG cc_start: 0.6179 (mtp-110) cc_final: 0.5654 (mtt180) REVERT: Q 44 LEU cc_start: 0.7685 (mt) cc_final: 0.7450 (mt) REVERT: R 50 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6250 (tttt) REVERT: R 57 ARG cc_start: 0.6777 (ttm110) cc_final: 0.6265 (mtm-85) REVERT: R 73 ARG cc_start: 0.5324 (ttp-110) cc_final: 0.4834 (ptm-80) REVERT: S 20 GLU cc_start: 0.5301 (pt0) cc_final: 0.4986 (pt0) REVERT: T 24 ARG cc_start: 0.6555 (mmm160) cc_final: 0.6218 (mmm-85) REVERT: T 29 ARG cc_start: 0.6996 (mtm-85) cc_final: 0.6560 (mtt180) REVERT: T 52 ASN cc_start: 0.5596 (m110) cc_final: 0.5095 (t0) REVERT: U 44 GLU cc_start: 0.6195 (pp20) cc_final: 0.5865 (pp20) REVERT: c 97 LYS cc_start: 0.7202 (ttmm) cc_final: 0.6908 (mmtt) REVERT: c 182 ARG cc_start: 0.8276 (ttt90) cc_final: 0.8054 (tpt90) REVERT: c 187 ASP cc_start: 0.7285 (m-30) cc_final: 0.7034 (m-30) REVERT: d 128 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6976 (mmp-170) REVERT: e 123 LYS cc_start: 0.5928 (tttm) cc_final: 0.5681 (mptt) REVERT: e 148 ILE cc_start: 0.7266 (mt) cc_final: 0.7049 (mm) REVERT: e 154 ASP cc_start: 0.4305 (OUTLIER) cc_final: 0.4017 (p0) REVERT: e 169 VAL cc_start: 0.7137 (t) cc_final: 0.6672 (m) REVERT: f 51 ASP cc_start: 0.6284 (m-30) cc_final: 0.6022 (m-30) REVERT: f 98 GLU cc_start: 0.6667 (mt-10) cc_final: 0.6193 (mt-10) REVERT: f 101 GLU cc_start: 0.6733 (tt0) cc_final: 0.6473 (tm-30) REVERT: f 112 ARG cc_start: 0.5094 (mmm-85) cc_final: 0.4239 (mmm-85) REVERT: f 120 LYS cc_start: 0.7012 (ptpp) cc_final: 0.6622 (pptt) REVERT: f 134 GLU cc_start: 0.5889 (mt-10) cc_final: 0.5605 (mt-10) REVERT: f 147 ASP cc_start: 0.3521 (p0) cc_final: 0.3314 (t0) REVERT: f 167 ARG cc_start: 0.6517 (ttm110) cc_final: 0.5721 (ttp-170) REVERT: f 177 PHE cc_start: 0.6903 (m-80) cc_final: 0.6642 (m-80) REVERT: g 69 ARG cc_start: 0.7930 (tmt170) cc_final: 0.7675 (tpt90) REVERT: g 74 SER cc_start: 0.6592 (m) cc_final: 0.6360 (t) REVERT: g 94 TYR cc_start: 0.7226 (m-10) cc_final: 0.6952 (m-10) REVERT: g 99 LYS cc_start: 0.5555 (tppp) cc_final: 0.4748 (pttt) REVERT: g 112 PRO cc_start: 0.6162 (Cg_endo) cc_final: 0.5804 (Cg_exo) REVERT: i 1 MET cc_start: 0.5274 (mtt) cc_final: 0.5060 (mtt) REVERT: i 95 ARG cc_start: 0.6949 (ttp-110) cc_final: 0.6355 (ttm-80) REVERT: j 45 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6304 (pm20) REVERT: j 73 ASP cc_start: 0.7879 (p0) cc_final: 0.7465 (p0) REVERT: j 117 SER cc_start: 0.7108 (p) cc_final: 0.6777 (m) REVERT: k 84 LYS cc_start: 0.7291 (ptpt) cc_final: 0.6688 (ptmt) REVERT: k 129 LYS cc_start: 0.6602 (mtpp) cc_final: 0.6283 (mptt) REVERT: l 6 ARG cc_start: 0.7106 (ptt90) cc_final: 0.6109 (ptm-80) REVERT: l 58 LYS cc_start: 0.7324 (mttm) cc_final: 0.7081 (mtpt) REVERT: l 110 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6508 (tt0) REVERT: l 118 LYS cc_start: 0.7686 (ttpp) cc_final: 0.7387 (tttm) REVERT: l 127 LYS cc_start: 0.7438 (mtpp) cc_final: 0.6932 (mtpp) REVERT: m 89 SER cc_start: 0.6886 (p) cc_final: 0.6551 (m) REVERT: n 16 ARG cc_start: 0.7079 (mmp80) cc_final: 0.6666 (mmt-90) REVERT: n 26 LEU cc_start: 0.7772 (tp) cc_final: 0.7519 (tp) REVERT: n 36 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.6016 (m-80) REVERT: n 46 GLU cc_start: 0.6456 (mm-30) cc_final: 0.5803 (mt-10) REVERT: n 108 ASP cc_start: 0.7307 (m-30) cc_final: 0.7063 (m-30) REVERT: o 6 LYS cc_start: 0.7023 (mtmm) cc_final: 0.6465 (mtmm) REVERT: o 7 GLN cc_start: 0.6910 (tm-30) cc_final: 0.6450 (tp40) REVERT: o 37 LYS cc_start: 0.5759 (ptpt) cc_final: 0.5408 (ptpp) REVERT: o 38 LYS cc_start: 0.7150 (ptmt) cc_final: 0.6876 (ptmm) REVERT: o 82 ASP cc_start: 0.7498 (t70) cc_final: 0.7077 (t70) REVERT: o 89 ARG cc_start: 0.7017 (mtm-85) cc_final: 0.6486 (mtp180) REVERT: o 111 LYS cc_start: 0.7189 (ttpp) cc_final: 0.6845 (ttpt) REVERT: o 112 GLU cc_start: 0.6976 (tt0) cc_final: 0.6672 (tt0) REVERT: p 13 ARG cc_start: 0.7551 (mtp85) cc_final: 0.7138 (mtt-85) REVERT: p 84 LYS cc_start: 0.7641 (tttm) cc_final: 0.6938 (tppt) REVERT: q 46 GLU cc_start: 0.5586 (OUTLIER) cc_final: 0.5024 (tt0) REVERT: q 48 LYS cc_start: 0.7490 (mtpt) cc_final: 0.7180 (mttp) REVERT: r 77 ASP cc_start: 0.8101 (m-30) cc_final: 0.7816 (m-30) REVERT: s 1 MET cc_start: 0.4040 (tpt) cc_final: 0.3684 (tpt) REVERT: t 46 GLN cc_start: 0.6861 (tp-100) cc_final: 0.6602 (tp40) REVERT: t 91 LYS cc_start: 0.5701 (mmtt) cc_final: 0.4986 (mptt) REVERT: u 50 MET cc_start: 0.7311 (ttm) cc_final: 0.6771 (ttm) REVERT: u 85 LYS cc_start: 0.7510 (mtpp) cc_final: 0.6991 (mtmt) REVERT: u 90 ASP cc_start: 0.8020 (m-30) cc_final: 0.7403 (m-30) REVERT: v 17 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7133 (tp30) REVERT: v 25 ARG cc_start: 0.7338 (mmt-90) cc_final: 0.6947 (mmt180) REVERT: v 44 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7559 (ptpp) REVERT: x 5 GLU cc_start: 0.5714 (mm-30) cc_final: 0.5276 (mp0) REVERT: x 23 ARG cc_start: 0.7133 (mtt90) cc_final: 0.6461 (ttp-110) REVERT: y 6 LYS cc_start: 0.7758 (mmtp) cc_final: 0.7129 (tppt) REVERT: y 19 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.6928 (ttpt) REVERT: y 56 LYS cc_start: 0.7675 (ttpt) cc_final: 0.7174 (tttt) REVERT: 0 35 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6631 (tm-30) REVERT: 1 41 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6989 (mpp-170) REVERT: 2 15 LYS cc_start: 0.7881 (mmtt) cc_final: 0.7379 (mttt) REVERT: 2 52 LYS cc_start: 0.6849 (ttpt) cc_final: 0.6645 (ttpt) REVERT: 2 59 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7624 (mt) REVERT: 3 9 LYS cc_start: 0.7961 (mttp) cc_final: 0.7702 (mttm) REVERT: 3 19 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7664 (mtm180) outliers start: 93 outliers final: 50 residues processed: 919 average time/residue: 2.3618 time to fit residues: 3037.0740 Evaluate side-chains 905 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 837 time to evaluate : 6.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 ARG Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 202 ILE Chi-restraints excluded: chain e residue 154 ASP Chi-restraints excluded: chain f residue 111 ILE Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain j residue 45 GLU Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain n residue 36 TYR Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain q residue 46 GLU Chi-restraints excluded: chain s residue 24 MET Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain u residue 8 VAL Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain v residue 44 LYS Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 1 residue 41 ARG Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 3 residue 19 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 886 optimal weight: 10.0000 chunk 583 optimal weight: 10.0000 chunk 940 optimal weight: 4.9990 chunk 573 optimal weight: 9.9990 chunk 446 optimal weight: 10.0000 chunk 653 optimal weight: 10.0000 chunk 986 optimal weight: 10.0000 chunk 907 optimal weight: 10.0000 chunk 785 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 606 optimal weight: 10.0000 overall best weight: 7.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN C 139 GLN D 54 GLN E 12 GLN F 3 HIS G 142 HIS I 75 GLN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS R 54 GLN T 20 HIS T 82 GLN f 81 GLN g 88 GLN g 116 GLN i 67 ASN ** j 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 89 ASN j 93 GLN n 38 GLN q 6 GLN q 86 GLN u 12 GLN ** u 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 75 GLN 1 29 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 153997 Z= 0.338 Angle : 0.844 19.155 230462 Z= 0.446 Chirality : 0.044 0.381 29304 Planarity : 0.008 0.150 12266 Dihedral : 23.172 179.127 77231 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.42 % Favored : 95.47 % Rotamer: Outliers : 2.25 % Allowed : 18.10 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.11), residues: 5480 helix: 1.11 (0.12), residues: 1857 sheet: -0.35 (0.15), residues: 1085 loop : -0.82 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP c 248 HIS 0.010 0.002 HIS u 44 PHE 0.031 0.003 PHE q 53 TYR 0.027 0.003 TYR p 32 ARG 0.011 0.001 ARG j 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 828 time to evaluate : 6.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 ASP cc_start: 0.3630 (p0) cc_final: 0.2370 (t70) REVERT: B 151 ILE cc_start: 0.4868 (pt) cc_final: 0.4639 (pp) REVERT: B 167 ASP cc_start: 0.3505 (m-30) cc_final: 0.2847 (m-30) REVERT: B 174 LYS cc_start: 0.3913 (tptp) cc_final: 0.2998 (tptm) REVERT: C 41 GLN cc_start: 0.6780 (tt0) cc_final: 0.6177 (tt0) REVERT: C 100 GLN cc_start: 0.6069 (tt0) cc_final: 0.5836 (tt0) REVERT: C 132 ARG cc_start: 0.5964 (mtp180) cc_final: 0.5340 (ttm170) REVERT: C 147 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7469 (mtpp) REVERT: D 8 LYS cc_start: 0.6212 (mmtp) cc_final: 0.5351 (mmtp) REVERT: D 45 LYS cc_start: 0.5889 (mtmm) cc_final: 0.5152 (mmtp) REVERT: D 124 MET cc_start: 0.6008 (ptp) cc_final: 0.5695 (ptt) REVERT: D 128 ARG cc_start: 0.5130 (ttm110) cc_final: 0.4482 (ttp80) REVERT: E 45 ARG cc_start: 0.7114 (mtp85) cc_final: 0.6659 (mtm180) REVERT: E 93 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7258 (mtp180) REVERT: E 146 ASN cc_start: 0.6636 (m-40) cc_final: 0.6378 (m110) REVERT: F 8 PHE cc_start: 0.7594 (p90) cc_final: 0.7150 (p90) REVERT: F 55 HIS cc_start: 0.6934 (m-70) cc_final: 0.6681 (m170) REVERT: G 41 SER cc_start: 0.7670 (m) cc_final: 0.7434 (m) REVERT: G 63 GLU cc_start: 0.6172 (mm-30) cc_final: 0.5809 (mm-30) REVERT: G 80 VAL cc_start: -0.0901 (OUTLIER) cc_final: -0.1595 (t) REVERT: G 106 GLU cc_start: 0.7299 (tt0) cc_final: 0.6777 (mm-30) REVERT: G 118 LEU cc_start: 0.7299 (tp) cc_final: 0.6775 (mt) REVERT: H 18 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7640 (mm-40) REVERT: H 21 ASN cc_start: 0.7748 (m110) cc_final: 0.7404 (m110) REVERT: I 36 GLU cc_start: 0.5989 (mm-30) cc_final: 0.5652 (mm-30) REVERT: I 72 ILE cc_start: 0.6960 (mt) cc_final: 0.6712 (mp) REVERT: I 97 GLU cc_start: 0.5479 (pm20) cc_final: 0.5252 (mm-30) REVERT: J 66 GLU cc_start: 0.7507 (pt0) cc_final: 0.7270 (pt0) REVERT: J 88 MET cc_start: 0.3823 (mmp) cc_final: 0.3529 (mmt) REVERT: J 99 GLN cc_start: 0.5999 (mt0) cc_final: 0.5583 (tt0) REVERT: K 56 ARG cc_start: 0.6898 (mtp-110) cc_final: 0.6468 (mtp85) REVERT: K 98 ARG cc_start: 0.6649 (mtt90) cc_final: 0.6288 (mtt-85) REVERT: K 106 ARG cc_start: 0.5542 (ttp-110) cc_final: 0.5041 (ttt-90) REVERT: L 62 GLU cc_start: 0.7367 (tt0) cc_final: 0.6902 (tt0) REVERT: L 111 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7178 (mmtt) REVERT: M 75 MET cc_start: 0.5968 (mtp) cc_final: 0.5180 (tmm) REVERT: N 30 ILE cc_start: 0.6623 (OUTLIER) cc_final: 0.6394 (mt) REVERT: N 41 ARG cc_start: 0.5435 (mtm-85) cc_final: 0.4951 (mtp180) REVERT: N 47 LYS cc_start: 0.5685 (tptp) cc_final: 0.5229 (mptt) REVERT: O 10 LYS cc_start: 0.6860 (mtpp) cc_final: 0.6238 (mptt) REVERT: O 26 GLU cc_start: 0.6792 (mp0) cc_final: 0.6474 (mp0) REVERT: O 62 GLN cc_start: 0.7191 (tt0) cc_final: 0.6622 (mm110) REVERT: Q 11 ARG cc_start: 0.6262 (mtp-110) cc_final: 0.5705 (mtt180) REVERT: Q 44 LEU cc_start: 0.7684 (mt) cc_final: 0.7455 (mt) REVERT: R 29 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6632 (mp) REVERT: R 50 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6454 (tttt) REVERT: T 24 ARG cc_start: 0.6532 (mmm160) cc_final: 0.6219 (mmm-85) REVERT: T 29 ARG cc_start: 0.6983 (mtm-85) cc_final: 0.6450 (mtt180) REVERT: U 44 GLU cc_start: 0.6189 (pp20) cc_final: 0.5844 (pp20) REVERT: c 97 LYS cc_start: 0.7250 (ttmm) cc_final: 0.6880 (mmtt) REVERT: c 187 ASP cc_start: 0.7336 (m-30) cc_final: 0.7066 (m-30) REVERT: d 128 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7228 (mmp-170) REVERT: e 123 LYS cc_start: 0.5994 (tttm) cc_final: 0.5719 (mptt) REVERT: f 48 LYS cc_start: 0.5893 (mmmt) cc_final: 0.5264 (ttpt) REVERT: f 51 ASP cc_start: 0.6295 (m-30) cc_final: 0.6048 (m-30) REVERT: f 98 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6229 (mt-10) REVERT: f 101 GLU cc_start: 0.6753 (tt0) cc_final: 0.6467 (tm-30) REVERT: f 112 ARG cc_start: 0.5045 (mmm-85) cc_final: 0.4309 (mmm-85) REVERT: f 120 LYS cc_start: 0.7058 (ptpp) cc_final: 0.6622 (pptt) REVERT: f 134 GLU cc_start: 0.5855 (mt-10) cc_final: 0.5483 (mt-10) REVERT: f 147 ASP cc_start: 0.3754 (p0) cc_final: 0.3539 (t0) REVERT: f 167 ARG cc_start: 0.6546 (ttm110) cc_final: 0.5772 (ttp-170) REVERT: f 177 PHE cc_start: 0.6942 (m-80) cc_final: 0.6675 (m-80) REVERT: g 69 ARG cc_start: 0.7971 (tmt170) cc_final: 0.7692 (tpt90) REVERT: g 74 SER cc_start: 0.6599 (m) cc_final: 0.6291 (t) REVERT: g 94 TYR cc_start: 0.7257 (m-10) cc_final: 0.6978 (m-10) REVERT: g 99 LYS cc_start: 0.5469 (tppp) cc_final: 0.4658 (pttt) REVERT: g 112 PRO cc_start: 0.6084 (Cg_endo) cc_final: 0.5725 (Cg_exo) REVERT: i 95 ARG cc_start: 0.6949 (ttp-110) cc_final: 0.6334 (ttm-80) REVERT: j 17 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6770 (mmt90) REVERT: j 20 MET cc_start: 0.8149 (ttp) cc_final: 0.7904 (ttm) REVERT: j 45 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6312 (pm20) REVERT: j 73 ASP cc_start: 0.7923 (p0) cc_final: 0.7519 (p0) REVERT: j 117 SER cc_start: 0.7084 (p) cc_final: 0.6748 (m) REVERT: k 84 LYS cc_start: 0.7226 (ptpt) cc_final: 0.6539 (ptmt) REVERT: k 129 LYS cc_start: 0.6846 (mtpp) cc_final: 0.6453 (mptt) REVERT: l 6 ARG cc_start: 0.7208 (ptt90) cc_final: 0.6178 (ptm-80) REVERT: l 58 LYS cc_start: 0.7406 (mttm) cc_final: 0.7149 (mtpt) REVERT: l 110 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6593 (tt0) REVERT: l 118 LYS cc_start: 0.7700 (ttpp) cc_final: 0.7388 (tttm) REVERT: l 127 LYS cc_start: 0.7444 (mtpp) cc_final: 0.7019 (mtpp) REVERT: m 89 SER cc_start: 0.6887 (p) cc_final: 0.6578 (m) REVERT: m 114 GLU cc_start: 0.7863 (pt0) cc_final: 0.7585 (pt0) REVERT: n 36 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.6188 (m-80) REVERT: n 46 GLU cc_start: 0.6512 (mm-30) cc_final: 0.5837 (mt-10) REVERT: n 92 PHE cc_start: 0.8100 (t80) cc_final: 0.7839 (t80) REVERT: n 108 ASP cc_start: 0.7352 (m-30) cc_final: 0.7094 (m-30) REVERT: o 6 LYS cc_start: 0.7005 (mtmm) cc_final: 0.6625 (mtmm) REVERT: o 7 GLN cc_start: 0.6917 (tm-30) cc_final: 0.6413 (tp40) REVERT: o 37 LYS cc_start: 0.5875 (OUTLIER) cc_final: 0.5524 (ptpp) REVERT: o 38 LYS cc_start: 0.7159 (ptmt) cc_final: 0.6867 (ptmm) REVERT: o 68 GLU cc_start: 0.5885 (mm-30) cc_final: 0.5681 (mm-30) REVERT: o 82 ASP cc_start: 0.7475 (t70) cc_final: 0.7033 (t70) REVERT: o 89 ARG cc_start: 0.7087 (mtm-85) cc_final: 0.6385 (mtt-85) REVERT: o 111 LYS cc_start: 0.7302 (ttpp) cc_final: 0.6886 (ttpt) REVERT: o 112 GLU cc_start: 0.7061 (tt0) cc_final: 0.6800 (tt0) REVERT: p 13 ARG cc_start: 0.7585 (mtp85) cc_final: 0.7295 (mtt180) REVERT: p 84 LYS cc_start: 0.7685 (tttm) cc_final: 0.6956 (tppt) REVERT: q 46 GLU cc_start: 0.5504 (OUTLIER) cc_final: 0.4977 (tt0) REVERT: q 48 LYS cc_start: 0.7510 (mtpt) cc_final: 0.7192 (mttp) REVERT: r 77 ASP cc_start: 0.8119 (m-30) cc_final: 0.7845 (m-30) REVERT: s 1 MET cc_start: 0.3986 (tpt) cc_final: 0.3642 (tpt) REVERT: t 46 GLN cc_start: 0.6905 (tp-100) cc_final: 0.6628 (tp40) REVERT: t 91 LYS cc_start: 0.5734 (mmtt) cc_final: 0.5002 (mptt) REVERT: u 50 MET cc_start: 0.7383 (ttm) cc_final: 0.6923 (ttm) REVERT: u 90 ASP cc_start: 0.8032 (m-30) cc_final: 0.7396 (m-30) REVERT: v 17 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7177 (tp30) REVERT: v 25 ARG cc_start: 0.7290 (mmt-90) cc_final: 0.6933 (mmt180) REVERT: v 44 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7591 (ptpp) REVERT: x 5 GLU cc_start: 0.5821 (mm-30) cc_final: 0.5451 (mp0) REVERT: x 23 ARG cc_start: 0.7130 (mtt90) cc_final: 0.6459 (ttp-110) REVERT: x 48 ARG cc_start: 0.6968 (mmt90) cc_final: 0.6587 (mmm-85) REVERT: y 6 LYS cc_start: 0.7747 (mmtp) cc_final: 0.7126 (mptt) REVERT: y 19 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6892 (ttpt) REVERT: y 37 GLU cc_start: 0.6586 (tt0) cc_final: 0.6083 (mt-10) REVERT: y 56 LYS cc_start: 0.7694 (ttpt) cc_final: 0.7103 (tttm) REVERT: 0 35 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6637 (tm-30) REVERT: 1 41 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7064 (mpp-170) REVERT: 2 15 LYS cc_start: 0.7939 (mmtt) cc_final: 0.7427 (mttt) REVERT: 2 52 LYS cc_start: 0.6932 (ttpt) cc_final: 0.6696 (ttpt) REVERT: 2 59 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7615 (mt) REVERT: 3 9 LYS cc_start: 0.7956 (mttp) cc_final: 0.7672 (mttm) REVERT: 3 19 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7810 (mtm180) outliers start: 103 outliers final: 63 residues processed: 894 average time/residue: 2.2873 time to fit residues: 2859.7604 Evaluate side-chains 903 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 820 time to evaluate : 6.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 ARG Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 202 ILE Chi-restraints excluded: chain e residue 154 ASP Chi-restraints excluded: chain f residue 111 ILE Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 161 LYS Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 24 ILE Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain j residue 17 ARG Chi-restraints excluded: chain j residue 45 GLU Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain n residue 36 TYR Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain o residue 37 LYS Chi-restraints excluded: chain q residue 46 GLU Chi-restraints excluded: chain s residue 24 MET Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain u residue 8 VAL Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain v residue 44 LYS Chi-restraints excluded: chain v residue 83 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 1 residue 41 ARG Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 3 residue 19 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 481 optimal weight: 10.0000 chunk 623 optimal weight: 10.0000 chunk 836 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 724 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 218 optimal weight: 5.9990 chunk 786 optimal weight: 4.9990 chunk 329 optimal weight: 5.9990 chunk 807 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN D 40 GLN D 54 GLN D 74 ASN E 12 GLN F 3 HIS G 97 ASN G 142 HIS ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS R 54 GLN T 20 HIS T 52 ASN f 81 GLN g 116 GLN i 67 ASN ** j 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 89 ASN j 93 GLN n 38 GLN q 6 GLN q 86 GLN u 12 GLN u 51 GLN u 75 GLN 1 29 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.160186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133752 restraints weight = 127963.303| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 0.35 r_work: 0.3267 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work: 0.3074 rms_B_bonded: 4.91 restraints_weight: 0.1250 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 153997 Z= 0.254 Angle : 0.761 17.192 230462 Z= 0.414 Chirality : 0.040 0.379 29304 Planarity : 0.008 0.145 12266 Dihedral : 23.145 179.751 77231 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 2.27 % Allowed : 18.34 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 5480 helix: 1.14 (0.12), residues: 1858 sheet: -0.32 (0.15), residues: 1073 loop : -0.80 (0.12), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP c 248 HIS 0.009 0.001 HIS u 44 PHE 0.037 0.002 PHE G 18 TYR 0.026 0.002 TYR p 32 ARG 0.012 0.001 ARG R 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44528.39 seconds wall clock time: 773 minutes 43.94 seconds (46423.94 seconds total)