Starting phenix.real_space_refine on Wed Mar 20 04:01:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7g_33664/03_2024/7y7g_33664_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7g_33664/03_2024/7y7g_33664.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7g_33664/03_2024/7y7g_33664_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7g_33664/03_2024/7y7g_33664_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7g_33664/03_2024/7y7g_33664_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7g_33664/03_2024/7y7g_33664.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7g_33664/03_2024/7y7g_33664.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7g_33664/03_2024/7y7g_33664_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7g_33664/03_2024/7y7g_33664_updated.pdb" } resolution = 2.34 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= 0.011 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 4557 5.49 5 Mg 256 5.21 5 S 150 5.16 5 C 71128 2.51 5 N 26435 2.21 5 O 39432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "E ASP 41": "OD1" <-> "OD2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "H ASP 48": "OD1" <-> "OD2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "I PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 62": "OD1" <-> "OD2" Residue "I ASP 91": "OD1" <-> "OD2" Residue "I ARG 95": "NH1" <-> "NH2" Residue "I ARG 124": "NH1" <-> "NH2" Residue "J ASP 14": "OD1" <-> "OD2" Residue "J ASP 97": "OD1" <-> "OD2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "L ARG 14": "NH1" <-> "NH2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "M ASP 42": "OD1" <-> "OD2" Residue "M GLU 50": "OE1" <-> "OE2" Residue "N GLU 10": "OE1" <-> "OE2" Residue "N PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 65": "NH1" <-> "NH2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "Q ASP 15": "OD1" <-> "OD2" Residue "S ARG 3": "NH1" <-> "NH2" Residue "S GLU 20": "OE1" <-> "OE2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "U ARG 35": "NH1" <-> "NH2" Residue "U ARG 66": "NH1" <-> "NH2" Residue "c GLU 23": "OE1" <-> "OE2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c GLU 100": "OE1" <-> "OE2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c GLU 194": "OE1" <-> "OE2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "c GLU 236": "OE1" <-> "OE2" Residue "c ASP 264": "OD1" <-> "OD2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ASP 39": "OD1" <-> "OD2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "e GLU 25": "OE1" <-> "OE2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e GLU 51": "OE1" <-> "OE2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e GLU 127": "OE1" <-> "OE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "e GLU 198": "OE1" <-> "OE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 101": "OE1" <-> "OE2" 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 165": "OE1" <-> "OE2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g GLU 32": "OE1" <-> "OE2" Residue "g GLU 42": "OE1" <-> "OE2" Residue "g ASP 114": "OD1" <-> "OD2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g GLU 167": "OE1" <-> "OE2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i ASP 19": "OD1" <-> "OD2" Residue "i ARG 37": "NH1" <-> "NH2" Residue "i TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 90": "OE1" <-> "OE2" Residue "i ARG 96": "NH1" <-> "NH2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "i ASP 141": "OD1" <-> "OD2" Residue "j GLU 45": "OE1" <-> "OE2" Residue "j GLU 106": "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 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 126": "NH1" <-> "NH2" Residue "l ARG 10": "NH1" <-> "NH2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ASP 25": "OD1" <-> "OD2" Residue "l ARG 40": "NH1" <-> "NH2" Residue "l ARG 44": "NH1" <-> "NH2" Residue "l GLU 47": "OE1" <-> "OE2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 104": "OE1" <-> "OE2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "l PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 58": "OD1" <-> "OD2" 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 GLU 74": "OE1" <-> "OE2" Residue "m ARG 96": "NH1" <-> "NH2" Residue "m GLU 114": "OE1" <-> "OE2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "n ARG 10": "NH1" <-> "NH2" Residue "n ARG 16": "NH1" <-> "NH2" Residue "n GLU 20": "OE1" <-> "OE2" Residue "n ARG 25": "NH1" <-> "NH2" Residue "n GLU 55": "OE1" <-> "OE2" Residue "n ARG 81": "NH1" <-> "NH2" Residue "n ARG 94": "NH1" <-> "NH2" Residue "n ARG 102": "NH1" <-> "NH2" Residue "n ARG 111": "NH1" <-> "NH2" Residue "o GLU 9": "OE1" <-> "OE2" Residue "o GLU 11": "OE1" <-> "OE2" Residue "o ARG 21": "NH1" <-> "NH2" Residue "o GLU 34": "OE1" <-> "OE2" Residue "o ARG 39": "NH1" <-> "NH2" Residue "o PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "o TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 102": "OD1" <-> "OD2" Residue "q TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q GLU 34": "OE1" <-> "OE2" Residue "q ARG 68": "NH1" <-> "NH2" Residue "q ARG 79": "NH1" <-> "NH2" Residue "q ARG 84": "NH1" <-> "NH2" Residue "r GLU 2": "OE1" <-> "OE2" Residue "r GLU 59": "OE1" <-> "OE2" Residue "r ASP 68": "OD1" <-> "OD2" Residue "r GLU 78": "OE1" <-> "OE2" 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 4": "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 GLU 60": "OE1" <-> "OE2" Residue "t GLU 62": "OE1" <-> "OE2" Residue "t ARG 82": "NH1" <-> "NH2" Residue "t ARG 86": "NH1" <-> "NH2" Residue "t ARG 94": "NH1" <-> "NH2" Residue "t GLU 101": "OE1" <-> "OE2" Residue "u GLU 35": "OE1" <-> "OE2" Residue "u TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 29": "OE1" <-> "OE2" Residue "v GLU 70": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "w ARG 3": "NH1" <-> "NH2" Residue "w ARG 11": "NH1" <-> "NH2" Residue "w ARG 37": "NH1" <-> "NH2" Residue "w ARG 50": "NH1" <-> "NH2" Residue "w ARG 57": "NH1" <-> "NH2" Residue "w GLU 70": "OE1" <-> "OE2" Residue "w ARG 74": "NH1" <-> "NH2" Residue "x GLU 13": "OE1" <-> "OE2" 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 GLU 39": "OE1" <-> "OE2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "z ASP 31": "OD1" <-> "OD2" Residue "z ARG 52": "NH1" <-> "NH2" Residue "0 ARG 44": "NH1" <-> "NH2" 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 "3 ARG 24": "NH1" <-> "NH2" Residue "3 GLU 30": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 141958 Number of models: 1 Model: "" Number of chains: 62 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': 120, 'rna2p_pyr': 82, 'rna3p': 10, 'rna3p_pur': 743, 'rna3p_pyr': 564} Link IDs: {'rna2p': 203, 'rna3p': 1316} 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': 139, 'rna3p': 17, 'rna3p_pur': 1318, 'rna3p_pyr': 1005} Link IDs: {'rna2p': 412, 'rna3p': 2340} 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: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 276 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 6} 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': 4, 'rna2p_pyr': 3, 'rna3p': 4, 'rna3p_pur': 35, '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: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1647 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p': 5, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p': 12, 'rna3p_pur': 27, 'rna3p_pyr': 25} Link IDs: {'rna2p': 12, 'rna3p': 63} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 11 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: "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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'GAL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 55.21, per 1000 atoms: 0.39 Number of scatterers: 141958 At special positions: 0 Unit cell: (249.378, 240.265, 248.55, 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 4557 15.00 Mg 256 11.99 O 39432 8.00 N 26435 7.00 C 71128 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: 52.72 Conformation dependent library (CDL) restraints added in 6.7 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 69 sheets defined 38.8% alpha, 19.2% beta 1586 base pairs and 2433 stacking pairs defined. Time for finding SS restraints: 72.79 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.674A pdb=" N MET B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 64 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 103 through 124 removed outlier: 3.543A pdb=" N VAL B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 148 removed outlier: 6.260A pdb=" N ALA B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 3.964A 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: 4.095A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 48 removed outlier: 4.400A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.652A 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: 3.551A 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: 4.723A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 4.005A 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: 5.088A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.912A 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: 3.652A pdb=" N LYS D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.885A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 3.716A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.533A pdb=" N LEU D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 4.791A 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: 4.206A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.933A pdb=" N MET E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 119 Processing helix chain 'E' and resid 132 through 147 removed outlier: 3.550A 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: 3.647A pdb=" N GLU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 55 Processing helix chain 'G' and resid 58 through 70 removed outlier: 3.739A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 111 removed outlier: 3.575A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.548A pdb=" N GLU G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 149 removed outlier: 3.598A pdb=" N ASN G 148 " --> pdb=" O MET G 144 " (cutoff:3.500A) removed outlier: 3.545A 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 92 removed outlier: 3.556A pdb=" N GLU I 92 " --> pdb=" O MET I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'J' and resid 14 through 33 removed outlier: 3.771A pdb=" N GLY J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 removed outlier: 3.549A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 51 removed outlier: 4.411A pdb=" N GLY K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.909A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.530A 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: 4.621A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 3.695A 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: 3.865A pdb=" N TYR L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.968A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 64 removed outlier: 3.924A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.605A pdb=" N GLY M 84 " --> pdb=" O LEU M 80 " (cutoff:3.500A) 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 Processing helix chain 'N' and resid 22 through 33 Processing helix chain 'N' and resid 37 through 51 removed outlier: 3.546A pdb=" N LEU N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 91 Processing helix chain 'N' and resid 52 through 57 Proline residue: N 57 - end of helix Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 44 removed outlier: 4.161A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.940A 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: 3.524A pdb=" N ASN P 79 " --> pdb=" O ILE P 75 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS P 80 " --> pdb=" O LYS P 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.649A pdb=" N GLU R 16 " --> pdb=" O ARG R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 34 removed outlier: 4.257A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 5.811A 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: 4.688A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 4.274A 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 42 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: 3.667A 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: 4.873A pdb=" N PHE U 37 " --> pdb=" O ARG U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 69 removed outlier: 3.990A pdb=" N THR U 68 " --> pdb=" O ASN U 64 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ARG U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 15 removed outlier: 5.162A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 4.027A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.823A 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: 3.746A 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: 3.743A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY c 215 " --> pdb=" O ALA c 211 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 3.995A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.513A 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: 3.550A pdb=" N ASP c 264 " --> pdb=" O ASN c 260 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.631A 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: 4.159A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 61 removed outlier: 3.507A pdb=" N VAL d 60 " --> pdb=" O LYS d 56 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 56 through 61' Processing helix chain 'd' and resid 62 through 72 Processing helix chain 'd' and resid 98 through 103 removed outlier: 4.313A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 5.122A 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 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 40 removed outlier: 3.943A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 53 removed outlier: 6.465A pdb=" N THR e 53 " --> pdb=" O ARG e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 116 Processing helix chain 'e' and resid 130 through 142 removed outlier: 3.552A pdb=" N LEU e 134 " --> pdb=" O LYS e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 163 removed outlier: 4.938A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 184 removed outlier: 5.825A pdb=" N ASP e 184 " --> pdb=" O LEU e 180 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'f' and resid 2 through 21 removed outlier: 4.877A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 47 removed outlier: 3.683A pdb=" N ASP f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) removed outlier: 3.985A 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: 4.612A 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 removed outlier: 3.762A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP f 174 " --> pdb=" O LEU f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 134 through 139 removed outlier: 3.966A 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: 3.725A 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: 5.181A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR g 80 " --> pdb=" O VAL g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 4.199A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 28 Processing helix chain 'h' and resid 29 through 34 removed outlier: 3.574A pdb=" N GLN h 33 " --> pdb=" O PHE h 29 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY h 34 " --> pdb=" O LEU h 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 29 through 34' Processing helix chain 'i' and resid 24 through 38 removed outlier: 4.168A 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: 4.290A 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: 3.963A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 104 through 109 removed outlier: 4.905A pdb=" N ARG j 108 " --> pdb=" O THR j 104 " (cutoff:3.500A) removed outlier: 5.746A 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 56 through 62 removed outlier: 3.697A 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: 3.989A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR k 74 " --> pdb=" O LYS k 70 " (cutoff:3.500A) removed outlier: 5.620A 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: 3.810A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 4.096A 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: 3.581A pdb=" N ALA l 122 " --> pdb=" O LYS l 118 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 4.020A 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: 4.267A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 4.529A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASP m 58 " --> pdb=" O LEU m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 4.357A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 4.756A 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: 4.603A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 5.214A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 5.687A 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: 3.617A pdb=" N GLY n 114 " --> pdb=" O ALA n 110 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 13 removed outlier: 4.130A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.650A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.282A 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: 4.046A pdb=" N LYS p 22 " --> pdb=" O LEU p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.683A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 32 through 37 removed outlier: 3.831A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 73 removed outlier: 3.794A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN p 72 " --> pdb=" O ALA p 68 " (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: 3.763A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) removed outlier: 3.717A 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: 3.575A pdb=" N VAL r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 65 through 70 removed outlier: 3.917A pdb=" N LEU r 69 " --> pdb=" O ASP r 65 " (cutoff:3.500A) removed outlier: 5.565A 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: 4.188A 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: 4.020A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.327A 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: 3.586A pdb=" N ASN u 24 " --> pdb=" O LEU u 20 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 53 removed outlier: 3.640A pdb=" N ALA u 52 " --> pdb=" O MET u 48 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 4.264A pdb=" N SER u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) 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: 4.066A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N SER x 10 " --> pdb=" O LEU x 6 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 35 Processing helix chain 'x' and resid 40 through 62 removed outlier: 4.233A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (cutoff:3.500A) removed outlier: 3.610A 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 removed outlier: 3.512A pdb=" N VAL y 51 " --> pdb=" O MET y 47 " (cutoff:3.500A) Processing helix chain 'z' and resid 9 through 19 removed outlier: 4.710A 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: 4.333A 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: 3.876A 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: 4.736A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 5.095A 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: 3.696A pdb=" N ASN 4 65 " --> pdb=" O ASN 4 61 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 90 through 93 removed outlier: 3.586A pdb=" N PHE B 90 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 185 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 53 through 59 Processing sheet with id= 3, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.617A pdb=" N GLY C 194 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 141 through 144 removed outlier: 4.145A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'E' and resid 12 through 16 removed outlier: 6.713A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 84 through 88 removed outlier: 3.694A pdb=" N ALA E 99 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 33 through 40 Processing sheet with id= 8, first strand: chain 'F' and resid 38 through 42 removed outlier: 5.570A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 43 through 47 removed outlier: 4.023A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G' and resid 72 through 79 removed outlier: 6.297A pdb=" N THR G 72 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'H' and resid 23 through 29 removed outlier: 6.649A pdb=" N ALA H 23 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.654A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I' and resid 5 through 11 removed outlier: 3.999A pdb=" N LYS I 27 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'J' and resid 39 through 42 removed outlier: 4.643A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE J 76 " --> pdb=" O ILE J 6 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'J' and resid 44 through 52 Processing sheet with id= 16, first strand: chain 'K' and resid 42 through 45 removed outlier: 7.137A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'L' and resid 29 through 32 removed outlier: 5.103A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'L' and resid 36 through 41 removed outlier: 5.168A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'P' and resid 4 through 10 removed outlier: 3.527A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'Q' and resid 7 through 11 removed outlier: 7.142A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'Q' and resid 19 through 30 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'S' and resid 30 through 33 Processing sheet with id= 23, first strand: chain 'c' and resid 2 through 6 removed outlier: 5.747A pdb=" N VAL c 16 " --> pdb=" O CYS c 6 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'c' and resid 80 through 83 removed outlier: 3.683A pdb=" N ARG c 80 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'c' and resid 138 through 142 removed outlier: 4.211A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'c' and resid 90 through 96 removed outlier: 5.409A pdb=" N ASN c 90 " --> pdb=" O ALA c 106 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU c 100 " --> pdb=" O TYR c 96 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'd' and resid 11 through 16 removed outlier: 4.052A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL d 26 " --> pdb=" O VAL d 9 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER d 199 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU d 168 " --> pdb=" O SER d 113 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'd' and resid 36 through 40 removed outlier: 3.841A pdb=" N LEU d 40 " --> pdb=" O TYR d 45 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR d 45 " --> pdb=" O LEU d 40 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'd' and resid 179 through 182 Processing sheet with id= 30, first strand: chain 'd' and resid 24 through 28 No H-bonds generated for sheet with id= 30 Processing sheet with id= 31, first strand: chain 'd' and resid 46 through 51 removed outlier: 5.996A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'd' and resid 105 through 108 removed outlier: 6.575A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'e' and resid 1 through 6 removed outlier: 4.415A pdb=" N MET e 1 " --> pdb=" O VAL e 14 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL e 14 " --> pdb=" O MET e 1 " (cutoff:3.500A) removed outlier: 4.905A 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: 3.714A pdb=" N LYS e 185 " --> pdb=" O ASP e 145 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'f' and resid 65 through 69 removed outlier: 3.651A pdb=" N GLY f 86 " --> pdb=" O THR f 68 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.645A 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 removed outlier: 3.648A pdb=" N LEU g 33 " --> pdb=" O ILE g 26 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'g' and resid 41 through 44 removed outlier: 3.517A pdb=" N LYS g 44 " --> pdb=" O THR g 51 " (cutoff:3.500A) removed outlier: 5.413A 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: 5.973A 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: 3.602A 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: 4.093A pdb=" N ASP h 17 " --> pdb=" O LEU h 5 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LYS h 35 " --> pdb=" O LEU h 6 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'i' and resid 52 through 57 removed outlier: 4.622A 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: 7.554A 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: 4.303A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 5.878A 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: 3.554A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU l 33 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS l 100 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'l' and resid 73 through 76 removed outlier: 6.910A pdb=" N ILE l 73 " --> pdb=" O GLU l 90 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN l 88 " --> pdb=" O GLU l 75 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'l' and resid 30 through 36 removed outlier: 7.599A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'm' and resid 33 through 37 removed outlier: 4.950A pdb=" N ARG m 103 " --> pdb=" O ASN m 107 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLY m 101 " --> pdb=" O PRO m 109 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA m 111 " --> pdb=" O LYS m 99 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS m 99 " --> pdb=" O ALA m 111 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE m 113 " --> pdb=" O ILE m 97 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE m 97 " --> pdb=" O ILE m 113 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU m 115 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR m 95 " --> pdb=" O LEU m 115 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'n' and resid 49 through 52 removed outlier: 3.653A pdb=" N VAL n 49 " --> pdb=" O VAL n 39 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'o' and resid 49 through 53 removed outlier: 3.722A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG o 53 " --> pdb=" O HIS o 56 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR o 60 " --> pdb=" O ILE o 48 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER o 83 " --> pdb=" O LYS o 29 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'o' and resid 57 through 64 removed outlier: 7.687A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'q' and resid 11 through 15 removed outlier: 3.636A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU q 39 " --> pdb=" O GLY q 50 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'q' and resid 17 through 22 removed outlier: 4.275A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU q 31 " --> pdb=" O VAL q 63 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 55, first strand: chain 'q' and resid 65 through 68 removed outlier: 3.544A pdb=" N GLY q 67 " --> pdb=" O PHE q 93 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.199A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'r' and resid 2 through 8 Processing sheet with id= 58, first strand: chain 's' and resid 28 through 33 removed outlier: 6.603A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 't' and resid 83 through 86 Processing sheet with id= 60, first strand: chain 'u' and resid 69 through 72 removed outlier: 6.594A pdb=" N ALA u 39 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'v' and resid 51 through 54 removed outlier: 4.192A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'v' and resid 67 through 71 Processing sheet with id= 63, first strand: chain 'w' and resid 12 through 19 removed outlier: 4.523A pdb=" N ASN w 23 " --> pdb=" O SER w 19 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.337A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'z' and resid 29 through 32 removed outlier: 4.163A pdb=" N GLU z 36 " --> pdb=" O ASP z 31 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain '0' and resid 19 through 24 removed outlier: 5.935A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE 0 48 " --> pdb=" O SER 0 14 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '2' and resid 22 through 25 removed outlier: 5.627A pdb=" N PHE 2 22 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '3' and resid 1 through 5 removed outlier: 6.562A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '4' and resid 20 through 25 removed outlier: 4.388A pdb=" N ASN 4 20 " --> pdb=" O CYS 4 16 " (cutoff:3.500A) 1888 hydrogen bonds defined for protein. 5568 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3989 hydrogen bonds 6248 hydrogen bond angles 0 basepair planarities 1586 basepair parallelities 2433 stacking parallelities Total time for adding SS restraints: 265.61 Time building geometry restraints manager: 57.41 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: 11893 1.29 - 1.43: 69631 1.43 - 1.56: 63129 1.56 - 1.70: 9115 1.70 - 1.84: 264 Bond restraints: 154032 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 2.07e+02 bond pdb=" C5 5MU V 53 " pdb=" C6 5MU V 53 " ideal model delta sigma weight residual 1.155 1.442 -0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" C5 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.155 1.439 -0.284 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C5 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.155 1.437 -0.282 2.00e-02 2.50e+03 1.99e+02 bond pdb=" C MS6 l 82 " pdb=" S MS6 l 82 " ideal model delta sigma weight residual 1.829 1.568 0.261 2.00e-02 2.50e+03 1.70e+02 ... (remaining 154027 not shown) Histogram of bond angle deviations from ideal: 97.70 - 106.64: 28268 106.64 - 115.57: 103200 115.57 - 124.51: 79981 124.51 - 133.45: 19021 133.45 - 142.39: 43 Bond angle restraints: 230513 Sorted by residual: angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C8 2MA a2503 " ideal model delta sigma weight residual 106.32 142.39 -36.07 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C4 2MA a2503 " ideal model delta sigma weight residual 138.88 110.25 28.63 3.00e+00 1.11e-01 9.11e+01 angle pdb=" C1' 1MA V 57 " pdb=" N9 1MA V 57 " pdb=" C8 1MA V 57 " ideal model delta sigma weight residual 100.68 128.40 -27.72 3.00e+00 1.11e-01 8.54e+01 angle pdb=" C1' 56B V 33 " pdb=" N9 56B V 33 " pdb=" C4 56B V 33 " ideal model delta sigma weight residual 105.37 127.93 -22.56 3.00e+00 1.11e-01 5.66e+01 angle pdb=" C1' 56B V 33 " pdb=" N9 56B V 33 " pdb=" C8 56B V 33 " ideal model delta sigma weight residual 146.55 124.02 22.53 3.00e+00 1.11e-01 5.64e+01 ... (remaining 230508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 87222 35.34 - 70.69: 9986 70.69 - 106.03: 1260 106.03 - 141.38: 20 141.38 - 176.72: 10 Dihedral angle restraints: 98498 sinusoidal: 82577 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 -117.30 -62.70 0 5.00e+00 4.00e-02 1.57e+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 -132.97 -47.03 0 5.00e+00 4.00e-02 8.85e+01 dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 48.93 151.07 1 1.50e+01 4.44e-03 8.00e+01 ... (remaining 98495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 26485 0.077 - 0.154: 2587 0.154 - 0.231: 201 0.231 - 0.308: 18 0.308 - 0.385: 5 Chirality restraints: 29296 Sorted by residual: 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 2.16 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C3 GAL V 101 " pdb=" C2 GAL V 101 " pdb=" C4 GAL V 101 " pdb=" O3 GAL V 101 " both_signs ideal model delta sigma weight residual False 2.41 2.79 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C11 56B V 33 " pdb=" C10 56B V 33 " pdb=" C12 56B V 33 " pdb=" O11 56B V 33 " both_signs ideal model delta sigma weight residual False 2.63 3.00 -0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 29293 not shown) Planarity restraints: 12270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG V 9 " 0.127 2.00e-02 2.50e+03 6.68e-01 1.00e+04 pdb=" C4' 2MG V 9 " 0.518 2.00e-02 2.50e+03 pdb=" O4' 2MG V 9 " 0.772 2.00e-02 2.50e+03 pdb=" C3' 2MG V 9 " -0.553 2.00e-02 2.50e+03 pdb=" O3' 2MG V 9 " -0.725 2.00e-02 2.50e+03 pdb=" C2' 2MG V 9 " -0.183 2.00e-02 2.50e+03 pdb=" O2' 2MG V 9 " 1.015 2.00e-02 2.50e+03 pdb=" C1' 2MG V 9 " 0.133 2.00e-02 2.50e+03 pdb=" N9 2MG V 9 " -1.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.066 2.00e-02 2.50e+03 6.00e-01 8.11e+03 pdb=" C4' 2MG A1516 " -0.436 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " -0.604 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " 0.597 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " 0.652 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " 0.166 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " -0.996 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " -0.225 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " 0.913 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " -0.068 2.00e-02 2.50e+03 5.99e-01 8.08e+03 pdb=" C4' 5MC A1407 " -0.439 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " -0.611 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " 0.597 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " 0.650 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " 0.170 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " -0.986 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " -0.223 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " 0.911 2.00e-02 2.50e+03 ... (remaining 12267 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 669 2.49 - 3.09: 93100 3.09 - 3.70: 266581 3.70 - 4.30: 411943 4.30 - 4.90: 545803 Nonbonded interactions: 1318096 Sorted by model distance: nonbonded pdb=" OP1 C a 948 " pdb="MG MG a6030 " model vdw 1.891 2.170 nonbonded pdb=" OP1 A a2448 " pdb="MG MG a6083 " model vdw 1.906 2.170 nonbonded pdb=" OP2 G a1186 " pdb="MG MG a6072 " model vdw 1.906 2.170 nonbonded pdb=" OP1 U A1224 " pdb="MG MG A1621 " model vdw 1.907 2.170 nonbonded pdb=" OP1 U a2615 " pdb="MG MG a6096 " model vdw 1.909 2.170 ... (remaining 1318091 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: 10.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.200 Extract box with map and model: 36.250 Check model and map are aligned: 1.900 Set scattering table: 1.000 Process input model: 542.920 Find NCS groups from input model: 2.840 Set up NCS constraints: 0.380 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: 0.030 Load rotamer database and sin/cos tables:10.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 607.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 : 0.010 0.288 154032 Z= 0.637 Angle : 0.741 36.068 230513 Z= 0.378 Chirality : 0.047 0.385 29296 Planarity : 0.027 0.668 12270 Dihedral : 22.510 176.720 88228 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.81 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 0.22 (0.11), residues: 5480 helix: 1.20 (0.12), residues: 1850 sheet: -0.06 (0.15), residues: 1116 loop : -0.47 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 42 HIS 0.023 0.002 HIS K 118 PHE 0.020 0.002 PHE B 50 TYR 0.028 0.002 TYR c 161 ARG 0.017 0.001 ARG F 24 *********************** 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 1055 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1055 time to evaluate : 5.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 MET cc_start: 0.3010 (mtt) cc_final: 0.2666 (mtp) REVERT: B 100 MET cc_start: 0.4617 (ttm) cc_final: 0.4028 (mtp) REVERT: B 112 LYS cc_start: 0.3306 (ttpt) cc_final: 0.2852 (mmtp) REVERT: B 148 LEU cc_start: 0.3635 (mt) cc_final: 0.3400 (mp) REVERT: B 154 MET cc_start: 0.2618 (ttm) cc_final: 0.1925 (mtp) REVERT: B 161 LEU cc_start: 0.4512 (tp) cc_final: 0.4181 (tp) REVERT: B 174 LYS cc_start: 0.3437 (tmmt) cc_final: 0.3035 (mtmm) REVERT: B 212 LEU cc_start: 0.3638 (tp) cc_final: 0.3022 (mp) REVERT: C 16 LYS cc_start: 0.6992 (mmmt) cc_final: 0.6685 (mttt) REVERT: C 28 GLU cc_start: 0.5637 (mp0) cc_final: 0.5327 (mm-30) REVERT: C 32 ASN cc_start: 0.6991 (m-40) cc_final: 0.6603 (m-40) REVERT: C 45 LYS cc_start: 0.6084 (tttm) cc_final: 0.5824 (tppt) REVERT: C 72 ARG cc_start: 0.5825 (mtm-85) cc_final: 0.5205 (mtt180) REVERT: C 108 LYS cc_start: 0.6676 (mtmt) cc_final: 0.5928 (mmpt) REVERT: C 114 LYS cc_start: 0.7512 (tptt) cc_final: 0.7185 (tptt) REVERT: C 129 MET cc_start: 0.6377 (mtm) cc_final: 0.6024 (mtp) REVERT: C 134 MET cc_start: 0.7604 (mtp) cc_final: 0.7248 (mtp) REVERT: C 136 ARG cc_start: 0.6455 (ttm-80) cc_final: 0.6184 (ttm-80) REVERT: C 139 GLN cc_start: 0.6598 (mt0) cc_final: 0.5849 (pt0) REVERT: C 140 ASN cc_start: 0.7434 (m-40) cc_final: 0.7015 (m110) REVERT: C 142 MET cc_start: 0.7482 (mmm) cc_final: 0.7038 (mmm) REVERT: C 150 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8187 (ttpp) REVERT: C 185 ASN cc_start: 0.7930 (t0) cc_final: 0.7688 (t0) REVERT: C 193 TYR cc_start: 0.7049 (m-80) cc_final: 0.6697 (m-80) REVERT: D 15 GLU cc_start: 0.6202 (mm-30) cc_final: 0.5814 (mm-30) REVERT: D 54 GLN cc_start: 0.7064 (mt0) cc_final: 0.6814 (mt0) REVERT: D 70 ARG cc_start: 0.6458 (tpt-90) cc_final: 0.6067 (ttm170) REVERT: D 76 TYR cc_start: 0.6839 (t80) cc_final: 0.6637 (t80) REVERT: D 81 ARG cc_start: 0.5229 (ttp80) cc_final: 0.4534 (tmt170) REVERT: D 104 ARG cc_start: 0.6238 (mmt90) cc_final: 0.5934 (mmt180) REVERT: D 129 VAL cc_start: 0.5712 (t) cc_final: 0.5460 (p) REVERT: D 135 TYR cc_start: 0.6697 (t80) cc_final: 0.6106 (t80) REVERT: D 148 LYS cc_start: 0.5102 (tmtt) cc_final: 0.4372 (tppt) REVERT: D 151 LYS cc_start: 0.4238 (pttm) cc_final: 0.4028 (mptp) REVERT: D 163 GLU cc_start: 0.3658 (mm-30) cc_final: 0.3265 (mm-30) REVERT: E 12 GLN cc_start: 0.6479 (mt0) cc_final: 0.6111 (mt0) REVERT: E 43 ASN cc_start: 0.7113 (t0) cc_final: 0.6913 (t0) REVERT: E 54 ARG cc_start: 0.7050 (mmm-85) cc_final: 0.6768 (mmt90) REVERT: E 55 GLU cc_start: 0.6445 (mt-10) cc_final: 0.6160 (mp0) REVERT: E 61 GLN cc_start: 0.6676 (mm-40) cc_final: 0.6456 (mt0) REVERT: E 66 LYS cc_start: 0.6939 (mttm) cc_final: 0.6737 (mmmt) REVERT: E 70 ASN cc_start: 0.6669 (t0) cc_final: 0.6329 (m-40) REVERT: E 124 LEU cc_start: 0.7786 (mt) cc_final: 0.7566 (mp) REVERT: E 151 GLU cc_start: 0.6473 (mp0) cc_final: 0.5784 (mm-30) REVERT: E 159 LYS cc_start: 0.6572 (mttm) cc_final: 0.5932 (mttt) REVERT: F 1 MET cc_start: 0.4558 (tpp) cc_final: 0.3028 (ttm) REVERT: F 9 MET cc_start: 0.7016 (mtp) cc_final: 0.6755 (mtp) REVERT: F 21 MET cc_start: 0.5275 (mtm) cc_final: 0.4892 (mtm) REVERT: F 55 HIS cc_start: 0.6815 (m90) cc_final: 0.6317 (m170) REVERT: F 56 LYS cc_start: 0.6933 (mtpp) cc_final: 0.5999 (pttt) REVERT: F 58 HIS cc_start: 0.6935 (t-170) cc_final: 0.6112 (t70) REVERT: F 92 THR cc_start: 0.5826 (m) cc_final: 0.5320 (p) REVERT: G 60 GLU cc_start: 0.5349 (mp0) cc_final: 0.4800 (mt-10) REVERT: G 92 ARG cc_start: 0.5726 (ptt-90) cc_final: 0.5006 (ptp90) REVERT: G 97 ASN cc_start: 0.7394 (m-40) cc_final: 0.6970 (m-40) REVERT: G 101 MET cc_start: 0.7579 (mtt) cc_final: 0.7373 (mtp) REVERT: G 119 ARG cc_start: 0.6445 (mtm180) cc_final: 0.6199 (mtp180) REVERT: G 136 LYS cc_start: 0.5345 (mmtm) cc_final: 0.4726 (pptt) REVERT: G 137 LYS cc_start: 0.6492 (tptm) cc_final: 0.5711 (tptt) REVERT: G 143 ARG cc_start: 0.4747 (mtp-110) cc_final: 0.4389 (ttt180) REVERT: H 38 ASN cc_start: 0.6984 (t0) cc_final: 0.6663 (t0) REVERT: H 50 LYS cc_start: 0.6775 (ptmt) cc_final: 0.6426 (pttm) REVERT: H 58 GLU cc_start: 0.6061 (tp30) cc_final: 0.5763 (tt0) REVERT: H 89 LYS cc_start: 0.6934 (pttp) cc_final: 0.6734 (pttp) REVERT: H 117 ARG cc_start: 0.6856 (mtm-85) cc_final: 0.6594 (mtm180) REVERT: I 33 ARG cc_start: 0.6088 (mtm180) cc_final: 0.5386 (mtt90) REVERT: I 49 ARG cc_start: 0.5981 (mtm-85) cc_final: 0.5639 (mtm180) REVERT: I 88 MET cc_start: 0.6273 (mtm) cc_final: 0.5927 (mtm) REVERT: I 110 GLN cc_start: 0.7647 (mm110) cc_final: 0.7406 (mm110) REVERT: J 45 ARG cc_start: 0.7763 (ttt180) cc_final: 0.7450 (ttt-90) REVERT: J 47 GLU cc_start: 0.6640 (tt0) cc_final: 0.6215 (tt0) REVERT: J 66 GLU cc_start: 0.7438 (tt0) cc_final: 0.7226 (tt0) REVERT: J 68 ARG cc_start: 0.7312 (mtt180) cc_final: 0.6919 (mtt180) REVERT: K 53 ARG cc_start: 0.7136 (mmm160) cc_final: 0.6823 (mmp-170) REVERT: K 57 LYS cc_start: 0.7547 (ttpt) cc_final: 0.7194 (ttpp) REVERT: K 85 MET cc_start: 0.7222 (mtp) cc_final: 0.6779 (mtm) REVERT: K 87 LYS cc_start: 0.7493 (ttmt) cc_final: 0.7220 (ttmt) REVERT: K 116 ILE cc_start: 0.7142 (pt) cc_final: 0.6894 (mm) REVERT: K 126 LYS cc_start: 0.6672 (mmtt) cc_final: 0.6435 (tttp) REVERT: L 10 LYS cc_start: 0.6816 (ttpt) cc_final: 0.6537 (tptt) REVERT: L 61 PHE cc_start: 0.7348 (m-80) cc_final: 0.7138 (m-80) REVERT: L 111 LYS cc_start: 0.7427 (mmtm) cc_final: 0.7224 (mmtp) REVERT: L 116 LYS cc_start: 0.7752 (mttt) cc_final: 0.7412 (mtmm) REVERT: M 39 ILE cc_start: 0.5423 (tt) cc_final: 0.5176 (tp) REVERT: M 57 ARG cc_start: 0.6899 (mtm-85) cc_final: 0.6661 (mtm-85) REVERT: M 92 ARG cc_start: 0.6470 (mtt180) cc_final: 0.6207 (mtt180) REVERT: M 93 ARG cc_start: 0.6184 (mtt-85) cc_final: 0.5670 (mmm160) REVERT: M 95 LEU cc_start: 0.6879 (mt) cc_final: 0.6650 (mt) REVERT: M 103 LYS cc_start: 0.8061 (tttt) cc_final: 0.7826 (tttt) REVERT: N 6 MET cc_start: 0.7119 (mmm) cc_final: 0.6423 (mmm) REVERT: N 23 LYS cc_start: 0.6254 (tptt) cc_final: 0.5833 (mtpp) REVERT: N 47 LYS cc_start: 0.5868 (tppt) cc_final: 0.5473 (tppt) REVERT: N 89 MET cc_start: 0.7571 (mmp) cc_final: 0.7318 (mmp) REVERT: N 97 LYS cc_start: 0.7379 (ptmm) cc_final: 0.6908 (pttt) REVERT: O 11 ILE cc_start: 0.6263 (mt) cc_final: 0.5963 (mp) REVERT: O 38 HIS cc_start: 0.7456 (t70) cc_final: 0.7228 (t70) REVERT: O 62 GLN cc_start: 0.7169 (tt0) cc_final: 0.6735 (tp40) REVERT: P 5 ARG cc_start: 0.7136 (ptt180) cc_final: 0.6907 (ptt180) REVERT: Q 11 ARG cc_start: 0.6069 (mtp-110) cc_final: 0.5661 (mtp85) REVERT: Q 25 ILE cc_start: 0.6269 (mt) cc_final: 0.6025 (mm) REVERT: Q 33 ILE cc_start: 0.7937 (mt) cc_final: 0.7647 (mt) REVERT: Q 41 THR cc_start: 0.6771 (p) cc_final: 0.6493 (t) REVERT: Q 47 HIS cc_start: 0.6456 (t70) cc_final: 0.6246 (t70) REVERT: Q 62 ARG cc_start: 0.6541 (ttp80) cc_final: 0.6246 (ttp80) REVERT: R 48 ARG cc_start: 0.5635 (mtp180) cc_final: 0.5108 (mpt180) REVERT: R 57 ARG cc_start: 0.7356 (mtm-85) cc_final: 0.6970 (mtm180) REVERT: R 72 ASP cc_start: 0.6243 (p0) cc_final: 0.5975 (p0) REVERT: S 13 LEU cc_start: 0.6159 (tp) cc_final: 0.5887 (mt) REVERT: S 36 ARG cc_start: 0.7820 (mtp85) cc_final: 0.7297 (mtp-110) REVERT: S 41 PHE cc_start: 0.5924 (m-80) cc_final: 0.5717 (m-80) REVERT: S 81 ARG cc_start: 0.5926 (mtt90) cc_final: 0.5708 (mtt180) REVERT: T 5 LYS cc_start: 0.5923 (mtpt) cc_final: 0.5536 (tmmt) REVERT: T 13 GLN cc_start: 0.6788 (tt0) cc_final: 0.6541 (tt0) REVERT: T 16 LYS cc_start: 0.6657 (tttm) cc_final: 0.6216 (tmmt) REVERT: T 18 ARG cc_start: 0.6048 (ttp80) cc_final: 0.5439 (ttp80) REVERT: T 27 MET cc_start: 0.5692 (tmm) cc_final: 0.5491 (ttp) REVERT: T 29 ARG cc_start: 0.6811 (mtm-85) cc_final: 0.6505 (mtm-85) REVERT: T 31 PHE cc_start: 0.6395 (m-80) cc_final: 0.6167 (m-80) REVERT: U 21 ARG cc_start: 0.3789 (tpp80) cc_final: 0.3139 (mmp80) REVERT: U 34 ARG cc_start: 0.4939 (ttp-170) cc_final: 0.4172 (mtm-85) REVERT: U 47 ARG cc_start: 0.5386 (tmm-80) cc_final: 0.4357 (mtt180) REVERT: c 5 LYS cc_start: 0.7115 (ttmm) cc_final: 0.6908 (tptm) REVERT: c 23 GLU cc_start: 0.7058 (pt0) cc_final: 0.6663 (pt0) REVERT: c 102 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7964 (mtt180) REVERT: c 117 GLN cc_start: 0.7211 (pt0) cc_final: 0.6996 (pt0) REVERT: c 161 TYR cc_start: 0.8099 (p90) cc_final: 0.7792 (p90) REVERT: c 187 ASP cc_start: 0.7371 (m-30) cc_final: 0.7054 (m-30) REVERT: d 7 LYS cc_start: 0.8117 (ptmm) cc_final: 0.7876 (pttm) REVERT: d 11 MET cc_start: 0.8311 (mtp) cc_final: 0.7863 (mtp) REVERT: d 58 ASN cc_start: 0.5890 (p0) cc_final: 0.5601 (m110) REVERT: d 60 VAL cc_start: 0.7435 (p) cc_final: 0.7226 (t) REVERT: d 64 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6338 (mm-30) REVERT: d 94 GLN cc_start: 0.7465 (tt0) cc_final: 0.7107 (tt0) REVERT: d 103 ASP cc_start: 0.5714 (m-30) cc_final: 0.5503 (p0) REVERT: d 105 LYS cc_start: 0.7210 (mmtm) cc_final: 0.7005 (mttp) REVERT: d 128 ARG cc_start: 0.7593 (mtm-85) cc_final: 0.7373 (mmp80) REVERT: d 185 ASN cc_start: 0.7661 (m-40) cc_final: 0.7260 (m-40) REVERT: d 207 VAL cc_start: 0.7855 (p) cc_final: 0.7510 (m) REVERT: e 51 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7763 (mt-10) REVERT: e 61 ARG cc_start: 0.7276 (ptt-90) cc_final: 0.7019 (ptt90) REVERT: e 111 GLU cc_start: 0.6647 (tp30) cc_final: 0.6146 (mm-30) REVERT: e 120 VAL cc_start: 0.6895 (t) cc_final: 0.6542 (m) REVERT: e 123 LYS cc_start: 0.5639 (ttpp) cc_final: 0.5203 (tmmt) REVERT: e 133 LEU cc_start: 0.5862 (mt) cc_final: 0.5451 (mm) REVERT: e 166 LYS cc_start: 0.6639 (mttm) cc_final: 0.6431 (mttt) REVERT: e 178 VAL cc_start: 0.6895 (t) cc_final: 0.6506 (p) REVERT: e 184 ASP cc_start: 0.5951 (p0) cc_final: 0.5368 (p0) REVERT: f 16 LEU cc_start: 0.6218 (mt) cc_final: 0.6017 (mt) REVERT: f 17 MET cc_start: 0.6784 (ttt) cc_final: 0.6548 (ttm) REVERT: f 27 GLN cc_start: 0.7546 (mt0) cc_final: 0.7198 (mt0) REVERT: f 30 ARG cc_start: 0.7190 (mtm-85) cc_final: 0.6650 (mpp-170) REVERT: f 35 THR cc_start: 0.8216 (m) cc_final: 0.7981 (m) REVERT: f 51 ASP cc_start: 0.5954 (t0) cc_final: 0.5555 (t70) REVERT: f 78 LYS cc_start: 0.5519 (ptpp) cc_final: 0.4875 (mtpm) REVERT: f 94 GLU cc_start: 0.6184 (mm-30) cc_final: 0.5901 (tt0) REVERT: f 113 ASP cc_start: 0.5586 (t70) cc_final: 0.5385 (t70) REVERT: f 115 ARG cc_start: 0.5233 (mmm-85) cc_final: 0.5006 (mmm160) REVERT: f 128 TYR cc_start: 0.7711 (t80) cc_final: 0.7388 (t80) REVERT: f 133 ARG cc_start: 0.6092 (mtm-85) cc_final: 0.5854 (mtp180) REVERT: f 161 LYS cc_start: 0.5620 (mtpp) cc_final: 0.5263 (mmtt) REVERT: f 164 GLU cc_start: 0.5034 (tp30) cc_final: 0.4566 (mt-10) REVERT: g 35 ARG cc_start: 0.5772 (ptp-110) cc_final: 0.5458 (ptp-110) REVERT: g 75 MET cc_start: 0.7247 (ptm) cc_final: 0.7002 (ptp) REVERT: g 76 VAL cc_start: 0.5887 (t) cc_final: 0.5564 (p) REVERT: g 95 ARG cc_start: 0.5945 (ptm-80) cc_final: 0.5696 (ptp-110) REVERT: g 104 ASN cc_start: 0.6097 (m-40) cc_final: 0.5821 (m-40) REVERT: g 131 ILE cc_start: 0.7127 (mt) cc_final: 0.6699 (mp) REVERT: g 149 ARG cc_start: 0.7767 (ttt-90) cc_final: 0.7560 (ttt-90) REVERT: g 151 TYR cc_start: 0.7362 (m-80) cc_final: 0.6881 (m-80) REVERT: i 14 ASP cc_start: 0.7995 (m-30) cc_final: 0.7792 (m-30) REVERT: i 138 GLN cc_start: 0.7056 (mm-40) cc_final: 0.6681 (mt0) REVERT: j 7 MET cc_start: 0.7996 (mmm) cc_final: 0.7629 (mmm) REVERT: j 51 LYS cc_start: 0.7000 (mttp) cc_final: 0.6712 (mttm) REVERT: j 53 LYS cc_start: 0.6883 (pttp) cc_final: 0.6625 (mttp) REVERT: j 92 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6825 (mt-10) REVERT: j 93 GLN cc_start: 0.6817 (mm-40) cc_final: 0.6351 (mm110) REVERT: k 10 GLU cc_start: 0.6612 (mm-30) cc_final: 0.6353 (pm20) REVERT: k 121 THR cc_start: 0.6726 (m) cc_final: 0.6524 (m) REVERT: k 126 ARG cc_start: 0.7703 (mtp180) cc_final: 0.7407 (mtp180) REVERT: k 129 LYS cc_start: 0.6732 (mttp) cc_final: 0.6376 (mmmt) REVERT: l 5 LYS cc_start: 0.7102 (mttp) cc_final: 0.6422 (pttm) REVERT: l 58 LYS cc_start: 0.6647 (mmtp) cc_final: 0.6339 (tptt) REVERT: l 133 LYS cc_start: 0.6495 (ttpt) cc_final: 0.6185 (tptm) REVERT: m 1 MET cc_start: 0.7883 (mtm) cc_final: 0.7660 (mtm) REVERT: m 43 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7517 (tp30) REVERT: m 72 ASP cc_start: 0.7392 (t0) cc_final: 0.6981 (t70) REVERT: n 3 LYS cc_start: 0.6558 (mtpt) cc_final: 0.6252 (mtpt) REVERT: n 13 ARG cc_start: 0.7095 (ttt-90) cc_final: 0.6608 (ttm-80) REVERT: n 16 ARG cc_start: 0.6876 (mmp80) cc_final: 0.6210 (mmt90) REVERT: n 18 LEU cc_start: 0.7402 (mt) cc_final: 0.7200 (mt) REVERT: n 20 GLU cc_start: 0.6364 (tt0) cc_final: 0.6109 (mt-10) REVERT: n 46 GLU cc_start: 0.6379 (mm-30) cc_final: 0.5884 (mp0) REVERT: n 69 ASP cc_start: 0.6644 (m-30) cc_final: 0.6341 (m-30) REVERT: o 7 GLN cc_start: 0.6943 (tm-30) cc_final: 0.6583 (tm-30) REVERT: o 29 LYS cc_start: 0.7997 (mmtp) cc_final: 0.7751 (mttt) REVERT: o 38 LYS cc_start: 0.6612 (pttp) cc_final: 0.6330 (pttp) REVERT: o 63 LYS cc_start: 0.7962 (ptmt) cc_final: 0.7491 (ptmt) REVERT: o 68 GLU cc_start: 0.6290 (mm-30) cc_final: 0.5923 (tp30) REVERT: o 89 ARG cc_start: 0.7135 (mtm110) cc_final: 0.6492 (mtp85) REVERT: p 13 ARG cc_start: 0.7740 (ttt90) cc_final: 0.6964 (ttp80) REVERT: p 78 LYS cc_start: 0.7752 (mttt) cc_final: 0.7493 (mmpt) REVERT: p 87 SER cc_start: 0.7769 (m) cc_final: 0.7142 (t) REVERT: p 111 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6481 (mm-30) REVERT: q 1 MET cc_start: 0.6174 (ttt) cc_final: 0.5740 (ttm) REVERT: q 16 GLU cc_start: 0.6192 (mm-30) cc_final: 0.5868 (tt0) REVERT: q 62 GLU cc_start: 0.6576 (tt0) cc_final: 0.6354 (tt0) REVERT: q 73 LYS cc_start: 0.7676 (mtpt) cc_final: 0.7445 (mttt) REVERT: q 85 LYS cc_start: 0.8287 (ttmm) cc_final: 0.8058 (ttpt) REVERT: r 70 LYS cc_start: 0.7426 (mtmm) cc_final: 0.7054 (mttp) REVERT: s 1 MET cc_start: 0.3916 (pmm) cc_final: 0.2727 (ptt) REVERT: s 6 ARG cc_start: 0.7259 (tpt170) cc_final: 0.7047 (tpt170) REVERT: s 8 LEU cc_start: 0.7672 (mt) cc_final: 0.7421 (mt) REVERT: s 32 LEU cc_start: 0.8260 (mt) cc_final: 0.7847 (mp) REVERT: s 76 ARG cc_start: 0.7297 (ttt-90) cc_final: 0.7075 (ttt90) REVERT: t 7 ARG cc_start: 0.5677 (mtm110) cc_final: 0.5425 (ttm170) REVERT: t 22 ARG cc_start: 0.6714 (mtm-85) cc_final: 0.6305 (mtp180) REVERT: t 29 LEU cc_start: 0.7340 (mt) cc_final: 0.6892 (mp) REVERT: t 41 LEU cc_start: 0.7403 (mt) cc_final: 0.7170 (mp) REVERT: t 46 GLN cc_start: 0.7340 (tp40) cc_final: 0.6797 (tp-100) REVERT: t 47 LYS cc_start: 0.6443 (mttm) cc_final: 0.6139 (mttm) REVERT: t 79 LYS cc_start: 0.6691 (mttp) cc_final: 0.6409 (mttm) REVERT: u 1 MET cc_start: 0.2589 (ppp) cc_final: 0.2214 (tmm) REVERT: u 4 ILE cc_start: 0.7693 (mt) cc_final: 0.7458 (mt) REVERT: u 25 LYS cc_start: 0.7436 (mttm) cc_final: 0.7033 (mttm) REVERT: u 41 GLU cc_start: 0.7320 (pt0) cc_final: 0.7005 (pt0) REVERT: u 48 MET cc_start: 0.6868 (tpt) cc_final: 0.6564 (tpt) REVERT: u 53 LYS cc_start: 0.6046 (mttm) cc_final: 0.5818 (mmtp) REVERT: v 5 LYS cc_start: 0.5484 (mtpt) cc_final: 0.4745 (mmtp) REVERT: v 44 LYS cc_start: 0.7820 (ttmm) cc_final: 0.7505 (ttpt) REVERT: v 72 LYS cc_start: 0.7519 (mtpp) cc_final: 0.7129 (mtpt) REVERT: v 78 LYS cc_start: 0.8140 (mtmt) cc_final: 0.7865 (mttt) REVERT: x 17 GLU cc_start: 0.6235 (tp30) cc_final: 0.5684 (tp30) REVERT: x 26 PHE cc_start: 0.7916 (t80) cc_final: 0.7687 (t80) REVERT: x 49 ASP cc_start: 0.6663 (m-30) cc_final: 0.6459 (m-30) REVERT: y 39 GLU cc_start: 0.6548 (pt0) cc_final: 0.6306 (pt0) REVERT: y 45 ARG cc_start: 0.7969 (mmt180) cc_final: 0.7686 (mmt180) REVERT: y 56 LYS cc_start: 0.7682 (ttmt) cc_final: 0.7110 (ttpp) REVERT: z 34 SER cc_start: 0.7870 (p) cc_final: 0.7534 (m) REVERT: z 36 GLU cc_start: 0.7602 (pt0) cc_final: 0.7385 (pt0) REVERT: z 55 ILE cc_start: 0.6756 (mm) cc_final: 0.6505 (mm) REVERT: 0 36 LEU cc_start: 0.8305 (mt) cc_final: 0.7849 (mm) REVERT: 0 50 LYS cc_start: 0.7341 (mttp) cc_final: 0.7070 (mmtm) REVERT: 1 41 ARG cc_start: 0.6597 (mtm-85) cc_final: 0.6394 (mtp85) REVERT: 2 15 LYS cc_start: 0.8036 (mmtt) cc_final: 0.7404 (mtpp) REVERT: 2 52 LYS cc_start: 0.6870 (ttpp) cc_final: 0.6420 (tppt) REVERT: 2 55 LEU cc_start: 0.7685 (mt) cc_final: 0.7467 (mt) REVERT: 3 1 MET cc_start: 0.7805 (tpp) cc_final: 0.7427 (tpp) REVERT: 3 12 ARG cc_start: 0.5691 (ptm-80) cc_final: 0.5160 (ptp-170) REVERT: 3 15 LYS cc_start: 0.7763 (mmtp) cc_final: 0.7341 (mtpt) REVERT: 3 18 LYS cc_start: 0.8130 (tttt) cc_final: 0.7808 (tttt) REVERT: 3 26 ILE cc_start: 0.7930 (pt) cc_final: 0.7665 (pt) REVERT: 3 36 ARG cc_start: 0.7352 (ttp-110) cc_final: 0.7130 (ttt180) outliers start: 0 outliers final: 0 residues processed: 1055 average time/residue: 2.4122 time to fit residues: 3486.7490 Evaluate side-chains 864 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 864 time to evaluate : 5.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 835 optimal weight: 6.9990 chunk 750 optimal weight: 0.0970 chunk 416 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 506 optimal weight: 6.9990 chunk 400 optimal weight: 10.0000 chunk 775 optimal weight: 5.9990 chunk 300 optimal weight: 3.9990 chunk 471 optimal weight: 30.0000 chunk 577 optimal weight: 0.8980 chunk 899 optimal weight: 5.9990 overall best weight: 3.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN O 35 GLN O 40 GLN R 54 GLN c 21 ASN c 115 GLN ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 136 GLN j 89 ASN k 93 ASN q 6 GLN u 12 GLN x 27 ASN x 58 ASN 4 20 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 154032 Z= 0.191 Angle : 0.710 16.349 230513 Z= 0.390 Chirality : 0.037 0.374 29296 Planarity : 0.007 0.137 12270 Dihedral : 23.017 179.388 77190 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.07 % Favored : 96.84 % Rotamer: Outliers : 1.55 % Allowed : 9.22 % Favored : 89.22 % 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: 0.56 (0.11), residues: 5480 helix: 1.53 (0.12), residues: 1875 sheet: 0.00 (0.16), residues: 1049 loop : -0.26 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 248 HIS 0.011 0.001 HIS K 118 PHE 0.020 0.002 PHE F 8 TYR 0.016 0.002 TYR n 36 ARG 0.007 0.001 ARG O 17 *********************** 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 1007 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 936 time to evaluate : 5.939 Fit side-chains revert: symmetry clash REVERT: B 9 MET cc_start: 0.2393 (OUTLIER) cc_final: 0.2102 (mmm) REVERT: B 27 MET cc_start: 0.3720 (mmp) cc_final: 0.3045 (mmm) REVERT: B 49 MET cc_start: 0.2933 (mtt) cc_final: 0.2576 (mtp) REVERT: B 100 MET cc_start: 0.4569 (ttm) cc_final: 0.3828 (mtp) REVERT: B 112 LYS cc_start: 0.3526 (ttpt) cc_final: 0.3036 (mmtt) REVERT: B 148 LEU cc_start: 0.3882 (mt) cc_final: 0.3606 (mp) REVERT: B 154 MET cc_start: 0.2773 (ttm) cc_final: 0.1931 (mtt) REVERT: B 161 LEU cc_start: 0.4513 (tp) cc_final: 0.4220 (tp) REVERT: B 174 LYS cc_start: 0.3479 (tmmt) cc_final: 0.3108 (mtmm) REVERT: B 212 LEU cc_start: 0.3763 (tp) cc_final: 0.3328 (mt) REVERT: C 45 LYS cc_start: 0.6167 (tttm) cc_final: 0.5953 (tptm) REVERT: C 72 ARG cc_start: 0.5899 (mtm-85) cc_final: 0.5189 (mtm-85) REVERT: C 108 LYS cc_start: 0.6601 (mtmt) cc_final: 0.5911 (mmpt) REVERT: C 134 MET cc_start: 0.7603 (mtp) cc_final: 0.7216 (mtp) REVERT: C 136 ARG cc_start: 0.6372 (ttm-80) cc_final: 0.6149 (ttm-80) REVERT: C 139 GLN cc_start: 0.6867 (mt0) cc_final: 0.5919 (pt0) REVERT: C 140 ASN cc_start: 0.7329 (m-40) cc_final: 0.6994 (m110) REVERT: C 142 MET cc_start: 0.7616 (mmm) cc_final: 0.7176 (mmm) REVERT: C 193 TYR cc_start: 0.7152 (m-80) cc_final: 0.6750 (m-80) REVERT: D 8 LYS cc_start: 0.5932 (mttm) cc_final: 0.5658 (mttp) REVERT: D 54 GLN cc_start: 0.7019 (mt0) cc_final: 0.6757 (mt0) REVERT: D 77 LYS cc_start: 0.7035 (mtmm) cc_final: 0.6835 (ttmm) REVERT: D 81 ARG cc_start: 0.5166 (ttp80) cc_final: 0.4272 (tmm160) REVERT: D 104 ARG cc_start: 0.6106 (mmt90) cc_final: 0.5840 (mmt180) REVERT: D 129 VAL cc_start: 0.5747 (t) cc_final: 0.5486 (p) REVERT: D 135 TYR cc_start: 0.6680 (t80) cc_final: 0.6227 (t80) REVERT: D 148 LYS cc_start: 0.4808 (tmtt) cc_final: 0.4285 (tppt) REVERT: E 12 GLN cc_start: 0.6552 (mt0) cc_final: 0.6106 (mt0) REVERT: E 29 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7642 (mtt90) REVERT: E 54 ARG cc_start: 0.7126 (mmm-85) cc_final: 0.6711 (mmt90) REVERT: E 55 GLU cc_start: 0.6209 (mt-10) cc_final: 0.5897 (mt-10) REVERT: E 65 GLU cc_start: 0.5964 (OUTLIER) cc_final: 0.5607 (tp30) REVERT: E 66 LYS cc_start: 0.7008 (mttm) cc_final: 0.6762 (mmmt) REVERT: E 70 ASN cc_start: 0.6487 (t0) cc_final: 0.6206 (m-40) REVERT: E 124 LEU cc_start: 0.7810 (mt) cc_final: 0.7589 (mp) REVERT: E 151 GLU cc_start: 0.6602 (mp0) cc_final: 0.5956 (mm-30) REVERT: E 152 MET cc_start: 0.7103 (ptm) cc_final: 0.6847 (ptt) REVERT: E 156 LYS cc_start: 0.6420 (mtmt) cc_final: 0.6087 (mtmt) REVERT: E 159 LYS cc_start: 0.6322 (mttm) cc_final: 0.5898 (mttt) REVERT: F 1 MET cc_start: 0.4768 (tpp) cc_final: 0.3004 (ttm) REVERT: F 8 PHE cc_start: 0.7519 (p90) cc_final: 0.7184 (p90) REVERT: F 9 MET cc_start: 0.7013 (mtp) cc_final: 0.6774 (mtp) REVERT: F 21 MET cc_start: 0.5347 (mtm) cc_final: 0.4994 (mtm) REVERT: F 55 HIS cc_start: 0.6601 (m90) cc_final: 0.6066 (m170) REVERT: F 92 THR cc_start: 0.6048 (m) cc_final: 0.5442 (p) REVERT: G 97 ASN cc_start: 0.7289 (m-40) cc_final: 0.6883 (m-40) REVERT: G 119 ARG cc_start: 0.6474 (mtm180) cc_final: 0.6223 (mtp180) REVERT: G 137 LYS cc_start: 0.6548 (tptm) cc_final: 0.5958 (tptt) REVERT: H 38 ASN cc_start: 0.7037 (t0) cc_final: 0.6739 (t0) REVERT: H 50 LYS cc_start: 0.6605 (ptmt) cc_final: 0.6236 (pttm) REVERT: H 58 GLU cc_start: 0.5988 (tp30) cc_final: 0.5630 (tt0) REVERT: H 62 THR cc_start: 0.7460 (m) cc_final: 0.6905 (t) REVERT: I 33 ARG cc_start: 0.6197 (mtm180) cc_final: 0.5283 (mtt90) REVERT: I 46 MET cc_start: 0.6433 (ttt) cc_final: 0.6221 (ttt) REVERT: I 49 ARG cc_start: 0.6005 (mtm-85) cc_final: 0.5626 (mtm180) REVERT: I 88 MET cc_start: 0.6125 (mtm) cc_final: 0.5837 (mtm) REVERT: I 110 GLN cc_start: 0.7618 (mm110) cc_final: 0.7334 (mm-40) REVERT: J 45 ARG cc_start: 0.7632 (ttt180) cc_final: 0.7313 (ttt-90) REVERT: J 47 GLU cc_start: 0.6646 (tt0) cc_final: 0.6279 (tt0) REVERT: J 68 ARG cc_start: 0.7377 (mtt180) cc_final: 0.7028 (mtt180) REVERT: K 53 ARG cc_start: 0.7100 (mmm160) cc_final: 0.6762 (mmp-170) REVERT: K 57 LYS cc_start: 0.7438 (ttpt) cc_final: 0.6993 (ttpp) REVERT: K 85 MET cc_start: 0.7207 (mtp) cc_final: 0.6822 (mtm) REVERT: K 116 ILE cc_start: 0.7145 (pt) cc_final: 0.6852 (mm) REVERT: K 126 LYS cc_start: 0.6738 (mmtt) cc_final: 0.6474 (tttp) REVERT: L 10 LYS cc_start: 0.6914 (ttpt) cc_final: 0.6592 (tptt) REVERT: L 54 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6307 (mtp180) REVERT: L 61 PHE cc_start: 0.7483 (m-80) cc_final: 0.7183 (m-10) REVERT: M 39 ILE cc_start: 0.5270 (tt) cc_final: 0.5062 (tp) REVERT: M 92 ARG cc_start: 0.6680 (mtt180) cc_final: 0.6205 (mtt180) REVERT: M 93 ARG cc_start: 0.6262 (mtt-85) cc_final: 0.5776 (mmm160) REVERT: N 6 MET cc_start: 0.7047 (mmm) cc_final: 0.6082 (mpt) REVERT: N 23 LYS cc_start: 0.6086 (tptt) cc_final: 0.5850 (mtpp) REVERT: N 47 LYS cc_start: 0.6074 (tppt) cc_final: 0.5726 (tppt) REVERT: N 86 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7147 (mt-10) REVERT: N 89 MET cc_start: 0.7661 (mmp) cc_final: 0.7413 (mmp) REVERT: N 92 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: O 11 ILE cc_start: 0.6248 (mt) cc_final: 0.5948 (mp) REVERT: O 17 ARG cc_start: 0.4586 (ttp80) cc_final: 0.3776 (ttt-90) REVERT: O 26 GLU cc_start: 0.6626 (mp0) cc_final: 0.6373 (mp0) REVERT: O 45 GLU cc_start: 0.7200 (pp20) cc_final: 0.6543 (tm-30) REVERT: O 62 GLN cc_start: 0.7161 (tt0) cc_final: 0.6754 (tp40) REVERT: O 80 GLN cc_start: 0.5940 (mm-40) cc_final: 0.5658 (tp-100) REVERT: P 1 MET cc_start: 0.4713 (tpt) cc_final: 0.3899 (tpt) REVERT: Q 11 ARG cc_start: 0.5942 (mtp-110) cc_final: 0.5563 (mtp85) REVERT: R 48 ARG cc_start: 0.5421 (mtp180) cc_final: 0.4952 (mpt180) REVERT: R 57 ARG cc_start: 0.7351 (mtm-85) cc_final: 0.6961 (mtm180) REVERT: R 61 ARG cc_start: 0.7365 (mtm-85) cc_final: 0.6906 (mtm-85) REVERT: S 36 ARG cc_start: 0.7942 (mtp85) cc_final: 0.7384 (mtp-110) REVERT: S 41 PHE cc_start: 0.5867 (m-80) cc_final: 0.5622 (m-80) REVERT: S 43 ASN cc_start: 0.6629 (p0) cc_final: 0.5922 (p0) REVERT: T 5 LYS cc_start: 0.5625 (mtpt) cc_final: 0.5354 (tmmt) REVERT: T 13 GLN cc_start: 0.6637 (tt0) cc_final: 0.6431 (tt0) REVERT: T 16 LYS cc_start: 0.6792 (tttm) cc_final: 0.6376 (tmmt) REVERT: T 18 ARG cc_start: 0.6092 (ttp80) cc_final: 0.5525 (ttp80) REVERT: T 29 ARG cc_start: 0.6806 (mtm-85) cc_final: 0.6564 (mtm-85) REVERT: T 33 LYS cc_start: 0.6190 (ttmt) cc_final: 0.5879 (mmtt) REVERT: T 70 ASN cc_start: 0.6304 (m-40) cc_final: 0.5802 (m-40) REVERT: U 34 ARG cc_start: 0.5064 (ttp-170) cc_final: 0.4279 (mtm-85) REVERT: U 47 ARG cc_start: 0.5351 (tmm-80) cc_final: 0.4340 (mtt180) REVERT: c 117 GLN cc_start: 0.7153 (pt0) cc_final: 0.6811 (pt0) REVERT: c 182 ARG cc_start: 0.7821 (ttt90) cc_final: 0.7448 (tpt-90) REVERT: d 7 LYS cc_start: 0.8031 (ptmm) cc_final: 0.7568 (ptpt) REVERT: d 55 LYS cc_start: 0.7658 (tttp) cc_final: 0.7369 (tttp) REVERT: d 64 GLU cc_start: 0.6693 (mt-10) cc_final: 0.6348 (mm-30) REVERT: d 89 GLU cc_start: 0.5262 (mp0) cc_final: 0.4927 (mt-10) REVERT: d 94 GLN cc_start: 0.7462 (tt0) cc_final: 0.7120 (tt0) REVERT: d 103 ASP cc_start: 0.5817 (m-30) cc_final: 0.5565 (p0) REVERT: d 105 LYS cc_start: 0.7168 (mmtm) cc_final: 0.6882 (mttt) REVERT: d 168 GLU cc_start: 0.7710 (pt0) cc_final: 0.7415 (pt0) REVERT: d 184 ARG cc_start: 0.7112 (mtm-85) cc_final: 0.6881 (mtm-85) REVERT: d 185 ASN cc_start: 0.7675 (m-40) cc_final: 0.7268 (m-40) REVERT: d 207 VAL cc_start: 0.7825 (p) cc_final: 0.7495 (m) REVERT: e 61 ARG cc_start: 0.7333 (ptt-90) cc_final: 0.7094 (ptt90) REVERT: e 111 GLU cc_start: 0.6532 (tp30) cc_final: 0.6085 (mm-30) REVERT: e 123 LYS cc_start: 0.5681 (ttpp) cc_final: 0.5191 (tmmt) REVERT: e 176 ASP cc_start: 0.7111 (p0) cc_final: 0.6898 (p0) REVERT: e 178 VAL cc_start: 0.6984 (t) cc_final: 0.6575 (p) REVERT: e 184 ASP cc_start: 0.6021 (p0) cc_final: 0.5457 (p0) REVERT: f 27 GLN cc_start: 0.7525 (mt0) cc_final: 0.7196 (mt0) REVERT: f 30 ARG cc_start: 0.7163 (mtm-85) cc_final: 0.6610 (mpp-170) REVERT: f 35 THR cc_start: 0.8244 (m) cc_final: 0.8033 (m) REVERT: f 78 LYS cc_start: 0.5644 (ptpp) cc_final: 0.4990 (mtpm) REVERT: f 94 GLU cc_start: 0.6102 (mm-30) cc_final: 0.5813 (tt0) REVERT: f 113 ASP cc_start: 0.5376 (t70) cc_final: 0.5144 (t70) REVERT: f 115 ARG cc_start: 0.5226 (mmm-85) cc_final: 0.4952 (mmm160) REVERT: f 122 PHE cc_start: 0.6964 (m-80) cc_final: 0.6285 (m-80) REVERT: f 128 TYR cc_start: 0.7630 (t80) cc_final: 0.7374 (t80) REVERT: f 136 ILE cc_start: 0.6631 (OUTLIER) cc_final: 0.6357 (pp) REVERT: f 161 LYS cc_start: 0.5596 (mtpp) cc_final: 0.5212 (mmtt) REVERT: f 164 GLU cc_start: 0.4908 (tp30) cc_final: 0.4474 (mt-10) REVERT: g 75 MET cc_start: 0.7207 (ptm) cc_final: 0.6912 (ptp) REVERT: g 104 ASN cc_start: 0.6154 (m-40) cc_final: 0.5861 (t0) REVERT: g 131 ILE cc_start: 0.7274 (mt) cc_final: 0.6886 (mp) REVERT: g 149 ARG cc_start: 0.7566 (ttt-90) cc_final: 0.7332 (ttt-90) REVERT: g 151 TYR cc_start: 0.7222 (m-80) cc_final: 0.6793 (m-80) REVERT: i 92 MET cc_start: 0.7780 (mmm) cc_final: 0.7090 (mmm) REVERT: i 98 GLU cc_start: 0.7689 (mp0) cc_final: 0.7438 (mp0) REVERT: j 7 MET cc_start: 0.8086 (mmm) cc_final: 0.7741 (mmm) REVERT: j 51 LYS cc_start: 0.6901 (mttp) cc_final: 0.6600 (mttm) REVERT: j 91 SER cc_start: 0.6138 (p) cc_final: 0.5479 (t) REVERT: j 93 GLN cc_start: 0.6832 (mm-40) cc_final: 0.6475 (mm-40) REVERT: j 106 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: k 10 GLU cc_start: 0.6553 (mm-30) cc_final: 0.6217 (pm20) REVERT: k 106 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6730 (mm-30) REVERT: k 123 ARG cc_start: 0.6438 (ttm170) cc_final: 0.5913 (ttm170) REVERT: k 126 ARG cc_start: 0.7824 (mtp180) cc_final: 0.7564 (mtp180) REVERT: k 129 LYS cc_start: 0.6787 (mttp) cc_final: 0.6438 (mmmt) REVERT: l 5 LYS cc_start: 0.7059 (mttp) cc_final: 0.6417 (pttm) REVERT: l 58 LYS cc_start: 0.6634 (mmtp) cc_final: 0.6417 (tptt) REVERT: l 133 LYS cc_start: 0.6698 (ttpt) cc_final: 0.6293 (tptm) REVERT: m 1 MET cc_start: 0.7915 (mtm) cc_final: 0.7617 (mtm) REVERT: m 43 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7551 (tp30) REVERT: n 13 ARG cc_start: 0.7154 (ttt-90) cc_final: 0.6862 (ttt-90) REVERT: n 16 ARG cc_start: 0.6794 (mmp80) cc_final: 0.6308 (mmt90) REVERT: n 46 GLU cc_start: 0.6328 (mm-30) cc_final: 0.5894 (mp0) REVERT: n 69 ASP cc_start: 0.6593 (m-30) cc_final: 0.6291 (m-30) REVERT: o 7 GLN cc_start: 0.6742 (tm-30) cc_final: 0.6504 (tt0) REVERT: o 38 LYS cc_start: 0.6635 (pttp) cc_final: 0.6349 (pttp) REVERT: o 63 LYS cc_start: 0.8123 (ptmt) cc_final: 0.7872 (ptmt) REVERT: o 68 GLU cc_start: 0.6324 (mm-30) cc_final: 0.5912 (tp30) REVERT: o 89 ARG cc_start: 0.7092 (mtm110) cc_final: 0.6120 (mtt-85) REVERT: p 13 ARG cc_start: 0.7725 (ttt90) cc_final: 0.6980 (ttp80) REVERT: p 78 LYS cc_start: 0.7827 (mttt) cc_final: 0.7459 (mmpt) REVERT: p 87 SER cc_start: 0.7673 (m) cc_final: 0.7115 (t) REVERT: p 111 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6386 (mm-30) REVERT: q 1 MET cc_start: 0.6057 (ttt) cc_final: 0.5459 (ttm) REVERT: q 60 LYS cc_start: 0.6839 (mtmm) cc_final: 0.6198 (mttp) REVERT: q 62 GLU cc_start: 0.6672 (tt0) cc_final: 0.6442 (tt0) REVERT: q 73 LYS cc_start: 0.7727 (mtpt) cc_final: 0.7412 (mttt) REVERT: q 85 LYS cc_start: 0.8300 (ttmm) cc_final: 0.8091 (ttpt) REVERT: r 70 LYS cc_start: 0.7455 (mtmm) cc_final: 0.7010 (mttp) REVERT: r 95 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6793 (ttp80) REVERT: s 1 MET cc_start: 0.4154 (pmm) cc_final: 0.2926 (ptt) REVERT: s 6 ARG cc_start: 0.7421 (tpt170) cc_final: 0.7152 (tpt170) REVERT: s 8 LEU cc_start: 0.7683 (mt) cc_final: 0.7451 (mt) REVERT: s 32 LEU cc_start: 0.8228 (mt) cc_final: 0.7875 (mt) REVERT: s 76 ARG cc_start: 0.7232 (ttt-90) cc_final: 0.6931 (tmt90) REVERT: t 7 ARG cc_start: 0.5849 (mtm110) cc_final: 0.5412 (ttm170) REVERT: t 22 ARG cc_start: 0.6713 (mtm-85) cc_final: 0.6283 (mtp180) REVERT: t 46 GLN cc_start: 0.7253 (tp40) cc_final: 0.6797 (tp-100) REVERT: t 62 GLU cc_start: 0.6814 (mp0) cc_final: 0.6582 (mp0) REVERT: t 79 LYS cc_start: 0.6665 (mttp) cc_final: 0.6419 (mttm) REVERT: u 1 MET cc_start: 0.2810 (ppp) cc_final: 0.2356 (tmm) REVERT: u 4 ILE cc_start: 0.7740 (mt) cc_final: 0.7516 (mt) REVERT: u 25 LYS cc_start: 0.7370 (mttm) cc_final: 0.7156 (mtpp) REVERT: u 48 MET cc_start: 0.6892 (tpt) cc_final: 0.6577 (mmm) REVERT: u 61 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7262 (mt) REVERT: u 75 GLN cc_start: 0.7244 (tp40) cc_final: 0.6893 (tp-100) REVERT: v 5 LYS cc_start: 0.5659 (mtpt) cc_final: 0.4900 (mmtp) REVERT: v 44 LYS cc_start: 0.7780 (ttmm) cc_final: 0.7470 (ttpt) REVERT: v 72 LYS cc_start: 0.7495 (mtpp) cc_final: 0.7293 (mtpt) REVERT: v 78 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7964 (mttt) REVERT: v 83 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6945 (mt-10) REVERT: w 54 LYS cc_start: 0.8037 (tptp) cc_final: 0.7833 (tptm) REVERT: x 2 LYS cc_start: 0.4965 (tttp) cc_final: 0.4707 (ttpp) REVERT: x 17 GLU cc_start: 0.6300 (tp30) cc_final: 0.5701 (tp30) REVERT: x 26 PHE cc_start: 0.7950 (t80) cc_final: 0.7689 (t80) REVERT: y 39 GLU cc_start: 0.6677 (pt0) cc_final: 0.6398 (pt0) REVERT: y 56 LYS cc_start: 0.7678 (ttmt) cc_final: 0.7113 (ttpp) REVERT: z 34 SER cc_start: 0.7885 (p) cc_final: 0.7473 (m) REVERT: 0 37 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7803 (mttp) REVERT: 0 51 GLU cc_start: 0.7429 (tt0) cc_final: 0.7212 (tt0) REVERT: 1 1 MET cc_start: 0.7203 (mtm) cc_final: 0.6756 (mtp) REVERT: 2 15 LYS cc_start: 0.7925 (mmtt) cc_final: 0.7381 (mtpp) REVERT: 3 12 ARG cc_start: 0.5750 (ptm-80) cc_final: 0.5197 (ptp-170) REVERT: 3 15 LYS cc_start: 0.7772 (mmtp) cc_final: 0.7333 (mtpt) REVERT: 3 18 LYS cc_start: 0.7951 (tttt) cc_final: 0.7748 (tttm) REVERT: 3 26 ILE cc_start: 0.8012 (pt) cc_final: 0.7810 (pt) outliers start: 71 outliers final: 28 residues processed: 965 average time/residue: 2.4230 time to fit residues: 3208.0523 Evaluate side-chains 909 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 872 time to evaluate : 5.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain f residue 111 ILE Chi-restraints excluded: chain f residue 136 ILE Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain j residue 109 SER Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain o residue 25 THR Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 95 ARG Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 38 LYS Chi-restraints excluded: chain 3 residue 20 ASP 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: 5.9990 chunk 748 optimal weight: 0.9980 chunk 612 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 900 optimal weight: 5.9990 chunk 972 optimal weight: 20.0000 chunk 802 optimal weight: 0.0670 chunk 893 optimal weight: 5.9990 chunk 307 optimal weight: 20.0000 chunk 722 optimal weight: 8.9990 overall best weight: 3.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN D 152 GLN E 97 GLN E 148 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN K 15 GLN O 28 GLN O 35 GLN O 40 GLN Q 47 HIS R 54 GLN ** h 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 ASN q 6 GLN u 12 GLN x 27 ASN x 58 ASN 0 45 GLN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 154032 Z= 0.202 Angle : 0.707 14.854 230513 Z= 0.391 Chirality : 0.037 0.373 29296 Planarity : 0.008 0.141 12270 Dihedral : 22.963 176.332 77190 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.38 % Favored : 96.57 % Rotamer: Outliers : 2.49 % Allowed : 12.11 % Favored : 85.40 % 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: 0.54 (0.11), residues: 5480 helix: 1.49 (0.12), residues: 1872 sheet: -0.02 (0.15), residues: 1069 loop : -0.26 (0.12), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 248 HIS 0.012 0.001 HIS J 56 PHE 0.020 0.002 PHE d 118 TYR 0.016 0.002 TYR B 22 ARG 0.007 0.001 ARG y 11 *********************** 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 1003 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 889 time to evaluate : 5.371 Fit side-chains REVERT: B 27 MET cc_start: 0.3762 (mmp) cc_final: 0.3133 (mmm) REVERT: B 49 MET cc_start: 0.2951 (mtt) cc_final: 0.2622 (mtp) REVERT: B 68 LEU cc_start: 0.4254 (OUTLIER) cc_final: 0.4007 (tt) REVERT: B 100 MET cc_start: 0.4574 (ttm) cc_final: 0.3916 (mtp) REVERT: B 112 LYS cc_start: 0.3548 (ttpt) cc_final: 0.3000 (mmtt) REVERT: B 136 MET cc_start: 0.3645 (OUTLIER) cc_final: 0.3408 (ptm) REVERT: B 148 LEU cc_start: 0.4234 (mt) cc_final: 0.3950 (mp) REVERT: B 154 MET cc_start: 0.2618 (ttm) cc_final: 0.1948 (mtt) REVERT: B 161 LEU cc_start: 0.4441 (tp) cc_final: 0.4189 (tp) REVERT: B 174 LYS cc_start: 0.3497 (tmmt) cc_final: 0.3119 (mtmm) REVERT: B 212 LEU cc_start: 0.3855 (tp) cc_final: 0.3295 (mp) REVERT: C 45 LYS cc_start: 0.6192 (tttm) cc_final: 0.5944 (tptm) REVERT: C 72 ARG cc_start: 0.5776 (mtm-85) cc_final: 0.5047 (mtt180) REVERT: C 82 GLU cc_start: 0.4248 (OUTLIER) cc_final: 0.3905 (tp30) REVERT: C 134 MET cc_start: 0.7586 (mtp) cc_final: 0.7196 (mtp) REVERT: C 136 ARG cc_start: 0.6296 (ttm-80) cc_final: 0.6055 (ttm-80) REVERT: C 140 ASN cc_start: 0.7260 (m-40) cc_final: 0.7006 (m110) REVERT: C 193 TYR cc_start: 0.7280 (m-80) cc_final: 0.6894 (m-80) REVERT: D 8 LYS cc_start: 0.6013 (mttm) cc_final: 0.5518 (mttp) REVERT: D 15 GLU cc_start: 0.6191 (mm-30) cc_final: 0.5609 (mm-30) REVERT: D 20 PHE cc_start: 0.5571 (m-80) cc_final: 0.5348 (m-80) REVERT: D 54 GLN cc_start: 0.7029 (mt0) cc_final: 0.6625 (mt0) REVERT: D 81 ARG cc_start: 0.5113 (ttp80) cc_final: 0.4504 (tmt170) REVERT: D 104 ARG cc_start: 0.6099 (mmt90) cc_final: 0.5878 (mmt180) REVERT: D 129 VAL cc_start: 0.5787 (t) cc_final: 0.5520 (p) REVERT: D 148 LYS cc_start: 0.4643 (tmtt) cc_final: 0.4321 (tppt) REVERT: E 12 GLN cc_start: 0.6615 (mt0) cc_final: 0.6166 (mt0) REVERT: E 19 ASN cc_start: 0.7739 (OUTLIER) cc_final: 0.7111 (p0) REVERT: E 54 ARG cc_start: 0.7066 (mmm-85) cc_final: 0.6617 (mmt90) REVERT: E 55 GLU cc_start: 0.6292 (mt-10) cc_final: 0.5810 (mp0) REVERT: E 65 GLU cc_start: 0.6022 (OUTLIER) cc_final: 0.5707 (tp30) REVERT: E 70 ASN cc_start: 0.6682 (t0) cc_final: 0.6295 (m110) REVERT: E 124 LEU cc_start: 0.7772 (mt) cc_final: 0.7536 (mp) REVERT: E 152 MET cc_start: 0.7095 (ptm) cc_final: 0.6868 (ptt) REVERT: E 156 LYS cc_start: 0.6395 (mtmt) cc_final: 0.6087 (mtmt) REVERT: E 159 LYS cc_start: 0.6451 (mttm) cc_final: 0.6124 (mttt) REVERT: F 1 MET cc_start: 0.4924 (tpp) cc_final: 0.4630 (mmt) REVERT: F 8 PHE cc_start: 0.7430 (p90) cc_final: 0.7062 (p90) REVERT: F 21 MET cc_start: 0.5169 (mtm) cc_final: 0.4835 (mtm) REVERT: F 55 HIS cc_start: 0.6602 (m90) cc_final: 0.6153 (m170) REVERT: F 92 THR cc_start: 0.6022 (m) cc_final: 0.5463 (p) REVERT: G 4 ARG cc_start: 0.5447 (mmt180) cc_final: 0.5137 (mmt-90) REVERT: G 25 LYS cc_start: 0.6938 (tppt) cc_final: 0.6690 (mmtt) REVERT: G 114 LYS cc_start: 0.5211 (mmtp) cc_final: 0.4999 (tptt) REVERT: G 137 LYS cc_start: 0.6491 (tptm) cc_final: 0.5927 (tptt) REVERT: G 139 GLU cc_start: 0.5621 (OUTLIER) cc_final: 0.5314 (mt-10) REVERT: G 143 ARG cc_start: 0.4637 (OUTLIER) cc_final: 0.4402 (ttp-170) REVERT: H 38 ASN cc_start: 0.6977 (t0) cc_final: 0.6693 (t0) REVERT: H 50 LYS cc_start: 0.6497 (ptmt) cc_final: 0.6211 (pttt) REVERT: H 58 GLU cc_start: 0.6117 (tp30) cc_final: 0.5625 (tt0) REVERT: I 33 ARG cc_start: 0.6237 (mtm180) cc_final: 0.5295 (mtt90) REVERT: I 46 MET cc_start: 0.6413 (ttt) cc_final: 0.6175 (ttt) REVERT: I 49 ARG cc_start: 0.5983 (mtm-85) cc_final: 0.5631 (mtm180) REVERT: I 57 MET cc_start: 0.5534 (ptp) cc_final: 0.5047 (ptm) REVERT: I 68 LYS cc_start: 0.7239 (mtpt) cc_final: 0.6442 (mtpt) REVERT: I 88 MET cc_start: 0.6279 (mtm) cc_final: 0.6010 (mtm) REVERT: I 110 GLN cc_start: 0.7561 (mm110) cc_final: 0.7359 (mm-40) REVERT: J 47 GLU cc_start: 0.6642 (tt0) cc_final: 0.6274 (tt0) REVERT: J 68 ARG cc_start: 0.7372 (mtt180) cc_final: 0.7054 (mtt180) REVERT: K 40 ASN cc_start: 0.6345 (m110) cc_final: 0.5846 (m-40) REVERT: K 85 MET cc_start: 0.7152 (mtp) cc_final: 0.6756 (mtm) REVERT: K 112 ASP cc_start: 0.6994 (t70) cc_final: 0.6564 (t0) REVERT: K 116 ILE cc_start: 0.7259 (pt) cc_final: 0.6876 (mm) REVERT: K 126 LYS cc_start: 0.6930 (mmtt) cc_final: 0.6680 (tttp) REVERT: L 10 LYS cc_start: 0.7089 (ttpt) cc_final: 0.6695 (tptt) REVERT: L 54 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6265 (mmp-170) REVERT: M 92 ARG cc_start: 0.6694 (mtt180) cc_final: 0.6415 (mtt180) REVERT: M 93 ARG cc_start: 0.6348 (mtt-85) cc_final: 0.5979 (mtt180) REVERT: N 6 MET cc_start: 0.7105 (mmm) cc_final: 0.6168 (mpt) REVERT: N 21 PHE cc_start: 0.6485 (t80) cc_final: 0.6236 (t80) REVERT: N 47 LYS cc_start: 0.6209 (tppt) cc_final: 0.5939 (tppt) REVERT: N 86 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7143 (mt-10) REVERT: N 89 MET cc_start: 0.7635 (mmp) cc_final: 0.7398 (mmp) REVERT: N 92 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7371 (mt-10) REVERT: O 11 ILE cc_start: 0.6179 (mt) cc_final: 0.5905 (mp) REVERT: O 45 GLU cc_start: 0.7180 (pp20) cc_final: 0.6564 (tm-30) REVERT: O 48 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6877 (mptp) REVERT: O 58 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6927 (ttm170) REVERT: O 62 GLN cc_start: 0.7165 (tt0) cc_final: 0.6847 (tp40) REVERT: O 64 ARG cc_start: 0.7513 (tpp-160) cc_final: 0.7218 (tpp-160) REVERT: O 80 GLN cc_start: 0.5960 (mm-40) cc_final: 0.5610 (tp40) REVERT: Q 11 ARG cc_start: 0.5985 (mtp-110) cc_final: 0.5558 (mtp85) REVERT: R 48 ARG cc_start: 0.5462 (mtp180) cc_final: 0.4772 (mpt180) REVERT: R 57 ARG cc_start: 0.7464 (mtm-85) cc_final: 0.7021 (mtm180) REVERT: R 61 ARG cc_start: 0.7374 (mtm-85) cc_final: 0.6943 (mtm-85) REVERT: S 13 LEU cc_start: 0.6136 (tp) cc_final: 0.5737 (mt) REVERT: S 36 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7554 (mtp85) REVERT: S 44 MET cc_start: 0.5818 (mtt) cc_final: 0.5478 (mtt) REVERT: T 5 LYS cc_start: 0.5633 (mtpt) cc_final: 0.5364 (tmmt) REVERT: T 16 LYS cc_start: 0.6869 (tttm) cc_final: 0.6433 (tmmt) REVERT: T 18 ARG cc_start: 0.6150 (ttp80) cc_final: 0.5506 (ttp80) REVERT: T 29 ARG cc_start: 0.6611 (mtm-85) cc_final: 0.6400 (mtm-85) REVERT: T 33 LYS cc_start: 0.6159 (ttmt) cc_final: 0.5846 (mmtt) REVERT: U 47 ARG cc_start: 0.5400 (tmm-80) cc_final: 0.4266 (mtt180) REVERT: c 72 ASP cc_start: 0.7013 (m-30) cc_final: 0.6709 (m-30) REVERT: c 117 GLN cc_start: 0.7008 (pt0) cc_final: 0.6625 (pt0) REVERT: c 182 ARG cc_start: 0.7782 (ttt90) cc_final: 0.7442 (tpt-90) REVERT: d 7 LYS cc_start: 0.8041 (ptmm) cc_final: 0.7809 (ptmt) REVERT: d 55 LYS cc_start: 0.7695 (tttp) cc_final: 0.7346 (tttp) REVERT: d 59 ARG cc_start: 0.7269 (mmt180) cc_final: 0.6702 (mmt180) REVERT: d 64 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6476 (mm-30) REVERT: d 89 GLU cc_start: 0.5273 (mp0) cc_final: 0.4901 (mt-10) REVERT: d 94 GLN cc_start: 0.7372 (tt0) cc_final: 0.7079 (tt0) REVERT: d 103 ASP cc_start: 0.5913 (m-30) cc_final: 0.5610 (p0) REVERT: d 168 GLU cc_start: 0.7715 (pt0) cc_final: 0.7419 (pt0) REVERT: d 207 VAL cc_start: 0.7808 (p) cc_final: 0.7519 (m) REVERT: e 61 ARG cc_start: 0.7301 (ptt-90) cc_final: 0.7066 (ptt90) REVERT: e 88 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7300 (mmp80) REVERT: e 178 VAL cc_start: 0.7074 (t) cc_final: 0.6675 (p) REVERT: f 27 GLN cc_start: 0.7473 (mt0) cc_final: 0.7137 (mt0) REVERT: f 30 ARG cc_start: 0.7135 (mtm-85) cc_final: 0.6635 (mtp180) REVERT: f 35 THR cc_start: 0.8214 (m) cc_final: 0.7989 (m) REVERT: f 94 GLU cc_start: 0.6162 (mm-30) cc_final: 0.5859 (tt0) REVERT: f 113 ASP cc_start: 0.5380 (t70) cc_final: 0.5125 (t70) REVERT: f 115 ARG cc_start: 0.5337 (mmm-85) cc_final: 0.5031 (mmm-85) REVERT: f 122 PHE cc_start: 0.6863 (m-80) cc_final: 0.6252 (m-80) REVERT: f 128 TYR cc_start: 0.7750 (t80) cc_final: 0.7362 (t80) REVERT: f 130 MET cc_start: 0.7470 (ptm) cc_final: 0.6690 (ppp) REVERT: f 161 LYS cc_start: 0.5353 (mtpp) cc_final: 0.4979 (mmtm) REVERT: g 75 MET cc_start: 0.7039 (ptm) cc_final: 0.6833 (ptp) REVERT: g 131 ILE cc_start: 0.7235 (mt) cc_final: 0.6866 (mp) REVERT: g 151 TYR cc_start: 0.7133 (m-80) cc_final: 0.6761 (m-80) REVERT: h 27 ARG cc_start: 0.6924 (ttm110) cc_final: 0.6695 (ttm110) REVERT: i 92 MET cc_start: 0.7830 (mmm) cc_final: 0.7135 (mmm) REVERT: i 96 ARG cc_start: 0.6563 (ttp80) cc_final: 0.5991 (ttp80) REVERT: j 7 MET cc_start: 0.8079 (mmm) cc_final: 0.7683 (mmm) REVERT: j 51 LYS cc_start: 0.6818 (mttp) cc_final: 0.6599 (mttm) REVERT: j 91 SER cc_start: 0.6214 (p) cc_final: 0.5547 (t) REVERT: j 93 GLN cc_start: 0.6797 (mm-40) cc_final: 0.6358 (mm110) REVERT: j 106 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6400 (mp0) REVERT: k 123 ARG cc_start: 0.6447 (ttm170) cc_final: 0.5982 (ttm170) REVERT: k 129 LYS cc_start: 0.6790 (mttp) cc_final: 0.6453 (mmmt) REVERT: l 5 LYS cc_start: 0.7017 (mttp) cc_final: 0.6518 (pttm) REVERT: l 22 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6954 (mt0) REVERT: l 133 LYS cc_start: 0.6647 (ttpt) cc_final: 0.6235 (tptm) REVERT: m 1 MET cc_start: 0.7904 (mtm) cc_final: 0.7673 (mtm) REVERT: m 43 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7612 (tp30) REVERT: m 72 ASP cc_start: 0.7339 (t0) cc_final: 0.6903 (t70) REVERT: n 16 ARG cc_start: 0.6743 (mmp80) cc_final: 0.6328 (mmt90) REVERT: n 30 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7480 (ptt90) REVERT: n 46 GLU cc_start: 0.6368 (mm-30) cc_final: 0.6086 (mp0) REVERT: n 69 ASP cc_start: 0.6585 (m-30) cc_final: 0.6273 (m-30) REVERT: o 7 GLN cc_start: 0.6747 (tm-30) cc_final: 0.6465 (tt0) REVERT: o 63 LYS cc_start: 0.8116 (ptmt) cc_final: 0.7902 (ptmt) REVERT: o 68 GLU cc_start: 0.6529 (mm-30) cc_final: 0.5993 (tp30) REVERT: o 89 ARG cc_start: 0.7022 (mtm110) cc_final: 0.6416 (mtp85) REVERT: p 13 ARG cc_start: 0.7639 (ttt90) cc_final: 0.7000 (ttp80) REVERT: p 87 SER cc_start: 0.7741 (m) cc_final: 0.7122 (t) REVERT: p 103 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6450 (mptt) REVERT: p 111 GLU cc_start: 0.6763 (mm-30) cc_final: 0.6421 (mm-30) REVERT: q 1 MET cc_start: 0.5766 (ttt) cc_final: 0.5401 (ttm) REVERT: q 60 LYS cc_start: 0.6873 (mtmm) cc_final: 0.6418 (mttp) REVERT: q 62 GLU cc_start: 0.6790 (tt0) cc_final: 0.6471 (tt0) REVERT: q 73 LYS cc_start: 0.7717 (mtpt) cc_final: 0.7440 (mttt) REVERT: r 70 LYS cc_start: 0.7391 (mtmm) cc_final: 0.6910 (mttp) REVERT: r 86 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7168 (ttm) REVERT: r 95 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6590 (ttp80) REVERT: s 1 MET cc_start: 0.4164 (pmm) cc_final: 0.2742 (ptt) REVERT: s 8 LEU cc_start: 0.7753 (mt) cc_final: 0.7470 (mt) REVERT: s 76 ARG cc_start: 0.7177 (ttt-90) cc_final: 0.6833 (tmt90) REVERT: t 7 ARG cc_start: 0.5836 (mtm110) cc_final: 0.5399 (ttm170) REVERT: t 10 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.5834 (tm-30) REVERT: t 22 ARG cc_start: 0.6818 (mtm-85) cc_final: 0.6586 (mtp180) REVERT: t 27 ASN cc_start: 0.7359 (OUTLIER) cc_final: 0.6932 (m-40) REVERT: t 46 GLN cc_start: 0.7328 (tp40) cc_final: 0.6953 (tp-100) REVERT: t 79 LYS cc_start: 0.6662 (mttp) cc_final: 0.6155 (mttp) REVERT: u 1 MET cc_start: 0.2693 (ppp) cc_final: 0.2125 (tmm) REVERT: u 4 ILE cc_start: 0.7669 (mt) cc_final: 0.7452 (mt) REVERT: u 48 MET cc_start: 0.6784 (tpt) cc_final: 0.6514 (mmm) REVERT: u 70 ILE cc_start: 0.6815 (OUTLIER) cc_final: 0.6139 (tt) REVERT: u 75 GLN cc_start: 0.7352 (tp40) cc_final: 0.6945 (tp-100) REVERT: v 5 LYS cc_start: 0.5857 (mtpt) cc_final: 0.5051 (mmtp) REVERT: v 44 LYS cc_start: 0.7757 (ttmm) cc_final: 0.7443 (ttpt) REVERT: v 78 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7861 (mttt) REVERT: x 17 GLU cc_start: 0.6302 (tp30) cc_final: 0.5734 (tp30) REVERT: x 26 PHE cc_start: 0.7941 (t80) cc_final: 0.7690 (t80) REVERT: y 39 GLU cc_start: 0.6619 (pt0) cc_final: 0.6370 (pt0) REVERT: y 56 LYS cc_start: 0.7732 (ttmt) cc_final: 0.7163 (ttpp) REVERT: 0 35 GLU cc_start: 0.6901 (tt0) cc_final: 0.6529 (tt0) REVERT: 0 36 LEU cc_start: 0.8209 (mt) cc_final: 0.7943 (mm) REVERT: 2 15 LYS cc_start: 0.7960 (mmtt) cc_final: 0.7375 (mtpp) REVERT: 3 12 ARG cc_start: 0.5883 (ptm-80) cc_final: 0.5275 (ptp-170) REVERT: 3 18 LYS cc_start: 0.7875 (tttt) cc_final: 0.7567 (tttt) outliers start: 114 outliers final: 45 residues processed: 942 average time/residue: 2.4113 time to fit residues: 3117.4767 Evaluate side-chains 898 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 832 time to evaluate : 5.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain T residue 15 GLU Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 154 ASP Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain f residue 111 ILE Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 80 THR Chi-restraints excluded: chain g residue 175 LYS Chi-restraints excluded: chain i residue 13 ARG Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain j residue 109 SER Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain o residue 13 MET Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain p residue 103 LYS Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 86 MET Chi-restraints excluded: chain r residue 95 ARG Chi-restraints excluded: chain s residue 26 LYS Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain t residue 27 ASN Chi-restraints excluded: chain t residue 72 ILE Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 70 ILE Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain 0 residue 38 LYS 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: 4.9990 chunk 467 optimal weight: 20.0000 chunk 99 optimal weight: 30.0000 chunk 429 optimal weight: 10.0000 chunk 604 optimal weight: 10.0000 chunk 903 optimal weight: 10.0000 chunk 956 optimal weight: 10.0000 chunk 472 optimal weight: 30.0000 chunk 856 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN D 136 GLN E 97 GLN F 3 HIS F 68 GLN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 ASN O 28 GLN O 35 GLN R 54 GLN ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 90 ASN k 93 ASN q 6 GLN r 31 GLN u 12 GLN x 27 ASN x 39 GLN x 58 ASN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 154032 Z= 0.376 Angle : 0.922 21.363 230513 Z= 0.481 Chirality : 0.046 0.395 29296 Planarity : 0.009 0.156 12270 Dihedral : 23.169 177.003 77190 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.83 % Favored : 96.06 % Rotamer: Outliers : 3.72 % Allowed : 13.38 % Favored : 82.91 % 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: -0.07 (0.11), residues: 5480 helix: 0.82 (0.12), residues: 1861 sheet: -0.20 (0.16), residues: 1055 loop : -0.54 (0.12), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP c 248 HIS 0.011 0.002 HIS c 230 PHE 0.027 0.003 PHE d 118 TYR 0.023 0.003 TYR R 51 ARG 0.016 0.001 ARG p 92 *********************** 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 1006 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 836 time to evaluate : 6.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.3867 (mmp) cc_final: 0.3214 (mmm) REVERT: B 49 MET cc_start: 0.3044 (mtt) cc_final: 0.2686 (mtp) REVERT: B 68 LEU cc_start: 0.4177 (OUTLIER) cc_final: 0.3954 (tt) REVERT: B 100 MET cc_start: 0.4436 (ttm) cc_final: 0.3719 (ttp) REVERT: B 112 LYS cc_start: 0.3700 (ttpt) cc_final: 0.3223 (ttmt) REVERT: B 136 MET cc_start: 0.3431 (OUTLIER) cc_final: 0.3174 (ptm) REVERT: B 212 LEU cc_start: 0.3836 (tp) cc_final: 0.3417 (mt) REVERT: C 45 LYS cc_start: 0.6210 (tttm) cc_final: 0.5839 (ttmm) REVERT: C 82 GLU cc_start: 0.4580 (OUTLIER) cc_final: 0.4070 (tp30) REVERT: C 136 ARG cc_start: 0.6213 (ttm-80) cc_final: 0.5937 (ttm-80) REVERT: C 139 GLN cc_start: 0.7002 (mt0) cc_final: 0.6537 (mt0) REVERT: C 179 ARG cc_start: 0.6870 (ttp-170) cc_final: 0.6354 (ttm170) REVERT: D 8 LYS cc_start: 0.5845 (mttm) cc_final: 0.5459 (mttp) REVERT: D 40 GLN cc_start: 0.6434 (mt0) cc_final: 0.5549 (tt0) REVERT: D 54 GLN cc_start: 0.6988 (mt0) cc_final: 0.6573 (mt0) REVERT: D 81 ARG cc_start: 0.5010 (ttp80) cc_final: 0.4134 (tmm160) REVERT: D 104 ARG cc_start: 0.6115 (mmt90) cc_final: 0.5791 (mmt180) REVERT: D 148 LYS cc_start: 0.4808 (tmtt) cc_final: 0.4471 (tppt) REVERT: D 202 GLU cc_start: 0.5095 (mm-30) cc_final: 0.4875 (mt-10) REVERT: D 206 LYS cc_start: 0.5891 (ttpp) cc_final: 0.5625 (tttp) REVERT: E 12 GLN cc_start: 0.6616 (mt0) cc_final: 0.6137 (mt0) REVERT: E 54 ARG cc_start: 0.7181 (mmm-85) cc_final: 0.6682 (mtt180) REVERT: E 55 GLU cc_start: 0.6428 (mt-10) cc_final: 0.5685 (mp0) REVERT: E 65 GLU cc_start: 0.5918 (OUTLIER) cc_final: 0.5666 (tp30) REVERT: E 70 ASN cc_start: 0.6784 (OUTLIER) cc_final: 0.6399 (m110) REVERT: E 156 LYS cc_start: 0.6468 (mtmt) cc_final: 0.6117 (mtmt) REVERT: E 159 LYS cc_start: 0.6526 (mttm) cc_final: 0.6230 (mttt) REVERT: F 1 MET cc_start: 0.4903 (tpp) cc_final: 0.4517 (mmt) REVERT: F 8 PHE cc_start: 0.7497 (p90) cc_final: 0.7171 (p90) REVERT: F 21 MET cc_start: 0.5293 (mtm) cc_final: 0.5089 (mtm) REVERT: F 44 ARG cc_start: 0.5385 (mmt90) cc_final: 0.5145 (mtt180) REVERT: F 55 HIS cc_start: 0.6516 (m90) cc_final: 0.6163 (m170) REVERT: F 92 THR cc_start: 0.6147 (m) cc_final: 0.5600 (p) REVERT: G 4 ARG cc_start: 0.5566 (mmt180) cc_final: 0.5233 (mmt-90) REVERT: G 21 GLU cc_start: 0.5895 (OUTLIER) cc_final: 0.5401 (mm-30) REVERT: G 106 GLU cc_start: 0.6367 (tt0) cc_final: 0.6136 (tt0) REVERT: G 119 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6534 (mtp180) REVERT: G 137 LYS cc_start: 0.6489 (OUTLIER) cc_final: 0.6032 (tptt) REVERT: G 139 GLU cc_start: 0.5646 (OUTLIER) cc_final: 0.5352 (mt-10) REVERT: H 38 ASN cc_start: 0.7164 (t0) cc_final: 0.6840 (t0) REVERT: H 58 GLU cc_start: 0.6348 (tp30) cc_final: 0.5843 (tt0) REVERT: H 114 ARG cc_start: 0.6165 (ttm-80) cc_final: 0.5860 (ttt180) REVERT: I 33 ARG cc_start: 0.6274 (mtm180) cc_final: 0.5448 (mtt90) REVERT: I 49 ARG cc_start: 0.6008 (mtm-85) cc_final: 0.5693 (mtm180) REVERT: I 57 MET cc_start: 0.5462 (ptp) cc_final: 0.5103 (ptm) REVERT: I 68 LYS cc_start: 0.7177 (mtpt) cc_final: 0.6466 (mtpt) REVERT: I 88 MET cc_start: 0.6350 (mtm) cc_final: 0.6092 (mtm) REVERT: I 110 GLN cc_start: 0.7410 (mm110) cc_final: 0.7044 (mt0) REVERT: I 124 ARG cc_start: 0.7272 (ttm-80) cc_final: 0.7021 (mtp-110) REVERT: K 40 ASN cc_start: 0.6519 (m110) cc_final: 0.6148 (m-40) REVERT: K 85 MET cc_start: 0.7158 (mtp) cc_final: 0.6700 (mtm) REVERT: K 112 ASP cc_start: 0.6964 (t70) cc_final: 0.6564 (t0) REVERT: K 126 LYS cc_start: 0.6856 (mmtt) cc_final: 0.6654 (tttp) REVERT: L 10 LYS cc_start: 0.7047 (ttpt) cc_final: 0.6733 (tptt) REVERT: N 6 MET cc_start: 0.7136 (mmm) cc_final: 0.6057 (mpt) REVERT: N 86 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7165 (mt-10) REVERT: N 92 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: O 45 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6540 (tm-30) REVERT: O 48 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6731 (mptp) REVERT: O 80 GLN cc_start: 0.5939 (mm-40) cc_final: 0.5635 (tp-100) REVERT: P 5 ARG cc_start: 0.6904 (ptt180) cc_final: 0.6639 (ptt180) REVERT: Q 11 ARG cc_start: 0.5970 (mtp-110) cc_final: 0.5559 (mtp85) REVERT: Q 19 LYS cc_start: 0.6583 (mttt) cc_final: 0.6324 (mttt) REVERT: R 48 ARG cc_start: 0.5737 (mtp180) cc_final: 0.5097 (mpt180) REVERT: R 57 ARG cc_start: 0.7435 (mtm-85) cc_final: 0.7076 (mtm180) REVERT: R 61 ARG cc_start: 0.7355 (mtm-85) cc_final: 0.6794 (mtm-85) REVERT: S 13 LEU cc_start: 0.6449 (tp) cc_final: 0.6056 (mt) REVERT: S 36 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7550 (mtp85) REVERT: T 5 LYS cc_start: 0.5906 (mtpt) cc_final: 0.5657 (mmtt) REVERT: T 18 ARG cc_start: 0.6221 (ttp80) cc_final: 0.5446 (ttp80) REVERT: U 17 ARG cc_start: 0.4942 (mtt90) cc_final: 0.4364 (mmt180) REVERT: U 47 ARG cc_start: 0.5450 (tmm-80) cc_final: 0.4143 (mtt180) REVERT: c 72 ASP cc_start: 0.6973 (m-30) cc_final: 0.6629 (m-30) REVERT: c 117 GLN cc_start: 0.7142 (pt0) cc_final: 0.6734 (pt0) REVERT: c 182 ARG cc_start: 0.7945 (ttt90) cc_final: 0.7625 (ttt-90) REVERT: c 223 THR cc_start: 0.8282 (p) cc_final: 0.7808 (t) REVERT: d 55 LYS cc_start: 0.7752 (tttp) cc_final: 0.7533 (tttp) REVERT: d 64 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6560 (mm-30) REVERT: d 89 GLU cc_start: 0.5244 (mp0) cc_final: 0.4870 (mt-10) REVERT: d 94 GLN cc_start: 0.7445 (tt0) cc_final: 0.7162 (tt0) REVERT: d 128 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.7452 (mmp80) REVERT: d 168 GLU cc_start: 0.7760 (pt0) cc_final: 0.7432 (pt0) REVERT: d 207 VAL cc_start: 0.7852 (p) cc_final: 0.7589 (m) REVERT: e 61 ARG cc_start: 0.7327 (ptt-90) cc_final: 0.7073 (ptt90) REVERT: e 88 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7249 (mmp80) REVERT: e 154 ASP cc_start: 0.4611 (OUTLIER) cc_final: 0.4367 (p0) REVERT: e 178 VAL cc_start: 0.7286 (t) cc_final: 0.6838 (p) REVERT: f 27 GLN cc_start: 0.7488 (mt0) cc_final: 0.7063 (mt0) REVERT: f 30 ARG cc_start: 0.7247 (mtm-85) cc_final: 0.6690 (mpp-170) REVERT: f 35 THR cc_start: 0.8270 (m) cc_final: 0.8039 (m) REVERT: f 94 GLU cc_start: 0.6130 (mm-30) cc_final: 0.5758 (tt0) REVERT: f 113 ASP cc_start: 0.5268 (t70) cc_final: 0.5023 (t70) REVERT: f 122 PHE cc_start: 0.6802 (m-80) cc_final: 0.6101 (m-80) REVERT: f 128 TYR cc_start: 0.7697 (t80) cc_final: 0.7366 (t80) REVERT: f 161 LYS cc_start: 0.5467 (mtpp) cc_final: 0.4953 (mmtt) REVERT: g 39 ASP cc_start: 0.5428 (m-30) cc_final: 0.5215 (t0) REVERT: g 130 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5784 (tt0) REVERT: g 131 ILE cc_start: 0.7286 (mt) cc_final: 0.6944 (mp) REVERT: h 27 ARG cc_start: 0.6902 (ttm110) cc_final: 0.6641 (ttm110) REVERT: i 96 ARG cc_start: 0.6621 (ttp80) cc_final: 0.6057 (ttp80) REVERT: j 7 MET cc_start: 0.8080 (mmm) cc_final: 0.7753 (mmm) REVERT: j 49 ARG cc_start: 0.6134 (mtm-85) cc_final: 0.5528 (mpp-170) REVERT: j 51 LYS cc_start: 0.6823 (mttp) cc_final: 0.6592 (mttm) REVERT: j 93 GLN cc_start: 0.6770 (mm-40) cc_final: 0.6366 (mm110) REVERT: j 106 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6401 (mp0) REVERT: k 1 MET cc_start: 0.6685 (OUTLIER) cc_final: 0.5969 (ptt) REVERT: k 123 ARG cc_start: 0.6390 (ttm170) cc_final: 0.5996 (ttm170) REVERT: k 129 LYS cc_start: 0.6831 (mttp) cc_final: 0.6476 (mmmt) REVERT: l 5 LYS cc_start: 0.7070 (mttp) cc_final: 0.6560 (pttm) REVERT: l 22 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6946 (mt0) REVERT: l 133 LYS cc_start: 0.6710 (ttpt) cc_final: 0.6241 (tptm) REVERT: m 1 MET cc_start: 0.7913 (mtm) cc_final: 0.7664 (mtm) REVERT: m 43 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7579 (tp30) REVERT: m 72 ASP cc_start: 0.7375 (t0) cc_final: 0.6937 (t70) REVERT: n 3 LYS cc_start: 0.6473 (mtpt) cc_final: 0.6257 (mttm) REVERT: n 16 ARG cc_start: 0.6852 (mmp80) cc_final: 0.6417 (mmt90) REVERT: n 46 GLU cc_start: 0.6331 (mm-30) cc_final: 0.5926 (mp0) REVERT: n 69 ASP cc_start: 0.6638 (m-30) cc_final: 0.6354 (m-30) REVERT: o 7 GLN cc_start: 0.6939 (tm-30) cc_final: 0.6680 (tm-30) REVERT: o 63 LYS cc_start: 0.8179 (ptmt) cc_final: 0.7972 (ptmt) REVERT: o 68 GLU cc_start: 0.6359 (mm-30) cc_final: 0.5943 (tm-30) REVERT: o 89 ARG cc_start: 0.7054 (mtm110) cc_final: 0.6160 (mtt-85) REVERT: p 13 ARG cc_start: 0.7824 (ttt90) cc_final: 0.7108 (ttp80) REVERT: p 103 LYS cc_start: 0.6884 (OUTLIER) cc_final: 0.6383 (mptt) REVERT: p 111 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6436 (mm-30) REVERT: q 1 MET cc_start: 0.5771 (ttt) cc_final: 0.5423 (ttm) REVERT: q 60 LYS cc_start: 0.7042 (mtmm) cc_final: 0.6547 (mttp) REVERT: q 62 GLU cc_start: 0.6616 (tt0) cc_final: 0.6266 (tt0) REVERT: q 73 LYS cc_start: 0.7731 (mtpt) cc_final: 0.7507 (mttt) REVERT: r 70 LYS cc_start: 0.7456 (mtmm) cc_final: 0.6973 (mttp) REVERT: r 86 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7334 (ttm) REVERT: r 95 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6717 (ttp-170) REVERT: s 4 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.5651 (tp30) REVERT: s 8 LEU cc_start: 0.7776 (mt) cc_final: 0.7513 (mt) REVERT: s 37 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7386 (p0) REVERT: s 76 ARG cc_start: 0.7244 (ttt-90) cc_final: 0.6934 (tmt90) REVERT: t 10 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.5877 (tm-30) REVERT: t 22 ARG cc_start: 0.6748 (mtm-85) cc_final: 0.6474 (mtp180) REVERT: t 54 GLN cc_start: 0.3030 (OUTLIER) cc_final: 0.2603 (mt0) REVERT: t 79 LYS cc_start: 0.6715 (mttp) cc_final: 0.6288 (mttp) REVERT: u 1 MET cc_start: 0.2793 (ppp) cc_final: 0.2231 (tmm) REVERT: u 70 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6211 (tt) REVERT: u 75 GLN cc_start: 0.7351 (tp40) cc_final: 0.6894 (tp-100) REVERT: v 44 LYS cc_start: 0.7818 (ttmm) cc_final: 0.7481 (ttpt) REVERT: v 72 LYS cc_start: 0.7587 (mtpt) cc_final: 0.7136 (mtpt) REVERT: v 78 LYS cc_start: 0.8078 (mtmt) cc_final: 0.7840 (mttt) REVERT: x 17 GLU cc_start: 0.6662 (tp30) cc_final: 0.6131 (tp30) REVERT: y 39 GLU cc_start: 0.6635 (pt0) cc_final: 0.6382 (pt0) REVERT: y 56 LYS cc_start: 0.7799 (ttmt) cc_final: 0.7219 (ttpp) REVERT: 0 50 LYS cc_start: 0.7408 (mttm) cc_final: 0.7028 (mtpp) REVERT: 2 15 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7533 (mptp) REVERT: 3 12 ARG cc_start: 0.6027 (ptm-80) cc_final: 0.5422 (ptp-170) REVERT: 3 18 LYS cc_start: 0.7923 (tttt) cc_final: 0.7554 (tttt) outliers start: 170 outliers final: 91 residues processed: 937 average time/residue: 2.3667 time to fit residues: 3060.1249 Evaluate side-chains 926 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 809 time to evaluate : 5.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 114 LYS Chi-restraints excluded: chain N residue 10 GLU Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 75 HIS Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 154 ASP Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain f residue 111 ILE Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 146 VAL Chi-restraints excluded: chain f residue 157 THR Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 24 ILE Chi-restraints excluded: chain g residue 80 THR Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 175 LYS Chi-restraints excluded: chain i residue 13 ARG Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain j residue 109 SER Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain n residue 85 LYS Chi-restraints excluded: chain o residue 13 MET Chi-restraints excluded: chain o residue 25 THR Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain p residue 103 LYS Chi-restraints excluded: chain p residue 104 VAL Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 86 MET Chi-restraints excluded: chain r residue 95 ARG Chi-restraints excluded: chain s residue 4 GLU Chi-restraints excluded: chain s residue 26 LYS Chi-restraints excluded: chain s residue 37 ASP Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain t residue 27 ASN Chi-restraints excluded: chain t residue 54 GLN Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain t residue 61 LYS Chi-restraints excluded: chain t residue 72 ILE Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 70 ILE Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain z residue 34 SER Chi-restraints excluded: chain 0 residue 38 LYS Chi-restraints excluded: chain 3 residue 36 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 796 optimal weight: 10.0000 chunk 543 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 712 optimal weight: 10.0000 chunk 394 optimal weight: 10.0000 chunk 816 optimal weight: 8.9990 chunk 661 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 488 optimal weight: 20.0000 chunk 858 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN E 73 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN O 40 GLN O 62 GLN R 54 GLN j 90 ASN k 93 ASN q 6 GLN t 46 GLN u 12 GLN x 27 ASN x 58 ASN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 154032 Z= 0.344 Angle : 0.880 18.505 230513 Z= 0.463 Chirality : 0.045 0.405 29296 Planarity : 0.009 0.151 12270 Dihedral : 23.140 177.158 77190 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 4.00 % Allowed : 14.64 % Favored : 81.36 % 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: -0.23 (0.11), residues: 5480 helix: 0.69 (0.12), residues: 1870 sheet: -0.33 (0.15), residues: 1081 loop : -0.62 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP c 248 HIS 0.010 0.002 HIS c 230 PHE 0.027 0.003 PHE F 8 TYR 0.021 0.003 TYR R 51 ARG 0.013 0.001 ARG p 92 *********************** 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 1023 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 840 time to evaluate : 6.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.3867 (mmp) cc_final: 0.3243 (mmm) REVERT: B 49 MET cc_start: 0.3099 (mtt) cc_final: 0.2767 (mtp) REVERT: B 68 LEU cc_start: 0.4153 (OUTLIER) cc_final: 0.3922 (tt) REVERT: B 100 MET cc_start: 0.4427 (ttm) cc_final: 0.3764 (ttp) REVERT: B 112 LYS cc_start: 0.3516 (ttpt) cc_final: 0.3086 (tttt) REVERT: B 154 MET cc_start: 0.3431 (mtt) cc_final: 0.3203 (ttp) REVERT: B 167 ASP cc_start: 0.3076 (OUTLIER) cc_final: 0.2866 (m-30) REVERT: C 45 LYS cc_start: 0.6209 (tttm) cc_final: 0.5827 (ttmm) REVERT: C 72 ARG cc_start: 0.5710 (mtm-85) cc_final: 0.5404 (mtm-85) REVERT: C 82 GLU cc_start: 0.4556 (OUTLIER) cc_final: 0.4156 (tp30) REVERT: C 132 ARG cc_start: 0.6332 (OUTLIER) cc_final: 0.5791 (ptp-170) REVERT: C 136 ARG cc_start: 0.6294 (ttm-80) cc_final: 0.5953 (ttm-80) REVERT: C 139 GLN cc_start: 0.6930 (mt0) cc_final: 0.6008 (pt0) REVERT: C 179 ARG cc_start: 0.6888 (ttp-170) cc_final: 0.6402 (ttm170) REVERT: D 8 LYS cc_start: 0.5895 (mttm) cc_final: 0.5515 (mttp) REVERT: D 40 GLN cc_start: 0.6520 (mt0) cc_final: 0.5622 (tt0) REVERT: D 54 GLN cc_start: 0.7078 (mt0) cc_final: 0.6765 (mt0) REVERT: D 81 ARG cc_start: 0.4962 (ttp80) cc_final: 0.4316 (tmt170) REVERT: D 104 ARG cc_start: 0.6194 (mmt90) cc_final: 0.5830 (mmt180) REVERT: D 128 ARG cc_start: 0.4854 (mtp-110) cc_final: 0.4567 (mtt-85) REVERT: D 129 VAL cc_start: 0.5707 (t) cc_final: 0.5455 (p) REVERT: D 148 LYS cc_start: 0.4764 (tmtt) cc_final: 0.4412 (tppt) REVERT: D 206 LYS cc_start: 0.5905 (ttpp) cc_final: 0.5609 (tttp) REVERT: E 12 GLN cc_start: 0.6643 (mt0) cc_final: 0.6152 (mt0) REVERT: E 19 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7144 (p0) REVERT: E 29 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7679 (mtt90) REVERT: E 54 ARG cc_start: 0.7212 (mmm-85) cc_final: 0.6751 (mtt180) REVERT: E 55 GLU cc_start: 0.6411 (mt-10) cc_final: 0.6038 (mt-10) REVERT: E 65 GLU cc_start: 0.5983 (OUTLIER) cc_final: 0.5711 (tp30) REVERT: E 70 ASN cc_start: 0.6805 (OUTLIER) cc_final: 0.6444 (m110) REVERT: E 152 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6963 (ptp) REVERT: E 156 LYS cc_start: 0.6499 (mtmt) cc_final: 0.6182 (mtmt) REVERT: E 159 LYS cc_start: 0.6575 (mttm) cc_final: 0.6114 (mttt) REVERT: F 1 MET cc_start: 0.4853 (tpp) cc_final: 0.4429 (mmt) REVERT: F 44 ARG cc_start: 0.5321 (mmt90) cc_final: 0.5017 (mtt180) REVERT: F 55 HIS cc_start: 0.6407 (m90) cc_final: 0.6091 (m170) REVERT: F 92 THR cc_start: 0.6225 (m) cc_final: 0.5661 (p) REVERT: G 4 ARG cc_start: 0.5656 (mmt180) cc_final: 0.5250 (mmt-90) REVERT: G 21 GLU cc_start: 0.5914 (OUTLIER) cc_final: 0.5356 (mm-30) REVERT: G 59 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.6058 (mm) REVERT: G 66 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6175 (tp) REVERT: G 106 GLU cc_start: 0.6379 (tt0) cc_final: 0.6132 (tt0) REVERT: G 119 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.6347 (mtp180) REVERT: G 137 LYS cc_start: 0.6422 (tptm) cc_final: 0.5934 (tptt) REVERT: G 139 GLU cc_start: 0.5528 (OUTLIER) cc_final: 0.5239 (mt-10) REVERT: G 154 TYR cc_start: 0.4490 (OUTLIER) cc_final: 0.3057 (m-10) REVERT: H 38 ASN cc_start: 0.7123 (t0) cc_final: 0.6809 (t0) REVERT: H 58 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.6023 (tt0) REVERT: H 114 ARG cc_start: 0.6196 (ttm-80) cc_final: 0.5940 (ttt180) REVERT: I 33 ARG cc_start: 0.6186 (mtm180) cc_final: 0.5445 (mtt180) REVERT: I 49 ARG cc_start: 0.6062 (mtm-85) cc_final: 0.5753 (mtm180) REVERT: I 57 MET cc_start: 0.5556 (ptp) cc_final: 0.5176 (ptm) REVERT: I 68 LYS cc_start: 0.7195 (mtpt) cc_final: 0.6438 (mtpt) REVERT: I 88 MET cc_start: 0.6361 (mtm) cc_final: 0.6103 (mtm) REVERT: I 110 GLN cc_start: 0.7408 (mm110) cc_final: 0.7116 (mt0) REVERT: I 124 ARG cc_start: 0.7293 (ttm-80) cc_final: 0.7034 (mtp-110) REVERT: K 40 ASN cc_start: 0.6521 (m110) cc_final: 0.6162 (m-40) REVERT: K 85 MET cc_start: 0.7119 (mtp) cc_final: 0.6910 (mtt) REVERT: K 112 ASP cc_start: 0.6964 (t70) cc_final: 0.6596 (t0) REVERT: L 10 LYS cc_start: 0.7072 (ttpt) cc_final: 0.6759 (tptt) REVERT: L 18 LYS cc_start: 0.3721 (OUTLIER) cc_final: 0.2852 (ptmm) REVERT: M 114 LYS cc_start: 0.5599 (OUTLIER) cc_final: 0.5390 (mttp) REVERT: N 6 MET cc_start: 0.7094 (mmm) cc_final: 0.6035 (mpt) REVERT: N 86 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7225 (mt-10) REVERT: N 92 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: N 97 LYS cc_start: 0.7389 (ptmm) cc_final: 0.6914 (pttt) REVERT: O 45 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6377 (tm-30) REVERT: O 48 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6721 (mptp) REVERT: O 73 LYS cc_start: 0.6512 (mmmt) cc_final: 0.5893 (ttmt) REVERT: P 1 MET cc_start: 0.4850 (OUTLIER) cc_final: 0.4045 (tpp) REVERT: P 34 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5497 (tm-30) REVERT: Q 11 ARG cc_start: 0.5993 (mtp-110) cc_final: 0.5639 (mtp85) REVERT: Q 18 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5501 (mt-10) REVERT: Q 19 LYS cc_start: 0.6581 (mttt) cc_final: 0.6288 (mttt) REVERT: R 48 ARG cc_start: 0.5674 (mtp180) cc_final: 0.5055 (mpt180) REVERT: R 57 ARG cc_start: 0.7390 (mtm-85) cc_final: 0.7100 (mtm180) REVERT: R 61 ARG cc_start: 0.7346 (mtm-85) cc_final: 0.7051 (mtm-85) REVERT: S 6 LYS cc_start: 0.6779 (pttt) cc_final: 0.6560 (pttp) REVERT: S 13 LEU cc_start: 0.6414 (tp) cc_final: 0.6004 (mt) REVERT: S 44 MET cc_start: 0.5243 (mtt) cc_final: 0.4793 (mtt) REVERT: S 58 VAL cc_start: 0.6602 (OUTLIER) cc_final: 0.6310 (m) REVERT: T 5 LYS cc_start: 0.5818 (mtpt) cc_final: 0.5599 (mmtt) REVERT: T 18 ARG cc_start: 0.6208 (ttp80) cc_final: 0.5526 (ttp80) REVERT: U 17 ARG cc_start: 0.5097 (mtt90) cc_final: 0.4469 (mmt180) REVERT: U 47 ARG cc_start: 0.5428 (tmm-80) cc_final: 0.4179 (mtt180) REVERT: c 72 ASP cc_start: 0.6873 (m-30) cc_final: 0.6494 (m-30) REVERT: c 117 GLN cc_start: 0.7061 (pt0) cc_final: 0.6643 (pt0) REVERT: c 182 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7666 (ttt180) REVERT: c 223 THR cc_start: 0.8231 (p) cc_final: 0.7847 (t) REVERT: d 55 LYS cc_start: 0.7826 (tttp) cc_final: 0.7626 (tttp) REVERT: d 59 ARG cc_start: 0.7312 (mmt180) cc_final: 0.6948 (mmt180) REVERT: d 64 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6487 (mm-30) REVERT: d 89 GLU cc_start: 0.5330 (OUTLIER) cc_final: 0.4934 (mt-10) REVERT: d 94 GLN cc_start: 0.7565 (tt0) cc_final: 0.7316 (tt0) REVERT: d 128 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7431 (mmp80) REVERT: d 168 GLU cc_start: 0.7782 (pt0) cc_final: 0.7442 (pt0) REVERT: d 207 VAL cc_start: 0.7969 (p) cc_final: 0.7674 (m) REVERT: e 61 ARG cc_start: 0.7336 (ptt-90) cc_final: 0.7086 (ptp90) REVERT: e 88 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7296 (mmp80) REVERT: e 178 VAL cc_start: 0.7347 (t) cc_final: 0.6893 (p) REVERT: f 27 GLN cc_start: 0.7481 (mt0) cc_final: 0.7019 (mt0) REVERT: f 30 ARG cc_start: 0.7239 (mtm-85) cc_final: 0.6651 (mpp-170) REVERT: f 35 THR cc_start: 0.8252 (m) cc_final: 0.8006 (m) REVERT: f 94 GLU cc_start: 0.6073 (mm-30) cc_final: 0.5776 (tt0) REVERT: f 113 ASP cc_start: 0.5266 (t70) cc_final: 0.5062 (t70) REVERT: f 122 PHE cc_start: 0.6792 (m-80) cc_final: 0.6183 (m-80) REVERT: f 161 LYS cc_start: 0.5483 (mtpp) cc_final: 0.4996 (mmtt) REVERT: g 131 ILE cc_start: 0.7208 (mt) cc_final: 0.6820 (mp) REVERT: g 149 ARG cc_start: 0.7600 (ttt-90) cc_final: 0.7323 (ttt-90) REVERT: i 92 MET cc_start: 0.7791 (mmm) cc_final: 0.6918 (mmm) REVERT: i 96 ARG cc_start: 0.6597 (ttp80) cc_final: 0.6031 (ttp80) REVERT: j 7 MET cc_start: 0.8074 (mmm) cc_final: 0.7541 (mmm) REVERT: j 49 ARG cc_start: 0.6087 (mtm-85) cc_final: 0.5484 (mpp-170) REVERT: j 51 LYS cc_start: 0.6820 (mttp) cc_final: 0.6571 (mttm) REVERT: j 93 GLN cc_start: 0.6772 (mm-40) cc_final: 0.6391 (mm110) REVERT: j 106 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: k 123 ARG cc_start: 0.6426 (ttm170) cc_final: 0.6023 (ttm170) REVERT: k 129 LYS cc_start: 0.6823 (mttp) cc_final: 0.6463 (mmmt) REVERT: l 5 LYS cc_start: 0.7078 (mttp) cc_final: 0.6566 (pttm) REVERT: l 22 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6930 (mt0) REVERT: l 127 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7551 (tttt) REVERT: l 133 LYS cc_start: 0.6835 (ttpt) cc_final: 0.6287 (tptm) REVERT: l 134 THR cc_start: 0.7380 (m) cc_final: 0.6867 (t) REVERT: m 1 MET cc_start: 0.7929 (mtm) cc_final: 0.7626 (mtm) REVERT: m 43 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7568 (tp30) REVERT: m 72 ASP cc_start: 0.7352 (t0) cc_final: 0.6895 (t70) REVERT: n 16 ARG cc_start: 0.6829 (mmp80) cc_final: 0.6401 (mmt90) REVERT: n 30 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7431 (ptt90) REVERT: n 46 GLU cc_start: 0.6347 (mm-30) cc_final: 0.5940 (mp0) REVERT: n 69 ASP cc_start: 0.6642 (m-30) cc_final: 0.6356 (m-30) REVERT: o 7 GLN cc_start: 0.6822 (tm-30) cc_final: 0.6583 (tm-30) REVERT: o 38 LYS cc_start: 0.6772 (OUTLIER) cc_final: 0.6564 (pttp) REVERT: o 89 ARG cc_start: 0.7020 (mtm110) cc_final: 0.6128 (mtt-85) REVERT: p 13 ARG cc_start: 0.7840 (ttt90) cc_final: 0.7182 (ttp80) REVERT: p 103 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6414 (mptt) REVERT: p 111 GLU cc_start: 0.6758 (mm-30) cc_final: 0.6387 (mm-30) REVERT: q 1 MET cc_start: 0.5698 (ttt) cc_final: 0.5455 (ttm) REVERT: q 62 GLU cc_start: 0.6632 (tt0) cc_final: 0.6245 (tt0) REVERT: q 73 LYS cc_start: 0.7743 (mtpt) cc_final: 0.7518 (mttt) REVERT: r 70 LYS cc_start: 0.7450 (mtmm) cc_final: 0.6986 (mttp) REVERT: r 95 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6705 (ttp-170) REVERT: s 4 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.5584 (tp30) REVERT: s 8 LEU cc_start: 0.7734 (mt) cc_final: 0.7446 (mt) REVERT: s 76 ARG cc_start: 0.7212 (ttt-90) cc_final: 0.6890 (tmt90) REVERT: t 7 ARG cc_start: 0.6634 (ttt-90) cc_final: 0.5925 (ttt90) REVERT: t 10 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.5899 (tm-30) REVERT: t 22 ARG cc_start: 0.6803 (mtm-85) cc_final: 0.6588 (mtp180) REVERT: t 54 GLN cc_start: 0.2983 (OUTLIER) cc_final: 0.2743 (mp10) REVERT: t 60 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6516 (mt-10) REVERT: t 79 LYS cc_start: 0.6471 (mttp) cc_final: 0.6158 (mttp) REVERT: u 70 ILE cc_start: 0.6905 (OUTLIER) cc_final: 0.6244 (tt) REVERT: u 75 GLN cc_start: 0.7453 (tp40) cc_final: 0.7006 (tp-100) REVERT: v 44 LYS cc_start: 0.7827 (ttmm) cc_final: 0.7498 (ttpt) REVERT: v 72 LYS cc_start: 0.7601 (mtpt) cc_final: 0.7156 (mtmt) REVERT: v 78 LYS cc_start: 0.8068 (mtmt) cc_final: 0.7821 (mttt) REVERT: v 83 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7073 (mt-10) REVERT: x 2 LYS cc_start: 0.5485 (tttp) cc_final: 0.5169 (ttpp) REVERT: x 17 GLU cc_start: 0.6740 (tp30) cc_final: 0.6334 (tp30) REVERT: y 39 GLU cc_start: 0.6644 (pt0) cc_final: 0.6396 (pt0) REVERT: y 56 LYS cc_start: 0.7790 (ttmt) cc_final: 0.7229 (ttpp) REVERT: 0 50 LYS cc_start: 0.7411 (mttm) cc_final: 0.7087 (mtpp) REVERT: 1 1 MET cc_start: 0.7272 (mtp) cc_final: 0.7060 (mtp) REVERT: 2 15 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7529 (mptp) REVERT: 3 12 ARG cc_start: 0.6085 (ptm-80) cc_final: 0.5574 (ptp-170) REVERT: 3 18 LYS cc_start: 0.7905 (tttt) cc_final: 0.7563 (tttt) REVERT: 4 39 LYS cc_start: 0.5486 (pttt) cc_final: 0.5206 (pttm) outliers start: 183 outliers final: 89 residues processed: 951 average time/residue: 2.4094 time to fit residues: 3158.6508 Evaluate side-chains 948 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 820 time to evaluate : 5.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 114 LYS Chi-restraints excluded: chain N residue 10 GLU Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 75 HIS Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 18 LYS Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 89 GLU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain f residue 111 ILE Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 157 THR Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 24 ILE Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 80 THR Chi-restraints excluded: chain g residue 163 ARG Chi-restraints excluded: chain g residue 175 LYS Chi-restraints excluded: chain i residue 13 ARG Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain j residue 109 SER Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 127 LYS Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 85 LYS Chi-restraints excluded: chain o residue 13 MET Chi-restraints excluded: chain o residue 25 THR Chi-restraints excluded: chain o residue 38 LYS Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain p residue 103 LYS Chi-restraints excluded: chain p residue 104 VAL Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 95 ARG Chi-restraints excluded: chain s residue 4 GLU Chi-restraints excluded: chain s residue 26 LYS Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain t residue 27 ASN Chi-restraints excluded: chain t residue 54 GLN Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain t residue 60 GLU Chi-restraints excluded: chain t residue 72 ILE Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 70 ILE Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain 0 residue 38 LYS Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 22 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 321 optimal weight: 5.9990 chunk 861 optimal weight: 5.9990 chunk 189 optimal weight: 30.0000 chunk 561 optimal weight: 10.0000 chunk 236 optimal weight: 0.9990 chunk 957 optimal weight: 8.9990 chunk 795 optimal weight: 8.9990 chunk 443 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 316 optimal weight: 2.9990 chunk 502 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN O 35 GLN O 40 GLN O 62 GLN R 54 GLN j 90 ASN k 93 ASN q 6 GLN t 46 GLN u 12 GLN x 27 ASN x 58 ASN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 154032 Z= 0.243 Angle : 0.771 15.331 230513 Z= 0.418 Chirality : 0.040 0.400 29296 Planarity : 0.008 0.143 12270 Dihedral : 23.066 177.413 77190 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.91 % Favored : 96.02 % Rotamer: Outliers : 3.76 % Allowed : 15.67 % Favored : 80.57 % 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: 0.01 (0.11), residues: 5480 helix: 0.97 (0.12), residues: 1872 sheet: -0.22 (0.15), residues: 1076 loop : -0.54 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 248 HIS 0.008 0.001 HIS c 230 PHE 0.022 0.002 PHE F 8 TYR 0.017 0.002 TYR r 38 ARG 0.008 0.001 ARG p 92 *********************** 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 996 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 824 time to evaluate : 5.500 Fit side-chains revert: symmetry clash REVERT: B 27 MET cc_start: 0.3820 (mmp) cc_final: 0.3225 (mmm) REVERT: B 49 MET cc_start: 0.3022 (mtt) cc_final: 0.2725 (mtp) REVERT: B 68 LEU cc_start: 0.4074 (OUTLIER) cc_final: 0.3824 (tt) REVERT: B 112 LYS cc_start: 0.3610 (ttpt) cc_final: 0.3184 (tttp) REVERT: B 154 MET cc_start: 0.3319 (mtt) cc_final: 0.3080 (ttp) REVERT: B 212 LEU cc_start: 0.3481 (tp) cc_final: 0.3003 (mt) REVERT: C 45 LYS cc_start: 0.6124 (tttm) cc_final: 0.5757 (ttmm) REVERT: C 46 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5903 (tt0) REVERT: C 82 GLU cc_start: 0.4351 (OUTLIER) cc_final: 0.4046 (tp30) REVERT: C 136 ARG cc_start: 0.6309 (ttm-80) cc_final: 0.5955 (ttm-80) REVERT: C 139 GLN cc_start: 0.6948 (mt0) cc_final: 0.5989 (pt0) REVERT: C 179 ARG cc_start: 0.6846 (ttp-170) cc_final: 0.6349 (ttm170) REVERT: D 8 LYS cc_start: 0.5823 (mttm) cc_final: 0.5475 (mttp) REVERT: D 40 GLN cc_start: 0.6442 (mt0) cc_final: 0.5553 (tt0) REVERT: D 54 GLN cc_start: 0.7053 (mt0) cc_final: 0.6715 (mt0) REVERT: D 81 ARG cc_start: 0.4988 (ttp80) cc_final: 0.4369 (tmt170) REVERT: D 104 ARG cc_start: 0.6199 (mmt90) cc_final: 0.5843 (mmt180) REVERT: D 129 VAL cc_start: 0.5509 (t) cc_final: 0.5294 (p) REVERT: D 148 LYS cc_start: 0.4787 (tmtt) cc_final: 0.4427 (tppt) REVERT: D 206 LYS cc_start: 0.5821 (ttpp) cc_final: 0.5555 (tttp) REVERT: E 12 GLN cc_start: 0.6621 (mt0) cc_final: 0.6132 (mt0) REVERT: E 19 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.7146 (p0) REVERT: E 29 ARG cc_start: 0.8028 (mtt180) cc_final: 0.7680 (mtt90) REVERT: E 54 ARG cc_start: 0.7185 (mmm-85) cc_final: 0.6733 (mtt180) REVERT: E 55 GLU cc_start: 0.6395 (mt-10) cc_final: 0.5936 (mm-30) REVERT: E 65 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.5697 (tp30) REVERT: E 70 ASN cc_start: 0.6673 (OUTLIER) cc_final: 0.6324 (m110) REVERT: E 152 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6907 (ptp) REVERT: E 156 LYS cc_start: 0.6513 (mtmt) cc_final: 0.6230 (mtmt) REVERT: E 159 LYS cc_start: 0.6515 (mttm) cc_final: 0.6142 (mttt) REVERT: F 1 MET cc_start: 0.4849 (tpp) cc_final: 0.4494 (mmt) REVERT: F 55 HIS cc_start: 0.6452 (m90) cc_final: 0.6129 (m170) REVERT: F 92 THR cc_start: 0.6211 (m) cc_final: 0.5645 (p) REVERT: G 4 ARG cc_start: 0.5682 (mmt180) cc_final: 0.5262 (mmt-90) REVERT: G 59 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.6013 (mm) REVERT: G 66 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6185 (tp) REVERT: G 106 GLU cc_start: 0.6371 (tt0) cc_final: 0.6117 (tt0) REVERT: G 119 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.6334 (mtp180) REVERT: G 137 LYS cc_start: 0.6396 (OUTLIER) cc_final: 0.5947 (tptt) REVERT: G 154 TYR cc_start: 0.4365 (OUTLIER) cc_final: 0.3025 (m-10) REVERT: H 38 ASN cc_start: 0.7105 (t0) cc_final: 0.6776 (t0) REVERT: H 58 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6018 (tt0) REVERT: H 114 ARG cc_start: 0.6135 (ttm-80) cc_final: 0.5879 (ttt180) REVERT: I 33 ARG cc_start: 0.6179 (mtm180) cc_final: 0.5447 (mtt180) REVERT: I 49 ARG cc_start: 0.5964 (mtm-85) cc_final: 0.5639 (mtm180) REVERT: I 57 MET cc_start: 0.5338 (ptp) cc_final: 0.4960 (ptm) REVERT: I 68 LYS cc_start: 0.7215 (mtpt) cc_final: 0.6453 (mtpt) REVERT: I 88 MET cc_start: 0.6350 (mtm) cc_final: 0.6086 (mtm) REVERT: I 110 GLN cc_start: 0.7407 (mm110) cc_final: 0.7108 (mt0) REVERT: I 124 ARG cc_start: 0.7275 (ttm-80) cc_final: 0.7020 (mtp-110) REVERT: J 66 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7226 (pt0) REVERT: K 40 ASN cc_start: 0.6460 (m110) cc_final: 0.6023 (m-40) REVERT: K 112 ASP cc_start: 0.6933 (t70) cc_final: 0.6567 (t0) REVERT: L 10 LYS cc_start: 0.7045 (ttpt) cc_final: 0.6736 (tptt) REVERT: L 18 LYS cc_start: 0.3667 (OUTLIER) cc_final: 0.2866 (ptmm) REVERT: L 54 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6058 (mmp-170) REVERT: M 93 ARG cc_start: 0.6433 (mtt-85) cc_final: 0.6143 (mtt180) REVERT: M 114 LYS cc_start: 0.5591 (OUTLIER) cc_final: 0.5362 (mttp) REVERT: N 6 MET cc_start: 0.7108 (mmm) cc_final: 0.6067 (mpt) REVERT: N 86 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7153 (mt-10) REVERT: N 92 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: N 97 LYS cc_start: 0.7379 (ptmm) cc_final: 0.6910 (pttt) REVERT: O 45 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6380 (tm-30) REVERT: O 48 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6736 (mptp) REVERT: O 58 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6988 (ttm170) REVERT: O 73 LYS cc_start: 0.6453 (mmmt) cc_final: 0.5876 (ttmt) REVERT: O 80 GLN cc_start: 0.5963 (mm-40) cc_final: 0.5641 (tp40) REVERT: P 1 MET cc_start: 0.4826 (OUTLIER) cc_final: 0.3944 (tpp) REVERT: Q 11 ARG cc_start: 0.5966 (mtp-110) cc_final: 0.5632 (mtp85) REVERT: Q 18 GLU cc_start: 0.5879 (OUTLIER) cc_final: 0.5508 (mt-10) REVERT: Q 19 LYS cc_start: 0.6558 (mttt) cc_final: 0.6224 (mttt) REVERT: R 48 ARG cc_start: 0.5680 (mtp180) cc_final: 0.5105 (mpt180) REVERT: R 57 ARG cc_start: 0.7352 (mtm-85) cc_final: 0.7061 (mtm180) REVERT: R 61 ARG cc_start: 0.7362 (mtm-85) cc_final: 0.6844 (mtm-85) REVERT: T 5 LYS cc_start: 0.5861 (mtpt) cc_final: 0.5649 (mmtt) REVERT: T 18 ARG cc_start: 0.6206 (ttp80) cc_final: 0.5496 (ttp80) REVERT: U 17 ARG cc_start: 0.5138 (mtt90) cc_final: 0.4515 (mmt180) REVERT: U 47 ARG cc_start: 0.5481 (tmm-80) cc_final: 0.4201 (mtt180) REVERT: U 60 LEU cc_start: 0.3236 (OUTLIER) cc_final: 0.2937 (mm) REVERT: c 117 GLN cc_start: 0.6968 (pt0) cc_final: 0.6561 (pt0) REVERT: c 182 ARG cc_start: 0.7890 (ttt90) cc_final: 0.7532 (ttt-90) REVERT: c 223 THR cc_start: 0.8175 (p) cc_final: 0.7783 (t) REVERT: d 59 ARG cc_start: 0.7317 (mmt180) cc_final: 0.6990 (mmt180) REVERT: d 64 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6478 (mm-30) REVERT: d 89 GLU cc_start: 0.5350 (OUTLIER) cc_final: 0.4958 (mt-10) REVERT: d 94 GLN cc_start: 0.7624 (tt0) cc_final: 0.7366 (tt0) REVERT: d 128 ARG cc_start: 0.7678 (mtm-85) cc_final: 0.7423 (mmp80) REVERT: d 168 GLU cc_start: 0.7715 (pt0) cc_final: 0.7389 (pt0) REVERT: d 207 VAL cc_start: 0.7976 (p) cc_final: 0.7682 (m) REVERT: e 61 ARG cc_start: 0.7329 (ptt-90) cc_final: 0.7078 (ptp90) REVERT: e 88 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7293 (mmp80) REVERT: e 149 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6174 (mp) REVERT: e 178 VAL cc_start: 0.7283 (t) cc_final: 0.6870 (p) REVERT: f 27 GLN cc_start: 0.7476 (mt0) cc_final: 0.7018 (mt0) REVERT: f 30 ARG cc_start: 0.7266 (mtm-85) cc_final: 0.6796 (mpp-170) REVERT: f 35 THR cc_start: 0.8232 (m) cc_final: 0.7989 (m) REVERT: f 94 GLU cc_start: 0.6037 (mm-30) cc_final: 0.5741 (tt0) REVERT: f 113 ASP cc_start: 0.5264 (t70) cc_final: 0.5063 (t70) REVERT: f 122 PHE cc_start: 0.6770 (m-80) cc_final: 0.6172 (m-80) REVERT: f 161 LYS cc_start: 0.5477 (mtpp) cc_final: 0.5016 (mmtt) REVERT: g 39 ASP cc_start: 0.5511 (m-30) cc_final: 0.5160 (t0) REVERT: g 130 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5829 (tt0) REVERT: g 131 ILE cc_start: 0.7222 (mt) cc_final: 0.6845 (mp) REVERT: i 92 MET cc_start: 0.7794 (mmm) cc_final: 0.6962 (mmm) REVERT: i 96 ARG cc_start: 0.6603 (ttp80) cc_final: 0.6042 (ttp80) REVERT: j 7 MET cc_start: 0.8086 (mmm) cc_final: 0.7739 (mmm) REVERT: j 49 ARG cc_start: 0.6070 (mtm-85) cc_final: 0.5464 (mpp-170) REVERT: j 51 LYS cc_start: 0.6809 (mttp) cc_final: 0.6572 (mttm) REVERT: j 93 GLN cc_start: 0.6759 (mm-40) cc_final: 0.6387 (mm110) REVERT: j 106 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6351 (mp0) REVERT: k 123 ARG cc_start: 0.6468 (ttm170) cc_final: 0.6042 (ttm170) REVERT: k 129 LYS cc_start: 0.6757 (mttp) cc_final: 0.6403 (mmmt) REVERT: l 5 LYS cc_start: 0.7039 (mttp) cc_final: 0.6568 (pttm) REVERT: l 22 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6883 (mt0) REVERT: l 127 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7538 (tttt) REVERT: l 133 LYS cc_start: 0.6795 (ttpt) cc_final: 0.6252 (tptm) REVERT: l 134 THR cc_start: 0.7297 (m) cc_final: 0.6764 (t) REVERT: m 1 MET cc_start: 0.7936 (mtm) cc_final: 0.7625 (mtm) REVERT: m 43 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7599 (tp30) REVERT: m 72 ASP cc_start: 0.7284 (t0) cc_final: 0.6826 (t70) REVERT: n 16 ARG cc_start: 0.6826 (mmp80) cc_final: 0.6389 (mmt90) REVERT: n 30 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7359 (ptt90) REVERT: n 46 GLU cc_start: 0.6386 (mm-30) cc_final: 0.6000 (mp0) REVERT: o 7 GLN cc_start: 0.6782 (tm-30) cc_final: 0.6572 (tt0) REVERT: o 38 LYS cc_start: 0.6760 (OUTLIER) cc_final: 0.6544 (pttp) REVERT: o 89 ARG cc_start: 0.7019 (mtm110) cc_final: 0.6131 (mtt-85) REVERT: p 13 ARG cc_start: 0.7815 (ttt90) cc_final: 0.7132 (ttp80) REVERT: p 87 SER cc_start: 0.7717 (m) cc_final: 0.7017 (t) REVERT: p 103 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6425 (mptt) REVERT: p 111 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6408 (mm-30) REVERT: q 1 MET cc_start: 0.5717 (ttt) cc_final: 0.5448 (ttm) REVERT: q 62 GLU cc_start: 0.6656 (tt0) cc_final: 0.6264 (tt0) REVERT: q 73 LYS cc_start: 0.7711 (mtpt) cc_final: 0.7455 (mttt) REVERT: r 70 LYS cc_start: 0.7453 (mtmm) cc_final: 0.6984 (mttp) REVERT: r 95 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6711 (ttp-170) REVERT: s 4 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.5572 (tp30) REVERT: s 8 LEU cc_start: 0.7762 (mt) cc_final: 0.7497 (mt) REVERT: s 76 ARG cc_start: 0.7224 (ttt-90) cc_final: 0.6905 (tmt90) REVERT: s 89 GLU cc_start: 0.5532 (OUTLIER) cc_final: 0.4681 (tt0) REVERT: t 7 ARG cc_start: 0.6583 (ttt-90) cc_final: 0.6052 (ttt90) REVERT: t 10 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.5891 (tm-30) REVERT: t 22 ARG cc_start: 0.6790 (mtm-85) cc_final: 0.6590 (mtp180) REVERT: t 54 GLN cc_start: 0.2932 (OUTLIER) cc_final: 0.2615 (mp10) REVERT: t 79 LYS cc_start: 0.6474 (mttp) cc_final: 0.6135 (mttp) REVERT: u 70 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6224 (tt) REVERT: u 75 GLN cc_start: 0.7473 (tp40) cc_final: 0.7031 (tp-100) REVERT: v 44 LYS cc_start: 0.7815 (ttmm) cc_final: 0.7472 (ttpt) REVERT: v 72 LYS cc_start: 0.7614 (mtpt) cc_final: 0.7189 (mtmt) REVERT: v 78 LYS cc_start: 0.8066 (mtmt) cc_final: 0.7833 (mttt) REVERT: v 83 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6945 (mt-10) REVERT: x 17 GLU cc_start: 0.6675 (tp30) cc_final: 0.6234 (tp30) REVERT: y 39 GLU cc_start: 0.6623 (pt0) cc_final: 0.6368 (pt0) REVERT: y 56 LYS cc_start: 0.7776 (ttmt) cc_final: 0.7223 (ttpp) REVERT: 0 50 LYS cc_start: 0.7434 (mttm) cc_final: 0.7053 (mtpp) REVERT: 0 51 GLU cc_start: 0.7556 (tt0) cc_final: 0.7351 (tt0) REVERT: 1 1 MET cc_start: 0.7321 (mtp) cc_final: 0.7121 (mtp) REVERT: 2 15 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7475 (mptp) REVERT: 3 18 LYS cc_start: 0.7879 (tttt) cc_final: 0.7537 (tttt) outliers start: 172 outliers final: 84 residues processed: 930 average time/residue: 2.4393 time to fit residues: 3125.5621 Evaluate side-chains 939 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 815 time to evaluate : 5.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 114 LYS Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 75 HIS Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 18 LYS Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain d residue 89 GLU Chi-restraints excluded: chain e residue 53 THR Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 149 ILE Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 24 ILE Chi-restraints excluded: chain g residue 80 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 163 ARG Chi-restraints excluded: chain g residue 175 LYS Chi-restraints excluded: chain i residue 13 ARG Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain j residue 109 SER Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 127 LYS Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 85 LYS Chi-restraints excluded: chain o residue 13 MET Chi-restraints excluded: chain o residue 38 LYS Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain p residue 103 LYS Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 95 ARG Chi-restraints excluded: chain s residue 4 GLU Chi-restraints excluded: chain s residue 7 LEU Chi-restraints excluded: chain s residue 89 GLU Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain t residue 27 ASN Chi-restraints excluded: chain t residue 54 GLN Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain t residue 72 ILE Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain u residue 70 ILE Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 38 LYS Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 22 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 923 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 545 optimal weight: 10.0000 chunk 699 optimal weight: 0.9990 chunk 541 optimal weight: 10.0000 chunk 806 optimal weight: 20.0000 chunk 534 optimal weight: 10.0000 chunk 954 optimal weight: 20.0000 chunk 597 optimal weight: 20.0000 chunk 581 optimal weight: 10.0000 chunk 440 optimal weight: 9.9990 overall best weight: 7.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN O 40 GLN O 62 GLN R 54 GLN f 81 GLN j 90 ASN k 93 ASN q 6 GLN t 46 GLN u 12 GLN x 27 ASN x 58 ASN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 154032 Z= 0.326 Angle : 0.867 19.076 230513 Z= 0.458 Chirality : 0.044 0.396 29296 Planarity : 0.009 0.151 12270 Dihedral : 23.143 177.851 77190 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.47 % Rotamer: Outliers : 4.17 % Allowed : 16.00 % Favored : 79.83 % 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: -0.22 (0.11), residues: 5480 helix: 0.75 (0.12), residues: 1870 sheet: -0.25 (0.16), residues: 1049 loop : -0.69 (0.12), residues: 2561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP c 248 HIS 0.009 0.002 HIS c 230 PHE 0.024 0.003 PHE U 12 TYR 0.022 0.003 TYR R 51 ARG 0.013 0.001 ARG p 92 *********************** 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 1015 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 824 time to evaluate : 6.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.3873 (mmp) cc_final: 0.3210 (mmm) REVERT: B 49 MET cc_start: 0.3163 (mtt) cc_final: 0.2811 (mtp) REVERT: B 68 LEU cc_start: 0.4187 (OUTLIER) cc_final: 0.3895 (tt) REVERT: B 112 LYS cc_start: 0.3660 (ttpt) cc_final: 0.3230 (tttp) REVERT: B 154 MET cc_start: 0.3327 (mtt) cc_final: 0.3065 (ttp) REVERT: B 212 LEU cc_start: 0.3604 (tp) cc_final: 0.3125 (mt) REVERT: C 45 LYS cc_start: 0.6228 (tttm) cc_final: 0.5724 (mtmm) REVERT: C 46 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.6058 (tt0) REVERT: C 72 ARG cc_start: 0.5631 (mtm-85) cc_final: 0.5256 (mtm-85) REVERT: C 82 GLU cc_start: 0.4324 (OUTLIER) cc_final: 0.4014 (tp30) REVERT: C 136 ARG cc_start: 0.6233 (ttm-80) cc_final: 0.5901 (ttm-80) REVERT: C 139 GLN cc_start: 0.6952 (mt0) cc_final: 0.6021 (pt0) REVERT: C 179 ARG cc_start: 0.6926 (ttp-170) cc_final: 0.6385 (ttm170) REVERT: D 8 LYS cc_start: 0.5809 (mttm) cc_final: 0.5454 (mttp) REVERT: D 40 GLN cc_start: 0.6455 (mt0) cc_final: 0.6180 (mt0) REVERT: D 54 GLN cc_start: 0.7201 (mt0) cc_final: 0.6890 (mt0) REVERT: D 60 LYS cc_start: 0.6486 (OUTLIER) cc_final: 0.6145 (ttmm) REVERT: D 81 ARG cc_start: 0.4989 (ttp80) cc_final: 0.4373 (tmt170) REVERT: D 104 ARG cc_start: 0.6138 (mmt90) cc_final: 0.5741 (mmt180) REVERT: D 129 VAL cc_start: 0.5618 (t) cc_final: 0.5404 (p) REVERT: D 148 LYS cc_start: 0.4590 (tmtt) cc_final: 0.4220 (tppt) REVERT: D 206 LYS cc_start: 0.5845 (ttpp) cc_final: 0.5554 (tttp) REVERT: E 12 GLN cc_start: 0.6754 (mt0) cc_final: 0.6221 (mt0) REVERT: E 19 ASN cc_start: 0.7791 (OUTLIER) cc_final: 0.7154 (p0) REVERT: E 29 ARG cc_start: 0.8049 (mtt180) cc_final: 0.7604 (mtt90) REVERT: E 54 ARG cc_start: 0.7201 (mmm-85) cc_final: 0.6748 (mtt180) REVERT: E 55 GLU cc_start: 0.6432 (mt-10) cc_final: 0.6025 (mt-10) REVERT: E 65 GLU cc_start: 0.5973 (OUTLIER) cc_final: 0.5704 (tp30) REVERT: E 70 ASN cc_start: 0.6913 (OUTLIER) cc_final: 0.6521 (m110) REVERT: E 152 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6957 (ptp) REVERT: E 156 LYS cc_start: 0.6472 (mtmt) cc_final: 0.6187 (mtmt) REVERT: E 159 LYS cc_start: 0.6529 (mttm) cc_final: 0.6172 (mttt) REVERT: F 1 MET cc_start: 0.4800 (tpp) cc_final: 0.4461 (mmt) REVERT: F 55 HIS cc_start: 0.6428 (m90) cc_final: 0.6106 (m170) REVERT: F 92 THR cc_start: 0.6250 (m) cc_final: 0.5672 (p) REVERT: G 4 ARG cc_start: 0.5642 (mmt180) cc_final: 0.5246 (mmt-90) REVERT: G 21 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.5280 (mm-30) REVERT: G 59 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.6078 (mm) REVERT: G 66 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6288 (tp) REVERT: G 119 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6366 (mtp180) REVERT: G 137 LYS cc_start: 0.6429 (OUTLIER) cc_final: 0.5996 (tptt) REVERT: G 146 GLU cc_start: 0.5668 (OUTLIER) cc_final: 0.5067 (mp0) REVERT: G 154 TYR cc_start: 0.4303 (OUTLIER) cc_final: 0.2985 (m-10) REVERT: H 38 ASN cc_start: 0.7118 (t0) cc_final: 0.6806 (t0) REVERT: H 58 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.6034 (tt0) REVERT: I 33 ARG cc_start: 0.6247 (mtm180) cc_final: 0.5510 (mtt180) REVERT: I 49 ARG cc_start: 0.5991 (mtm-85) cc_final: 0.5671 (mtm180) REVERT: I 57 MET cc_start: 0.5436 (ptp) cc_final: 0.4897 (ptm) REVERT: I 60 LYS cc_start: 0.4847 (OUTLIER) cc_final: 0.4563 (mptt) REVERT: I 88 MET cc_start: 0.6328 (mtm) cc_final: 0.6076 (mtm) REVERT: I 110 GLN cc_start: 0.7388 (mm110) cc_final: 0.7087 (mt0) REVERT: I 124 ARG cc_start: 0.7288 (ttm-80) cc_final: 0.7029 (mtp-110) REVERT: K 40 ASN cc_start: 0.6481 (m110) cc_final: 0.6049 (m-40) REVERT: K 112 ASP cc_start: 0.6929 (t70) cc_final: 0.6546 (t0) REVERT: L 10 LYS cc_start: 0.7052 (ttpt) cc_final: 0.6747 (tptt) REVERT: L 18 LYS cc_start: 0.3687 (OUTLIER) cc_final: 0.2797 (ptmm) REVERT: L 88 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7508 (mmmt) REVERT: N 6 MET cc_start: 0.7090 (mmm) cc_final: 0.6023 (mpt) REVERT: N 86 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7186 (mt-10) REVERT: N 89 MET cc_start: 0.7691 (mmp) cc_final: 0.7451 (mmp) REVERT: N 92 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7432 (mt-10) REVERT: N 97 LYS cc_start: 0.7374 (ptmm) cc_final: 0.6900 (pttt) REVERT: O 11 ILE cc_start: 0.6334 (mt) cc_final: 0.6075 (mp) REVERT: O 45 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6558 (tm-30) REVERT: O 48 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6688 (mptp) REVERT: O 58 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6991 (ttm170) REVERT: O 73 LYS cc_start: 0.6519 (mmmt) cc_final: 0.5909 (ttmt) REVERT: P 1 MET cc_start: 0.4833 (OUTLIER) cc_final: 0.4052 (tpp) REVERT: Q 11 ARG cc_start: 0.5989 (mtp-110) cc_final: 0.5637 (mtp85) REVERT: Q 18 GLU cc_start: 0.5844 (OUTLIER) cc_final: 0.5609 (mt-10) REVERT: Q 19 LYS cc_start: 0.6566 (mttt) cc_final: 0.6225 (mttt) REVERT: R 48 ARG cc_start: 0.5758 (mtp180) cc_final: 0.4917 (mtt-85) REVERT: R 57 ARG cc_start: 0.7408 (mtm-85) cc_final: 0.7126 (mtm180) REVERT: R 61 ARG cc_start: 0.7360 (mtm-85) cc_final: 0.6858 (mtm-85) REVERT: S 18 LYS cc_start: 0.6466 (mtpp) cc_final: 0.6161 (mtpp) REVERT: S 32 ARG cc_start: 0.6302 (OUTLIER) cc_final: 0.5570 (mtm180) REVERT: S 44 MET cc_start: 0.5111 (mtt) cc_final: 0.4545 (mtt) REVERT: S 58 VAL cc_start: 0.6596 (OUTLIER) cc_final: 0.6302 (m) REVERT: T 5 LYS cc_start: 0.5847 (mtpt) cc_final: 0.5600 (mmtt) REVERT: T 9 LYS cc_start: 0.6292 (tptp) cc_final: 0.5916 (tppp) REVERT: T 18 ARG cc_start: 0.6260 (ttp80) cc_final: 0.5497 (ttp80) REVERT: U 17 ARG cc_start: 0.5146 (mtt90) cc_final: 0.4532 (mmt180) REVERT: U 47 ARG cc_start: 0.5454 (tmm-80) cc_final: 0.4226 (mtt180) REVERT: U 60 LEU cc_start: 0.3251 (OUTLIER) cc_final: 0.2941 (mm) REVERT: c 117 GLN cc_start: 0.7073 (pt0) cc_final: 0.6647 (pt0) REVERT: c 182 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7555 (ttt180) REVERT: c 223 THR cc_start: 0.8215 (p) cc_final: 0.7866 (t) REVERT: d 59 ARG cc_start: 0.7277 (mmt180) cc_final: 0.6985 (mmt180) REVERT: d 64 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6509 (mm-30) REVERT: d 89 GLU cc_start: 0.5285 (OUTLIER) cc_final: 0.4906 (mt-10) REVERT: d 94 GLN cc_start: 0.7609 (tt0) cc_final: 0.7382 (tt0) REVERT: d 128 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.7429 (mmp80) REVERT: d 207 VAL cc_start: 0.7935 (p) cc_final: 0.7665 (m) REVERT: e 61 ARG cc_start: 0.7265 (ptt-90) cc_final: 0.7016 (ptp90) REVERT: e 88 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7288 (mmp80) REVERT: e 149 ILE cc_start: 0.6772 (OUTLIER) cc_final: 0.6114 (mp) REVERT: e 178 VAL cc_start: 0.7342 (t) cc_final: 0.6893 (p) REVERT: f 27 GLN cc_start: 0.7477 (mt0) cc_final: 0.7012 (mt0) REVERT: f 30 ARG cc_start: 0.7291 (mtm-85) cc_final: 0.6811 (mpp-170) REVERT: f 94 GLU cc_start: 0.6039 (mm-30) cc_final: 0.5764 (tt0) REVERT: f 113 ASP cc_start: 0.5254 (t70) cc_final: 0.5047 (t70) REVERT: f 122 PHE cc_start: 0.6766 (m-80) cc_final: 0.6207 (m-80) REVERT: f 161 LYS cc_start: 0.5447 (mtpp) cc_final: 0.4986 (mmtt) REVERT: g 9 VAL cc_start: 0.4904 (OUTLIER) cc_final: 0.4247 (t) REVERT: g 39 ASP cc_start: 0.5693 (m-30) cc_final: 0.5311 (t0) REVERT: g 130 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5814 (tt0) REVERT: g 131 ILE cc_start: 0.7189 (mt) cc_final: 0.6824 (mp) REVERT: i 92 MET cc_start: 0.7765 (mmm) cc_final: 0.6928 (mmm) REVERT: i 96 ARG cc_start: 0.6699 (ttp80) cc_final: 0.6088 (ttp80) REVERT: j 7 MET cc_start: 0.8086 (mmm) cc_final: 0.7543 (mmm) REVERT: j 49 ARG cc_start: 0.6132 (mtm-85) cc_final: 0.5506 (mpp-170) REVERT: j 51 LYS cc_start: 0.6735 (mttp) cc_final: 0.6491 (mttm) REVERT: j 93 GLN cc_start: 0.6795 (mm-40) cc_final: 0.6429 (mm110) REVERT: j 106 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6338 (mp0) REVERT: k 1 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.5678 (ptp) REVERT: k 123 ARG cc_start: 0.6483 (ttm170) cc_final: 0.6069 (ttm170) REVERT: k 129 LYS cc_start: 0.6850 (mttp) cc_final: 0.6481 (mmmt) REVERT: l 5 LYS cc_start: 0.7030 (mttp) cc_final: 0.6568 (pttm) REVERT: l 22 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6946 (mt0) REVERT: l 133 LYS cc_start: 0.6775 (ttpt) cc_final: 0.6224 (tptm) REVERT: l 134 THR cc_start: 0.7285 (m) cc_final: 0.6762 (t) REVERT: m 1 MET cc_start: 0.7944 (mtm) cc_final: 0.7629 (mtm) REVERT: m 43 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7540 (tp30) REVERT: m 72 ASP cc_start: 0.7236 (t0) cc_final: 0.6794 (t70) REVERT: n 16 ARG cc_start: 0.6825 (mmp80) cc_final: 0.6394 (mmt90) REVERT: n 46 GLU cc_start: 0.6336 (mm-30) cc_final: 0.5929 (mp0) REVERT: n 69 ASP cc_start: 0.6598 (m-30) cc_final: 0.6358 (m-30) REVERT: o 7 GLN cc_start: 0.6779 (tm-30) cc_final: 0.6544 (tm-30) REVERT: o 38 LYS cc_start: 0.6732 (OUTLIER) cc_final: 0.6459 (pttp) REVERT: o 89 ARG cc_start: 0.7012 (mtm110) cc_final: 0.6057 (mtt-85) REVERT: p 13 ARG cc_start: 0.7830 (ttt90) cc_final: 0.7175 (ttp80) REVERT: p 103 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6409 (mptt) REVERT: p 111 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6429 (mm-30) REVERT: q 1 MET cc_start: 0.5835 (ttt) cc_final: 0.5592 (ttm) REVERT: q 62 GLU cc_start: 0.6616 (tt0) cc_final: 0.6222 (tt0) REVERT: q 73 LYS cc_start: 0.7670 (mtpt) cc_final: 0.7438 (mttt) REVERT: r 70 LYS cc_start: 0.7448 (mtmm) cc_final: 0.6985 (mttp) REVERT: r 95 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6666 (ttp-170) REVERT: s 4 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.5616 (tp30) REVERT: s 8 LEU cc_start: 0.7729 (mt) cc_final: 0.7468 (mt) REVERT: s 76 ARG cc_start: 0.7221 (ttt-90) cc_final: 0.6912 (tmt90) REVERT: s 89 GLU cc_start: 0.5501 (OUTLIER) cc_final: 0.4664 (tt0) REVERT: t 7 ARG cc_start: 0.6611 (ttt-90) cc_final: 0.6063 (ttt90) REVERT: t 10 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.5893 (tm-30) REVERT: t 54 GLN cc_start: 0.2991 (OUTLIER) cc_final: 0.2660 (mp10) REVERT: t 79 LYS cc_start: 0.6481 (mttp) cc_final: 0.6148 (mttp) REVERT: u 70 ILE cc_start: 0.6840 (OUTLIER) cc_final: 0.6304 (tt) REVERT: u 75 GLN cc_start: 0.7491 (tp40) cc_final: 0.7073 (tp40) REVERT: v 44 LYS cc_start: 0.7839 (ttmm) cc_final: 0.7504 (ttpt) REVERT: v 70 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6490 (tt0) REVERT: v 83 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6917 (mt-10) REVERT: x 2 LYS cc_start: 0.5495 (tttp) cc_final: 0.5175 (ttpp) REVERT: x 17 GLU cc_start: 0.6654 (tp30) cc_final: 0.6329 (tp30) REVERT: y 39 GLU cc_start: 0.6612 (pt0) cc_final: 0.6365 (pt0) REVERT: y 56 LYS cc_start: 0.7780 (ttmt) cc_final: 0.7225 (ttpp) REVERT: 0 50 LYS cc_start: 0.7434 (mttm) cc_final: 0.7084 (mtpp) REVERT: 2 15 LYS cc_start: 0.8018 (mmtt) cc_final: 0.7548 (mptp) REVERT: 3 18 LYS cc_start: 0.7928 (tttt) cc_final: 0.7548 (tttt) REVERT: 4 39 LYS cc_start: 0.5514 (pttt) cc_final: 0.5220 (pttm) outliers start: 191 outliers final: 114 residues processed: 946 average time/residue: 2.4220 time to fit residues: 3161.0990 Evaluate side-chains 970 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 810 time to evaluate : 5.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 114 LYS Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 75 HIS Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 18 LYS Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 89 GLU Chi-restraints excluded: chain e residue 53 THR Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 149 ILE Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 157 THR Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 24 ILE Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 80 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 163 ARG Chi-restraints excluded: chain g residue 175 LYS Chi-restraints excluded: chain i residue 13 ARG Chi-restraints excluded: chain i residue 43 GLU Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain j residue 109 SER Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain n residue 85 LYS Chi-restraints excluded: chain o residue 13 MET Chi-restraints excluded: chain o residue 25 THR Chi-restraints excluded: chain o residue 38 LYS Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain p residue 103 LYS Chi-restraints excluded: chain p residue 104 VAL Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 95 ARG Chi-restraints excluded: chain s residue 4 GLU Chi-restraints excluded: chain s residue 7 LEU Chi-restraints excluded: chain s residue 26 LYS Chi-restraints excluded: chain s residue 89 GLU Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain t residue 27 ASN Chi-restraints excluded: chain t residue 54 GLN Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain t residue 72 ILE Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain u residue 70 ILE Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 5 ILE Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 38 LYS Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 22 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: 0.0870 chunk 569 optimal weight: 10.0000 chunk 287 optimal weight: 30.0000 chunk 187 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 606 optimal weight: 10.0000 chunk 650 optimal weight: 10.0000 chunk 471 optimal weight: 40.0000 chunk 88 optimal weight: 10.0000 chunk 750 optimal weight: 2.9990 overall best weight: 5.2168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN O 35 GLN O 40 GLN O 62 GLN R 54 GLN j 90 ASN k 93 ASN t 46 GLN u 12 GLN x 27 ASN x 58 ASN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 154032 Z= 0.252 Angle : 0.782 15.645 230513 Z= 0.423 Chirality : 0.040 0.400 29296 Planarity : 0.008 0.144 12270 Dihedral : 23.066 177.663 77190 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.00 % Favored : 95.93 % Rotamer: Outliers : 3.76 % Allowed : 16.85 % 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: -0.03 (0.11), residues: 5480 helix: 0.98 (0.12), residues: 1866 sheet: -0.23 (0.15), residues: 1081 loop : -0.60 (0.12), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 248 HIS 0.008 0.001 HIS c 230 PHE 0.021 0.002 PHE U 12 TYR 0.018 0.002 TYR r 38 ARG 0.009 0.001 ARG p 92 *********************** 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 992 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 820 time to evaluate : 6.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.3820 (mmp) cc_final: 0.3215 (mmm) REVERT: B 49 MET cc_start: 0.3111 (mtt) cc_final: 0.2809 (mtp) REVERT: B 68 LEU cc_start: 0.4078 (OUTLIER) cc_final: 0.3812 (tt) REVERT: B 112 LYS cc_start: 0.3670 (ttpt) cc_final: 0.3234 (tttp) REVERT: B 154 MET cc_start: 0.3146 (OUTLIER) cc_final: 0.2891 (ttp) REVERT: B 212 LEU cc_start: 0.3609 (tp) cc_final: 0.3130 (mt) REVERT: C 45 LYS cc_start: 0.6120 (tttm) cc_final: 0.5641 (mtmm) REVERT: C 46 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6041 (tt0) REVERT: C 82 GLU cc_start: 0.4273 (OUTLIER) cc_final: 0.3981 (tp30) REVERT: C 136 ARG cc_start: 0.6268 (ttm-80) cc_final: 0.5940 (ttm-80) REVERT: C 139 GLN cc_start: 0.6954 (mt0) cc_final: 0.6008 (pt0) REVERT: C 179 ARG cc_start: 0.6930 (ttp-170) cc_final: 0.6412 (ttm170) REVERT: D 8 LYS cc_start: 0.5824 (mttm) cc_final: 0.5470 (mttp) REVERT: D 40 GLN cc_start: 0.6404 (mt0) cc_final: 0.6185 (mt0) REVERT: D 54 GLN cc_start: 0.7193 (mt0) cc_final: 0.6931 (mt0) REVERT: D 81 ARG cc_start: 0.4964 (ttp80) cc_final: 0.4349 (tmt170) REVERT: D 104 ARG cc_start: 0.6140 (mmt90) cc_final: 0.5759 (mmt180) REVERT: D 129 VAL cc_start: 0.5609 (t) cc_final: 0.5406 (p) REVERT: D 148 LYS cc_start: 0.4703 (tmtt) cc_final: 0.4176 (tppt) REVERT: D 197 GLU cc_start: 0.4701 (pm20) cc_final: 0.4259 (pm20) REVERT: D 206 LYS cc_start: 0.5778 (ttpp) cc_final: 0.5526 (tttp) REVERT: E 12 GLN cc_start: 0.6737 (mt0) cc_final: 0.6203 (mt0) REVERT: E 19 ASN cc_start: 0.7739 (OUTLIER) cc_final: 0.7134 (p0) REVERT: E 29 ARG cc_start: 0.8023 (mtt180) cc_final: 0.7664 (mtt90) REVERT: E 54 ARG cc_start: 0.7196 (mmm-85) cc_final: 0.6745 (mtt180) REVERT: E 55 GLU cc_start: 0.6384 (mt-10) cc_final: 0.5979 (mt-10) REVERT: E 65 GLU cc_start: 0.5941 (OUTLIER) cc_final: 0.5667 (tp30) REVERT: E 70 ASN cc_start: 0.6752 (t0) cc_final: 0.6360 (m110) REVERT: E 152 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6905 (ptp) REVERT: E 156 LYS cc_start: 0.6495 (mtmt) cc_final: 0.6236 (mtmt) REVERT: E 159 LYS cc_start: 0.6525 (mttm) cc_final: 0.6180 (mttt) REVERT: F 1 MET cc_start: 0.4790 (tpp) cc_final: 0.4463 (mmt) REVERT: F 55 HIS cc_start: 0.6446 (m90) cc_final: 0.6118 (m170) REVERT: F 92 THR cc_start: 0.6190 (m) cc_final: 0.5645 (p) REVERT: G 4 ARG cc_start: 0.5669 (mmt180) cc_final: 0.5282 (mmt-90) REVERT: G 21 GLU cc_start: 0.5744 (OUTLIER) cc_final: 0.5356 (mm-30) REVERT: G 59 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.6041 (mm) REVERT: G 66 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6332 (tp) REVERT: G 119 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.6289 (mtp180) REVERT: G 137 LYS cc_start: 0.6400 (OUTLIER) cc_final: 0.5844 (tptt) REVERT: G 146 GLU cc_start: 0.5697 (OUTLIER) cc_final: 0.5122 (mp0) REVERT: G 154 TYR cc_start: 0.4316 (OUTLIER) cc_final: 0.3009 (m-10) REVERT: H 38 ASN cc_start: 0.7064 (t0) cc_final: 0.6750 (t0) REVERT: H 58 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.6028 (tt0) REVERT: I 33 ARG cc_start: 0.6154 (mtm180) cc_final: 0.5447 (mtt180) REVERT: I 49 ARG cc_start: 0.5984 (mtm-85) cc_final: 0.5667 (mtm180) REVERT: I 57 MET cc_start: 0.5304 (ptp) cc_final: 0.4831 (ptm) REVERT: I 60 LYS cc_start: 0.4801 (OUTLIER) cc_final: 0.4533 (mptt) REVERT: I 88 MET cc_start: 0.6343 (mtm) cc_final: 0.6077 (mtm) REVERT: I 110 GLN cc_start: 0.7412 (mm110) cc_final: 0.7110 (mt0) REVERT: I 124 ARG cc_start: 0.7275 (ttm-80) cc_final: 0.7018 (mtp-110) REVERT: K 40 ASN cc_start: 0.6471 (m110) cc_final: 0.6008 (m-40) REVERT: K 112 ASP cc_start: 0.6928 (t70) cc_final: 0.6556 (t0) REVERT: L 10 LYS cc_start: 0.7053 (ttpt) cc_final: 0.6741 (tptt) REVERT: L 18 LYS cc_start: 0.3570 (OUTLIER) cc_final: 0.2707 (ptmm) REVERT: L 54 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.5481 (mmp-170) REVERT: M 114 LYS cc_start: 0.5587 (OUTLIER) cc_final: 0.5378 (mttp) REVERT: N 6 MET cc_start: 0.7109 (mmm) cc_final: 0.6067 (mpt) REVERT: N 86 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7179 (mt-10) REVERT: N 92 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7378 (mt-10) REVERT: O 11 ILE cc_start: 0.6422 (mt) cc_final: 0.6166 (mp) REVERT: O 45 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6360 (tm-30) REVERT: O 48 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6725 (mptp) REVERT: O 58 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6995 (ttm170) REVERT: O 73 LYS cc_start: 0.6508 (mmmt) cc_final: 0.5925 (ttmt) REVERT: O 80 GLN cc_start: 0.5947 (mm-40) cc_final: 0.5643 (tp40) REVERT: P 1 MET cc_start: 0.4818 (OUTLIER) cc_final: 0.3937 (tpp) REVERT: Q 11 ARG cc_start: 0.5986 (mtp-110) cc_final: 0.5634 (mtp85) REVERT: Q 18 GLU cc_start: 0.5862 (OUTLIER) cc_final: 0.5563 (mt-10) REVERT: R 48 ARG cc_start: 0.5736 (mtp180) cc_final: 0.5160 (mpt180) REVERT: R 57 ARG cc_start: 0.7371 (mtm-85) cc_final: 0.7093 (mtm180) REVERT: R 61 ARG cc_start: 0.7372 (mtm-85) cc_final: 0.6891 (mtm-85) REVERT: S 32 ARG cc_start: 0.6218 (OUTLIER) cc_final: 0.5510 (mtm180) REVERT: T 5 LYS cc_start: 0.5790 (mtpt) cc_final: 0.5579 (mmtt) REVERT: T 9 LYS cc_start: 0.6195 (tptp) cc_final: 0.5782 (tppp) REVERT: T 18 ARG cc_start: 0.6266 (ttp80) cc_final: 0.5517 (ttp80) REVERT: U 17 ARG cc_start: 0.5152 (mtt90) cc_final: 0.4529 (mmt180) REVERT: U 47 ARG cc_start: 0.5458 (tmm-80) cc_final: 0.4216 (mtt180) REVERT: U 60 LEU cc_start: 0.3227 (OUTLIER) cc_final: 0.2933 (mm) REVERT: c 117 GLN cc_start: 0.6964 (pt0) cc_final: 0.6554 (pt0) REVERT: c 182 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7524 (ttt-90) REVERT: c 223 THR cc_start: 0.8179 (p) cc_final: 0.7786 (t) REVERT: d 59 ARG cc_start: 0.7307 (mmt180) cc_final: 0.7028 (mmt180) REVERT: d 64 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6480 (mm-30) REVERT: d 89 GLU cc_start: 0.5305 (OUTLIER) cc_final: 0.4919 (mt-10) REVERT: d 94 GLN cc_start: 0.7623 (tt0) cc_final: 0.7386 (tt0) REVERT: d 128 ARG cc_start: 0.7678 (mtm-85) cc_final: 0.7424 (mmp80) REVERT: d 207 VAL cc_start: 0.7896 (p) cc_final: 0.7634 (m) REVERT: e 61 ARG cc_start: 0.7316 (ptt-90) cc_final: 0.7065 (ptp90) REVERT: e 88 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7285 (mmp80) REVERT: e 149 ILE cc_start: 0.6766 (OUTLIER) cc_final: 0.6104 (mp) REVERT: e 178 VAL cc_start: 0.7316 (t) cc_final: 0.6860 (p) REVERT: f 27 GLN cc_start: 0.7452 (mt0) cc_final: 0.6993 (mt0) REVERT: f 30 ARG cc_start: 0.7309 (mtm-85) cc_final: 0.6823 (mpp-170) REVERT: f 94 GLU cc_start: 0.6000 (mm-30) cc_final: 0.5723 (tt0) REVERT: f 122 PHE cc_start: 0.6771 (m-80) cc_final: 0.6165 (m-80) REVERT: f 161 LYS cc_start: 0.5447 (mtpp) cc_final: 0.4986 (mmtm) REVERT: g 39 ASP cc_start: 0.5604 (m-30) cc_final: 0.5246 (t0) REVERT: g 131 ILE cc_start: 0.7199 (mt) cc_final: 0.6814 (mp) REVERT: i 92 MET cc_start: 0.7767 (mmm) cc_final: 0.6948 (mmm) REVERT: i 96 ARG cc_start: 0.6645 (ttp80) cc_final: 0.6133 (ttp80) REVERT: j 7 MET cc_start: 0.8085 (mmm) cc_final: 0.7618 (mmm) REVERT: j 49 ARG cc_start: 0.6069 (mtm-85) cc_final: 0.5462 (mpp-170) REVERT: j 51 LYS cc_start: 0.6888 (mttp) cc_final: 0.6661 (mttm) REVERT: j 93 GLN cc_start: 0.6757 (mm-40) cc_final: 0.6384 (mm110) REVERT: j 106 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6337 (mp0) REVERT: k 123 ARG cc_start: 0.6506 (ttm170) cc_final: 0.6101 (ttm170) REVERT: k 129 LYS cc_start: 0.6835 (mttp) cc_final: 0.6470 (mmmt) REVERT: l 5 LYS cc_start: 0.7026 (mttp) cc_final: 0.6562 (pttm) REVERT: l 22 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6884 (mt0) REVERT: l 127 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7540 (tttt) REVERT: l 133 LYS cc_start: 0.6774 (ttpt) cc_final: 0.6234 (tptm) REVERT: l 134 THR cc_start: 0.7234 (m) cc_final: 0.6721 (t) REVERT: m 1 MET cc_start: 0.7947 (mtm) cc_final: 0.7638 (mtm) REVERT: m 43 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7546 (tp30) REVERT: m 72 ASP cc_start: 0.7284 (t0) cc_final: 0.6823 (t70) REVERT: m 86 ARG cc_start: 0.7617 (mtp180) cc_final: 0.7380 (mtp180) REVERT: n 16 ARG cc_start: 0.6835 (mmp80) cc_final: 0.6403 (mmt90) REVERT: n 30 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7339 (ptt90) REVERT: n 46 GLU cc_start: 0.6366 (mm-30) cc_final: 0.5951 (mp0) REVERT: o 38 LYS cc_start: 0.6750 (OUTLIER) cc_final: 0.6540 (pttp) REVERT: o 89 ARG cc_start: 0.7015 (mtm110) cc_final: 0.6127 (mtt-85) REVERT: p 13 ARG cc_start: 0.7904 (ttt90) cc_final: 0.7147 (ttp80) REVERT: p 87 SER cc_start: 0.7723 (m) cc_final: 0.7005 (t) REVERT: p 103 LYS cc_start: 0.6949 (OUTLIER) cc_final: 0.6415 (mptt) REVERT: p 111 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6473 (mm-30) REVERT: q 1 MET cc_start: 0.6034 (ttt) cc_final: 0.5783 (ttm) REVERT: q 62 GLU cc_start: 0.6641 (tt0) cc_final: 0.6245 (tt0) REVERT: q 73 LYS cc_start: 0.7720 (mtpt) cc_final: 0.7466 (mttt) REVERT: r 70 LYS cc_start: 0.7452 (mtmm) cc_final: 0.6983 (mttp) REVERT: r 95 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6635 (ttp80) REVERT: s 4 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.5548 (tp30) REVERT: s 8 LEU cc_start: 0.7755 (mt) cc_final: 0.7481 (mt) REVERT: s 54 GLU cc_start: 0.5977 (OUTLIER) cc_final: 0.5728 (mm-30) REVERT: s 76 ARG cc_start: 0.7228 (ttt-90) cc_final: 0.6921 (tmt90) REVERT: s 89 GLU cc_start: 0.5499 (OUTLIER) cc_final: 0.4637 (tt0) REVERT: t 7 ARG cc_start: 0.6581 (ttt-90) cc_final: 0.6039 (ttt90) REVERT: t 10 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.5903 (tm-30) REVERT: t 54 GLN cc_start: 0.2968 (OUTLIER) cc_final: 0.2605 (mt0) REVERT: u 70 ILE cc_start: 0.6894 (OUTLIER) cc_final: 0.6350 (tt) REVERT: u 75 GLN cc_start: 0.7504 (tp40) cc_final: 0.7034 (tp-100) REVERT: v 44 LYS cc_start: 0.7830 (ttmm) cc_final: 0.7476 (ttpt) REVERT: v 70 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6520 (tt0) REVERT: v 72 LYS cc_start: 0.7599 (mtpt) cc_final: 0.7138 (mtmt) REVERT: v 78 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7737 (mttt) REVERT: v 83 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6884 (mt-10) REVERT: x 2 LYS cc_start: 0.5528 (tttp) cc_final: 0.5228 (ttpp) REVERT: x 17 GLU cc_start: 0.6642 (tp30) cc_final: 0.6297 (tp30) REVERT: y 39 GLU cc_start: 0.6622 (pt0) cc_final: 0.6372 (pt0) REVERT: y 56 LYS cc_start: 0.7769 (ttmt) cc_final: 0.7221 (ttpp) REVERT: 0 50 LYS cc_start: 0.7442 (mttm) cc_final: 0.7060 (mtpp) REVERT: 2 15 LYS cc_start: 0.7976 (mmtt) cc_final: 0.7514 (mptp) REVERT: 3 18 LYS cc_start: 0.7881 (tttt) cc_final: 0.7529 (tttt) outliers start: 172 outliers final: 109 residues processed: 928 average time/residue: 2.4380 time to fit residues: 3116.5290 Evaluate side-chains 959 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 805 time to evaluate : 5.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 114 LYS Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 75 HIS Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 18 LYS Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 89 GLU Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 149 ILE Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain f residue 111 ILE Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 157 THR Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 24 ILE Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 80 THR Chi-restraints excluded: chain g residue 163 ARG Chi-restraints excluded: chain g residue 175 LYS Chi-restraints excluded: chain i residue 13 ARG Chi-restraints excluded: chain i residue 43 GLU Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain j residue 109 SER Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain k residue 141 LYS Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 127 LYS Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain n residue 85 LYS Chi-restraints excluded: chain o residue 13 MET Chi-restraints excluded: chain o residue 38 LYS Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain p residue 103 LYS Chi-restraints excluded: chain p residue 104 VAL Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 95 ARG Chi-restraints excluded: chain s residue 4 GLU Chi-restraints excluded: chain s residue 7 LEU Chi-restraints excluded: chain s residue 54 GLU Chi-restraints excluded: chain s residue 89 GLU Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain t residue 27 ASN Chi-restraints excluded: chain t residue 41 LEU Chi-restraints excluded: chain t residue 54 GLN Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain t residue 72 ILE Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain u residue 70 ILE Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 5 ILE Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 38 LYS Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 36 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 868 optimal weight: 9.9990 chunk 914 optimal weight: 2.9990 chunk 834 optimal weight: 8.9990 chunk 889 optimal weight: 4.9990 chunk 913 optimal weight: 6.9990 chunk 535 optimal weight: 20.0000 chunk 387 optimal weight: 10.0000 chunk 698 optimal weight: 10.0000 chunk 272 optimal weight: 5.9990 chunk 803 optimal weight: 10.0000 chunk 840 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN O 40 GLN O 62 GLN R 54 GLN j 90 ASN k 93 ASN q 6 GLN t 46 GLN u 12 GLN x 27 ASN x 58 ASN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 154032 Z= 0.279 Angle : 0.813 17.259 230513 Z= 0.436 Chirality : 0.042 0.396 29296 Planarity : 0.008 0.147 12270 Dihedral : 23.089 177.868 77190 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 3.91 % Allowed : 17.03 % Favored : 79.06 % 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: -0.10 (0.11), residues: 5480 helix: 0.90 (0.12), residues: 1864 sheet: -0.26 (0.15), residues: 1081 loop : -0.63 (0.12), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 248 HIS 0.008 0.002 HIS B 39 PHE 0.022 0.002 PHE U 12 TYR 0.020 0.002 TYR R 51 ARG 0.010 0.001 ARG p 92 *********************** 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 983 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 804 time to evaluate : 6.034 Fit side-chains revert: symmetry clash REVERT: B 27 MET cc_start: 0.3739 (mmp) cc_final: 0.3107 (mmm) REVERT: B 49 MET cc_start: 0.3099 (mtt) cc_final: 0.2789 (mtp) REVERT: B 68 LEU cc_start: 0.4124 (OUTLIER) cc_final: 0.3838 (tt) REVERT: B 100 MET cc_start: 0.4533 (ttm) cc_final: 0.3831 (mtp) REVERT: B 112 LYS cc_start: 0.3710 (ttpt) cc_final: 0.3266 (tttp) REVERT: B 154 MET cc_start: 0.3069 (OUTLIER) cc_final: 0.2840 (ttp) REVERT: B 212 LEU cc_start: 0.3571 (tp) cc_final: 0.3097 (mt) REVERT: C 45 LYS cc_start: 0.6145 (tttm) cc_final: 0.5664 (mtmm) REVERT: C 46 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6039 (tt0) REVERT: C 82 GLU cc_start: 0.4322 (OUTLIER) cc_final: 0.4022 (tp30) REVERT: C 136 ARG cc_start: 0.6268 (ttm-80) cc_final: 0.5942 (ttm-80) REVERT: C 139 GLN cc_start: 0.6950 (mt0) cc_final: 0.6015 (pt0) REVERT: C 179 ARG cc_start: 0.6934 (ttp-170) cc_final: 0.6387 (ttm170) REVERT: D 8 LYS cc_start: 0.5833 (mttm) cc_final: 0.5480 (mttp) REVERT: D 40 GLN cc_start: 0.6386 (mt0) cc_final: 0.6172 (mt0) REVERT: D 60 LYS cc_start: 0.6529 (OUTLIER) cc_final: 0.6113 (ttmm) REVERT: D 73 ARG cc_start: 0.6267 (ttp80) cc_final: 0.5419 (ttm170) REVERT: D 81 ARG cc_start: 0.4965 (ttp80) cc_final: 0.4346 (tmt170) REVERT: D 104 ARG cc_start: 0.6110 (mmt90) cc_final: 0.5718 (mmt180) REVERT: D 148 LYS cc_start: 0.4633 (tmtt) cc_final: 0.4193 (tppt) REVERT: D 197 GLU cc_start: 0.4694 (pm20) cc_final: 0.4282 (pm20) REVERT: D 206 LYS cc_start: 0.5714 (ttpp) cc_final: 0.5465 (tttp) REVERT: E 12 GLN cc_start: 0.6759 (mt0) cc_final: 0.6223 (mt0) REVERT: E 19 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7144 (p0) REVERT: E 29 ARG cc_start: 0.8026 (mtt180) cc_final: 0.7664 (mtt90) REVERT: E 54 ARG cc_start: 0.7210 (mmm-85) cc_final: 0.6758 (mtt180) REVERT: E 55 GLU cc_start: 0.6402 (mt-10) cc_final: 0.5994 (mt-10) REVERT: E 65 GLU cc_start: 0.5973 (OUTLIER) cc_final: 0.5701 (tp30) REVERT: E 70 ASN cc_start: 0.6906 (OUTLIER) cc_final: 0.6521 (m110) REVERT: E 156 LYS cc_start: 0.6454 (mtmt) cc_final: 0.6201 (mtmt) REVERT: E 159 LYS cc_start: 0.6526 (mttm) cc_final: 0.6181 (mttt) REVERT: F 1 MET cc_start: 0.4791 (tpp) cc_final: 0.4468 (mmt) REVERT: F 55 HIS cc_start: 0.6432 (m90) cc_final: 0.6105 (m170) REVERT: F 92 THR cc_start: 0.6210 (m) cc_final: 0.5655 (p) REVERT: G 4 ARG cc_start: 0.5666 (mmt180) cc_final: 0.5277 (mmt-90) REVERT: G 21 GLU cc_start: 0.5714 (OUTLIER) cc_final: 0.5314 (mm-30) REVERT: G 59 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.6067 (mm) REVERT: G 66 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6286 (tp) REVERT: G 119 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6295 (mtp180) REVERT: G 137 LYS cc_start: 0.6411 (OUTLIER) cc_final: 0.5977 (tptt) REVERT: G 146 GLU cc_start: 0.5660 (OUTLIER) cc_final: 0.5065 (mp0) REVERT: G 154 TYR cc_start: 0.4326 (OUTLIER) cc_final: 0.3026 (m-10) REVERT: H 38 ASN cc_start: 0.7070 (t0) cc_final: 0.6762 (t0) REVERT: H 58 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.6024 (tt0) REVERT: I 33 ARG cc_start: 0.6239 (mtm180) cc_final: 0.5510 (mtt180) REVERT: I 34 SER cc_start: 0.6064 (OUTLIER) cc_final: 0.5855 (t) REVERT: I 49 ARG cc_start: 0.5988 (mtm-85) cc_final: 0.5669 (mtm180) REVERT: I 57 MET cc_start: 0.5539 (ptp) cc_final: 0.5048 (ptm) REVERT: I 60 LYS cc_start: 0.4779 (OUTLIER) cc_final: 0.4508 (mptt) REVERT: I 88 MET cc_start: 0.6315 (mtm) cc_final: 0.6053 (mtm) REVERT: I 110 GLN cc_start: 0.7400 (mm110) cc_final: 0.7115 (mt0) REVERT: I 124 ARG cc_start: 0.7276 (ttm-80) cc_final: 0.7019 (mtp-110) REVERT: K 40 ASN cc_start: 0.6471 (m110) cc_final: 0.6015 (m-40) REVERT: K 112 ASP cc_start: 0.6924 (t70) cc_final: 0.6554 (t0) REVERT: L 10 LYS cc_start: 0.7058 (ttpt) cc_final: 0.6748 (tptt) REVERT: L 18 LYS cc_start: 0.3681 (OUTLIER) cc_final: 0.2775 (ptmm) REVERT: L 54 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.5966 (mmp-170) REVERT: M 114 LYS cc_start: 0.5588 (OUTLIER) cc_final: 0.5377 (mttp) REVERT: N 6 MET cc_start: 0.7093 (mmm) cc_final: 0.6046 (mpt) REVERT: N 86 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7187 (mt-10) REVERT: N 89 MET cc_start: 0.7694 (mmp) cc_final: 0.7465 (mmp) REVERT: N 92 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: N 97 LYS cc_start: 0.7350 (ptmm) cc_final: 0.6885 (pttt) REVERT: O 11 ILE cc_start: 0.6409 (mt) cc_final: 0.6147 (mp) REVERT: O 45 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6544 (tm-30) REVERT: O 48 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6742 (mptp) REVERT: O 58 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7004 (ttm170) REVERT: O 73 LYS cc_start: 0.6514 (mmmt) cc_final: 0.5915 (ttmt) REVERT: P 1 MET cc_start: 0.4775 (OUTLIER) cc_final: 0.3854 (tpp) REVERT: Q 11 ARG cc_start: 0.5989 (mtp-110) cc_final: 0.5635 (mtp85) REVERT: Q 18 GLU cc_start: 0.5822 (OUTLIER) cc_final: 0.5536 (mt-10) REVERT: R 48 ARG cc_start: 0.5763 (mtp180) cc_final: 0.5192 (mpt180) REVERT: R 57 ARG cc_start: 0.7373 (mtm-85) cc_final: 0.7101 (mtm180) REVERT: R 61 ARG cc_start: 0.7375 (mtm-85) cc_final: 0.6898 (mtm-85) REVERT: S 32 ARG cc_start: 0.6241 (OUTLIER) cc_final: 0.5537 (mtm180) REVERT: T 5 LYS cc_start: 0.5815 (mtpt) cc_final: 0.5591 (mmtt) REVERT: T 9 LYS cc_start: 0.6232 (tptp) cc_final: 0.5819 (tppp) REVERT: T 18 ARG cc_start: 0.6287 (ttp80) cc_final: 0.5503 (ttp80) REVERT: U 17 ARG cc_start: 0.5022 (mtt90) cc_final: 0.4486 (mmt180) REVERT: U 47 ARG cc_start: 0.5447 (tmm-80) cc_final: 0.4206 (mtt180) REVERT: U 60 LEU cc_start: 0.3252 (OUTLIER) cc_final: 0.2935 (mm) REVERT: c 117 GLN cc_start: 0.6843 (pt0) cc_final: 0.6418 (pt0) REVERT: c 182 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7535 (ttt180) REVERT: c 223 THR cc_start: 0.8198 (p) cc_final: 0.7833 (t) REVERT: d 59 ARG cc_start: 0.7316 (mmt180) cc_final: 0.7034 (mmt180) REVERT: d 64 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6521 (mm-30) REVERT: d 89 GLU cc_start: 0.5303 (OUTLIER) cc_final: 0.4917 (mt-10) REVERT: d 94 GLN cc_start: 0.7614 (tt0) cc_final: 0.7379 (tt0) REVERT: d 128 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7423 (mmp80) REVERT: d 207 VAL cc_start: 0.7872 (p) cc_final: 0.7608 (m) REVERT: e 61 ARG cc_start: 0.7267 (ptt-90) cc_final: 0.7019 (ptp90) REVERT: e 88 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7281 (mmp80) REVERT: e 149 ILE cc_start: 0.6766 (OUTLIER) cc_final: 0.6156 (mp) REVERT: e 178 VAL cc_start: 0.7337 (t) cc_final: 0.6885 (p) REVERT: f 27 GLN cc_start: 0.7482 (mt0) cc_final: 0.7021 (mt0) REVERT: f 30 ARG cc_start: 0.7323 (mtm-85) cc_final: 0.6834 (mpp-170) REVERT: f 94 GLU cc_start: 0.6006 (mm-30) cc_final: 0.5734 (tt0) REVERT: f 122 PHE cc_start: 0.6738 (m-80) cc_final: 0.6112 (m-80) REVERT: f 134 GLU cc_start: 0.5810 (mt-10) cc_final: 0.5484 (mp0) REVERT: f 161 LYS cc_start: 0.5447 (mtpp) cc_final: 0.4983 (mmtm) REVERT: g 130 GLU cc_start: 0.6158 (OUTLIER) cc_final: 0.5672 (tt0) REVERT: g 131 ILE cc_start: 0.7202 (mt) cc_final: 0.6822 (mp) REVERT: i 92 MET cc_start: 0.7756 (mmm) cc_final: 0.6933 (mmm) REVERT: i 96 ARG cc_start: 0.6691 (ttp80) cc_final: 0.6175 (ttp80) REVERT: j 7 MET cc_start: 0.8105 (mmm) cc_final: 0.7743 (mmm) REVERT: j 49 ARG cc_start: 0.6108 (mtm-85) cc_final: 0.5492 (mpp-170) REVERT: j 51 LYS cc_start: 0.6826 (mttp) cc_final: 0.6597 (mttm) REVERT: j 93 GLN cc_start: 0.6804 (mm-40) cc_final: 0.6412 (mm110) REVERT: j 106 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6335 (mp0) REVERT: k 123 ARG cc_start: 0.6509 (ttm170) cc_final: 0.6108 (ttm170) REVERT: k 129 LYS cc_start: 0.6824 (mttp) cc_final: 0.6459 (mmmt) REVERT: l 5 LYS cc_start: 0.7027 (mttp) cc_final: 0.6557 (pttm) REVERT: l 22 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6927 (mt0) REVERT: l 127 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7585 (tttt) REVERT: l 133 LYS cc_start: 0.6764 (ttpt) cc_final: 0.6216 (tptm) REVERT: l 134 THR cc_start: 0.7165 (m) cc_final: 0.6656 (t) REVERT: m 1 MET cc_start: 0.7947 (mtm) cc_final: 0.7635 (mtm) REVERT: m 43 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7538 (tp30) REVERT: m 72 ASP cc_start: 0.7235 (t0) cc_final: 0.6766 (t70) REVERT: n 16 ARG cc_start: 0.6835 (mmp80) cc_final: 0.6403 (mmt90) REVERT: n 30 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7332 (ptt90) REVERT: n 46 GLU cc_start: 0.6348 (mm-30) cc_final: 0.5929 (mp0) REVERT: n 69 ASP cc_start: 0.6607 (m-30) cc_final: 0.6361 (m-30) REVERT: o 38 LYS cc_start: 0.6706 (OUTLIER) cc_final: 0.6505 (pttp) REVERT: o 89 ARG cc_start: 0.7009 (mtm110) cc_final: 0.6121 (mtt-85) REVERT: p 13 ARG cc_start: 0.7896 (ttt90) cc_final: 0.7138 (ttp80) REVERT: p 103 LYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6383 (mptt) REVERT: p 111 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6449 (mm-30) REVERT: q 1 MET cc_start: 0.6056 (ttt) cc_final: 0.5779 (ttm) REVERT: q 62 GLU cc_start: 0.6652 (tt0) cc_final: 0.6243 (tt0) REVERT: q 73 LYS cc_start: 0.7718 (mtpt) cc_final: 0.7462 (mttt) REVERT: r 70 LYS cc_start: 0.7445 (mtmm) cc_final: 0.6978 (mttp) REVERT: r 86 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7233 (ttm) REVERT: r 95 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6643 (ttp-170) REVERT: s 4 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.5601 (tp30) REVERT: s 8 LEU cc_start: 0.7760 (mt) cc_final: 0.7520 (mt) REVERT: s 76 ARG cc_start: 0.7228 (ttt-90) cc_final: 0.6922 (tmt90) REVERT: s 89 GLU cc_start: 0.5482 (OUTLIER) cc_final: 0.4610 (tt0) REVERT: t 7 ARG cc_start: 0.6606 (ttt-90) cc_final: 0.6065 (ttt90) REVERT: t 10 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.5931 (tm-30) REVERT: t 54 GLN cc_start: 0.2989 (OUTLIER) cc_final: 0.2616 (mt0) REVERT: u 70 ILE cc_start: 0.6865 (OUTLIER) cc_final: 0.6332 (tt) REVERT: u 75 GLN cc_start: 0.7503 (tp40) cc_final: 0.7008 (tp-100) REVERT: v 44 LYS cc_start: 0.7834 (ttmm) cc_final: 0.7498 (ttpt) REVERT: v 70 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6448 (tt0) REVERT: v 83 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6868 (mt-10) REVERT: x 2 LYS cc_start: 0.5554 (tttp) cc_final: 0.5239 (ttpp) REVERT: x 17 GLU cc_start: 0.6645 (tp30) cc_final: 0.6288 (tp30) REVERT: y 39 GLU cc_start: 0.6623 (pt0) cc_final: 0.6376 (pt0) REVERT: y 56 LYS cc_start: 0.7773 (ttmt) cc_final: 0.7222 (ttpp) REVERT: 0 50 LYS cc_start: 0.7440 (mttm) cc_final: 0.7077 (mtpp) REVERT: 2 15 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7525 (mptp) REVERT: 3 18 LYS cc_start: 0.7888 (tttt) cc_final: 0.7531 (tttt) outliers start: 179 outliers final: 115 residues processed: 919 average time/residue: 2.4908 time to fit residues: 3147.7917 Evaluate side-chains 962 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 799 time to evaluate : 5.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 114 LYS Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 75 HIS Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 18 LYS Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 89 GLU Chi-restraints excluded: chain e residue 53 THR Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 149 ILE Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 155 GLU Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 157 THR Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 24 ILE Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 80 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 163 ARG Chi-restraints excluded: chain g residue 175 LYS Chi-restraints excluded: chain i residue 13 ARG Chi-restraints excluded: chain i residue 43 GLU Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain j residue 109 SER Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain k residue 141 LYS Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 127 LYS Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 85 LYS Chi-restraints excluded: chain o residue 13 MET Chi-restraints excluded: chain o residue 38 LYS Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain p residue 103 LYS Chi-restraints excluded: chain p residue 104 VAL Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 86 MET Chi-restraints excluded: chain r residue 95 ARG Chi-restraints excluded: chain s residue 4 GLU Chi-restraints excluded: chain s residue 7 LEU Chi-restraints excluded: chain s residue 89 GLU Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain t residue 27 ASN Chi-restraints excluded: chain t residue 41 LEU Chi-restraints excluded: chain t residue 54 GLN Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain t residue 72 ILE Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain u residue 70 ILE Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 5 ILE Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 38 LYS Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 22 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 886 optimal weight: 0.8980 chunk 583 optimal weight: 10.0000 chunk 940 optimal weight: 3.9990 chunk 573 optimal weight: 10.0000 chunk 446 optimal weight: 10.0000 chunk 653 optimal weight: 10.0000 chunk 986 optimal weight: 20.0000 chunk 907 optimal weight: 5.9990 chunk 785 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 606 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN O 40 GLN O 62 GLN R 54 GLN j 90 ASN k 93 ASN s 48 GLN t 46 GLN u 12 GLN x 27 ASN x 58 ASN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 154032 Z= 0.224 Angle : 0.753 15.893 230513 Z= 0.412 Chirality : 0.039 0.393 29296 Planarity : 0.008 0.143 12270 Dihedral : 23.066 177.641 77190 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.91 % Rotamer: Outliers : 3.72 % Allowed : 17.14 % Favored : 79.15 % 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: 0.00 (0.11), residues: 5480 helix: 1.03 (0.12), residues: 1866 sheet: -0.23 (0.15), residues: 1081 loop : -0.59 (0.12), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 248 HIS 0.007 0.001 HIS B 39 PHE 0.030 0.002 PHE F 78 TYR 0.019 0.002 TYR F 4 ARG 0.016 0.001 ARG J 45 ********************** 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 977 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 807 time to evaluate : 6.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.3757 (mmp) cc_final: 0.3176 (mmm) REVERT: B 49 MET cc_start: 0.3111 (mtt) cc_final: 0.2792 (mtp) REVERT: B 68 LEU cc_start: 0.4070 (OUTLIER) cc_final: 0.3799 (tt) REVERT: B 112 LYS cc_start: 0.3704 (ttpt) cc_final: 0.3260 (tttp) REVERT: B 154 MET cc_start: 0.3097 (OUTLIER) cc_final: 0.2871 (ttp) REVERT: B 212 LEU cc_start: 0.3563 (tp) cc_final: 0.3090 (mt) REVERT: C 45 LYS cc_start: 0.6143 (tttm) cc_final: 0.5658 (mtmm) REVERT: C 82 GLU cc_start: 0.4278 (OUTLIER) cc_final: 0.3999 (tp30) REVERT: C 136 ARG cc_start: 0.6306 (ttm-80) cc_final: 0.5943 (ttm-80) REVERT: C 139 GLN cc_start: 0.6950 (mt0) cc_final: 0.6010 (pt0) REVERT: C 179 ARG cc_start: 0.6914 (ttp-170) cc_final: 0.6416 (ttm170) REVERT: D 8 LYS cc_start: 0.5827 (mttm) cc_final: 0.5473 (mttp) REVERT: D 54 GLN cc_start: 0.7187 (mt0) cc_final: 0.6911 (mt0) REVERT: D 60 LYS cc_start: 0.6566 (OUTLIER) cc_final: 0.6140 (ttmm) REVERT: D 73 ARG cc_start: 0.6283 (ttp80) cc_final: 0.5435 (ttm170) REVERT: D 81 ARG cc_start: 0.4961 (ttp80) cc_final: 0.4333 (tmt170) REVERT: D 104 ARG cc_start: 0.6123 (mmt90) cc_final: 0.5736 (mmt180) REVERT: D 135 TYR cc_start: 0.6313 (t80) cc_final: 0.6083 (t80) REVERT: D 148 LYS cc_start: 0.4627 (tmtt) cc_final: 0.4183 (tppt) REVERT: D 197 GLU cc_start: 0.4697 (pm20) cc_final: 0.4256 (pm20) REVERT: D 206 LYS cc_start: 0.5745 (ttpp) cc_final: 0.5484 (tttp) REVERT: E 12 GLN cc_start: 0.6753 (mt0) cc_final: 0.6218 (mt0) REVERT: E 19 ASN cc_start: 0.7751 (OUTLIER) cc_final: 0.7129 (p0) REVERT: E 29 ARG cc_start: 0.8026 (mtt180) cc_final: 0.7670 (mtt90) REVERT: E 54 ARG cc_start: 0.7192 (mmm-85) cc_final: 0.6741 (mtt180) REVERT: E 55 GLU cc_start: 0.6386 (mt-10) cc_final: 0.5978 (mt-10) REVERT: E 65 GLU cc_start: 0.5993 (OUTLIER) cc_final: 0.5711 (tp30) REVERT: E 70 ASN cc_start: 0.6892 (OUTLIER) cc_final: 0.6510 (m110) REVERT: E 156 LYS cc_start: 0.6429 (mtmt) cc_final: 0.6212 (mtmt) REVERT: E 159 LYS cc_start: 0.6520 (mttm) cc_final: 0.6180 (mttt) REVERT: F 1 MET cc_start: 0.4763 (tpp) cc_final: 0.4442 (mmt) REVERT: F 55 HIS cc_start: 0.6439 (m90) cc_final: 0.6114 (m170) REVERT: F 92 THR cc_start: 0.6240 (m) cc_final: 0.5673 (p) REVERT: G 4 ARG cc_start: 0.5674 (mmt180) cc_final: 0.5285 (mmt-90) REVERT: G 21 GLU cc_start: 0.5728 (OUTLIER) cc_final: 0.5340 (mm-30) REVERT: G 59 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.6037 (mm) REVERT: G 66 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6294 (tp) REVERT: G 119 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6290 (mtp180) REVERT: G 137 LYS cc_start: 0.6409 (OUTLIER) cc_final: 0.5859 (tptt) REVERT: G 146 GLU cc_start: 0.5672 (OUTLIER) cc_final: 0.5081 (mp0) REVERT: G 154 TYR cc_start: 0.4342 (OUTLIER) cc_final: 0.3048 (m-10) REVERT: H 38 ASN cc_start: 0.7061 (t0) cc_final: 0.6745 (t0) REVERT: H 58 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.6016 (tt0) REVERT: I 33 ARG cc_start: 0.6229 (mtm180) cc_final: 0.5505 (mtt180) REVERT: I 49 ARG cc_start: 0.5965 (mtm-85) cc_final: 0.5645 (mtm180) REVERT: I 57 MET cc_start: 0.5557 (ptp) cc_final: 0.5062 (ptm) REVERT: I 60 LYS cc_start: 0.4779 (OUTLIER) cc_final: 0.4514 (mptt) REVERT: I 88 MET cc_start: 0.6311 (mtm) cc_final: 0.6050 (mtm) REVERT: I 110 GLN cc_start: 0.7395 (mm110) cc_final: 0.7102 (mt0) REVERT: I 124 ARG cc_start: 0.7276 (ttm-80) cc_final: 0.7019 (mtp-110) REVERT: K 40 ASN cc_start: 0.6467 (m110) cc_final: 0.6003 (m-40) REVERT: K 112 ASP cc_start: 0.6923 (t70) cc_final: 0.6556 (t0) REVERT: L 10 LYS cc_start: 0.7066 (ttpt) cc_final: 0.6752 (tptt) REVERT: L 18 LYS cc_start: 0.3543 (OUTLIER) cc_final: 0.2671 (ptmm) REVERT: L 54 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.5952 (mmp-170) REVERT: M 114 LYS cc_start: 0.5565 (OUTLIER) cc_final: 0.5352 (mttp) REVERT: N 6 MET cc_start: 0.7099 (mmm) cc_final: 0.6055 (mpt) REVERT: N 86 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7141 (mt-10) REVERT: N 92 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7399 (mt-10) REVERT: N 97 LYS cc_start: 0.7348 (ptmm) cc_final: 0.6887 (pttt) REVERT: O 11 ILE cc_start: 0.6411 (mt) cc_final: 0.6175 (mp) REVERT: O 45 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6333 (tm-30) REVERT: O 48 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6728 (mptp) REVERT: O 58 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6986 (ttm170) REVERT: O 73 LYS cc_start: 0.6508 (mmmt) cc_final: 0.5927 (ttmt) REVERT: O 80 GLN cc_start: 0.5948 (mm-40) cc_final: 0.5644 (tp40) REVERT: P 1 MET cc_start: 0.4815 (OUTLIER) cc_final: 0.3948 (tpp) REVERT: Q 11 ARG cc_start: 0.5982 (mtp-110) cc_final: 0.5629 (mtp85) REVERT: Q 18 GLU cc_start: 0.5848 (OUTLIER) cc_final: 0.5539 (mt-10) REVERT: R 48 ARG cc_start: 0.5732 (mtp180) cc_final: 0.5168 (mpt180) REVERT: R 57 ARG cc_start: 0.7368 (mtm-85) cc_final: 0.7088 (mtm180) REVERT: R 61 ARG cc_start: 0.7368 (mtm-85) cc_final: 0.6892 (mtm-85) REVERT: S 32 ARG cc_start: 0.6211 (OUTLIER) cc_final: 0.5503 (mtm180) REVERT: T 5 LYS cc_start: 0.5791 (mtpt) cc_final: 0.5578 (mmtt) REVERT: T 9 LYS cc_start: 0.6178 (tptp) cc_final: 0.5794 (tppp) REVERT: T 18 ARG cc_start: 0.6281 (ttp80) cc_final: 0.5510 (ttp80) REVERT: U 17 ARG cc_start: 0.5014 (mtt90) cc_final: 0.4481 (mmt180) REVERT: U 47 ARG cc_start: 0.5479 (tmm-80) cc_final: 0.4224 (mtt180) REVERT: U 60 LEU cc_start: 0.3160 (OUTLIER) cc_final: 0.2876 (mm) REVERT: c 117 GLN cc_start: 0.6820 (pt0) cc_final: 0.6397 (pt0) REVERT: c 182 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7471 (ttt180) REVERT: c 223 THR cc_start: 0.8161 (p) cc_final: 0.7802 (t) REVERT: d 59 ARG cc_start: 0.7302 (mmt180) cc_final: 0.7028 (mmt180) REVERT: d 64 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6513 (mm-30) REVERT: d 89 GLU cc_start: 0.5303 (OUTLIER) cc_final: 0.4919 (mt-10) REVERT: d 94 GLN cc_start: 0.7618 (tt0) cc_final: 0.7380 (tt0) REVERT: d 128 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.7417 (mmp80) REVERT: d 207 VAL cc_start: 0.7892 (p) cc_final: 0.7632 (m) REVERT: e 61 ARG cc_start: 0.7313 (ptt-90) cc_final: 0.7066 (ptp90) REVERT: e 88 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7285 (mmp80) REVERT: e 111 GLU cc_start: 0.6726 (tp30) cc_final: 0.6316 (tp30) REVERT: e 149 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6118 (mp) REVERT: e 178 VAL cc_start: 0.7310 (t) cc_final: 0.6857 (p) REVERT: f 27 GLN cc_start: 0.7483 (mt0) cc_final: 0.7031 (mt0) REVERT: f 30 ARG cc_start: 0.7319 (mtm-85) cc_final: 0.6831 (mpp-170) REVERT: f 94 GLU cc_start: 0.5999 (mm-30) cc_final: 0.5720 (tt0) REVERT: f 122 PHE cc_start: 0.6736 (m-80) cc_final: 0.6118 (m-80) REVERT: f 161 LYS cc_start: 0.5448 (mtpp) cc_final: 0.5003 (mmtt) REVERT: g 130 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.5782 (tt0) REVERT: g 131 ILE cc_start: 0.7196 (mt) cc_final: 0.6821 (mp) REVERT: i 92 MET cc_start: 0.7758 (mmm) cc_final: 0.6928 (mmm) REVERT: i 96 ARG cc_start: 0.6642 (ttp80) cc_final: 0.6137 (ttp80) REVERT: j 7 MET cc_start: 0.8098 (mmm) cc_final: 0.7750 (mmm) REVERT: j 49 ARG cc_start: 0.6090 (mtm-85) cc_final: 0.5460 (mpp-170) REVERT: j 51 LYS cc_start: 0.6884 (mttp) cc_final: 0.6660 (mttm) REVERT: j 93 GLN cc_start: 0.6783 (mm-40) cc_final: 0.6368 (mm110) REVERT: j 106 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: k 123 ARG cc_start: 0.6511 (ttm170) cc_final: 0.6113 (ttm170) REVERT: k 129 LYS cc_start: 0.6772 (mttp) cc_final: 0.6419 (mmmt) REVERT: l 5 LYS cc_start: 0.7021 (mttp) cc_final: 0.6551 (pttm) REVERT: l 22 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6899 (mt0) REVERT: l 133 LYS cc_start: 0.6764 (ttpt) cc_final: 0.6192 (tptm) REVERT: l 134 THR cc_start: 0.7193 (m) cc_final: 0.6680 (t) REVERT: m 1 MET cc_start: 0.7954 (mtm) cc_final: 0.7639 (mtm) REVERT: m 43 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7550 (tp30) REVERT: m 72 ASP cc_start: 0.7225 (t0) cc_final: 0.6762 (t70) REVERT: m 86 ARG cc_start: 0.7616 (mtp180) cc_final: 0.7350 (mtp180) REVERT: n 16 ARG cc_start: 0.6832 (mmp80) cc_final: 0.6400 (mmt90) REVERT: n 30 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7336 (ptt90) REVERT: n 46 GLU cc_start: 0.6374 (mm-30) cc_final: 0.5952 (mp0) REVERT: n 69 ASP cc_start: 0.6617 (m-30) cc_final: 0.6375 (m-30) REVERT: o 89 ARG cc_start: 0.7010 (mtm110) cc_final: 0.6125 (mtt-85) REVERT: p 13 ARG cc_start: 0.7903 (ttt90) cc_final: 0.7139 (ttp80) REVERT: p 87 SER cc_start: 0.7718 (m) cc_final: 0.7003 (t) REVERT: p 103 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6411 (mptt) REVERT: p 111 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6462 (mm-30) REVERT: q 1 MET cc_start: 0.6009 (ttt) cc_final: 0.5736 (ttm) REVERT: q 62 GLU cc_start: 0.6664 (tt0) cc_final: 0.6263 (tt0) REVERT: q 73 LYS cc_start: 0.7649 (mtpt) cc_final: 0.7385 (mttt) REVERT: r 70 LYS cc_start: 0.7452 (mtmm) cc_final: 0.6983 (mttp) REVERT: r 86 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7177 (ttm) REVERT: r 95 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6613 (ttp80) REVERT: s 4 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.5582 (tp30) REVERT: s 8 LEU cc_start: 0.7749 (mt) cc_final: 0.7475 (mt) REVERT: s 76 ARG cc_start: 0.7212 (ttt-90) cc_final: 0.6908 (tmt90) REVERT: s 89 GLU cc_start: 0.5518 (OUTLIER) cc_final: 0.4657 (tt0) REVERT: t 10 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.5900 (tm-30) REVERT: t 54 GLN cc_start: 0.2965 (OUTLIER) cc_final: 0.2655 (mp10) REVERT: u 70 ILE cc_start: 0.6829 (OUTLIER) cc_final: 0.6309 (tt) REVERT: u 75 GLN cc_start: 0.7434 (tp40) cc_final: 0.6973 (tp-100) REVERT: v 44 LYS cc_start: 0.7834 (ttmm) cc_final: 0.7508 (ttpt) REVERT: v 70 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6491 (tt0) REVERT: v 83 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6867 (mt-10) REVERT: x 2 LYS cc_start: 0.5546 (tttp) cc_final: 0.5239 (ttpp) REVERT: x 17 GLU cc_start: 0.6640 (tp30) cc_final: 0.6286 (tp30) REVERT: y 39 GLU cc_start: 0.6617 (pt0) cc_final: 0.6369 (pt0) REVERT: y 56 LYS cc_start: 0.7764 (ttmt) cc_final: 0.7214 (ttpp) REVERT: 0 50 LYS cc_start: 0.7451 (mttm) cc_final: 0.7156 (mttm) REVERT: 2 15 LYS cc_start: 0.7990 (mmtt) cc_final: 0.7521 (mptp) REVERT: 3 18 LYS cc_start: 0.7881 (tttt) cc_final: 0.7524 (tttt) outliers start: 170 outliers final: 102 residues processed: 914 average time/residue: 2.4339 time to fit residues: 3059.3790 Evaluate side-chains 949 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 803 time to evaluate : 5.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 114 LYS Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 75 HIS Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 18 LYS Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 89 GLU Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 149 ILE Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 155 GLU Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 157 THR Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 24 ILE Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 80 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 175 LYS Chi-restraints excluded: chain i residue 13 ARG Chi-restraints excluded: chain i residue 43 GLU Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain j residue 109 SER Chi-restraints excluded: chain k residue 94 THR Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain k residue 141 LYS Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 85 LYS Chi-restraints excluded: chain o residue 13 MET Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain p residue 103 LYS Chi-restraints excluded: chain p residue 104 VAL Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 86 MET Chi-restraints excluded: chain r residue 95 ARG Chi-restraints excluded: chain s residue 4 GLU Chi-restraints excluded: chain s residue 7 LEU Chi-restraints excluded: chain s residue 89 GLU Chi-restraints excluded: chain t residue 10 GLU Chi-restraints excluded: chain t residue 27 ASN Chi-restraints excluded: chain t residue 54 GLN Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain u residue 70 ILE Chi-restraints excluded: chain v residue 70 GLU Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 38 LYS Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 22 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 481 optimal weight: 9.9990 chunk 623 optimal weight: 10.0000 chunk 836 optimal weight: 20.0000 chunk 240 optimal weight: 0.1980 chunk 724 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 786 optimal weight: 10.0000 chunk 329 optimal weight: 7.9990 chunk 807 optimal weight: 8.9990 chunk 99 optimal weight: 30.0000 overall best weight: 6.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN O 40 GLN O 62 GLN R 54 GLN j 90 ASN k 93 ASN q 6 GLN s 48 GLN t 46 GLN u 12 GLN x 27 ASN x 58 ASN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.162926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.133881 restraints weight = 123125.570| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 0.81 r_work: 0.3152 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 154032 Z= 0.311 Angle : 0.849 18.261 230513 Z= 0.451 Chirality : 0.043 0.398 29296 Planarity : 0.009 0.149 12270 Dihedral : 23.115 178.104 77190 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.36 % Favored : 95.55 % Rotamer: Outliers : 3.56 % Allowed : 17.60 % Favored : 78.84 % 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: -0.19 (0.11), residues: 5480 helix: 0.80 (0.12), residues: 1870 sheet: -0.27 (0.16), residues: 1051 loop : -0.68 (0.12), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP c 248 HIS 0.009 0.002 HIS v 57 PHE 0.023 0.003 PHE U 12 TYR 0.022 0.003 TYR G 154 ARG 0.011 0.001 ARG p 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43826.18 seconds wall clock time: 760 minutes 41.32 seconds (45641.32 seconds total)