Starting phenix.real_space_refine on Wed Mar 20 03:29:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7e_33662/03_2024/7y7e_33662_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7e_33662/03_2024/7y7e_33662.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7e_33662/03_2024/7y7e_33662_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7e_33662/03_2024/7y7e_33662_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7e_33662/03_2024/7y7e_33662_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7e_33662/03_2024/7y7e_33662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7e_33662/03_2024/7y7e_33662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7e_33662/03_2024/7y7e_33662_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7e_33662/03_2024/7y7e_33662_updated.pdb" } resolution = 2.41 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 4556 5.49 5 Mg 248 5.21 5 S 150 5.16 5 C 71109 2.51 5 N 26433 2.21 5 O 39422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 192": "OD1" <-> "OD2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "C GLU 28": "OE1" <-> "OE2" 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 "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "E GLU 13": "OE1" <-> "OE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 40": "OE1" <-> "OE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "I ARG 95": "NH1" <-> "NH2" Residue "I ARG 124": "NH1" <-> "NH2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "L ARG 14": "NH1" <-> "NH2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M GLU 59": "OE1" <-> "OE2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "N ARG 65": "NH1" <-> "NH2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O GLU 45": "OE1" <-> "OE2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "Q ASP 15": "OD1" <-> "OD2" Residue "Q GLU 26": "OE1" <-> "OE2" Residue "Q ASP 48": "OD1" <-> "OD2" Residue "Q GLU 63": "OE1" <-> "OE2" Residue "Q GLU 80": "OE1" <-> "OE2" Residue "R TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 72": "OD1" <-> "OD2" Residue "S ARG 3": "NH1" <-> "NH2" Residue "S GLU 20": "OE1" <-> "OE2" Residue "S GLU 24": "OE1" <-> "OE2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "S ASP 64": "OD1" <-> "OD2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "U GLU 39": "OE1" <-> "OE2" 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 82": "OE1" <-> "OE2" Residue "c ASP 98": "OD1" <-> "OD2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c GLU 145": "OE1" <-> "OE2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c GLU 180": "OE1" <-> "OE2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c GLU 199": "OE1" <-> "OE2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "c GLU 236": "OE1" <-> "OE2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d GLU 28": "OE1" <-> "OE2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d GLU 64": "OE1" <-> "OE2" Residue "d GLU 74": "OE1" <-> "OE2" Residue "d GLU 81": "OE1" <-> "OE2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d GLU 89": "OE1" <-> "OE2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 94": "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 134": "OE1" <-> "OE2" Residue "g ARG 3": "NH1" <-> "NH2" 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 TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "i GLU 9": "OE1" <-> "OE2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i ARG 37": "NH1" <-> "NH2" Residue "i GLU 43": "OE1" <-> "OE2" Residue "i ASP 60": "OD1" <-> "OD2" Residue "i GLU 90": "OE1" <-> "OE2" Residue "i GLU 91": "OE1" <-> "OE2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "i GLU 129": "OE1" <-> "OE2" Residue "j ASP 12": "OD1" <-> "OD2" Residue "j GLU 106": "OE1" <-> "OE2" Residue "j GLU 110": "OE1" <-> "OE2" Residue "k GLU 10": "OE1" <-> "OE2" Residue "k ARG 21": "NH1" <-> "NH2" Residue "k ARG 33": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k ARG 47": "NH1" <-> "NH2" Residue "k GLU 51": "OE1" <-> "OE2" Residue "k ARG 60": "NH1" <-> "NH2" Residue "k PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 78": "NH1" <-> "NH2" Residue "k GLU 106": "OE1" <-> "OE2" Residue "k ARG 123": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "k GLU 136": "OE1" <-> "OE2" Residue "l ARG 10": "NH1" <-> "NH2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ARG 40": "NH1" <-> "NH2" Residue "l ARG 44": "NH1" <-> "NH2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l GLU 90": "OE1" <-> "OE2" Residue "l TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "m ARG 12": "NH1" <-> "NH2" Residue "m ARG 17": "NH1" <-> "NH2" Residue "m ARG 22": "NH1" <-> "NH2" Residue "m GLU 43": "OE1" <-> "OE2" Residue "m ARG 46": "NH1" <-> "NH2" Residue "m GLU 49": "OE1" <-> "OE2" Residue "m ARG 63": "NH1" <-> "NH2" Residue "m ARG 64": "NH1" <-> "NH2" Residue "m ARG 69": "NH1" <-> "NH2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m ARG 96": "NH1" <-> "NH2" 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 ARG 81": "NH1" <-> "NH2" Residue "n ASP 89": "OD1" <-> "OD2" Residue "n ASP 93": "OD1" <-> "OD2" Residue "n ARG 94": "NH1" <-> "NH2" Residue "n ARG 102": "NH1" <-> "NH2" Residue "n ARG 111": "NH1" <-> "NH2" Residue "o GLU 9": "OE1" <-> "OE2" Residue "o GLU 11": "OE1" <-> "OE2" Residue "o ARG 21": "NH1" <-> "NH2" Residue "o ASP 24": "OD1" <-> "OD2" Residue "o ARG 39": "NH1" <-> "NH2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "o ARG 101": "NH1" <-> "NH2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "p ARG 3": "NH1" <-> "NH2" Residue "p ARG 6": "NH1" <-> "NH2" Residue "p ARG 13": "NH1" <-> "NH2" Residue "p ARG 33": "NH1" <-> "NH2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p TYR 76": "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 ASP 65": "OD1" <-> "OD2" Residue "r ASP 77": "OD1" <-> "OD2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r ARG 88": "NH1" <-> "NH2" Residue "r ARG 95": "NH1" <-> "NH2" Residue "r ARG 110": "NH1" <-> "NH2" Residue "s GLU 4": "OE1" <-> "OE2" Residue "s GLU 18": "OE1" <-> "OE2" Residue "s GLU 42": "OE1" <-> "OE2" Residue "s ARG 73": "NH1" <-> "NH2" Residue "t ARG 6": "NH1" <-> "NH2" Residue "t ARG 7": "NH1" <-> "NH2" Residue "t GLU 10": "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 "v GLU 29": "OE1" <-> "OE2" Residue "w ARG 3": "NH1" <-> "NH2" Residue "w ARG 11": "NH1" <-> "NH2" Residue "w ARG 37": "NH1" <-> "NH2" Residue "w GLU 41": "OE1" <-> "OE2" Residue "w ARG 50": "NH1" <-> "NH2" Residue "w ARG 57": "NH1" <-> "NH2" Residue "w ARG 74": "NH1" <-> "NH2" Residue "x GLU 5": "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 ASP 40": "OD1" <-> "OD2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "z ARG 52": "NH1" <-> "NH2" Residue "0 GLU 7": "OE1" <-> "OE2" Residue "0 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "4 GLU 11": "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: 141918 Number of models: 1 Model: "" Number of chains: 63 Chain: "A" Number of atoms: 32634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1520, 32634 Classifications: {'RNA': 1520} Modifications used: {'rna2p': 1, 'rna2p_pur': 121, 'rna2p_pyr': 82, 'rna3p': 10, 'rna3p_pur': 742, 'rna3p_pyr': 564} Link IDs: {'rna2p': 204, 'rna3p': 1315} 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': 141, 'rna3p': 17, 'rna3p_pur': 1318, 'rna3p_pyr': 1003} Link IDs: {'rna2p': 414, 'rna3p': 2338} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "b" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "h" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "i" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "j" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "k" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "l" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Unusual residues: {'MS6': 1} Classifications: {'peptide': 135, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126, None: 2} Not linked: pdbres="4D4 l 81 " pdbres="MS6 l 82 " Not linked: pdbres="MS6 l 82 " pdbres="GLY l 83 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "n" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "o" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "p" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "r" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "s" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "t" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "u" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "v" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 628 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "x" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "y" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "0" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "2" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "3" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "4" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 480 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 1 Chain: "X" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 279 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 10} Chain: "Z" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1645 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p': 4, 'rna3p_pur': 34, 'rna3p_pyr': 30} Link IDs: {'rna2p': 8, 'rna3p': 68} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "V" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1612 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p': 3, 'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p': 8, 'rna3p_pur': 31, 'rna3p_pyr': 27} Link IDs: {'rna2p': 9, 'rna3p': 65} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Unusual residues: {' MG': 56} Classifications: {'undetermined': 56} Link IDs: {None: 55} Chain: "a" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 181 Unusual residues: {' MG': 181} Classifications: {'undetermined': 181} Link IDs: {None: 180} Chain: "b" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' MG': 2, 'MAN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 53.64, per 1000 atoms: 0.38 Number of scatterers: 141918 At special positions: 0 Unit cell: (250.207, 239.436, 247.721, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 150 16.00 P 4556 15.00 Mg 248 11.99 O 39422 8.00 N 26433 7.00 C 71109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 55.22 Conformation dependent library (CDL) restraints added in 7.4 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: 172 helices and 69 sheets defined 39.1% alpha, 19.3% beta 1585 base pairs and 2411 stacking pairs defined. Time for finding SS restraints: 69.40 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.652A pdb=" N MET B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.712A pdb=" N ILE B 31 " --> pdb=" O MET B 27 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N PHE B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 32' Processing helix chain 'B' and resid 42 through 64 Proline residue: B 48 - end of helix removed outlier: 3.555A pdb=" N LYS B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 removed outlier: 3.911A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 124 removed outlier: 3.622A pdb=" N VAL B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 148 removed outlier: 6.353A pdb=" N ALA B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 3.973A 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: 4.038A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 48 removed outlier: 3.519A pdb=" N ALA C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.522A 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 108 through 113 removed outlier: 4.413A pdb=" N ASP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 113' Processing helix chain 'C' and resid 114 through 127 removed outlier: 3.547A 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: 4.564A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.782A 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: 5.094A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.889A 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: 3.587A pdb=" N LYS D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.833A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 3.755A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.683A pdb=" N LEU D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 5.030A 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: 4.023A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 4.034A 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 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: 3.637A 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 57 through 70 removed outlier: 3.752A pdb=" N ALA G 61 " --> pdb=" O SER G 57 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 112 removed outlier: 3.556A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLY G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.584A pdb=" N GLU G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 153 removed outlier: 3.813A pdb=" N ASN G 148 " --> pdb=" O MET G 144 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS G 149 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ALA G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N HIS G 153 " --> pdb=" O LYS G 149 " (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 40 removed outlier: 4.143A pdb=" N GLY I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) 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: 3.826A pdb=" N GLU I 92 " --> pdb=" O MET I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 102 removed outlier: 4.619A pdb=" N GLU I 97 " --> pdb=" O SER I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 33 removed outlier: 3.573A pdb=" N ILE J 18 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 removed outlier: 3.772A pdb=" N ARG J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 51 removed outlier: 4.478A pdb=" N GLY K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.902A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.384A 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: 3.979A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 3.771A 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: 3.866A pdb=" N TYR L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.782A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.562A 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: 3.936A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 21 removed outlier: 3.542A pdb=" N PHE N 21 " --> pdb=" O ALA N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 33 Processing helix chain 'N' and resid 37 through 51 removed outlier: 3.800A pdb=" N ARG N 41 " --> pdb=" O SER N 37 " (cutoff:3.500A) removed outlier: 3.704A 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: 4.180A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.803A 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 removed outlier: 3.737A pdb=" N ILE P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 80 removed outlier: 4.152A pdb=" N LYS P 80 " --> pdb=" O LYS P 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.510A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 34 removed outlier: 4.441A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 5.528A 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: 4.651A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA S 75 " --> pdb=" O LEU S 71 " (cutoff:3.500A) Proline residue: S 76 - end of helix No H-bonds generated for 'chain 'S' and resid 70 through 76' Processing helix chain 'T' and resid 4 through 41 Processing helix chain 'T' and resid 44 through 65 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 removed outlier: 3.533A 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: 4.823A pdb=" N PHE U 37 " --> pdb=" O ARG U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 69 removed outlier: 3.997A pdb=" N THR U 68 " --> pdb=" O ASN U 64 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ARG U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 15 removed outlier: 5.233A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 3.660A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.489A 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: 3.670A 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: 3.728A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY c 215 " --> pdb=" O ALA c 211 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 4.006A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.498A 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: 3.530A pdb=" N ASP c 264 " --> pdb=" O ASN c 260 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.653A 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: 4.242A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 61 removed outlier: 5.898A pdb=" N THR d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 72 Processing helix chain 'd' and resid 98 through 103 removed outlier: 4.327A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP d 103 " --> pdb=" O GLU d 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 98 through 103' Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'd' and resid 39 through 44 Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 40 removed outlier: 3.559A pdb=" N ALA e 39 " --> pdb=" O TYR e 35 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 53 removed outlier: 6.545A 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: 3.558A pdb=" N LEU e 134 " --> pdb=" O LYS e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 163 removed outlier: 4.838A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'f' and resid 2 through 21 removed outlier: 3.503A pdb=" N ASP f 6 " --> pdb=" O ALA f 2 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 47 removed outlier: 3.709A pdb=" N ASP f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) removed outlier: 3.885A 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: 5.747A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 Processing helix chain 'f' and resid 134 through 139 removed outlier: 3.845A 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: 3.516A 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: 5.216A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL g 79 " --> pdb=" O MET g 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 4.123A 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: 3.607A pdb=" N GLN h 33 " --> pdb=" O PHE h 29 " (cutoff:3.500A) Processing helix chain 'i' and resid 24 through 38 removed outlier: 4.011A 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: 4.273A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 3.652A 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: 3.964A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 67 through 72 removed outlier: 4.627A pdb=" N LYS i 72 " --> pdb=" O ASN i 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 67 through 72' Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'k' and resid 56 through 62 removed outlier: 3.680A pdb=" N LEU k 61 " --> pdb=" O LEU k 57 " (cutoff:3.500A) Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 4.108A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR k 74 " --> pdb=" O LYS k 70 " (cutoff:3.500A) removed outlier: 5.535A 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: 3.725A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 4.057A 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: 3.573A pdb=" N ALA l 122 " --> pdb=" O LYS l 118 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 3.998A 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: 4.305A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 4.599A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASP m 58 " --> pdb=" O LEU m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 4.471A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 4.966A 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: 4.674A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 5.100A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 5.750A 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: 3.627A pdb=" N GLY n 114 " --> pdb=" O ALA n 110 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 13 removed outlier: 3.619A pdb=" N GLU o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET o 13 " --> pdb=" O GLU o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.704A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N THR o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 97 through 104' Processing helix chain 'p' and resid 6 through 22 removed outlier: 3.928A pdb=" N LYS p 22 " --> pdb=" O LEU p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.763A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 32 through 37 removed outlier: 3.834A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 73 removed outlier: 3.847A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) removed outlier: 3.560A 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: 3.747A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) removed outlier: 3.830A 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: 3.700A pdb=" N VAL r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 65 through 70 removed outlier: 3.840A pdb=" N LEU r 69 " --> pdb=" O ASP r 65 " (cutoff:3.500A) removed outlier: 5.881A 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: 4.230A pdb=" N LEU s 11 " --> pdb=" O LEU s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 17 through 27 Processing helix chain 's' and resid 39 through 51 Processing helix chain 't' and resid 66 through 71 removed outlier: 3.932A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.410A 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: 3.624A pdb=" N ASN u 24 " --> pdb=" O LEU u 20 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 53 removed outlier: 4.137A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 3.999A 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: 3.536A pdb=" N LEU x 6 " --> pdb=" O LYS x 2 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N SER x 10 " --> pdb=" O LEU x 6 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 35 removed outlier: 3.611A pdb=" N GLY x 35 " --> pdb=" O GLN x 31 " (cutoff:3.500A) Processing helix chain 'x' and resid 40 through 62 removed outlier: 4.242A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY x 62 " --> pdb=" O ASN x 58 " (cutoff:3.500A) Processing helix chain 'y' and resid 17 through 28 Processing helix chain 'y' and resid 41 through 52 Processing helix chain 'z' and resid 9 through 19 removed outlier: 4.775A 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: 4.257A 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: 3.878A 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: 4.452A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU 2 57 " --> pdb=" O GLY 2 53 " (cutoff:3.500A) Proline residue: 2 63 - end of helix Processing helix chain '4' and resid 41 through 46 Processing helix chain '4' and resid 55 through 65 removed outlier: 4.315A pdb=" N ARG 4 59 " --> pdb=" O GLY 4 55 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN 4 65 " --> pdb=" O ASN 4 61 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 15 through 18 removed outlier: 5.395A pdb=" N HIS B 15 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N HIS B 39 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 90 through 93 removed outlier: 4.001A pdb=" N PHE B 90 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 198 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA B 185 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 53 through 59 Processing sheet with id= 4, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.566A pdb=" N GLY C 194 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 141 through 144 removed outlier: 4.035A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 12 through 16 removed outlier: 6.658A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 84 through 88 removed outlier: 3.664A pdb=" N ALA E 99 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 33 through 40 Processing sheet with id= 9, first strand: chain 'F' and resid 38 through 42 removed outlier: 5.674A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 43 through 47 removed outlier: 3.686A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 72 through 79 removed outlier: 6.597A pdb=" N THR G 72 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 23 through 29 removed outlier: 6.240A pdb=" N ALA H 23 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.635A pdb=" N SER H 74 " --> pdb=" O ALA H 130 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'I' and resid 5 through 11 Processing sheet with id= 15, first strand: chain 'I' and resid 26 through 30 removed outlier: 3.548A pdb=" N LYS I 27 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'J' and resid 39 through 42 removed outlier: 3.552A pdb=" N LEU J 42 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 44 through 52 Processing sheet with id= 18, first strand: chain 'K' and resid 30 through 35 Processing sheet with id= 19, first strand: chain 'L' and resid 29 through 33 removed outlier: 5.129A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'L' and resid 35 through 41 removed outlier: 5.175A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'P' and resid 4 through 11 removed outlier: 3.600A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'Q' and resid 7 through 11 removed outlier: 6.704A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'Q' and resid 19 through 30 No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 'S' and resid 30 through 33 Processing sheet with id= 25, first strand: chain 'c' and resid 2 through 6 removed outlier: 5.612A pdb=" N VAL c 16 " --> pdb=" O CYS c 6 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'c' and resid 80 through 83 removed outlier: 3.640A pdb=" N ARG c 80 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'c' and resid 138 through 142 removed outlier: 4.277A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'c' and resid 91 through 96 removed outlier: 4.154A pdb=" N GLU c 100 " --> pdb=" O TYR c 96 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'd' and resid 11 through 16 removed outlier: 4.166A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL d 26 " --> pdb=" O VAL d 9 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER d 199 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'd' and resid 79 through 84 removed outlier: 5.990A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'd' and resid 179 through 182 Processing sheet with id= 32, first strand: chain 'd' and resid 24 through 28 No H-bonds generated for sheet with id= 32 Processing sheet with id= 33, first strand: chain 'd' and resid 105 through 108 removed outlier: 6.624A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'e' and resid 1 through 6 removed outlier: 3.772A pdb=" N LEU e 3 " --> pdb=" O LEU e 12 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'e' and resid 117 through 120 removed outlier: 5.520A pdb=" N ARG e 117 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'f' and resid 65 through 69 removed outlier: 4.951A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'g' and resid 16 through 19 Processing sheet with id= 38, first strand: chain 'g' and resid 41 through 44 removed outlier: 3.588A pdb=" N LYS g 44 " --> pdb=" O THR g 51 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N THR g 51 " --> pdb=" O LYS g 44 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'g' and resid 94 through 99 removed outlier: 3.844A pdb=" N VAL g 102 " --> pdb=" O LYS g 99 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL g 113 " --> pdb=" O LEU g 105 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'g' and resid 121 through 125 removed outlier: 6.014A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'h' and resid 1 through 5 removed outlier: 4.575A pdb=" N ASP h 17 " --> pdb=" O LEU h 5 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'i' and resid 52 through 57 removed outlier: 4.825A pdb=" N ASP i 19 " --> pdb=" O LEU i 140 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.370A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'j' and resid 56 through 60 removed outlier: 4.577A pdb=" N ASP j 56 " --> pdb=" O ILE j 43 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS j 40 " --> pdb=" O ILE j 22 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASN j 82 " --> pdb=" O MET j 7 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'l' and resid 62 through 66 removed outlier: 6.608A pdb=" N LEU l 102 " --> pdb=" O ARG l 66 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'l' and resid 73 through 76 removed outlier: 6.872A pdb=" N ILE l 73 " --> pdb=" O GLU l 90 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN l 88 " --> pdb=" O GLU l 75 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'm' and resid 33 through 37 removed outlier: 5.036A pdb=" N ARG m 103 " --> pdb=" O ASN m 107 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLY m 101 " --> pdb=" O PRO m 109 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA m 111 " --> pdb=" O LYS m 99 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS m 99 " --> pdb=" O ALA m 111 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE m 113 " --> pdb=" O ILE m 97 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE m 97 " --> pdb=" O ILE m 113 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU m 115 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR m 95 " --> pdb=" O LEU m 115 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'n' and resid 49 through 53 removed outlier: 3.774A pdb=" N VAL n 49 " --> pdb=" O VAL n 39 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE n 35 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'o' and resid 38 through 45 removed outlier: 6.496A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER o 83 " --> pdb=" O LYS o 29 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.755A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'q' and resid 11 through 15 removed outlier: 3.548A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU q 39 " --> pdb=" O GLY q 50 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU q 46 " --> pdb=" O ASN q 43 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'q' and resid 18 through 23 removed outlier: 4.066A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 54, first strand: chain 'q' and resid 65 through 68 Processing sheet with id= 55, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.147A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'r' and resid 2 through 8 Processing sheet with id= 57, first strand: chain 's' and resid 28 through 33 removed outlier: 6.348A 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: 6.139A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 't' and resid 40 through 45 No H-bonds generated for sheet with id= 58 Processing sheet with id= 59, first strand: chain 't' and resid 83 through 87 Processing sheet with id= 60, first strand: chain 'u' and resid 69 through 72 removed outlier: 3.513A pdb=" N GLU u 7 " --> pdb=" O GLU u 41 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA u 39 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'v' and resid 51 through 54 removed outlier: 4.233A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'v' and resid 65 through 71 Processing sheet with id= 63, first strand: chain 'w' and resid 12 through 19 removed outlier: 4.521A pdb=" N ASN w 23 " --> pdb=" O SER w 19 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'w' and resid 34 through 41 removed outlier: 3.725A pdb=" N ARG w 45 " --> pdb=" O VAL w 40 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.414A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain '0' and resid 19 through 24 removed outlier: 6.186A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE 0 48 " --> pdb=" O SER 0 14 " (cutoff:3.500A) removed outlier: 6.504A 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: 5.644A pdb=" N PHE 2 22 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '3' and resid 14 through 19 Processing sheet with id= 69, first strand: chain '4' and resid 20 through 25 removed outlier: 3.749A pdb=" N ASN 4 20 " --> pdb=" O CYS 4 16 " (cutoff:3.500A) 1879 hydrogen bonds defined for protein. 5547 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3989 hydrogen bonds 6248 hydrogen bond angles 0 basepair planarities 1585 basepair parallelities 2411 stacking parallelities Total time for adding SS restraints: 240.73 Time building geometry restraints manager: 59.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 12480 1.30 - 1.43: 69295 1.43 - 1.57: 62845 1.57 - 1.70: 9113 1.70 - 1.84: 264 Bond restraints: 153997 Sorted by residual: bond pdb=" C5 5MU Z 55 " pdb=" C6 5MU Z 55 " ideal model delta sigma weight residual 1.155 1.444 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C5 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.155 1.441 -0.286 2.00e-02 2.50e+03 2.04e+02 bond pdb=" C5 5MU V 53 " pdb=" C6 5MU V 53 " ideal model delta sigma weight residual 1.155 1.440 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C5 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.155 1.439 -0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" C MS6 l 82 " pdb=" S MS6 l 82 " ideal model delta sigma weight residual 1.829 1.570 0.259 2.00e-02 2.50e+03 1.68e+02 ... (remaining 153992 not shown) Histogram of bond angle deviations from ideal: 98.17 - 106.93: 29308 106.93 - 115.69: 102762 115.69 - 124.45: 79140 124.45 - 133.21: 19201 133.21 - 141.97: 51 Bond angle restraints: 230462 Sorted by residual: angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C8 2MA a2503 " ideal model delta sigma weight residual 106.32 141.97 -35.65 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C4 2MA a2503 " ideal model delta sigma weight residual 138.88 110.47 28.41 3.00e+00 1.11e-01 8.97e+01 angle pdb=" C1' 1MA V 9 " pdb=" N9 1MA V 9 " pdb=" C8 1MA V 9 " ideal model delta sigma weight residual 100.68 128.70 -28.02 3.00e+00 1.11e-01 8.73e+01 angle pdb=" C1' 1MA V 57 " pdb=" N9 1MA V 57 " pdb=" C8 1MA V 57 " ideal model delta sigma weight residual 100.68 128.29 -27.61 3.00e+00 1.11e-01 8.47e+01 angle pdb=" C1' 56B V 34 " pdb=" N9 56B V 34 " pdb=" C8 56B V 34 " ideal model delta sigma weight residual 146.55 124.93 21.62 3.00e+00 1.11e-01 5.19e+01 ... (remaining 230457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 87492 35.88 - 71.75: 9844 71.75 - 107.63: 1177 107.63 - 143.50: 15 143.50 - 179.38: 11 Dihedral angle restraints: 98539 sinusoidal: 82618 harmonic: 15921 Sorted by residual: dihedral pdb=" CA ASP g 47 " pdb=" C ASP g 47 " pdb=" N ASN g 48 " pdb=" CA ASN g 48 " ideal model delta harmonic sigma weight residual -180.00 -116.59 -63.41 0 5.00e+00 4.00e-02 1.61e+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 -133.99 -46.01 0 5.00e+00 4.00e-02 8.47e+01 dihedral pdb=" O4' C V 73 " pdb=" C1' C V 73 " pdb=" N1 C V 73 " pdb=" C2 C V 73 " ideal model delta sinusoidal sigma weight residual -160.00 8.32 -168.32 1 1.50e+01 4.44e-03 8.44e+01 ... (remaining 98536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 26105 0.071 - 0.143: 2922 0.143 - 0.214: 242 0.214 - 0.285: 26 0.285 - 0.357: 9 Chirality restraints: 29304 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 2.19 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C1' A a 983 " pdb=" O4' A a 983 " pdb=" C2' A a 983 " pdb=" N9 A a 983 " both_signs ideal model delta sigma weight residual False 2.46 2.11 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C1* PSU A 516 " pdb=" O4* PSU A 516 " pdb=" C2* PSU A 516 " pdb=" C5 PSU A 516 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 29301 not shown) Planarity restraints: 12266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC V 47 " 0.911 2.00e-02 2.50e+03 6.00e-01 8.09e+03 pdb=" C4' 5MC V 47 " -0.199 2.00e-02 2.50e+03 pdb=" O4' 5MC V 47 " -0.795 2.00e-02 2.50e+03 pdb=" C3' 5MC V 47 " 0.241 2.00e-02 2.50e+03 pdb=" O3' 5MC V 47 " -0.869 2.00e-02 2.50e+03 pdb=" C2' 5MC V 47 " 0.607 2.00e-02 2.50e+03 pdb=" O2' 5MC V 47 " 0.582 2.00e-02 2.50e+03 pdb=" C1' 5MC V 47 " -0.462 2.00e-02 2.50e+03 pdb=" N1 5MC V 47 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " -0.066 2.00e-02 2.50e+03 5.94e-01 7.95e+03 pdb=" C4' 5MC A1407 " -0.436 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " -0.608 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " 0.597 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " 0.638 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " 0.175 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " -0.977 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " -0.227 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " 0.904 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC a2498 " 0.061 2.00e-02 2.50e+03 5.94e-01 7.93e+03 pdb=" C4' OMC a2498 " 0.433 2.00e-02 2.50e+03 pdb=" O4' OMC a2498 " 0.609 2.00e-02 2.50e+03 pdb=" C3' OMC a2498 " -0.600 2.00e-02 2.50e+03 pdb=" O3' OMC a2498 " -0.635 2.00e-02 2.50e+03 pdb=" C2' OMC a2498 " -0.175 2.00e-02 2.50e+03 pdb=" O2' OMC a2498 " 0.976 2.00e-02 2.50e+03 pdb=" C1' OMC a2498 " 0.229 2.00e-02 2.50e+03 pdb=" N1 OMC a2498 " -0.900 2.00e-02 2.50e+03 ... (remaining 12263 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 666 2.48 - 3.09: 90931 3.09 - 3.69: 264300 3.69 - 4.30: 413054 4.30 - 4.90: 548055 Nonbonded interactions: 1317006 Sorted by model distance: nonbonded pdb=" OP2 G a1186 " pdb="MG MG a6072 " model vdw 1.875 2.170 nonbonded pdb=" O6 G a 776 " pdb="MG MG a6144 " model vdw 1.888 2.170 nonbonded pdb=" OP1 G a1026 " pdb="MG MG a6119 " model vdw 1.889 2.170 nonbonded pdb=" OP1 G a1332 " pdb="MG MG a6097 " model vdw 1.898 2.170 nonbonded pdb=" OP1 U A1224 " pdb="MG MG A1621 " model vdw 1.899 2.170 ... (remaining 1317001 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: 9.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 35.790 Check model and map are aligned: 2.010 Set scattering table: 1.060 Process input model: 517.850 Find NCS groups from input model: 2.940 Set up NCS constraints: 0.400 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:14.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 584.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 0.289 153997 Z= 0.605 Angle : 0.724 35.655 230462 Z= 0.373 Chirality : 0.046 0.357 29304 Planarity : 0.025 0.600 12266 Dihedral : 22.460 179.380 88269 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 0.04 % Allowed : 0.33 % Favored : 99.63 % 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: 0.13 (0.11), residues: 5480 helix: 1.10 (0.12), residues: 1846 sheet: -0.11 (0.15), residues: 1142 loop : -0.50 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 104 HIS 0.039 0.001 HIS K 118 PHE 0.018 0.002 PHE f 100 TYR 0.022 0.002 TYR i 125 ARG 0.024 0.001 ARG t 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1055 time to evaluate : 5.605 Fit side-chains revert: symmetry clash REVERT: B 9 MET cc_start: 0.2505 (mtp) cc_final: 0.1312 (mmm) REVERT: B 49 MET cc_start: 0.3337 (mmt) cc_final: 0.2787 (mmt) REVERT: B 115 LYS cc_start: 0.3068 (mttm) cc_final: 0.2638 (ttpt) REVERT: B 174 LYS cc_start: 0.3115 (tptp) cc_final: 0.2852 (tttm) REVERT: C 25 ASN cc_start: 0.7261 (m110) cc_final: 0.6343 (m-40) REVERT: C 65 ARG cc_start: 0.6299 (ttp80) cc_final: 0.6090 (ttp80) REVERT: C 72 ARG cc_start: 0.5636 (mtp85) cc_final: 0.4926 (mtp180) REVERT: C 86 LYS cc_start: 0.6237 (ttmm) cc_final: 0.5565 (tptp) REVERT: C 89 LYS cc_start: 0.6264 (mtmt) cc_final: 0.5486 (tptm) REVERT: C 112 ASP cc_start: 0.7048 (t70) cc_final: 0.6803 (t70) REVERT: C 118 ASP cc_start: 0.6345 (m-30) cc_final: 0.6035 (m-30) REVERT: C 127 ARG cc_start: 0.6508 (mtt90) cc_final: 0.5298 (mtp-110) REVERT: C 134 MET cc_start: 0.6911 (mtp) cc_final: 0.6545 (mtm) REVERT: C 135 LYS cc_start: 0.7178 (mttt) cc_final: 0.6386 (tttm) REVERT: C 136 ARG cc_start: 0.6397 (ttm110) cc_final: 0.5935 (tpt90) REVERT: C 177 THR cc_start: 0.7662 (t) cc_final: 0.7442 (t) REVERT: D 73 ARG cc_start: 0.6601 (tpt-90) cc_final: 0.6177 (ttp-170) REVERT: D 104 ARG cc_start: 0.6014 (mmt180) cc_final: 0.5803 (mmt180) REVERT: D 128 ARG cc_start: 0.5129 (mtp-110) cc_final: 0.4722 (tmt-80) REVERT: D 151 LYS cc_start: 0.5012 (pptt) cc_final: 0.4395 (mmpt) REVERT: D 155 VAL cc_start: 0.6509 (t) cc_final: 0.6186 (t) REVERT: D 159 LEU cc_start: 0.4488 (mt) cc_final: 0.4122 (mt) REVERT: D 160 GLU cc_start: 0.4632 (mm-30) cc_final: 0.4368 (tp30) REVERT: D 166 GLU cc_start: 0.4834 (tp30) cc_final: 0.4493 (tm-30) REVERT: D 185 LYS cc_start: 0.4560 (tptt) cc_final: 0.4158 (ttmt) REVERT: E 13 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6485 (mt-10) REVERT: E 14 LYS cc_start: 0.7515 (mtpp) cc_final: 0.7301 (mttp) REVERT: E 68 ARG cc_start: 0.6881 (mtt90) cc_final: 0.6637 (mtm110) REVERT: E 93 ARG cc_start: 0.7568 (mtm110) cc_final: 0.7314 (mtm110) REVERT: F 29 ILE cc_start: 0.5801 (mt) cc_final: 0.5585 (mm) REVERT: F 74 LEU cc_start: 0.6289 (tt) cc_final: 0.5877 (mt) REVERT: G 21 GLU cc_start: 0.5853 (mt-10) cc_final: 0.5610 (mt-10) REVERT: G 22 LEU cc_start: 0.7183 (tp) cc_final: 0.6803 (tp) REVERT: G 40 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6636 (mm-30) REVERT: G 63 GLU cc_start: 0.5200 (tm-30) cc_final: 0.4739 (tp30) REVERT: G 101 MET cc_start: 0.7280 (mtt) cc_final: 0.7039 (mtt) REVERT: G 106 GLU cc_start: 0.6837 (pt0) cc_final: 0.6275 (mt-10) REVERT: H 3 MET cc_start: 0.7621 (tpp) cc_final: 0.6994 (tpp) REVERT: H 9 ASP cc_start: 0.7691 (t0) cc_final: 0.7418 (t0) REVERT: H 22 LYS cc_start: 0.7192 (mmmm) cc_final: 0.6958 (mmtt) REVERT: H 27 MET cc_start: 0.7320 (ptp) cc_final: 0.6778 (ptp) REVERT: H 31 LYS cc_start: 0.6793 (mtmt) cc_final: 0.6106 (mmtp) REVERT: H 85 ILE cc_start: 0.7759 (mm) cc_final: 0.7513 (mp) REVERT: H 88 ARG cc_start: 0.6204 (mtm110) cc_final: 0.5558 (mtp85) REVERT: H 89 LYS cc_start: 0.6560 (ttpt) cc_final: 0.6136 (tptm) REVERT: H 90 ASP cc_start: 0.5710 (p0) cc_final: 0.5351 (t0) REVERT: H 92 LEU cc_start: 0.7559 (mt) cc_final: 0.7286 (mp) REVERT: H 94 LYS cc_start: 0.6897 (mtpp) cc_final: 0.6680 (mttp) REVERT: H 114 ARG cc_start: 0.6365 (ttm110) cc_final: 0.5980 (ttt180) REVERT: H 117 ARG cc_start: 0.6611 (mtm-85) cc_final: 0.6320 (mtm-85) REVERT: I 41 ARG cc_start: 0.5433 (ttt90) cc_final: 0.4967 (tpt90) REVERT: I 49 ARG cc_start: 0.6411 (mtm-85) cc_final: 0.5800 (mtt-85) REVERT: I 57 MET cc_start: 0.5069 (mtp) cc_final: 0.4847 (mtp) REVERT: I 64 TYR cc_start: 0.6934 (t80) cc_final: 0.6583 (t80) REVERT: I 68 LYS cc_start: 0.6918 (mtpp) cc_final: 0.6531 (mttp) REVERT: I 88 MET cc_start: 0.6581 (mtm) cc_final: 0.6380 (mtp) REVERT: J 15 HIS cc_start: 0.6987 (p-80) cc_final: 0.6558 (p-80) REVERT: J 48 ARG cc_start: 0.7941 (mtt180) cc_final: 0.7565 (mmt90) REVERT: J 68 ARG cc_start: 0.7091 (mtt180) cc_final: 0.6842 (mtm-85) REVERT: J 88 MET cc_start: 0.2646 (mmp) cc_final: 0.2161 (mpm) REVERT: K 32 VAL cc_start: 0.7550 (t) cc_final: 0.7298 (t) REVERT: K 83 GLU cc_start: 0.5729 (mt-10) cc_final: 0.5375 (mt-10) REVERT: K 98 ARG cc_start: 0.5360 (ttm-80) cc_final: 0.5056 (ttm110) REVERT: L 10 LYS cc_start: 0.7769 (ttpp) cc_final: 0.7538 (ttpp) REVERT: L 77 HIS cc_start: 0.6244 (m-70) cc_final: 0.6004 (m170) REVERT: L 81 LEU cc_start: 0.7646 (tp) cc_final: 0.7406 (tp) REVERT: L 102 LEU cc_start: 0.6306 (mt) cc_final: 0.6043 (mt) REVERT: L 121 ARG cc_start: 0.6233 (ttt90) cc_final: 0.5809 (ttt-90) REVERT: M 21 SER cc_start: 0.8105 (m) cc_final: 0.7803 (t) REVERT: M 56 LEU cc_start: 0.6396 (mt) cc_final: 0.6159 (tp) REVERT: M 79 ARG cc_start: 0.6694 (ptm-80) cc_final: 0.6409 (ttt-90) REVERT: M 93 ARG cc_start: 0.6196 (mmp80) cc_final: 0.5478 (mmm-85) REVERT: N 6 MET cc_start: 0.7402 (mmm) cc_final: 0.7077 (mmp) REVERT: N 92 GLU cc_start: 0.6459 (mt-10) cc_final: 0.6074 (mm-30) REVERT: N 97 LYS cc_start: 0.7286 (pttt) cc_final: 0.7072 (pttp) REVERT: N 100 SER cc_start: 0.7545 (p) cc_final: 0.7077 (t) REVERT: O 35 GLN cc_start: 0.7493 (tp40) cc_final: 0.7078 (tp-100) REVERT: O 38 HIS cc_start: 0.7222 (t70) cc_final: 0.6581 (t70) REVERT: O 58 ARG cc_start: 0.6974 (ttt180) cc_final: 0.6624 (ttp-170) REVERT: O 59 MET cc_start: 0.7721 (mtt) cc_final: 0.7390 (mtt) REVERT: O 71 LYS cc_start: 0.7374 (tttm) cc_final: 0.6828 (tptp) REVERT: O 82 ILE cc_start: 0.6678 (pt) cc_final: 0.6377 (pp) REVERT: O 84 ARG cc_start: 0.4937 (ttt90) cc_final: 0.4562 (tmt-80) REVERT: P 24 SER cc_start: 0.7063 (t) cc_final: 0.6664 (p) REVERT: Q 11 ARG cc_start: 0.5648 (mtp-110) cc_final: 0.5176 (mtm180) REVERT: R 34 THR cc_start: 0.6613 (m) cc_final: 0.6311 (p) REVERT: R 38 LYS cc_start: 0.7513 (mttm) cc_final: 0.7110 (mttp) REVERT: R 55 LEU cc_start: 0.7713 (tp) cc_final: 0.7471 (tp) REVERT: S 17 LYS cc_start: 0.6381 (mttp) cc_final: 0.6118 (mmmt) REVERT: S 20 GLU cc_start: 0.5095 (mm-30) cc_final: 0.4668 (mt-10) REVERT: T 54 MET cc_start: 0.6554 (ttp) cc_final: 0.6283 (tmm) REVERT: T 60 ARG cc_start: 0.7212 (ttm110) cc_final: 0.6908 (ttm110) REVERT: T 85 LYS cc_start: 0.5918 (ptmm) cc_final: 0.5295 (mttt) REVERT: U 17 ARG cc_start: 0.4609 (ptp-110) cc_final: 0.3936 (mmt-90) REVERT: U 21 ARG cc_start: 0.4425 (mmp80) cc_final: 0.4195 (mmp80) REVERT: U 33 ARG cc_start: 0.4381 (mtt180) cc_final: 0.3882 (mtt90) REVERT: U 34 ARG cc_start: 0.5560 (mpt180) cc_final: 0.4495 (ptp90) REVERT: U 39 GLU cc_start: 0.7014 (tt0) cc_final: 0.6572 (tt0) REVERT: c 97 LYS cc_start: 0.7457 (mmmm) cc_final: 0.7163 (mptt) REVERT: c 100 GLU cc_start: 0.7357 (tt0) cc_final: 0.6839 (tt0) REVERT: c 111 LYS cc_start: 0.7257 (mtmm) cc_final: 0.6840 (pttt) REVERT: c 115 GLN cc_start: 0.6937 (mm-40) cc_final: 0.6546 (tt0) REVERT: c 167 ARG cc_start: 0.7051 (ttp-170) cc_final: 0.6823 (ttm-80) REVERT: c 175 ARG cc_start: 0.7937 (ttm-80) cc_final: 0.7602 (ttm-80) REVERT: c 185 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6477 (mt-10) REVERT: c 255 LYS cc_start: 0.8173 (tttp) cc_final: 0.7780 (ttmp) REVERT: c 269 ARG cc_start: 0.7019 (ttp-110) cc_final: 0.6532 (ttm170) REVERT: d 1 MET cc_start: 0.5136 (tpt) cc_final: 0.4846 (tpt) REVERT: d 28 GLU cc_start: 0.7327 (tt0) cc_final: 0.6893 (tt0) REVERT: d 40 LEU cc_start: 0.7629 (mt) cc_final: 0.7325 (mm) REVERT: d 74 GLU cc_start: 0.6756 (mm-30) cc_final: 0.6302 (tp30) REVERT: d 105 LYS cc_start: 0.7445 (mmtm) cc_final: 0.7206 (mmtm) REVERT: d 128 ARG cc_start: 0.7329 (mmt-90) cc_final: 0.7051 (mpt90) REVERT: d 181 ASP cc_start: 0.6363 (t0) cc_final: 0.6062 (t0) REVERT: d 185 ASN cc_start: 0.6848 (m110) cc_final: 0.6341 (m110) REVERT: e 1 MET cc_start: 0.3691 (pmm) cc_final: 0.3447 (pmm) REVERT: e 22 ASP cc_start: 0.5540 (t0) cc_final: 0.5294 (p0) REVERT: e 88 ARG cc_start: 0.7547 (mmp80) cc_final: 0.7252 (mmp80) REVERT: e 137 LYS cc_start: 0.6219 (ttmm) cc_final: 0.5929 (ttmm) REVERT: e 149 ILE cc_start: 0.7358 (mt) cc_final: 0.7019 (mt) REVERT: e 184 ASP cc_start: 0.6883 (m-30) cc_final: 0.6427 (m-30) REVERT: e 194 LYS cc_start: 0.6216 (ttpp) cc_final: 0.5995 (tmtm) REVERT: f 17 MET cc_start: 0.6736 (mmm) cc_final: 0.5984 (mmt) REVERT: f 32 GLU cc_start: 0.6024 (tt0) cc_final: 0.5734 (tm-30) REVERT: f 46 ASP cc_start: 0.4959 (t0) cc_final: 0.4620 (m-30) REVERT: f 69 LYS cc_start: 0.6550 (mptt) cc_final: 0.5842 (mtmm) REVERT: f 72 LYS cc_start: 0.6660 (mtpp) cc_final: 0.5860 (mmmm) REVERT: f 96 MET cc_start: 0.7594 (ttp) cc_final: 0.7223 (ttp) REVERT: f 101 GLU cc_start: 0.6343 (tt0) cc_final: 0.6124 (tm-30) REVERT: f 130 MET cc_start: 0.7535 (ptm) cc_final: 0.7038 (ppp) REVERT: f 148 ARG cc_start: 0.5024 (mtp-110) cc_final: 0.4797 (mtm110) REVERT: f 150 ARG cc_start: 0.6502 (ptp90) cc_final: 0.6152 (ptp90) REVERT: f 167 ARG cc_start: 0.6079 (ttp-110) cc_final: 0.5021 (ttt180) REVERT: g 3 ARG cc_start: 0.5002 (ttm170) cc_final: 0.4546 (mtt180) REVERT: g 37 LEU cc_start: 0.6756 (mp) cc_final: 0.6541 (mt) REVERT: g 86 LYS cc_start: 0.5326 (mtpt) cc_final: 0.5121 (mtpt) REVERT: g 115 HIS cc_start: 0.7102 (t-90) cc_final: 0.6651 (t-90) REVERT: g 152 ARG cc_start: 0.6872 (tpp-160) cc_final: 0.6389 (tpp80) REVERT: h 1 MET cc_start: 0.4244 (pmm) cc_final: 0.4012 (pmm) REVERT: i 10 THR cc_start: 0.7068 (m) cc_final: 0.6781 (t) REVERT: i 23 LYS cc_start: 0.7747 (mttp) cc_final: 0.7416 (mttm) REVERT: i 49 ASP cc_start: 0.8015 (t0) cc_final: 0.7691 (t0) REVERT: i 61 LYS cc_start: 0.7846 (mttp) cc_final: 0.7560 (mttm) REVERT: i 131 ASN cc_start: 0.6208 (t0) cc_final: 0.5605 (t0) REVERT: i 138 GLN cc_start: 0.7688 (mt0) cc_final: 0.7410 (mt0) REVERT: j 53 LYS cc_start: 0.7122 (mmtm) cc_final: 0.6732 (mppt) REVERT: j 93 GLN cc_start: 0.7039 (mm-40) cc_final: 0.6710 (mm-40) REVERT: j 121 GLU cc_start: 0.6326 (pt0) cc_final: 0.6023 (pt0) REVERT: k 82 LEU cc_start: 0.7130 (mt) cc_final: 0.6885 (mt) REVERT: k 91 ASP cc_start: 0.6321 (t70) cc_final: 0.5917 (m-30) REVERT: k 107 PHE cc_start: 0.7930 (m-80) cc_final: 0.7538 (m-80) REVERT: k 123 ARG cc_start: 0.6586 (ttm-80) cc_final: 0.6264 (ttm-80) REVERT: l 47 GLU cc_start: 0.7978 (tp30) cc_final: 0.7753 (tp30) REVERT: l 53 MET cc_start: 0.8019 (ptp) cc_final: 0.7601 (ptm) REVERT: l 90 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7312 (mm-30) REVERT: l 133 LYS cc_start: 0.7491 (ttpt) cc_final: 0.7044 (ttpt) REVERT: m 20 MET cc_start: 0.8059 (ttp) cc_final: 0.7710 (ttp) REVERT: n 13 ARG cc_start: 0.7068 (ttp80) cc_final: 0.6248 (ttm-80) REVERT: n 18 LEU cc_start: 0.8177 (mp) cc_final: 0.7854 (mm) REVERT: n 19 GLN cc_start: 0.6882 (tt0) cc_final: 0.6548 (tp40) REVERT: n 24 THR cc_start: 0.7508 (m) cc_final: 0.7007 (p) REVERT: n 81 ARG cc_start: 0.7150 (mtt180) cc_final: 0.6893 (mtm180) REVERT: o 6 LYS cc_start: 0.6416 (ttpp) cc_final: 0.6108 (ttpt) REVERT: o 9 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6937 (mt-10) REVERT: o 11 GLU cc_start: 0.6953 (pt0) cc_final: 0.6742 (pt0) REVERT: o 38 LYS cc_start: 0.6698 (ptmm) cc_final: 0.5904 (pttm) REVERT: o 44 GLU cc_start: 0.7729 (tt0) cc_final: 0.7478 (tt0) REVERT: o 111 LYS cc_start: 0.6836 (ttpp) cc_final: 0.6451 (tttt) REVERT: p 19 LYS cc_start: 0.8250 (tttm) cc_final: 0.8040 (tmtm) REVERT: p 59 GLN cc_start: 0.7715 (mt0) cc_final: 0.6765 (mm-40) REVERT: p 84 LYS cc_start: 0.7166 (mmtt) cc_final: 0.6214 (ttpt) REVERT: q 6 GLN cc_start: 0.7106 (tt0) cc_final: 0.6805 (tt0) REVERT: q 18 GLN cc_start: 0.6843 (tt0) cc_final: 0.6295 (mt0) REVERT: q 85 LYS cc_start: 0.8235 (ttpt) cc_final: 0.8015 (ttpt) REVERT: q 97 LYS cc_start: 0.7173 (ttmm) cc_final: 0.6957 (ttpp) REVERT: r 31 GLN cc_start: 0.6592 (tt0) cc_final: 0.6237 (tt0) REVERT: s 1 MET cc_start: 0.4049 (ttp) cc_final: 0.3604 (tmm) REVERT: s 2 ILE cc_start: 0.6970 (mp) cc_final: 0.6651 (mt) REVERT: s 4 GLU cc_start: 0.5919 (tt0) cc_final: 0.5356 (tt0) REVERT: s 42 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7697 (mt-10) REVERT: s 54 GLU cc_start: 0.6057 (mm-30) cc_final: 0.5840 (mm-30) REVERT: s 76 ARG cc_start: 0.7329 (ttt-90) cc_final: 0.6889 (ttt180) REVERT: t 10 GLU cc_start: 0.6792 (tp30) cc_final: 0.6571 (mm-30) REVERT: t 24 LYS cc_start: 0.7607 (ttmm) cc_final: 0.7261 (ttmt) REVERT: t 66 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7886 (mm-40) REVERT: t 94 ARG cc_start: 0.7046 (mtm180) cc_final: 0.6667 (mtm180) REVERT: u 2 PHE cc_start: 0.6671 (m-80) cc_final: 0.6198 (m-10) REVERT: u 7 GLU cc_start: 0.6432 (pt0) cc_final: 0.6116 (pt0) REVERT: u 24 ASN cc_start: 0.7153 (m110) cc_final: 0.6700 (m-40) REVERT: u 25 LYS cc_start: 0.7759 (mtpt) cc_final: 0.7344 (mttm) REVERT: u 48 MET cc_start: 0.7082 (tpt) cc_final: 0.6852 (tpt) REVERT: u 50 MET cc_start: 0.6968 (mtp) cc_final: 0.6242 (ttm) REVERT: u 71 LYS cc_start: 0.6793 (mmtp) cc_final: 0.6238 (mppt) REVERT: u 76 ASP cc_start: 0.6508 (t70) cc_final: 0.6165 (t70) REVERT: u 85 LYS cc_start: 0.7338 (mttm) cc_final: 0.6931 (mttm) REVERT: v 44 LYS cc_start: 0.7818 (ttmt) cc_final: 0.7550 (tttt) REVERT: v 64 ASP cc_start: 0.7293 (m-30) cc_final: 0.7015 (m-30) REVERT: v 68 LYS cc_start: 0.7649 (tttp) cc_final: 0.7355 (tttp) REVERT: w 68 LEU cc_start: 0.6931 (mt) cc_final: 0.6711 (mt) REVERT: x 22 LEU cc_start: 0.7535 (mt) cc_final: 0.7133 (mt) REVERT: x 30 MET cc_start: 0.6138 (mmm) cc_final: 0.5725 (mtm) REVERT: x 31 GLN cc_start: 0.6501 (mt0) cc_final: 0.6238 (mt0) REVERT: x 45 GLN cc_start: 0.6822 (mt0) cc_final: 0.6499 (mt0) REVERT: x 49 ASP cc_start: 0.6673 (m-30) cc_final: 0.6411 (m-30) REVERT: y 11 ARG cc_start: 0.7983 (mtt-85) cc_final: 0.7736 (mtt90) REVERT: y 47 MET cc_start: 0.8691 (mtm) cc_final: 0.8491 (mtm) REVERT: y 49 ASN cc_start: 0.8150 (t0) cc_final: 0.7861 (t0) REVERT: 0 38 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8231 (mtpp) REVERT: 0 45 GLN cc_start: 0.7419 (mm110) cc_final: 0.7015 (mt0) REVERT: 1 29 GLN cc_start: 0.7999 (mt0) cc_final: 0.7773 (mt0) REVERT: 2 16 LYS cc_start: 0.8220 (tttp) cc_final: 0.7766 (tttt) REVERT: 2 19 LYS cc_start: 0.7745 (mtmt) cc_final: 0.7520 (mtmt) REVERT: 4 22 MET cc_start: 0.5768 (mtm) cc_final: 0.3947 (mmm) outliers start: 2 outliers final: 0 residues processed: 1057 average time/residue: 2.4085 time to fit residues: 3495.9574 Evaluate side-chains 872 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 872 time to evaluate : 6.182 ------------------------------------------------------------------------------- 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: 7.9990 chunk 750 optimal weight: 6.9990 chunk 416 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 506 optimal weight: 8.9990 chunk 400 optimal weight: 10.0000 chunk 775 optimal weight: 1.9990 chunk 300 optimal weight: 0.9990 chunk 471 optimal weight: 30.0000 chunk 577 optimal weight: 1.9990 chunk 899 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 GLN E 70 ASN E 97 GLN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN I 75 GLN K 64 GLN L 5 ASN R 52 GLN d 32 ASN e 115 GLN f 37 ASN f 63 GLN g 64 GLN g 139 GLN k 93 ASN n 38 GLN n 104 GLN ** n 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 ASN s 28 ASN s 59 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 153997 Z= 0.216 Angle : 0.724 15.309 230462 Z= 0.394 Chirality : 0.038 0.353 29304 Planarity : 0.007 0.137 12266 Dihedral : 22.982 177.852 77231 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.53 % Rotamer: Outliers : 2.23 % Allowed : 9.60 % Favored : 88.17 % 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: 0.31 (0.11), residues: 5480 helix: 1.19 (0.12), residues: 1892 sheet: 0.04 (0.15), residues: 1128 loop : -0.41 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 104 HIS 0.020 0.001 HIS K 118 PHE 0.021 0.002 PHE S 10 TYR 0.022 0.002 TYR I 90 ARG 0.009 0.001 ARG F 44 *********************** 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 1021 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 919 time to evaluate : 5.514 Fit side-chains revert: symmetry clash REVERT: B 115 LYS cc_start: 0.2753 (mttm) cc_final: 0.2417 (ttpt) REVERT: B 161 LEU cc_start: 0.4722 (mp) cc_final: 0.4393 (mm) REVERT: B 174 LYS cc_start: 0.3301 (tptp) cc_final: 0.3001 (tttm) REVERT: C 45 LYS cc_start: 0.6468 (tmtt) cc_final: 0.6141 (mptt) REVERT: C 72 ARG cc_start: 0.5703 (mtp85) cc_final: 0.5101 (mtp85) REVERT: C 86 LYS cc_start: 0.6329 (ttmm) cc_final: 0.5626 (tptp) REVERT: C 89 LYS cc_start: 0.6158 (mtmt) cc_final: 0.5364 (ttmt) REVERT: C 108 LYS cc_start: 0.6618 (OUTLIER) cc_final: 0.6388 (ptmt) REVERT: C 134 MET cc_start: 0.7356 (mtp) cc_final: 0.6912 (mtm) REVERT: C 135 LYS cc_start: 0.7144 (mttt) cc_final: 0.6408 (tttm) REVERT: C 142 MET cc_start: 0.6794 (mmm) cc_final: 0.6543 (mmp) REVERT: C 161 GLU cc_start: 0.6450 (mt-10) cc_final: 0.6043 (pm20) REVERT: D 73 ARG cc_start: 0.6647 (tpt-90) cc_final: 0.6164 (ttp-170) REVERT: D 104 ARG cc_start: 0.6095 (mmt180) cc_final: 0.5623 (mmt90) REVERT: D 151 LYS cc_start: 0.4983 (pptt) cc_final: 0.4437 (mmpt) REVERT: D 155 VAL cc_start: 0.6421 (t) cc_final: 0.6119 (t) REVERT: D 156 LYS cc_start: 0.5142 (tptp) cc_final: 0.4769 (tmtt) REVERT: D 159 LEU cc_start: 0.4303 (mt) cc_final: 0.3908 (mt) REVERT: D 160 GLU cc_start: 0.4798 (mm-30) cc_final: 0.4200 (tp30) REVERT: D 185 LYS cc_start: 0.4848 (tptt) cc_final: 0.4331 (ttmt) REVERT: D 200 ILE cc_start: 0.5905 (mm) cc_final: 0.5498 (mt) REVERT: E 14 LYS cc_start: 0.7519 (mtpp) cc_final: 0.7297 (mttm) REVERT: E 70 ASN cc_start: 0.6226 (m-40) cc_final: 0.5892 (m-40) REVERT: E 93 ARG cc_start: 0.7577 (mtm110) cc_final: 0.7368 (mtm110) REVERT: E 116 GLU cc_start: 0.6548 (mt-10) cc_final: 0.6302 (mt-10) REVERT: E 146 ASN cc_start: 0.6589 (m-40) cc_final: 0.5449 (p0) REVERT: F 74 LEU cc_start: 0.6491 (tt) cc_final: 0.6047 (mt) REVERT: F 102 MET cc_start: 0.5506 (OUTLIER) cc_final: 0.5182 (ptp) REVERT: G 40 GLU cc_start: 0.6506 (mm-30) cc_final: 0.6126 (mm-30) REVERT: G 63 GLU cc_start: 0.5249 (tm-30) cc_final: 0.4284 (tm-30) REVERT: G 75 VAL cc_start: 0.8008 (m) cc_final: 0.7706 (p) REVERT: G 92 ARG cc_start: 0.4663 (mtm110) cc_final: 0.4371 (ptp-170) REVERT: G 101 MET cc_start: 0.7335 (mtt) cc_final: 0.6971 (mtt) REVERT: G 106 GLU cc_start: 0.6938 (pt0) cc_final: 0.6656 (pt0) REVERT: G 110 LYS cc_start: 0.6295 (mtmm) cc_final: 0.6009 (mttp) REVERT: G 144 MET cc_start: 0.4140 (mmt) cc_final: 0.3704 (mmp) REVERT: H 3 MET cc_start: 0.7616 (tpp) cc_final: 0.7002 (tpp) REVERT: H 5 ASP cc_start: 0.7526 (t0) cc_final: 0.7277 (t0) REVERT: H 9 ASP cc_start: 0.7775 (t0) cc_final: 0.7527 (t0) REVERT: H 27 MET cc_start: 0.7412 (ptp) cc_final: 0.6867 (ptp) REVERT: H 88 ARG cc_start: 0.6192 (mtm110) cc_final: 0.5376 (mtp85) REVERT: H 89 LYS cc_start: 0.6640 (ttpt) cc_final: 0.6045 (tptm) REVERT: H 90 ASP cc_start: 0.5845 (p0) cc_final: 0.5298 (t0) REVERT: H 92 LEU cc_start: 0.7504 (mt) cc_final: 0.7281 (mp) REVERT: H 114 ARG cc_start: 0.6338 (ttm110) cc_final: 0.5973 (ttt180) REVERT: I 41 ARG cc_start: 0.5527 (ttt90) cc_final: 0.5172 (ttt180) REVERT: I 49 ARG cc_start: 0.6424 (mtm-85) cc_final: 0.5887 (mtt-85) REVERT: I 64 TYR cc_start: 0.6901 (t80) cc_final: 0.6407 (t80) REVERT: I 68 LYS cc_start: 0.6859 (mtpp) cc_final: 0.6309 (mttt) REVERT: J 11 LYS cc_start: 0.7964 (mttt) cc_final: 0.7651 (mmtp) REVERT: J 15 HIS cc_start: 0.6881 (p-80) cc_final: 0.6421 (p-80) REVERT: J 42 LEU cc_start: 0.7016 (mt) cc_final: 0.6792 (mm) REVERT: J 48 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7726 (mmt90) REVERT: J 68 ARG cc_start: 0.7191 (mtt180) cc_final: 0.6978 (mtm-85) REVERT: J 88 MET cc_start: 0.2820 (mmp) cc_final: 0.2379 (mpm) REVERT: K 32 VAL cc_start: 0.7559 (t) cc_final: 0.7312 (t) REVERT: K 83 GLU cc_start: 0.5985 (mt-10) cc_final: 0.5599 (mt-10) REVERT: K 98 ARG cc_start: 0.5605 (ttm-80) cc_final: 0.5097 (ttm170) REVERT: L 10 LYS cc_start: 0.7417 (ttpp) cc_final: 0.7149 (ttpp) REVERT: L 62 GLU cc_start: 0.6674 (tt0) cc_final: 0.6193 (tt0) REVERT: L 88 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7081 (tmmt) REVERT: M 21 SER cc_start: 0.7998 (m) cc_final: 0.7710 (t) REVERT: M 56 LEU cc_start: 0.6392 (mt) cc_final: 0.6138 (tp) REVERT: M 79 ARG cc_start: 0.6656 (ptm-80) cc_final: 0.6288 (ttt-90) REVERT: M 83 LEU cc_start: 0.7023 (tt) cc_final: 0.6788 (tt) REVERT: M 93 ARG cc_start: 0.6133 (mmp80) cc_final: 0.5566 (mmm-85) REVERT: N 6 MET cc_start: 0.7556 (mmm) cc_final: 0.7310 (mmp) REVERT: N 16 LEU cc_start: 0.7592 (mt) cc_final: 0.7153 (mp) REVERT: N 96 LEU cc_start: 0.7977 (tp) cc_final: 0.7703 (tp) REVERT: N 100 SER cc_start: 0.7557 (p) cc_final: 0.7077 (t) REVERT: O 47 LYS cc_start: 0.7345 (mmmt) cc_final: 0.7126 (mttp) REVERT: O 58 ARG cc_start: 0.6937 (ttt180) cc_final: 0.6550 (ttp-170) REVERT: O 59 MET cc_start: 0.7853 (mtt) cc_final: 0.7362 (mtt) REVERT: O 71 LYS cc_start: 0.7373 (tttm) cc_final: 0.6894 (tptp) REVERT: O 82 ILE cc_start: 0.6723 (pt) cc_final: 0.6400 (pp) REVERT: P 24 SER cc_start: 0.7050 (t) cc_final: 0.6825 (p) REVERT: Q 11 ARG cc_start: 0.5792 (mtp-110) cc_final: 0.5240 (ttm170) REVERT: R 34 THR cc_start: 0.6692 (m) cc_final: 0.6203 (p) REVERT: R 38 LYS cc_start: 0.7518 (mttm) cc_final: 0.7062 (mtpp) REVERT: R 55 LEU cc_start: 0.7660 (tp) cc_final: 0.7352 (tp) REVERT: S 15 LEU cc_start: 0.6911 (tp) cc_final: 0.6690 (tp) REVERT: T 28 MET cc_start: 0.6610 (ttp) cc_final: 0.6111 (ptm) REVERT: T 60 ARG cc_start: 0.7248 (ttm110) cc_final: 0.6967 (ttm110) REVERT: T 82 GLN cc_start: 0.6678 (mt0) cc_final: 0.6393 (mt0) REVERT: U 17 ARG cc_start: 0.4596 (ptp-110) cc_final: 0.3869 (mmt-90) REVERT: U 21 ARG cc_start: 0.4539 (mmp80) cc_final: 0.4277 (mmp80) REVERT: U 34 ARG cc_start: 0.5359 (mpt180) cc_final: 0.4454 (ptp90) REVERT: U 39 GLU cc_start: 0.7069 (tt0) cc_final: 0.6638 (tt0) REVERT: c 97 LYS cc_start: 0.7434 (mmmm) cc_final: 0.6969 (mtpp) REVERT: c 98 ASP cc_start: 0.7799 (p0) cc_final: 0.7429 (p0) REVERT: c 100 GLU cc_start: 0.7331 (tt0) cc_final: 0.6828 (tt0) REVERT: c 111 LYS cc_start: 0.7057 (mtmm) cc_final: 0.6651 (pttt) REVERT: c 115 GLN cc_start: 0.6956 (mm-40) cc_final: 0.6489 (tt0) REVERT: c 167 ARG cc_start: 0.7049 (ttp-170) cc_final: 0.6805 (tpp80) REVERT: c 183 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7809 (mtmt) REVERT: c 255 LYS cc_start: 0.8063 (tttp) cc_final: 0.7631 (ttmp) REVERT: c 269 ARG cc_start: 0.7181 (ttp-110) cc_final: 0.6602 (ttm170) REVERT: d 39 ASP cc_start: 0.6832 (p0) cc_final: 0.6622 (p0) REVERT: d 40 LEU cc_start: 0.7719 (mt) cc_final: 0.7382 (mm) REVERT: d 74 GLU cc_start: 0.6727 (mm-30) cc_final: 0.6162 (tp30) REVERT: d 105 LYS cc_start: 0.7478 (mmtm) cc_final: 0.7168 (mmtm) REVERT: d 128 ARG cc_start: 0.7259 (mmt-90) cc_final: 0.6841 (mpt90) REVERT: d 181 ASP cc_start: 0.5933 (t0) cc_final: 0.5664 (t0) REVERT: e 1 MET cc_start: 0.3787 (pmm) cc_final: 0.3571 (pmm) REVERT: e 22 ASP cc_start: 0.5474 (t0) cc_final: 0.5128 (p0) REVERT: e 115 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7423 (mt0) REVERT: e 140 ASP cc_start: 0.5380 (m-30) cc_final: 0.5129 (m-30) REVERT: e 154 ASP cc_start: 0.4604 (p0) cc_final: 0.3766 (t70) REVERT: f 32 GLU cc_start: 0.5828 (tt0) cc_final: 0.5526 (tm-30) REVERT: f 46 ASP cc_start: 0.4852 (t0) cc_final: 0.4518 (m-30) REVERT: f 69 LYS cc_start: 0.6765 (mptt) cc_final: 0.6478 (mptt) REVERT: f 72 LYS cc_start: 0.6776 (mtpp) cc_final: 0.5947 (mmmm) REVERT: f 96 MET cc_start: 0.7559 (ttp) cc_final: 0.7203 (ttp) REVERT: f 101 GLU cc_start: 0.6624 (tt0) cc_final: 0.6337 (tm-30) REVERT: f 130 MET cc_start: 0.7712 (ptm) cc_final: 0.7204 (ptm) REVERT: f 148 ARG cc_start: 0.4990 (mtp-110) cc_final: 0.4745 (ttp80) REVERT: f 150 ARG cc_start: 0.6503 (ptp90) cc_final: 0.6179 (ptp90) REVERT: f 167 ARG cc_start: 0.6097 (ttp-110) cc_final: 0.5073 (ttt180) REVERT: g 115 HIS cc_start: 0.7053 (t-90) cc_final: 0.6668 (t-90) REVERT: g 155 GLU cc_start: 0.6654 (pp20) cc_final: 0.6344 (pp20) REVERT: i 61 LYS cc_start: 0.7845 (mttp) cc_final: 0.7623 (mttm) REVERT: i 96 ARG cc_start: 0.6458 (mmm160) cc_final: 0.5877 (ptt-90) REVERT: i 131 ASN cc_start: 0.6388 (t0) cc_final: 0.6179 (m-40) REVERT: j 53 LYS cc_start: 0.7077 (mmtm) cc_final: 0.6542 (mmtt) REVERT: j 71 ARG cc_start: 0.7552 (mmt90) cc_final: 0.7162 (mpt-90) REVERT: j 93 GLN cc_start: 0.7086 (mm-40) cc_final: 0.6777 (mm-40) REVERT: j 121 GLU cc_start: 0.6449 (pt0) cc_final: 0.6192 (pt0) REVERT: k 2 ARG cc_start: 0.5884 (mmm-85) cc_final: 0.5378 (mmt-90) REVERT: k 82 LEU cc_start: 0.7234 (mt) cc_final: 0.7032 (mt) REVERT: k 91 ASP cc_start: 0.6255 (t70) cc_final: 0.5913 (m-30) REVERT: l 47 GLU cc_start: 0.8044 (tp30) cc_final: 0.7836 (tp30) REVERT: l 115 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6527 (tm-30) REVERT: l 133 LYS cc_start: 0.7531 (ttpt) cc_final: 0.7129 (ttpt) REVERT: m 20 MET cc_start: 0.7953 (ttp) cc_final: 0.7623 (ttp) REVERT: m 65 LEU cc_start: 0.8079 (mt) cc_final: 0.7817 (mp) REVERT: n 13 ARG cc_start: 0.7076 (ttp80) cc_final: 0.6340 (ttm-80) REVERT: n 19 GLN cc_start: 0.6822 (tt0) cc_final: 0.6527 (tp40) REVERT: n 24 THR cc_start: 0.7636 (m) cc_final: 0.7178 (p) REVERT: n 68 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7390 (mtmp) REVERT: n 81 ARG cc_start: 0.7194 (mtt180) cc_final: 0.6961 (mtt180) REVERT: o 6 LYS cc_start: 0.6301 (ttpp) cc_final: 0.5936 (mtpt) REVERT: o 9 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7101 (mt-10) REVERT: o 11 GLU cc_start: 0.7076 (pt0) cc_final: 0.6729 (pt0) REVERT: o 38 LYS cc_start: 0.6888 (ptmm) cc_final: 0.6070 (pttm) REVERT: o 44 GLU cc_start: 0.7679 (tt0) cc_final: 0.7433 (tt0) REVERT: o 106 LYS cc_start: 0.7597 (mmtt) cc_final: 0.7363 (mptm) REVERT: o 110 ILE cc_start: 0.7950 (mm) cc_final: 0.7726 (mp) REVERT: o 111 LYS cc_start: 0.6773 (ttpp) cc_final: 0.6379 (tmtt) REVERT: p 59 GLN cc_start: 0.7761 (mt0) cc_final: 0.6926 (mm-40) REVERT: p 84 LYS cc_start: 0.7328 (mmtt) cc_final: 0.6403 (ttpt) REVERT: p 117 LEU cc_start: 0.7272 (mt) cc_final: 0.7041 (mt) REVERT: q 6 GLN cc_start: 0.6983 (tt0) cc_final: 0.6606 (tm-30) REVERT: q 18 GLN cc_start: 0.6907 (tt0) cc_final: 0.6386 (mt0) REVERT: q 60 LYS cc_start: 0.7083 (mptt) cc_final: 0.6688 (mmtt) REVERT: q 85 LYS cc_start: 0.8211 (ttpt) cc_final: 0.8006 (ttpt) REVERT: q 97 LYS cc_start: 0.7355 (ttmm) cc_final: 0.6956 (tttp) REVERT: s 1 MET cc_start: 0.4045 (ttp) cc_final: 0.3485 (tmm) REVERT: s 4 GLU cc_start: 0.5608 (tt0) cc_final: 0.5122 (tt0) REVERT: s 54 GLU cc_start: 0.6233 (mm-30) cc_final: 0.5937 (mm-30) REVERT: s 76 ARG cc_start: 0.7324 (ttt-90) cc_final: 0.6950 (ttt180) REVERT: t 10 GLU cc_start: 0.6774 (tp30) cc_final: 0.6524 (mm-30) REVERT: t 24 LYS cc_start: 0.7584 (ttmm) cc_final: 0.7160 (ttmt) REVERT: t 43 LYS cc_start: 0.7118 (mtmt) cc_final: 0.6793 (mttm) REVERT: t 61 LYS cc_start: 0.6690 (mtpt) cc_final: 0.6312 (mttm) REVERT: t 66 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8079 (mm-40) REVERT: u 25 LYS cc_start: 0.7559 (mtpt) cc_final: 0.7190 (mttm) REVERT: u 42 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7399 (mt) REVERT: u 48 MET cc_start: 0.7058 (tpt) cc_final: 0.6829 (tpt) REVERT: u 50 MET cc_start: 0.6800 (mtp) cc_final: 0.6020 (mtp) REVERT: u 59 GLU cc_start: 0.6317 (pm20) cc_final: 0.5696 (mp0) REVERT: u 71 LYS cc_start: 0.6904 (mmtp) cc_final: 0.6367 (mppt) REVERT: u 76 ASP cc_start: 0.6608 (t70) cc_final: 0.6329 (t70) REVERT: u 85 LYS cc_start: 0.7293 (mttm) cc_final: 0.7033 (mtpp) REVERT: v 29 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7798 (mt-10) REVERT: v 64 ASP cc_start: 0.7434 (m-30) cc_final: 0.7175 (m-30) REVERT: v 66 LYS cc_start: 0.7944 (mttm) cc_final: 0.7562 (mtmt) REVERT: w 39 TRP cc_start: 0.7490 (t-100) cc_final: 0.6974 (t-100) REVERT: w 68 LEU cc_start: 0.6830 (mt) cc_final: 0.6580 (mt) REVERT: x 2 LYS cc_start: 0.5267 (tptp) cc_final: 0.5003 (tptp) REVERT: x 30 MET cc_start: 0.6191 (mmm) cc_final: 0.5451 (mtm) REVERT: x 31 GLN cc_start: 0.6520 (mt0) cc_final: 0.6266 (mt0) REVERT: x 45 GLN cc_start: 0.6772 (mt0) cc_final: 0.6413 (mt0) REVERT: x 49 ASP cc_start: 0.6654 (m-30) cc_final: 0.6387 (m-30) REVERT: x 58 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.7048 (t0) REVERT: y 49 ASN cc_start: 0.8091 (t0) cc_final: 0.7821 (t0) REVERT: 0 27 LYS cc_start: 0.7124 (ptpt) cc_final: 0.6514 (mtpp) REVERT: 0 45 GLN cc_start: 0.7460 (mm110) cc_final: 0.7121 (mm-40) REVERT: 0 50 LYS cc_start: 0.7684 (mmtt) cc_final: 0.7478 (mmtt) REVERT: 1 29 GLN cc_start: 0.7868 (mt0) cc_final: 0.7612 (mt0) REVERT: 2 16 LYS cc_start: 0.8092 (tttp) cc_final: 0.7664 (tttt) REVERT: 2 19 LYS cc_start: 0.7721 (mtmt) cc_final: 0.7399 (mtmt) REVERT: 4 22 MET cc_start: 0.5992 (mtm) cc_final: 0.3957 (mmm) outliers start: 102 outliers final: 48 residues processed: 967 average time/residue: 2.3292 time to fit residues: 3123.3746 Evaluate side-chains 921 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 864 time to evaluate : 6.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 68 ASP Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 13 LYS Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 68 LYS Chi-restraints excluded: chain n residue 116 GLN Chi-restraints excluded: chain p residue 71 GLN Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 27 SER Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain t residue 35 ILE Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 42 LEU Chi-restraints excluded: chain v residue 29 GLU Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain x residue 58 ASN Chi-restraints excluded: chain z residue 46 ASP Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 51 SER Chi-restraints excluded: chain 2 residue 54 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: 6.9990 chunk 748 optimal weight: 9.9990 chunk 612 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 900 optimal weight: 0.7980 chunk 972 optimal weight: 10.0000 chunk 802 optimal weight: 10.0000 chunk 893 optimal weight: 1.9990 chunk 307 optimal weight: 9.9990 chunk 722 optimal weight: 4.9990 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 140 ASN D 116 GLN D 198 HIS E 12 GLN E 97 GLN F 11 HIS ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN G 148 ASN I 75 GLN I 126 GLN K 64 GLN L 112 GLN N 49 GLN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 HIS d 32 ASN d 94 GLN g 64 GLN g 101 ASN k 93 ASN n 38 GLN n 104 GLN s 28 ASN x 20 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 153997 Z= 0.225 Angle : 0.717 15.097 230462 Z= 0.392 Chirality : 0.038 0.372 29304 Planarity : 0.008 0.141 12266 Dihedral : 22.970 178.225 77231 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.56 % Favored : 96.39 % Rotamer: Outliers : 3.15 % Allowed : 12.83 % Favored : 84.02 % 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: 0.26 (0.11), residues: 5480 helix: 1.17 (0.12), residues: 1894 sheet: -0.02 (0.15), residues: 1115 loop : -0.43 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 248 HIS 0.013 0.001 HIS K 118 PHE 0.020 0.002 PHE S 10 TYR 0.020 0.002 TYR C 42 ARG 0.008 0.001 ARG e 114 *********************** 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 1054 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 910 time to evaluate : 6.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 LYS cc_start: 0.4397 (ttmm) cc_final: 0.3842 (tmtt) REVERT: B 153 ASP cc_start: 0.2988 (m-30) cc_final: 0.2378 (t0) REVERT: B 161 LEU cc_start: 0.4711 (mp) cc_final: 0.4386 (mm) REVERT: B 174 LYS cc_start: 0.3407 (tptp) cc_final: 0.3058 (tttm) REVERT: B 197 ASP cc_start: 0.2928 (OUTLIER) cc_final: 0.1474 (m-30) REVERT: C 38 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.5692 (mptp) REVERT: C 45 LYS cc_start: 0.6519 (tmtt) cc_final: 0.6110 (mptt) REVERT: C 72 ARG cc_start: 0.5482 (mtp85) cc_final: 0.4802 (mtp85) REVERT: C 86 LYS cc_start: 0.6440 (ttmm) cc_final: 0.5679 (tptp) REVERT: C 89 LYS cc_start: 0.6111 (mtmt) cc_final: 0.5319 (ttmt) REVERT: C 108 LYS cc_start: 0.6620 (OUTLIER) cc_final: 0.6363 (ptmt) REVERT: C 134 MET cc_start: 0.7515 (mtp) cc_final: 0.7019 (mtm) REVERT: C 135 LYS cc_start: 0.7128 (mttt) cc_final: 0.6487 (tttm) REVERT: C 142 MET cc_start: 0.6840 (mmm) cc_final: 0.6640 (mmp) REVERT: D 60 LYS cc_start: 0.6622 (ttpt) cc_final: 0.6360 (ttmm) REVERT: D 73 ARG cc_start: 0.6682 (tpt-90) cc_final: 0.6186 (ttp-170) REVERT: D 151 LYS cc_start: 0.5038 (pptt) cc_final: 0.4484 (mmpt) REVERT: D 156 LYS cc_start: 0.5476 (tptp) cc_final: 0.5052 (tmtt) REVERT: D 159 LEU cc_start: 0.4228 (mt) cc_final: 0.3819 (mt) REVERT: D 160 GLU cc_start: 0.4926 (mm-30) cc_final: 0.4512 (mm-30) REVERT: D 165 ARG cc_start: 0.3903 (ttp-170) cc_final: 0.3517 (ttp-110) REVERT: D 179 GLU cc_start: 0.5155 (OUTLIER) cc_final: 0.4499 (tt0) REVERT: D 185 LYS cc_start: 0.4911 (tptt) cc_final: 0.4491 (tttt) REVERT: D 200 ILE cc_start: 0.5912 (mm) cc_final: 0.5619 (mt) REVERT: E 68 ARG cc_start: 0.6951 (mtm-85) cc_final: 0.6503 (mtm110) REVERT: E 70 ASN cc_start: 0.6196 (m-40) cc_final: 0.5904 (m-40) REVERT: E 93 ARG cc_start: 0.7443 (mtm110) cc_final: 0.7240 (mtm110) REVERT: E 116 GLU cc_start: 0.6612 (mt-10) cc_final: 0.6354 (mt-10) REVERT: E 146 ASN cc_start: 0.6525 (m-40) cc_final: 0.5457 (p0) REVERT: F 74 LEU cc_start: 0.6561 (tt) cc_final: 0.6191 (tp) REVERT: F 90 MET cc_start: 0.6620 (mtm) cc_final: 0.6334 (mtp) REVERT: F 102 MET cc_start: 0.5615 (OUTLIER) cc_final: 0.5158 (ptp) REVERT: G 40 GLU cc_start: 0.6524 (mm-30) cc_final: 0.6133 (mm-30) REVERT: G 63 GLU cc_start: 0.4894 (tm-30) cc_final: 0.4147 (tm-30) REVERT: G 75 VAL cc_start: 0.7933 (m) cc_final: 0.7630 (p) REVERT: G 92 ARG cc_start: 0.4683 (mtm110) cc_final: 0.4379 (ptp-170) REVERT: G 101 MET cc_start: 0.7216 (mtt) cc_final: 0.6808 (mtt) REVERT: G 106 GLU cc_start: 0.6868 (pt0) cc_final: 0.6532 (pt0) REVERT: G 110 LYS cc_start: 0.6266 (mtmm) cc_final: 0.5887 (mmpt) REVERT: G 144 MET cc_start: 0.4179 (mmt) cc_final: 0.3854 (mmp) REVERT: H 3 MET cc_start: 0.7521 (tpp) cc_final: 0.6865 (tpp) REVERT: H 5 ASP cc_start: 0.7568 (t0) cc_final: 0.7289 (t0) REVERT: H 26 THR cc_start: 0.6692 (OUTLIER) cc_final: 0.6415 (p) REVERT: H 27 MET cc_start: 0.7450 (ptp) cc_final: 0.7058 (ptp) REVERT: H 88 ARG cc_start: 0.6166 (mtm110) cc_final: 0.5420 (mtp85) REVERT: H 89 LYS cc_start: 0.6697 (ttpt) cc_final: 0.6040 (tptm) REVERT: H 90 ASP cc_start: 0.5980 (p0) cc_final: 0.5348 (t0) REVERT: H 114 ARG cc_start: 0.6423 (ttm110) cc_final: 0.6102 (ttt180) REVERT: H 117 ARG cc_start: 0.6599 (mtm-85) cc_final: 0.6384 (mtm-85) REVERT: I 41 ARG cc_start: 0.5622 (ttt90) cc_final: 0.5305 (ttt180) REVERT: I 45 ARG cc_start: 0.5862 (ptp-170) cc_final: 0.5509 (mtm180) REVERT: I 49 ARG cc_start: 0.6529 (mtm-85) cc_final: 0.5950 (mtt-85) REVERT: I 64 TYR cc_start: 0.6951 (t80) cc_final: 0.6329 (t80) REVERT: I 68 LYS cc_start: 0.6965 (mtpp) cc_final: 0.6458 (mttt) REVERT: J 15 HIS cc_start: 0.6910 (p-80) cc_final: 0.6366 (p-80) REVERT: J 48 ARG cc_start: 0.7864 (mtt180) cc_final: 0.7622 (mmt90) REVERT: J 88 MET cc_start: 0.2716 (mmp) cc_final: 0.2506 (mmt) REVERT: K 32 VAL cc_start: 0.7539 (t) cc_final: 0.7287 (t) REVERT: K 83 GLU cc_start: 0.6080 (mt-10) cc_final: 0.5676 (mt-10) REVERT: K 98 ARG cc_start: 0.5619 (ttm-80) cc_final: 0.5030 (ttm170) REVERT: L 10 LYS cc_start: 0.7485 (ttpp) cc_final: 0.7211 (ttpp) REVERT: L 88 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7194 (tmmt) REVERT: L 102 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6189 (mt) REVERT: L 121 ARG cc_start: 0.6416 (ttt90) cc_final: 0.5902 (ttt-90) REVERT: M 93 ARG cc_start: 0.5974 (mmp80) cc_final: 0.5349 (mpt-90) REVERT: M 104 THR cc_start: 0.6707 (OUTLIER) cc_final: 0.6151 (p) REVERT: N 6 MET cc_start: 0.7586 (mmm) cc_final: 0.7280 (mmp) REVERT: N 16 LEU cc_start: 0.7615 (mt) cc_final: 0.7184 (mp) REVERT: N 96 LEU cc_start: 0.8004 (tp) cc_final: 0.7735 (tp) REVERT: N 100 SER cc_start: 0.7467 (p) cc_final: 0.6892 (t) REVERT: O 14 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5783 (tm-30) REVERT: O 58 ARG cc_start: 0.6902 (ttt180) cc_final: 0.6547 (ttp-170) REVERT: O 59 MET cc_start: 0.7940 (mtt) cc_final: 0.7459 (mtt) REVERT: O 71 LYS cc_start: 0.7401 (tttm) cc_final: 0.6891 (tptp) REVERT: O 82 ILE cc_start: 0.6759 (pt) cc_final: 0.6365 (pp) REVERT: O 84 ARG cc_start: 0.5084 (ttp80) cc_final: 0.4719 (ttt90) REVERT: Q 11 ARG cc_start: 0.5803 (mtp-110) cc_final: 0.4954 (mmm-85) REVERT: R 34 THR cc_start: 0.6576 (m) cc_final: 0.6079 (p) REVERT: R 38 LYS cc_start: 0.7385 (mttm) cc_final: 0.6874 (mtpp) REVERT: R 55 LEU cc_start: 0.7596 (tp) cc_final: 0.7315 (tp) REVERT: T 54 MET cc_start: 0.6364 (tmm) cc_final: 0.5725 (tmm) REVERT: T 60 ARG cc_start: 0.7286 (ttm110) cc_final: 0.6980 (ttm110) REVERT: T 82 GLN cc_start: 0.6661 (mt0) cc_final: 0.6387 (mt0) REVERT: U 34 ARG cc_start: 0.5497 (mpt180) cc_final: 0.4416 (ptp90) REVERT: c 97 LYS cc_start: 0.7459 (mmmm) cc_final: 0.7215 (mptt) REVERT: c 98 ASP cc_start: 0.7730 (p0) cc_final: 0.7360 (p0) REVERT: c 100 GLU cc_start: 0.7431 (tt0) cc_final: 0.6863 (tt0) REVERT: c 111 LYS cc_start: 0.7151 (mtmm) cc_final: 0.6733 (mtmt) REVERT: c 115 GLN cc_start: 0.7030 (mm-40) cc_final: 0.6557 (tt0) REVERT: c 183 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7838 (mtmt) REVERT: c 187 ASP cc_start: 0.6917 (m-30) cc_final: 0.6502 (m-30) REVERT: c 255 LYS cc_start: 0.8076 (tttp) cc_final: 0.7629 (tttp) REVERT: c 269 ARG cc_start: 0.7177 (ttp-110) cc_final: 0.6608 (ttm170) REVERT: d 1 MET cc_start: 0.5472 (tpt) cc_final: 0.5122 (tpt) REVERT: d 40 LEU cc_start: 0.7646 (mt) cc_final: 0.7329 (mm) REVERT: d 74 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6093 (tp30) REVERT: d 100 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7632 (tp) REVERT: d 128 ARG cc_start: 0.7290 (mmt-90) cc_final: 0.6887 (mpt90) REVERT: e 1 MET cc_start: 0.3809 (pmm) cc_final: 0.2195 (mpp) REVERT: e 22 ASP cc_start: 0.5577 (t0) cc_final: 0.5257 (p0) REVERT: e 140 ASP cc_start: 0.5341 (m-30) cc_final: 0.5046 (m-30) REVERT: f 69 LYS cc_start: 0.6830 (mptt) cc_final: 0.6560 (mptt) REVERT: f 96 MET cc_start: 0.7572 (ttp) cc_final: 0.7165 (ttp) REVERT: f 101 GLU cc_start: 0.6592 (tt0) cc_final: 0.6249 (tm-30) REVERT: f 130 MET cc_start: 0.7714 (ptm) cc_final: 0.7245 (ptm) REVERT: f 134 GLU cc_start: 0.6372 (mp0) cc_final: 0.6068 (mt-10) REVERT: f 148 ARG cc_start: 0.4941 (mtp-110) cc_final: 0.4697 (mmm160) REVERT: f 167 ARG cc_start: 0.6209 (ttp-110) cc_final: 0.5150 (ttt180) REVERT: g 115 HIS cc_start: 0.6928 (t-90) cc_final: 0.6597 (t-90) REVERT: g 155 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6001 (pp20) REVERT: i 49 ASP cc_start: 0.8214 (t0) cc_final: 0.7985 (t70) REVERT: i 61 LYS cc_start: 0.7860 (mttp) cc_final: 0.7637 (mttm) REVERT: i 96 ARG cc_start: 0.6409 (mmm160) cc_final: 0.5847 (ptt-90) REVERT: i 136 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7538 (mt0) REVERT: j 14 SER cc_start: 0.8472 (p) cc_final: 0.8232 (p) REVERT: j 53 LYS cc_start: 0.7135 (mmtm) cc_final: 0.6578 (mmtt) REVERT: j 93 GLN cc_start: 0.6993 (mm-40) cc_final: 0.6732 (mm-40) REVERT: j 100 PHE cc_start: 0.7943 (m-80) cc_final: 0.7716 (m-80) REVERT: k 2 ARG cc_start: 0.6133 (mmm-85) cc_final: 0.5568 (mmt-90) REVERT: k 82 LEU cc_start: 0.7243 (mt) cc_final: 0.7024 (mt) REVERT: k 91 ASP cc_start: 0.6241 (t70) cc_final: 0.5908 (m-30) REVERT: l 53 MET cc_start: 0.7639 (ptp) cc_final: 0.7367 (ptm) REVERT: l 115 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6559 (tm-30) REVERT: l 133 LYS cc_start: 0.7529 (ttpt) cc_final: 0.7105 (ttpt) REVERT: m 20 MET cc_start: 0.7950 (ttp) cc_final: 0.7749 (ttp) REVERT: m 65 LEU cc_start: 0.8113 (mt) cc_final: 0.7885 (mp) REVERT: m 98 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7785 (mt) REVERT: n 13 ARG cc_start: 0.6969 (ttp80) cc_final: 0.6269 (ttm-80) REVERT: n 19 GLN cc_start: 0.7001 (tt0) cc_final: 0.6557 (tp40) REVERT: n 24 THR cc_start: 0.7658 (m) cc_final: 0.7245 (p) REVERT: n 68 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7442 (mtmp) REVERT: n 98 GLN cc_start: 0.7908 (tp40) cc_final: 0.7187 (mm-40) REVERT: o 6 LYS cc_start: 0.6436 (ttpp) cc_final: 0.6089 (ttpt) REVERT: o 11 GLU cc_start: 0.7133 (pt0) cc_final: 0.6822 (pt0) REVERT: o 38 LYS cc_start: 0.6893 (ptmm) cc_final: 0.6204 (pttm) REVERT: o 44 GLU cc_start: 0.7660 (tt0) cc_final: 0.7409 (tt0) REVERT: o 106 LYS cc_start: 0.7592 (mmtt) cc_final: 0.7326 (mptm) REVERT: o 110 ILE cc_start: 0.8007 (mm) cc_final: 0.7780 (mp) REVERT: o 111 LYS cc_start: 0.6849 (ttpp) cc_final: 0.6461 (tmtt) REVERT: p 84 LYS cc_start: 0.7318 (mmtt) cc_final: 0.6379 (ttpt) REVERT: p 117 LEU cc_start: 0.7308 (mt) cc_final: 0.7100 (mt) REVERT: q 6 GLN cc_start: 0.6876 (tt0) cc_final: 0.6548 (tm-30) REVERT: q 18 GLN cc_start: 0.6841 (tt0) cc_final: 0.6430 (mt0) REVERT: q 32 THR cc_start: 0.6866 (p) cc_final: 0.6575 (m) REVERT: q 60 LYS cc_start: 0.7116 (mptt) cc_final: 0.6764 (mmtt) REVERT: q 97 LYS cc_start: 0.7311 (ttmm) cc_final: 0.7021 (tttp) REVERT: s 1 MET cc_start: 0.3884 (ttp) cc_final: 0.3255 (tmm) REVERT: s 4 GLU cc_start: 0.5587 (tt0) cc_final: 0.4929 (tp30) REVERT: s 54 GLU cc_start: 0.6144 (mm-30) cc_final: 0.5911 (mm-30) REVERT: t 10 GLU cc_start: 0.6745 (tp30) cc_final: 0.6517 (mm-30) REVERT: t 24 LYS cc_start: 0.7669 (ttmm) cc_final: 0.7280 (ttmt) REVERT: t 43 LYS cc_start: 0.6939 (mtmt) cc_final: 0.6674 (mttm) REVERT: t 62 GLU cc_start: 0.6851 (mp0) cc_final: 0.6472 (mt-10) REVERT: u 42 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7407 (mt) REVERT: u 48 MET cc_start: 0.7119 (tpt) cc_final: 0.6814 (tpt) REVERT: u 50 MET cc_start: 0.6584 (mtp) cc_final: 0.5757 (ttm) REVERT: u 59 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5771 (mp0) REVERT: u 71 LYS cc_start: 0.6778 (mmtp) cc_final: 0.6249 (mppt) REVERT: u 76 ASP cc_start: 0.6665 (t70) cc_final: 0.6437 (t70) REVERT: u 85 LYS cc_start: 0.7276 (mttm) cc_final: 0.7049 (mtpp) REVERT: v 66 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7568 (mtmt) REVERT: x 2 LYS cc_start: 0.5269 (tptp) cc_final: 0.5066 (tptp) REVERT: x 31 GLN cc_start: 0.6479 (mt0) cc_final: 0.6232 (mt0) REVERT: x 45 GLN cc_start: 0.6993 (mt0) cc_final: 0.6724 (mt0) REVERT: x 49 ASP cc_start: 0.6655 (m-30) cc_final: 0.6395 (m-30) REVERT: x 58 ASN cc_start: 0.7520 (OUTLIER) cc_final: 0.7056 (t0) REVERT: y 11 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7622 (mtt90) REVERT: y 49 ASN cc_start: 0.8018 (t0) cc_final: 0.7749 (t0) REVERT: y 58 GLU cc_start: 0.5648 (tp30) cc_final: 0.5040 (mp0) REVERT: z 46 ASP cc_start: 0.6648 (OUTLIER) cc_final: 0.6222 (t70) REVERT: 0 27 LYS cc_start: 0.7145 (ptpt) cc_final: 0.6523 (mtpp) REVERT: 0 45 GLN cc_start: 0.7429 (mm110) cc_final: 0.7102 (mm-40) REVERT: 1 29 GLN cc_start: 0.8006 (mt0) cc_final: 0.7768 (mt0) REVERT: 2 16 LYS cc_start: 0.8069 (tttp) cc_final: 0.7658 (tttt) REVERT: 2 19 LYS cc_start: 0.7755 (mtmt) cc_final: 0.7402 (mtmt) outliers start: 144 outliers final: 49 residues processed: 978 average time/residue: 2.3143 time to fit residues: 3150.9737 Evaluate side-chains 954 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 883 time to evaluate : 6.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 85 CYS Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 68 ASP Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain i residue 136 GLN Chi-restraints excluded: chain k residue 13 LYS Chi-restraints excluded: chain k residue 74 THR Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 121 THR Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain m residue 98 LEU Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 68 LYS Chi-restraints excluded: chain n residue 116 GLN Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 27 SER Chi-restraints excluded: chain t residue 35 ILE Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 42 LEU Chi-restraints excluded: chain u residue 59 GLU Chi-restraints excluded: chain v residue 66 LYS Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain x residue 58 ASN Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain z residue 46 ASP Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 54 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 889 optimal weight: 8.9990 chunk 677 optimal weight: 10.0000 chunk 467 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 429 optimal weight: 10.0000 chunk 604 optimal weight: 10.0000 chunk 903 optimal weight: 10.0000 chunk 956 optimal weight: 10.0000 chunk 472 optimal weight: 30.0000 chunk 856 optimal weight: 0.8980 chunk 257 optimal weight: 5.9990 overall best weight: 7.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN C 140 ASN D 116 GLN D 198 HIS E 12 GLN E 43 ASN E 97 GLN F 3 HIS F 55 HIS ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN I 75 GLN K 64 GLN N 49 GLN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN ** Q 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN d 32 ASN d 94 GLN e 156 ASN g 64 GLN g 104 ASN g 115 HIS g 143 GLN n 38 GLN o 3 ASN r 61 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 153997 Z= 0.336 Angle : 0.844 17.242 230462 Z= 0.445 Chirality : 0.043 0.372 29304 Planarity : 0.008 0.151 12266 Dihedral : 23.123 177.914 77231 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.34 % Favored : 95.58 % Rotamer: Outliers : 4.04 % Allowed : 15.15 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.11), residues: 5480 helix: 0.74 (0.11), residues: 1892 sheet: -0.13 (0.15), residues: 1097 loop : -0.62 (0.12), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 248 HIS 0.010 0.002 HIS k 35 PHE 0.027 0.003 PHE S 10 TYR 0.027 0.003 TYR r 38 ARG 0.010 0.001 ARG D 56 *********************** 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 1060 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 875 time to evaluate : 6.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.3486 (OUTLIER) cc_final: 0.3268 (p) REVERT: B 112 LYS cc_start: 0.4505 (ttmm) cc_final: 0.3780 (tmtt) REVERT: B 153 ASP cc_start: 0.2870 (m-30) cc_final: 0.2322 (t0) REVERT: B 161 LEU cc_start: 0.4636 (mp) cc_final: 0.4342 (mm) REVERT: B 174 LYS cc_start: 0.3165 (tptp) cc_final: 0.2809 (tttp) REVERT: B 197 ASP cc_start: 0.2880 (OUTLIER) cc_final: 0.1483 (m-30) REVERT: C 45 LYS cc_start: 0.6549 (tmtt) cc_final: 0.6139 (mptt) REVERT: C 72 ARG cc_start: 0.5417 (mtp85) cc_final: 0.4783 (mtp85) REVERT: C 86 LYS cc_start: 0.6400 (ttmm) cc_final: 0.5677 (tptp) REVERT: C 89 LYS cc_start: 0.6099 (mtmt) cc_final: 0.5893 (mppt) REVERT: C 108 LYS cc_start: 0.6672 (OUTLIER) cc_final: 0.6415 (ptmt) REVERT: C 134 MET cc_start: 0.7610 (mtp) cc_final: 0.7113 (mtm) REVERT: C 135 LYS cc_start: 0.7047 (mttt) cc_final: 0.6447 (tttm) REVERT: C 142 MET cc_start: 0.7164 (mmm) cc_final: 0.6864 (mmm) REVERT: D 73 ARG cc_start: 0.6714 (tpt-90) cc_final: 0.6153 (ttp-170) REVERT: D 159 LEU cc_start: 0.4374 (mt) cc_final: 0.3899 (mt) REVERT: D 200 ILE cc_start: 0.6045 (OUTLIER) cc_final: 0.5739 (mp) REVERT: D 202 GLU cc_start: 0.6085 (mm-30) cc_final: 0.5555 (tt0) REVERT: E 116 GLU cc_start: 0.6592 (mt-10) cc_final: 0.6380 (mt-10) REVERT: F 74 LEU cc_start: 0.6531 (tt) cc_final: 0.6121 (tp) REVERT: F 102 MET cc_start: 0.5654 (OUTLIER) cc_final: 0.5189 (ptp) REVERT: G 40 GLU cc_start: 0.6491 (mm-30) cc_final: 0.6112 (mm-30) REVERT: G 63 GLU cc_start: 0.4882 (tm-30) cc_final: 0.4137 (tm-30) REVERT: G 92 ARG cc_start: 0.4585 (mtm110) cc_final: 0.4365 (ptp-170) REVERT: G 106 GLU cc_start: 0.6918 (pt0) cc_final: 0.6568 (pt0) REVERT: G 110 LYS cc_start: 0.6209 (mtmm) cc_final: 0.5842 (mmtt) REVERT: G 144 MET cc_start: 0.4164 (mmt) cc_final: 0.3933 (mmp) REVERT: H 3 MET cc_start: 0.7321 (tpp) cc_final: 0.6693 (tpp) REVERT: H 5 ASP cc_start: 0.7515 (t0) cc_final: 0.7248 (t0) REVERT: H 26 THR cc_start: 0.6652 (OUTLIER) cc_final: 0.6388 (p) REVERT: H 69 LYS cc_start: 0.6372 (mtpp) cc_final: 0.5950 (mptp) REVERT: H 88 ARG cc_start: 0.6234 (mtm110) cc_final: 0.5610 (mtp85) REVERT: H 89 LYS cc_start: 0.6755 (ttpt) cc_final: 0.6204 (tptm) REVERT: H 90 ASP cc_start: 0.6064 (p0) cc_final: 0.5392 (t0) REVERT: H 114 ARG cc_start: 0.6522 (ttm110) cc_final: 0.6254 (ttt180) REVERT: I 41 ARG cc_start: 0.5583 (ttt90) cc_final: 0.5260 (ttt180) REVERT: I 49 ARG cc_start: 0.6240 (mtm-85) cc_final: 0.5725 (mtt-85) REVERT: I 64 TYR cc_start: 0.6906 (t80) cc_final: 0.6390 (t80) REVERT: I 68 LYS cc_start: 0.6978 (mtpp) cc_final: 0.6509 (mttt) REVERT: J 15 HIS cc_start: 0.6934 (p-80) cc_final: 0.6376 (p-80) REVERT: J 48 ARG cc_start: 0.7859 (mtt180) cc_final: 0.7646 (mmt90) REVERT: J 68 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7128 (mtt-85) REVERT: J 88 MET cc_start: 0.2738 (mmp) cc_final: 0.2387 (mpm) REVERT: K 32 VAL cc_start: 0.7503 (t) cc_final: 0.7260 (t) REVERT: K 80 LYS cc_start: 0.6244 (mptt) cc_final: 0.5903 (mmtm) REVERT: K 83 GLU cc_start: 0.6000 (mt-10) cc_final: 0.5630 (mt-10) REVERT: K 98 ARG cc_start: 0.5538 (ttm-80) cc_final: 0.4956 (ttm170) REVERT: L 76 GLU cc_start: 0.5634 (mm-30) cc_final: 0.5418 (mm-30) REVERT: L 88 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7165 (tmmt) REVERT: L 102 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.6172 (mt) REVERT: L 121 ARG cc_start: 0.6396 (ttt90) cc_final: 0.5831 (ttt-90) REVERT: M 93 ARG cc_start: 0.5934 (mmp80) cc_final: 0.5311 (mpt-90) REVERT: M 104 THR cc_start: 0.6723 (OUTLIER) cc_final: 0.6290 (p) REVERT: N 6 MET cc_start: 0.7599 (mmm) cc_final: 0.7324 (mmp) REVERT: N 46 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.6135 (mt) REVERT: N 92 GLU cc_start: 0.6576 (mt-10) cc_final: 0.6110 (mm-30) REVERT: O 58 ARG cc_start: 0.6867 (ttt180) cc_final: 0.6478 (ttp-170) REVERT: O 59 MET cc_start: 0.7938 (mtt) cc_final: 0.7474 (mtt) REVERT: O 71 LYS cc_start: 0.7464 (tttm) cc_final: 0.6944 (tptp) REVERT: O 82 ILE cc_start: 0.6835 (pt) cc_final: 0.6557 (pp) REVERT: Q 11 ARG cc_start: 0.5882 (mtp-110) cc_final: 0.5333 (ttt90) REVERT: Q 41 THR cc_start: 0.7508 (m) cc_final: 0.7202 (p) REVERT: R 34 THR cc_start: 0.6543 (m) cc_final: 0.5974 (p) REVERT: R 38 LYS cc_start: 0.7391 (mttm) cc_final: 0.6962 (mtpp) REVERT: R 55 LEU cc_start: 0.7668 (tp) cc_final: 0.7441 (tp) REVERT: U 34 ARG cc_start: 0.5585 (mpt180) cc_final: 0.4552 (ptp90) REVERT: U 39 GLU cc_start: 0.7129 (tt0) cc_final: 0.6633 (tt0) REVERT: c 97 LYS cc_start: 0.7460 (mmmm) cc_final: 0.7220 (mptt) REVERT: c 111 LYS cc_start: 0.7141 (mtmm) cc_final: 0.6622 (mttm) REVERT: c 115 GLN cc_start: 0.7001 (mm-40) cc_final: 0.6510 (tt0) REVERT: c 183 LYS cc_start: 0.8123 (mtmm) cc_final: 0.7860 (mtmt) REVERT: c 187 ASP cc_start: 0.6925 (m-30) cc_final: 0.6508 (m-30) REVERT: c 255 LYS cc_start: 0.8086 (tttp) cc_final: 0.7713 (ttmp) REVERT: c 269 ARG cc_start: 0.7177 (ttp-110) cc_final: 0.6633 (ttm170) REVERT: d 18 ASP cc_start: 0.5837 (p0) cc_final: 0.5578 (p0) REVERT: d 40 LEU cc_start: 0.7602 (mt) cc_final: 0.7307 (mm) REVERT: d 74 GLU cc_start: 0.6707 (mm-30) cc_final: 0.6063 (tp30) REVERT: d 128 ARG cc_start: 0.7287 (mmt-90) cc_final: 0.6943 (mpt90) REVERT: e 22 ASP cc_start: 0.5596 (t0) cc_final: 0.5280 (p0) REVERT: e 140 ASP cc_start: 0.5405 (m-30) cc_final: 0.5071 (m-30) REVERT: f 42 GLU cc_start: 0.5824 (pm20) cc_final: 0.5530 (pm20) REVERT: f 56 ASP cc_start: 0.6544 (m-30) cc_final: 0.6247 (m-30) REVERT: f 69 LYS cc_start: 0.6817 (mptt) cc_final: 0.6570 (mptt) REVERT: f 81 GLN cc_start: 0.7769 (tt0) cc_final: 0.7552 (tt0) REVERT: f 96 MET cc_start: 0.7587 (ttp) cc_final: 0.7152 (ttp) REVERT: f 101 GLU cc_start: 0.6775 (tt0) cc_final: 0.6448 (tm-30) REVERT: f 130 MET cc_start: 0.7769 (ptm) cc_final: 0.7298 (ptm) REVERT: f 134 GLU cc_start: 0.6305 (mp0) cc_final: 0.6071 (mt-10) REVERT: f 148 ARG cc_start: 0.4905 (mtp-110) cc_final: 0.4133 (mmm-85) REVERT: f 167 ARG cc_start: 0.6233 (ttp-110) cc_final: 0.5142 (ttt180) REVERT: g 115 HIS cc_start: 0.6870 (t70) cc_final: 0.6606 (t-90) REVERT: g 155 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6039 (pp20) REVERT: i 49 ASP cc_start: 0.8168 (t0) cc_final: 0.7947 (t70) REVERT: i 61 LYS cc_start: 0.7860 (mttp) cc_final: 0.7632 (mttm) REVERT: i 96 ARG cc_start: 0.6420 (mmm160) cc_final: 0.5967 (ptt-90) REVERT: i 136 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7465 (mt0) REVERT: j 14 SER cc_start: 0.8481 (p) cc_final: 0.8223 (p) REVERT: j 53 LYS cc_start: 0.7164 (mmtm) cc_final: 0.6606 (mmtt) REVERT: j 93 GLN cc_start: 0.6864 (mm-40) cc_final: 0.6654 (mm-40) REVERT: j 100 PHE cc_start: 0.7944 (m-80) cc_final: 0.7735 (m-80) REVERT: k 2 ARG cc_start: 0.6254 (mmm-85) cc_final: 0.5532 (mmt-90) REVERT: l 115 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6542 (tm-30) REVERT: l 133 LYS cc_start: 0.7532 (ttpt) cc_final: 0.7286 (ttpp) REVERT: m 65 LEU cc_start: 0.8227 (mt) cc_final: 0.7947 (mp) REVERT: m 98 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7613 (mp) REVERT: n 13 ARG cc_start: 0.6904 (ttp80) cc_final: 0.6375 (ttm-80) REVERT: n 19 GLN cc_start: 0.7081 (tt0) cc_final: 0.6592 (tp40) REVERT: n 24 THR cc_start: 0.7638 (m) cc_final: 0.7236 (p) REVERT: n 68 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7481 (mtmp) REVERT: n 98 GLN cc_start: 0.7909 (tp40) cc_final: 0.7200 (mm-40) REVERT: o 6 LYS cc_start: 0.6332 (ttpp) cc_final: 0.6018 (ttpt) REVERT: o 38 LYS cc_start: 0.6855 (ptmm) cc_final: 0.6177 (pttm) REVERT: o 44 GLU cc_start: 0.7755 (tt0) cc_final: 0.7451 (tt0) REVERT: o 106 LYS cc_start: 0.7644 (mmtt) cc_final: 0.7377 (mmtp) REVERT: o 111 LYS cc_start: 0.6887 (ttpp) cc_final: 0.6524 (tmtt) REVERT: p 84 LYS cc_start: 0.7260 (mmtt) cc_final: 0.6274 (ttpm) REVERT: p 117 LEU cc_start: 0.7313 (mt) cc_final: 0.7103 (mt) REVERT: q 6 GLN cc_start: 0.6783 (tt0) cc_final: 0.6545 (tm-30) REVERT: q 18 GLN cc_start: 0.6896 (tt0) cc_final: 0.6516 (mt0) REVERT: q 32 THR cc_start: 0.6752 (p) cc_final: 0.6455 (m) REVERT: q 97 LYS cc_start: 0.7402 (ttmm) cc_final: 0.7149 (tttp) REVERT: s 1 MET cc_start: 0.3965 (ttp) cc_final: 0.3308 (tmm) REVERT: s 4 GLU cc_start: 0.5638 (tt0) cc_final: 0.4987 (tp30) REVERT: s 54 GLU cc_start: 0.6122 (mm-30) cc_final: 0.5839 (mm-30) REVERT: s 73 ARG cc_start: 0.6161 (ttm170) cc_final: 0.5893 (ttm-80) REVERT: t 10 GLU cc_start: 0.6682 (tp30) cc_final: 0.6407 (mm-30) REVERT: t 24 LYS cc_start: 0.7657 (ttmm) cc_final: 0.7232 (ttmt) REVERT: t 43 LYS cc_start: 0.6941 (mtmt) cc_final: 0.6701 (mttm) REVERT: u 1 MET cc_start: 0.4442 (OUTLIER) cc_final: 0.4202 (ttm) REVERT: u 25 LYS cc_start: 0.7483 (mtpt) cc_final: 0.6999 (mttm) REVERT: u 42 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7447 (mt) REVERT: u 48 MET cc_start: 0.7062 (tpt) cc_final: 0.6824 (tpt) REVERT: u 50 MET cc_start: 0.6428 (mtp) cc_final: 0.5849 (ttm) REVERT: u 59 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.5764 (mp0) REVERT: u 71 LYS cc_start: 0.6868 (mmtp) cc_final: 0.6331 (mppt) REVERT: u 85 LYS cc_start: 0.7300 (mttm) cc_final: 0.6862 (mttm) REVERT: v 44 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7641 (ttmm) REVERT: v 66 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7484 (mtmt) REVERT: x 2 LYS cc_start: 0.5247 (tptp) cc_final: 0.5038 (tptp) REVERT: x 45 GLN cc_start: 0.7089 (mt0) cc_final: 0.6826 (mt0) REVERT: x 49 ASP cc_start: 0.6667 (m-30) cc_final: 0.6393 (m-30) REVERT: x 58 ASN cc_start: 0.7434 (OUTLIER) cc_final: 0.6937 (t0) REVERT: y 11 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7637 (mtt90) REVERT: y 49 ASN cc_start: 0.8089 (t0) cc_final: 0.7877 (t0) REVERT: y 58 GLU cc_start: 0.5702 (tp30) cc_final: 0.4999 (mp0) REVERT: z 46 ASP cc_start: 0.6399 (OUTLIER) cc_final: 0.6164 (m-30) REVERT: 0 27 LYS cc_start: 0.7344 (ptpt) cc_final: 0.6715 (mtpp) REVERT: 0 45 GLN cc_start: 0.7434 (mm110) cc_final: 0.7166 (mm-40) REVERT: 1 29 GLN cc_start: 0.8050 (mt0) cc_final: 0.7807 (mt0) REVERT: 2 16 LYS cc_start: 0.8033 (tttp) cc_final: 0.7605 (tttt) REVERT: 2 19 LYS cc_start: 0.7727 (mtmt) cc_final: 0.7418 (mtmt) REVERT: 3 8 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7664 (ptmt) REVERT: 3 36 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6626 (ttp-170) REVERT: 4 22 MET cc_start: 0.6826 (mtt) cc_final: 0.6015 (mtp) REVERT: 4 33 ASN cc_start: 0.5376 (m-40) cc_final: 0.4919 (p0) REVERT: 4 59 ARG cc_start: 0.4518 (OUTLIER) cc_final: 0.4018 (ppt170) outliers start: 185 outliers final: 94 residues processed: 973 average time/residue: 2.2908 time to fit residues: 3116.5158 Evaluate side-chains 979 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 858 time to evaluate : 5.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 85 CYS Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 10 GLU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 68 ASP Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain f residue 78 LYS Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain i residue 98 GLU Chi-restraints excluded: chain i residue 136 GLN Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain j residue 114 LYS Chi-restraints excluded: chain k residue 13 LYS Chi-restraints excluded: chain k residue 74 THR Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain k residue 121 THR Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain l residue 136 MET Chi-restraints excluded: chain m residue 98 LEU Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 68 LYS Chi-restraints excluded: chain n residue 116 GLN Chi-restraints excluded: chain q residue 19 THR Chi-restraints excluded: chain q residue 40 MET Chi-restraints excluded: chain q residue 49 ILE Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 27 SER Chi-restraints excluded: chain t residue 35 ILE Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain t residue 88 GLU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 42 LEU Chi-restraints excluded: chain u residue 59 GLU Chi-restraints excluded: chain v residue 44 LYS Chi-restraints excluded: chain v residue 66 LYS Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain x residue 58 ASN Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain z residue 46 ASP Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 54 ASP Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 59 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 796 optimal weight: 7.9990 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: 9.9990 chunk 661 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 488 optimal weight: 30.0000 chunk 858 optimal weight: 6.9990 chunk 241 optimal weight: 1.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN C 140 ASN D 116 GLN D 136 GLN E 97 GLN F 55 HIS ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN I 75 GLN K 64 GLN L 73 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN d 42 ASN d 94 GLN e 156 ASN g 64 GLN g 143 GLN n 38 GLN v 3 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 153997 Z= 0.341 Angle : 0.847 17.899 230462 Z= 0.446 Chirality : 0.044 0.364 29304 Planarity : 0.008 0.152 12266 Dihedral : 23.126 177.837 77231 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % Rotamer: Outliers : 4.35 % Allowed : 16.42 % Favored : 79.23 % 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: -0.30 (0.11), residues: 5480 helix: 0.60 (0.11), residues: 1882 sheet: -0.27 (0.15), residues: 1114 loop : -0.69 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP c 248 HIS 0.010 0.002 HIS k 35 PHE 0.028 0.003 PHE B 50 TYR 0.029 0.003 TYR r 38 ARG 0.009 0.001 ARG D 56 *********************** 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 1058 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 859 time to evaluate : 6.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.3500 (OUTLIER) cc_final: 0.3286 (p) REVERT: B 112 LYS cc_start: 0.4501 (ttmm) cc_final: 0.3665 (tmtt) REVERT: B 161 LEU cc_start: 0.4617 (mp) cc_final: 0.4323 (mm) REVERT: B 174 LYS cc_start: 0.3323 (tptp) cc_final: 0.2935 (tttt) REVERT: B 178 ASN cc_start: 0.2028 (OUTLIER) cc_final: 0.1730 (p0) REVERT: C 45 LYS cc_start: 0.6541 (tmtt) cc_final: 0.6108 (mptt) REVERT: C 72 ARG cc_start: 0.5399 (mtp85) cc_final: 0.4841 (mtp85) REVERT: C 86 LYS cc_start: 0.6467 (ttmm) cc_final: 0.5675 (tptp) REVERT: C 89 LYS cc_start: 0.6046 (mtmt) cc_final: 0.5837 (mppt) REVERT: C 108 LYS cc_start: 0.6679 (OUTLIER) cc_final: 0.6422 (ptmt) REVERT: C 134 MET cc_start: 0.7607 (mtp) cc_final: 0.7119 (mtm) REVERT: C 135 LYS cc_start: 0.7058 (mttt) cc_final: 0.6460 (tttm) REVERT: C 142 MET cc_start: 0.7017 (mmm) cc_final: 0.6740 (mmm) REVERT: D 73 ARG cc_start: 0.6731 (tpt-90) cc_final: 0.6152 (ttp-170) REVERT: D 159 LEU cc_start: 0.4325 (mt) cc_final: 0.3842 (mt) REVERT: D 202 GLU cc_start: 0.6119 (mm-30) cc_final: 0.5623 (tt0) REVERT: E 116 GLU cc_start: 0.6541 (mt-10) cc_final: 0.6340 (mt-10) REVERT: F 74 LEU cc_start: 0.6494 (tt) cc_final: 0.6068 (tp) REVERT: F 102 MET cc_start: 0.5588 (OUTLIER) cc_final: 0.5202 (ptp) REVERT: G 40 GLU cc_start: 0.6495 (mm-30) cc_final: 0.6112 (mm-30) REVERT: G 63 GLU cc_start: 0.4756 (tm-30) cc_final: 0.4537 (tm-30) REVERT: G 92 ARG cc_start: 0.4615 (mtm110) cc_final: 0.4354 (ptp-170) REVERT: G 106 GLU cc_start: 0.6941 (pt0) cc_final: 0.6616 (pt0) REVERT: G 144 MET cc_start: 0.4167 (mmt) cc_final: 0.3612 (mmp) REVERT: H 3 MET cc_start: 0.7230 (tpp) cc_final: 0.6577 (tpp) REVERT: H 5 ASP cc_start: 0.7521 (t0) cc_final: 0.7229 (t0) REVERT: H 26 THR cc_start: 0.6670 (OUTLIER) cc_final: 0.6394 (p) REVERT: H 69 LYS cc_start: 0.6483 (mtpp) cc_final: 0.6071 (mptp) REVERT: H 88 ARG cc_start: 0.6270 (mtm110) cc_final: 0.5639 (mtp85) REVERT: H 89 LYS cc_start: 0.6790 (ttpt) cc_final: 0.6259 (tptm) REVERT: H 90 ASP cc_start: 0.6053 (p0) cc_final: 0.5367 (t0) REVERT: H 114 ARG cc_start: 0.6552 (ttm110) cc_final: 0.6302 (ttt180) REVERT: I 41 ARG cc_start: 0.5553 (ttt90) cc_final: 0.5236 (ttt180) REVERT: I 49 ARG cc_start: 0.6254 (mtm-85) cc_final: 0.5653 (mtt-85) REVERT: I 68 LYS cc_start: 0.6993 (mtpp) cc_final: 0.6506 (mttt) REVERT: J 15 HIS cc_start: 0.6974 (p-80) cc_final: 0.6456 (p-80) REVERT: J 68 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7157 (mtt-85) REVERT: K 80 LYS cc_start: 0.6275 (mptt) cc_final: 0.5921 (mmtm) REVERT: K 83 GLU cc_start: 0.6063 (mt-10) cc_final: 0.5696 (mt-10) REVERT: K 98 ARG cc_start: 0.5549 (ttm-80) cc_final: 0.4976 (ttm170) REVERT: L 76 GLU cc_start: 0.5640 (mm-30) cc_final: 0.5437 (mm-30) REVERT: L 88 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7145 (tmmt) REVERT: L 102 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.6231 (mt) REVERT: L 121 ARG cc_start: 0.6382 (ttt90) cc_final: 0.5819 (ttt-90) REVERT: M 93 ARG cc_start: 0.5928 (mmp80) cc_final: 0.5541 (mmm-85) REVERT: M 104 THR cc_start: 0.6766 (OUTLIER) cc_final: 0.6320 (p) REVERT: O 58 ARG cc_start: 0.6823 (ttt180) cc_final: 0.6473 (ttp-170) REVERT: O 59 MET cc_start: 0.7910 (mtt) cc_final: 0.7446 (mtt) REVERT: O 71 LYS cc_start: 0.7451 (tttm) cc_final: 0.6997 (tptp) REVERT: O 82 ILE cc_start: 0.6821 (pt) cc_final: 0.6535 (pp) REVERT: Q 11 ARG cc_start: 0.5931 (mtp-110) cc_final: 0.4996 (mmm-85) REVERT: Q 41 THR cc_start: 0.7555 (m) cc_final: 0.7291 (p) REVERT: R 38 LYS cc_start: 0.7280 (mttm) cc_final: 0.6993 (mtpp) REVERT: R 55 LEU cc_start: 0.7651 (tp) cc_final: 0.7438 (tp) REVERT: R 61 ARG cc_start: 0.7354 (mtt90) cc_final: 0.7099 (mtt90) REVERT: S 18 LYS cc_start: 0.6446 (mttm) cc_final: 0.6101 (mttm) REVERT: U 34 ARG cc_start: 0.5549 (mpt180) cc_final: 0.4326 (ptp90) REVERT: U 45 ARG cc_start: 0.5703 (OUTLIER) cc_final: 0.5044 (mtm-85) REVERT: c 97 LYS cc_start: 0.7446 (mmmm) cc_final: 0.7195 (mptt) REVERT: c 111 LYS cc_start: 0.7119 (mtmm) cc_final: 0.6627 (mttt) REVERT: c 115 GLN cc_start: 0.7057 (mm-40) cc_final: 0.6582 (tt0) REVERT: c 183 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7873 (mtmt) REVERT: c 187 ASP cc_start: 0.6965 (m-30) cc_final: 0.6538 (m-30) REVERT: c 255 LYS cc_start: 0.8136 (tttp) cc_final: 0.7776 (ttmp) REVERT: c 269 ARG cc_start: 0.7190 (ttp-110) cc_final: 0.6641 (ttm170) REVERT: d 18 ASP cc_start: 0.5799 (OUTLIER) cc_final: 0.5564 (p0) REVERT: d 40 LEU cc_start: 0.7480 (mt) cc_final: 0.7141 (mm) REVERT: d 74 GLU cc_start: 0.6718 (mm-30) cc_final: 0.6024 (tp30) REVERT: d 128 ARG cc_start: 0.7290 (mmt180) cc_final: 0.6938 (mpt90) REVERT: d 181 ASP cc_start: 0.6356 (t0) cc_final: 0.6120 (t0) REVERT: e 22 ASP cc_start: 0.5606 (t0) cc_final: 0.5284 (p0) REVERT: e 140 ASP cc_start: 0.5366 (m-30) cc_final: 0.5016 (m-30) REVERT: f 42 GLU cc_start: 0.5811 (pm20) cc_final: 0.5480 (pm20) REVERT: f 56 ASP cc_start: 0.6540 (m-30) cc_final: 0.6242 (m-30) REVERT: f 81 GLN cc_start: 0.7758 (tt0) cc_final: 0.7533 (tt0) REVERT: f 96 MET cc_start: 0.7644 (ttp) cc_final: 0.7220 (ttp) REVERT: f 101 GLU cc_start: 0.6744 (tt0) cc_final: 0.6415 (tm-30) REVERT: g 10 VAL cc_start: 0.5214 (OUTLIER) cc_final: 0.4987 (m) REVERT: g 115 HIS cc_start: 0.6900 (t70) cc_final: 0.6613 (t-90) REVERT: g 155 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6057 (pp20) REVERT: i 96 ARG cc_start: 0.6403 (mmm160) cc_final: 0.5950 (ptt-90) REVERT: i 136 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7510 (mt0) REVERT: j 14 SER cc_start: 0.8447 (p) cc_final: 0.8197 (p) REVERT: j 53 LYS cc_start: 0.7140 (mmtm) cc_final: 0.6629 (mmtt) REVERT: j 93 GLN cc_start: 0.6890 (mm-40) cc_final: 0.6690 (mm-40) REVERT: k 2 ARG cc_start: 0.6395 (mmm-85) cc_final: 0.5430 (mmt-90) REVERT: l 53 MET cc_start: 0.7749 (ptp) cc_final: 0.7527 (ptm) REVERT: l 106 ASP cc_start: 0.7791 (t0) cc_final: 0.7262 (t70) REVERT: l 115 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6551 (tm-30) REVERT: l 133 LYS cc_start: 0.7566 (ttpt) cc_final: 0.7154 (ttpt) REVERT: m 1 MET cc_start: 0.8545 (mtm) cc_final: 0.8343 (mtt) REVERT: m 65 LEU cc_start: 0.8240 (mt) cc_final: 0.7959 (mp) REVERT: m 98 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7627 (mp) REVERT: n 13 ARG cc_start: 0.6910 (ttp80) cc_final: 0.6405 (ttm-80) REVERT: n 19 GLN cc_start: 0.7084 (tt0) cc_final: 0.6568 (tp40) REVERT: n 24 THR cc_start: 0.7627 (m) cc_final: 0.7220 (p) REVERT: n 68 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7507 (mtmp) REVERT: n 98 GLN cc_start: 0.7937 (tp40) cc_final: 0.7230 (mm-40) REVERT: o 6 LYS cc_start: 0.6306 (ttpp) cc_final: 0.5886 (mtpt) REVERT: o 38 LYS cc_start: 0.6878 (ptmm) cc_final: 0.6201 (pttm) REVERT: o 44 GLU cc_start: 0.7782 (tt0) cc_final: 0.7479 (tt0) REVERT: o 106 LYS cc_start: 0.7600 (mmtt) cc_final: 0.7284 (mmtp) REVERT: o 111 LYS cc_start: 0.6855 (ttpp) cc_final: 0.6493 (tmtt) REVERT: p 84 LYS cc_start: 0.7253 (mmtt) cc_final: 0.6285 (ttpt) REVERT: q 6 GLN cc_start: 0.6794 (tt0) cc_final: 0.6587 (tm-30) REVERT: q 18 GLN cc_start: 0.6902 (tt0) cc_final: 0.6521 (mt0) REVERT: q 97 LYS cc_start: 0.7392 (ttmm) cc_final: 0.7138 (tttp) REVERT: q 101 ILE cc_start: 0.7528 (OUTLIER) cc_final: 0.7264 (mp) REVERT: s 1 MET cc_start: 0.4012 (ttp) cc_final: 0.3358 (tmm) REVERT: s 4 GLU cc_start: 0.5611 (tt0) cc_final: 0.5008 (tp30) REVERT: s 18 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6798 (tm-30) REVERT: s 73 ARG cc_start: 0.6181 (ttm170) cc_final: 0.5891 (ttm-80) REVERT: t 10 GLU cc_start: 0.6570 (tp30) cc_final: 0.6359 (mm-30) REVERT: t 24 LYS cc_start: 0.7661 (ttmm) cc_final: 0.7253 (ttmt) REVERT: t 43 LYS cc_start: 0.6907 (mtmt) cc_final: 0.6674 (mttm) REVERT: u 1 MET cc_start: 0.4435 (OUTLIER) cc_final: 0.4177 (ttm) REVERT: u 42 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7474 (mt) REVERT: u 48 MET cc_start: 0.7063 (tpt) cc_final: 0.6809 (tpt) REVERT: u 50 MET cc_start: 0.6336 (mtp) cc_final: 0.5830 (ttm) REVERT: u 59 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.5772 (mp0) REVERT: u 71 LYS cc_start: 0.6863 (mmtp) cc_final: 0.6304 (mppt) REVERT: v 3 HIS cc_start: 0.5698 (OUTLIER) cc_final: 0.4154 (t-170) REVERT: v 44 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7652 (ttmm) REVERT: v 66 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7689 (mtmt) REVERT: x 30 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.5915 (mmm) REVERT: x 45 GLN cc_start: 0.7090 (mt0) cc_final: 0.6843 (mt0) REVERT: x 49 ASP cc_start: 0.6610 (m-30) cc_final: 0.6355 (m-30) REVERT: x 58 ASN cc_start: 0.7444 (OUTLIER) cc_final: 0.6929 (t0) REVERT: y 11 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7637 (mtt90) REVERT: y 49 ASN cc_start: 0.8092 (t0) cc_final: 0.7863 (t0) REVERT: y 58 GLU cc_start: 0.5629 (tp30) cc_final: 0.5002 (mp0) REVERT: 0 27 LYS cc_start: 0.7349 (ptpt) cc_final: 0.6663 (mtpp) REVERT: 1 29 GLN cc_start: 0.8040 (mt0) cc_final: 0.7795 (mt0) REVERT: 2 16 LYS cc_start: 0.8051 (tttp) cc_final: 0.7603 (tttt) REVERT: 2 19 LYS cc_start: 0.7724 (mtmt) cc_final: 0.7416 (mtmt) REVERT: 3 8 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7620 (ptmt) REVERT: 3 36 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6639 (ttp-170) REVERT: 4 22 MET cc_start: 0.6803 (mtt) cc_final: 0.6002 (mtp) REVERT: 4 24 ILE cc_start: 0.6805 (pt) cc_final: 0.6582 (pt) REVERT: 4 33 ASN cc_start: 0.5382 (m-40) cc_final: 0.4955 (p0) REVERT: 4 59 ARG cc_start: 0.4437 (OUTLIER) cc_final: 0.4016 (ppt170) outliers start: 199 outliers final: 117 residues processed: 972 average time/residue: 2.3245 time to fit residues: 3159.8363 Evaluate side-chains 991 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 843 time to evaluate : 5.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 85 CYS Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 10 GLU Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 97 LYS Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 68 ASP Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain U residue 45 ARG Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 197 THR Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain f residue 78 LYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 153 ASP 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 92 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 98 GLU Chi-restraints excluded: chain i residue 136 GLN Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 13 LYS Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 74 THR Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain l residue 136 MET Chi-restraints excluded: chain m residue 98 LEU Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 68 LYS Chi-restraints excluded: chain n residue 116 GLN Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 19 THR Chi-restraints excluded: chain q residue 49 ILE Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain q residue 101 ILE Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain s residue 27 SER Chi-restraints excluded: chain t residue 35 ILE Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain t residue 88 GLU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 42 LEU Chi-restraints excluded: chain u residue 59 GLU Chi-restraints excluded: chain v residue 3 HIS Chi-restraints excluded: chain v residue 44 LYS Chi-restraints excluded: chain v residue 66 LYS Chi-restraints excluded: chain w residue 2 SER Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain x residue 30 MET Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain x residue 53 VAL Chi-restraints excluded: chain x residue 58 ASN Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 54 ASP Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 59 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 321 optimal weight: 9.9990 chunk 861 optimal weight: 6.9990 chunk 189 optimal weight: 8.9990 chunk 561 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 chunk 957 optimal weight: 10.0000 chunk 795 optimal weight: 4.9990 chunk 443 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 316 optimal weight: 0.8980 chunk 502 optimal weight: 10.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN C 140 ASN D 116 GLN D 136 GLN D 198 HIS E 12 GLN E 78 ASN E 97 GLN F 55 HIS ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN H 76 GLN K 64 GLN L 73 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS d 32 ASN d 42 ASN d 94 GLN e 156 ASN g 64 GLN n 38 GLN v 3 HIS 3 33 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 153997 Z= 0.270 Angle : 0.775 15.409 230462 Z= 0.416 Chirality : 0.040 0.359 29304 Planarity : 0.008 0.146 12266 Dihedral : 23.067 178.162 77231 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.16 % Favored : 95.77 % Rotamer: Outliers : 4.33 % Allowed : 17.33 % Favored : 78.34 % 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: -0.20 (0.11), residues: 5480 helix: 0.74 (0.11), residues: 1889 sheet: -0.23 (0.15), residues: 1098 loop : -0.67 (0.12), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 104 HIS 0.027 0.001 HIS v 3 PHE 0.023 0.002 PHE B 162 TYR 0.027 0.002 TYR r 38 ARG 0.010 0.001 ARG T 60 *********************** 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 1051 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 853 time to evaluate : 6.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.3506 (OUTLIER) cc_final: 0.3305 (p) REVERT: B 112 LYS cc_start: 0.4510 (ttmm) cc_final: 0.3693 (tmtt) REVERT: B 115 LYS cc_start: 0.2721 (mttm) cc_final: 0.2248 (ttpt) REVERT: B 161 LEU cc_start: 0.4597 (mp) cc_final: 0.4299 (mm) REVERT: B 174 LYS cc_start: 0.3199 (tptp) cc_final: 0.2705 (mmmm) REVERT: C 45 LYS cc_start: 0.6566 (tmtt) cc_final: 0.6156 (mptt) REVERT: C 72 ARG cc_start: 0.5393 (mtp85) cc_final: 0.4458 (mmt180) REVERT: C 86 LYS cc_start: 0.6433 (ttmm) cc_final: 0.5600 (tptp) REVERT: C 89 LYS cc_start: 0.6044 (mtmt) cc_final: 0.5167 (ttmt) REVERT: C 108 LYS cc_start: 0.6653 (OUTLIER) cc_final: 0.6410 (ptmt) REVERT: C 134 MET cc_start: 0.7553 (mtp) cc_final: 0.6950 (mtm) REVERT: C 135 LYS cc_start: 0.7054 (mttt) cc_final: 0.6452 (tttm) REVERT: D 73 ARG cc_start: 0.6687 (tpt-90) cc_final: 0.6050 (ttp-170) REVERT: D 159 LEU cc_start: 0.4279 (mt) cc_final: 0.3798 (mt) REVERT: D 179 GLU cc_start: 0.5016 (OUTLIER) cc_final: 0.4591 (tt0) REVERT: D 202 GLU cc_start: 0.6145 (mm-30) cc_final: 0.5680 (tt0) REVERT: E 116 GLU cc_start: 0.6532 (mt-10) cc_final: 0.6317 (mt-10) REVERT: F 29 ILE cc_start: 0.5856 (OUTLIER) cc_final: 0.5630 (mm) REVERT: F 74 LEU cc_start: 0.6655 (tt) cc_final: 0.6221 (tp) REVERT: F 102 MET cc_start: 0.5592 (OUTLIER) cc_final: 0.5210 (ptp) REVERT: G 40 GLU cc_start: 0.6446 (mm-30) cc_final: 0.6065 (mm-30) REVERT: G 92 ARG cc_start: 0.4601 (mtm110) cc_final: 0.4184 (ptp-170) REVERT: G 106 GLU cc_start: 0.6934 (pt0) cc_final: 0.6612 (pt0) REVERT: H 3 MET cc_start: 0.7208 (tpp) cc_final: 0.6564 (tpp) REVERT: H 5 ASP cc_start: 0.7493 (t0) cc_final: 0.7225 (t0) REVERT: H 26 THR cc_start: 0.6619 (OUTLIER) cc_final: 0.6348 (p) REVERT: H 69 LYS cc_start: 0.6488 (mtpp) cc_final: 0.6079 (mptp) REVERT: H 88 ARG cc_start: 0.6258 (mtm110) cc_final: 0.5632 (mtp85) REVERT: H 89 LYS cc_start: 0.6728 (ttpt) cc_final: 0.6204 (tptm) REVERT: H 90 ASP cc_start: 0.6002 (p0) cc_final: 0.5293 (t0) REVERT: H 114 ARG cc_start: 0.6550 (ttm110) cc_final: 0.6302 (ttt180) REVERT: I 41 ARG cc_start: 0.5532 (ttt90) cc_final: 0.5234 (ttt180) REVERT: I 49 ARG cc_start: 0.6331 (mtm-85) cc_final: 0.5795 (mtt-85) REVERT: I 68 LYS cc_start: 0.6939 (mtpp) cc_final: 0.6403 (mtpt) REVERT: I 88 MET cc_start: 0.6324 (mtp) cc_final: 0.6051 (mtp) REVERT: I 119 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.6339 (ptm160) REVERT: J 11 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7805 (mttp) REVERT: J 15 HIS cc_start: 0.6971 (p-80) cc_final: 0.6458 (p-80) REVERT: J 68 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.7091 (mtt-85) REVERT: K 32 VAL cc_start: 0.7513 (t) cc_final: 0.7261 (t) REVERT: K 80 LYS cc_start: 0.6265 (mptt) cc_final: 0.5908 (mmtm) REVERT: K 83 GLU cc_start: 0.6018 (mt-10) cc_final: 0.5700 (mt-10) REVERT: K 98 ARG cc_start: 0.5594 (ttm-80) cc_final: 0.5004 (ttm170) REVERT: L 88 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7152 (tmmt) REVERT: L 102 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6230 (mt) REVERT: L 121 ARG cc_start: 0.6382 (ttt90) cc_final: 0.5906 (ttt-90) REVERT: M 93 ARG cc_start: 0.5916 (mmp80) cc_final: 0.5531 (mmm-85) REVERT: M 104 THR cc_start: 0.6741 (OUTLIER) cc_final: 0.6294 (p) REVERT: N 6 MET cc_start: 0.7570 (mmm) cc_final: 0.7309 (mmp) REVERT: N 92 GLU cc_start: 0.6581 (mt-10) cc_final: 0.6106 (mm-30) REVERT: O 14 GLU cc_start: 0.6042 (OUTLIER) cc_final: 0.5791 (tm-30) REVERT: O 58 ARG cc_start: 0.6828 (ttt180) cc_final: 0.6483 (ttp-170) REVERT: O 59 MET cc_start: 0.7882 (mtt) cc_final: 0.7423 (mtt) REVERT: O 71 LYS cc_start: 0.7460 (tttm) cc_final: 0.6997 (tptp) REVERT: O 82 ILE cc_start: 0.6803 (pt) cc_final: 0.6467 (pp) REVERT: Q 11 ARG cc_start: 0.5714 (mtp-110) cc_final: 0.4936 (mmm-85) REVERT: Q 41 THR cc_start: 0.7566 (m) cc_final: 0.7262 (p) REVERT: Q 61 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7221 (pt) REVERT: R 38 LYS cc_start: 0.7353 (mttm) cc_final: 0.7022 (mtpp) REVERT: U 34 ARG cc_start: 0.5517 (mpt180) cc_final: 0.4266 (ptp90) REVERT: U 39 GLU cc_start: 0.7139 (tt0) cc_final: 0.6632 (tt0) REVERT: U 60 LEU cc_start: 0.4047 (OUTLIER) cc_final: 0.3404 (mp) REVERT: c 97 LYS cc_start: 0.7440 (mmmm) cc_final: 0.7195 (mptt) REVERT: c 111 LYS cc_start: 0.7181 (mtmm) cc_final: 0.6642 (mttt) REVERT: c 115 GLN cc_start: 0.7065 (mm-40) cc_final: 0.6560 (tt0) REVERT: c 183 LYS cc_start: 0.8156 (mtmm) cc_final: 0.7889 (mtmt) REVERT: c 187 ASP cc_start: 0.6994 (m-30) cc_final: 0.6572 (m-30) REVERT: c 269 ARG cc_start: 0.7180 (ttp-110) cc_final: 0.6601 (ttm170) REVERT: d 1 MET cc_start: 0.5453 (tpt) cc_final: 0.5237 (tpt) REVERT: d 18 ASP cc_start: 0.5802 (OUTLIER) cc_final: 0.5568 (p0) REVERT: d 40 LEU cc_start: 0.7525 (mt) cc_final: 0.7180 (mm) REVERT: d 74 GLU cc_start: 0.6731 (mm-30) cc_final: 0.6034 (tp30) REVERT: d 128 ARG cc_start: 0.7302 (mmt180) cc_final: 0.6944 (mpt90) REVERT: d 181 ASP cc_start: 0.6224 (t0) cc_final: 0.6008 (t0) REVERT: e 16 GLU cc_start: 0.5192 (OUTLIER) cc_final: 0.4858 (tm-30) REVERT: e 22 ASP cc_start: 0.5631 (t0) cc_final: 0.5254 (p0) REVERT: e 140 ASP cc_start: 0.5417 (m-30) cc_final: 0.5085 (m-30) REVERT: f 42 GLU cc_start: 0.5793 (pm20) cc_final: 0.5491 (pm20) REVERT: f 81 GLN cc_start: 0.7732 (tt0) cc_final: 0.7511 (tt0) REVERT: f 96 MET cc_start: 0.7632 (ttp) cc_final: 0.7201 (ttp) REVERT: f 101 GLU cc_start: 0.6717 (tt0) cc_final: 0.6370 (tm-30) REVERT: g 10 VAL cc_start: 0.5213 (OUTLIER) cc_final: 0.4718 (t) REVERT: g 115 HIS cc_start: 0.6893 (t70) cc_final: 0.6627 (t-90) REVERT: g 155 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6018 (pp20) REVERT: h 12 LEU cc_start: 0.4601 (OUTLIER) cc_final: 0.3550 (mm) REVERT: i 49 ASP cc_start: 0.8133 (t0) cc_final: 0.7907 (t70) REVERT: i 96 ARG cc_start: 0.6385 (mmm160) cc_final: 0.5921 (ptt-90) REVERT: i 136 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7541 (mt0) REVERT: j 14 SER cc_start: 0.8444 (p) cc_final: 0.8192 (p) REVERT: j 53 LYS cc_start: 0.7170 (mmtm) cc_final: 0.6666 (mmtt) REVERT: k 2 ARG cc_start: 0.6277 (mmm-85) cc_final: 0.5353 (mmt-90) REVERT: l 53 MET cc_start: 0.7714 (ptp) cc_final: 0.7479 (ptm) REVERT: l 106 ASP cc_start: 0.7812 (t0) cc_final: 0.7276 (t70) REVERT: l 115 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6503 (tm-30) REVERT: l 133 LYS cc_start: 0.7554 (ttpt) cc_final: 0.7130 (ttpt) REVERT: m 65 LEU cc_start: 0.8182 (mt) cc_final: 0.7894 (mp) REVERT: m 98 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7624 (mp) REVERT: n 13 ARG cc_start: 0.6907 (ttp80) cc_final: 0.6382 (ttm-80) REVERT: n 19 GLN cc_start: 0.7061 (tt0) cc_final: 0.6571 (tp40) REVERT: n 24 THR cc_start: 0.7655 (m) cc_final: 0.7239 (p) REVERT: n 68 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7489 (mtmp) REVERT: n 98 GLN cc_start: 0.7903 (tp40) cc_final: 0.7191 (mm-40) REVERT: o 6 LYS cc_start: 0.6264 (ttpp) cc_final: 0.5855 (mtpt) REVERT: o 38 LYS cc_start: 0.6906 (ptmm) cc_final: 0.6221 (pttm) REVERT: o 44 GLU cc_start: 0.7778 (tt0) cc_final: 0.7476 (tt0) REVERT: o 106 LYS cc_start: 0.7580 (mmtt) cc_final: 0.7213 (mmmm) REVERT: o 111 LYS cc_start: 0.6850 (ttpp) cc_final: 0.6469 (tmtt) REVERT: p 84 LYS cc_start: 0.7253 (mmtt) cc_final: 0.6259 (ttpm) REVERT: q 18 GLN cc_start: 0.6868 (tt0) cc_final: 0.6572 (mt0) REVERT: q 97 LYS cc_start: 0.7398 (ttmm) cc_final: 0.7126 (tttp) REVERT: s 1 MET cc_start: 0.3951 (ttp) cc_final: 0.3260 (tmm) REVERT: s 4 GLU cc_start: 0.5596 (tt0) cc_final: 0.4971 (tp30) REVERT: s 73 ARG cc_start: 0.6127 (ttm170) cc_final: 0.5871 (ttm-80) REVERT: t 10 GLU cc_start: 0.6608 (tp30) cc_final: 0.6358 (mm-30) REVERT: t 24 LYS cc_start: 0.7655 (ttmm) cc_final: 0.7257 (ttmt) REVERT: u 1 MET cc_start: 0.4410 (OUTLIER) cc_final: 0.4164 (ttm) REVERT: u 42 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7434 (mt) REVERT: u 48 MET cc_start: 0.7060 (tpt) cc_final: 0.6841 (tpt) REVERT: u 50 MET cc_start: 0.6256 (mtp) cc_final: 0.5797 (ttm) REVERT: u 59 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.5787 (mp0) REVERT: u 71 LYS cc_start: 0.6839 (mmtp) cc_final: 0.6320 (mppt) REVERT: v 44 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7635 (ttmm) REVERT: v 66 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7666 (mtmt) REVERT: x 45 GLN cc_start: 0.7072 (mt0) cc_final: 0.6836 (mt0) REVERT: x 49 ASP cc_start: 0.6596 (m-30) cc_final: 0.6355 (m-30) REVERT: x 58 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.6951 (t0) REVERT: y 11 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7599 (mtt90) REVERT: y 49 ASN cc_start: 0.8083 (t0) cc_final: 0.7839 (t0) REVERT: y 58 GLU cc_start: 0.5622 (tp30) cc_final: 0.4980 (mp0) REVERT: z 46 ASP cc_start: 0.6379 (OUTLIER) cc_final: 0.6133 (m-30) REVERT: 1 29 GLN cc_start: 0.8005 (mt0) cc_final: 0.7758 (mt0) REVERT: 2 16 LYS cc_start: 0.7967 (tttp) cc_final: 0.7575 (tttt) REVERT: 2 19 LYS cc_start: 0.7715 (mtmt) cc_final: 0.7413 (mtmt) REVERT: 3 8 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7730 (ptmt) REVERT: 3 36 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6622 (ttp-170) REVERT: 4 22 MET cc_start: 0.6851 (mtt) cc_final: 0.5983 (mtp) REVERT: 4 33 ASN cc_start: 0.5387 (m-40) cc_final: 0.4975 (p0) outliers start: 198 outliers final: 114 residues processed: 960 average time/residue: 2.3189 time to fit residues: 3119.4552 Evaluate side-chains 982 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 834 time to evaluate : 6.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 119 ARG Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 85 CYS Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 97 LYS Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 68 ASP Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 16 GLU Chi-restraints excluded: chain f residue 78 LYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 98 GLU Chi-restraints excluded: chain i residue 136 GLN Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 13 LYS Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 74 THR Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain l residue 136 MET Chi-restraints excluded: chain m residue 98 LEU Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 68 LYS Chi-restraints excluded: chain n residue 116 GLN Chi-restraints excluded: chain q residue 19 THR Chi-restraints excluded: chain q residue 49 ILE Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain r residue 28 LYS Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 27 SER Chi-restraints excluded: chain t residue 35 ILE Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain t residue 88 GLU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 42 LEU Chi-restraints excluded: chain u residue 59 GLU Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain v residue 44 LYS Chi-restraints excluded: chain v residue 66 LYS Chi-restraints excluded: chain w residue 2 SER Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain x residue 58 ASN Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain z residue 46 ASP Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 54 ASP Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 36 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 923 optimal weight: 9.9990 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: 10.0000 chunk 597 optimal weight: 20.0000 chunk 581 optimal weight: 10.0000 chunk 440 optimal weight: 9.9990 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN C 140 ASN D 116 GLN D 136 GLN E 78 ASN E 97 GLN F 55 HIS ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN I 75 GLN K 64 GLN L 73 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN d 42 ASN d 94 GLN e 156 ASN g 64 GLN g 143 GLN i 58 ASN n 38 GLN v 3 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 153997 Z= 0.375 Angle : 0.891 19.467 230462 Z= 0.464 Chirality : 0.045 0.363 29304 Planarity : 0.009 0.154 12266 Dihedral : 23.189 178.011 77231 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.60 % Favored : 95.29 % Rotamer: Outliers : 5.07 % Allowed : 17.44 % Favored : 77.49 % 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: -0.46 (0.11), residues: 5480 helix: 0.41 (0.11), residues: 1894 sheet: -0.32 (0.15), residues: 1094 loop : -0.77 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 104 HIS 0.012 0.002 HIS k 35 PHE 0.032 0.003 PHE B 50 TYR 0.031 0.003 TYR r 38 ARG 0.011 0.001 ARG T 60 *********************** 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 1093 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 861 time to evaluate : 6.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.3524 (OUTLIER) cc_final: 0.3304 (p) REVERT: B 112 LYS cc_start: 0.4646 (ttmm) cc_final: 0.3811 (tmtt) REVERT: B 115 LYS cc_start: 0.2712 (mttm) cc_final: 0.2370 (ttpt) REVERT: B 153 ASP cc_start: 0.2948 (m-30) cc_final: 0.2288 (t0) REVERT: B 161 LEU cc_start: 0.4625 (mp) cc_final: 0.4329 (mm) REVERT: B 174 LYS cc_start: 0.3225 (tptp) cc_final: 0.2714 (mmmm) REVERT: C 45 LYS cc_start: 0.6540 (tmtt) cc_final: 0.6096 (mptt) REVERT: C 72 ARG cc_start: 0.5491 (mtp85) cc_final: 0.4505 (mmt180) REVERT: C 86 LYS cc_start: 0.6478 (ttmm) cc_final: 0.5632 (tptp) REVERT: C 89 LYS cc_start: 0.6077 (mtmt) cc_final: 0.5265 (ttmt) REVERT: C 108 LYS cc_start: 0.6640 (OUTLIER) cc_final: 0.6083 (mtpp) REVERT: C 134 MET cc_start: 0.7619 (mtp) cc_final: 0.7135 (mtm) REVERT: C 135 LYS cc_start: 0.7062 (mttt) cc_final: 0.6423 (tttm) REVERT: D 73 ARG cc_start: 0.6746 (tpt-90) cc_final: 0.6155 (ttp-170) REVERT: D 126 ASN cc_start: 0.5977 (m-40) cc_final: 0.5392 (t0) REVERT: D 128 ARG cc_start: 0.5194 (ttt90) cc_final: 0.4930 (mmm-85) REVERT: D 156 LYS cc_start: 0.5527 (tptp) cc_final: 0.5134 (tmtt) REVERT: D 159 LEU cc_start: 0.4396 (mt) cc_final: 0.3878 (mt) REVERT: D 160 GLU cc_start: 0.4985 (mm-30) cc_final: 0.4655 (mm-30) REVERT: D 179 GLU cc_start: 0.5160 (OUTLIER) cc_final: 0.4601 (tt0) REVERT: F 74 LEU cc_start: 0.6553 (tt) cc_final: 0.6162 (tp) REVERT: F 102 MET cc_start: 0.5593 (OUTLIER) cc_final: 0.5231 (ptp) REVERT: G 40 GLU cc_start: 0.6498 (mm-30) cc_final: 0.6130 (mm-30) REVERT: G 92 ARG cc_start: 0.4572 (mtm110) cc_final: 0.4265 (ptp-170) REVERT: G 106 GLU cc_start: 0.6945 (pt0) cc_final: 0.6617 (pt0) REVERT: H 3 MET cc_start: 0.7159 (tpp) cc_final: 0.6593 (tpp) REVERT: H 5 ASP cc_start: 0.7501 (t0) cc_final: 0.7195 (t0) REVERT: H 26 THR cc_start: 0.6655 (OUTLIER) cc_final: 0.6375 (p) REVERT: H 69 LYS cc_start: 0.6427 (mtpp) cc_final: 0.6092 (mptp) REVERT: H 88 ARG cc_start: 0.6276 (mtm110) cc_final: 0.5647 (mtp85) REVERT: H 89 LYS cc_start: 0.6828 (ttpt) cc_final: 0.6264 (tptm) REVERT: H 90 ASP cc_start: 0.6040 (p0) cc_final: 0.5390 (t0) REVERT: H 94 LYS cc_start: 0.6942 (mtpp) cc_final: 0.6658 (mttt) REVERT: H 114 ARG cc_start: 0.6550 (ttm110) cc_final: 0.6311 (ttt180) REVERT: I 41 ARG cc_start: 0.5531 (ttt90) cc_final: 0.5300 (ttt180) REVERT: I 46 MET cc_start: 0.5116 (tpp) cc_final: 0.4788 (tpp) REVERT: I 49 ARG cc_start: 0.6204 (mtm-85) cc_final: 0.5718 (mtt-85) REVERT: I 68 LYS cc_start: 0.6987 (mtpp) cc_final: 0.6637 (mtpt) REVERT: I 112 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6524 (mt-10) REVERT: J 11 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7810 (mttp) REVERT: J 15 HIS cc_start: 0.6991 (p-80) cc_final: 0.6478 (p-80) REVERT: J 68 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7154 (mtt-85) REVERT: J 102 LEU cc_start: 0.3697 (OUTLIER) cc_final: 0.3462 (mm) REVERT: K 80 LYS cc_start: 0.6239 (mptt) cc_final: 0.5885 (mmtm) REVERT: K 83 GLU cc_start: 0.6051 (mt-10) cc_final: 0.5704 (mt-10) REVERT: K 98 ARG cc_start: 0.5589 (ttm-80) cc_final: 0.5005 (ttm170) REVERT: L 88 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7178 (tmmt) REVERT: L 102 LEU cc_start: 0.6375 (OUTLIER) cc_final: 0.6135 (mt) REVERT: L 108 LYS cc_start: 0.5558 (mmtt) cc_final: 0.5311 (mmtp) REVERT: L 121 ARG cc_start: 0.6416 (ttt90) cc_final: 0.5873 (ttt-90) REVERT: M 21 SER cc_start: 0.7949 (m) cc_final: 0.7588 (p) REVERT: M 93 ARG cc_start: 0.5892 (mmp80) cc_final: 0.5265 (mpt-90) REVERT: M 104 THR cc_start: 0.6805 (OUTLIER) cc_final: 0.6352 (p) REVERT: N 98 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7850 (mmtp) REVERT: O 58 ARG cc_start: 0.6823 (ttt180) cc_final: 0.6486 (ttp-170) REVERT: O 59 MET cc_start: 0.7915 (mtt) cc_final: 0.7434 (mtt) REVERT: O 71 LYS cc_start: 0.7447 (tttm) cc_final: 0.6991 (tptp) REVERT: O 82 ILE cc_start: 0.6838 (pt) cc_final: 0.6559 (pp) REVERT: Q 11 ARG cc_start: 0.5756 (mtp-110) cc_final: 0.4859 (mmm-85) REVERT: Q 41 THR cc_start: 0.7598 (m) cc_final: 0.7335 (p) REVERT: Q 61 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7175 (pt) REVERT: R 38 LYS cc_start: 0.7279 (mttm) cc_final: 0.6933 (mtpp) REVERT: S 18 LYS cc_start: 0.6786 (OUTLIER) cc_final: 0.6448 (mtmm) REVERT: U 45 ARG cc_start: 0.5716 (OUTLIER) cc_final: 0.5024 (mtm-85) REVERT: U 60 LEU cc_start: 0.4033 (OUTLIER) cc_final: 0.3363 (mp) REVERT: c 97 LYS cc_start: 0.7443 (mmmm) cc_final: 0.7197 (mptt) REVERT: c 111 LYS cc_start: 0.7125 (mtmm) cc_final: 0.6621 (mttt) REVERT: c 115 GLN cc_start: 0.7117 (mm-40) cc_final: 0.6592 (tt0) REVERT: c 183 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7902 (mtmt) REVERT: c 187 ASP cc_start: 0.6926 (m-30) cc_final: 0.6500 (m-30) REVERT: c 269 ARG cc_start: 0.7190 (ttp-110) cc_final: 0.6595 (ttm170) REVERT: d 18 ASP cc_start: 0.5760 (OUTLIER) cc_final: 0.5524 (p0) REVERT: d 40 LEU cc_start: 0.7622 (mt) cc_final: 0.7355 (mt) REVERT: d 128 ARG cc_start: 0.7288 (mmt180) cc_final: 0.6924 (mpt90) REVERT: d 181 ASP cc_start: 0.6129 (t0) cc_final: 0.5902 (t0) REVERT: e 1 MET cc_start: 0.3523 (OUTLIER) cc_final: 0.2182 (mpp) REVERT: e 22 ASP cc_start: 0.5642 (t0) cc_final: 0.5306 (p0) REVERT: e 140 ASP cc_start: 0.5419 (m-30) cc_final: 0.5059 (m-30) REVERT: f 42 GLU cc_start: 0.5806 (pm20) cc_final: 0.5469 (pm20) REVERT: f 56 ASP cc_start: 0.6472 (m-30) cc_final: 0.6187 (m-30) REVERT: f 81 GLN cc_start: 0.7788 (tt0) cc_final: 0.7581 (tt0) REVERT: f 96 MET cc_start: 0.7633 (ttp) cc_final: 0.7208 (ttp) REVERT: f 101 GLU cc_start: 0.6721 (tt0) cc_final: 0.6453 (tm-30) REVERT: g 115 HIS cc_start: 0.6902 (t70) cc_final: 0.6634 (t-90) REVERT: g 155 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6115 (pp20) REVERT: h 1 MET cc_start: 0.4109 (OUTLIER) cc_final: 0.2209 (ttt) REVERT: h 12 LEU cc_start: 0.4575 (OUTLIER) cc_final: 0.3510 (mm) REVERT: i 96 ARG cc_start: 0.6439 (mmm160) cc_final: 0.6016 (ptt-90) REVERT: i 136 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7503 (mt0) REVERT: j 14 SER cc_start: 0.8455 (p) cc_final: 0.8205 (p) REVERT: j 53 LYS cc_start: 0.7126 (mmtm) cc_final: 0.6926 (mmmt) REVERT: k 2 ARG cc_start: 0.6333 (mmm-85) cc_final: 0.5296 (mmt-90) REVERT: l 53 MET cc_start: 0.7784 (ptp) cc_final: 0.7498 (ptm) REVERT: l 106 ASP cc_start: 0.7795 (t0) cc_final: 0.7258 (t70) REVERT: l 115 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6558 (tm-30) REVERT: l 133 LYS cc_start: 0.7541 (ttpt) cc_final: 0.7188 (ttpt) REVERT: m 65 LEU cc_start: 0.8188 (mt) cc_final: 0.7904 (mp) REVERT: m 98 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7637 (mp) REVERT: n 13 ARG cc_start: 0.6886 (ttp80) cc_final: 0.6397 (ttm-80) REVERT: n 19 GLN cc_start: 0.7146 (tt0) cc_final: 0.6610 (tp40) REVERT: n 24 THR cc_start: 0.7584 (m) cc_final: 0.7190 (p) REVERT: n 68 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7512 (mtmp) REVERT: n 98 GLN cc_start: 0.7957 (tp40) cc_final: 0.7217 (mm-40) REVERT: o 6 LYS cc_start: 0.6276 (ttpp) cc_final: 0.5862 (mtpt) REVERT: o 38 LYS cc_start: 0.6956 (ptmm) cc_final: 0.6210 (pttm) REVERT: o 44 GLU cc_start: 0.7800 (tt0) cc_final: 0.7485 (tt0) REVERT: o 87 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7400 (mmmt) REVERT: o 106 LYS cc_start: 0.7590 (mmtt) cc_final: 0.7216 (mmtp) REVERT: o 111 LYS cc_start: 0.6872 (ttpp) cc_final: 0.6500 (tmtt) REVERT: p 84 LYS cc_start: 0.7294 (mmtt) cc_final: 0.6306 (ttpt) REVERT: q 13 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7728 (ttt90) REVERT: q 18 GLN cc_start: 0.6891 (tt0) cc_final: 0.6511 (mt0) REVERT: q 97 LYS cc_start: 0.7391 (ttmm) cc_final: 0.7137 (ttpp) REVERT: q 101 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7257 (mp) REVERT: s 1 MET cc_start: 0.3756 (ttp) cc_final: 0.3263 (tmm) REVERT: s 4 GLU cc_start: 0.5625 (tt0) cc_final: 0.5026 (tp30) REVERT: s 18 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6804 (tm-30) REVERT: s 73 ARG cc_start: 0.6039 (ttm170) cc_final: 0.5599 (ttm-80) REVERT: t 10 GLU cc_start: 0.6595 (tp30) cc_final: 0.6341 (mm-30) REVERT: t 24 LYS cc_start: 0.7657 (ttmm) cc_final: 0.7356 (ttmt) REVERT: u 1 MET cc_start: 0.4500 (OUTLIER) cc_final: 0.4253 (ttm) REVERT: u 42 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7460 (mt) REVERT: u 48 MET cc_start: 0.7063 (tpt) cc_final: 0.6835 (tpt) REVERT: u 50 MET cc_start: 0.6260 (mtp) cc_final: 0.5864 (ttm) REVERT: u 59 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.5780 (mp0) REVERT: u 68 LYS cc_start: 0.5581 (mmtm) cc_final: 0.5113 (mttt) REVERT: u 71 LYS cc_start: 0.6870 (mmtp) cc_final: 0.6311 (mppt) REVERT: v 44 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7645 (ttmm) REVERT: v 66 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7711 (mtmt) REVERT: x 5 GLU cc_start: 0.6477 (pp20) cc_final: 0.6092 (mm-30) REVERT: x 30 MET cc_start: 0.6251 (OUTLIER) cc_final: 0.5904 (mmm) REVERT: x 45 GLN cc_start: 0.7183 (mt0) cc_final: 0.6976 (mt0) REVERT: x 49 ASP cc_start: 0.6620 (m-30) cc_final: 0.6384 (m-30) REVERT: x 58 ASN cc_start: 0.7446 (OUTLIER) cc_final: 0.6920 (t0) REVERT: y 11 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7654 (mtt90) REVERT: y 49 ASN cc_start: 0.8109 (t0) cc_final: 0.7895 (t0) REVERT: z 46 ASP cc_start: 0.6347 (OUTLIER) cc_final: 0.6076 (m-30) REVERT: 0 27 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7137 (ptpp) REVERT: 1 29 GLN cc_start: 0.8061 (mt0) cc_final: 0.7790 (mt0) REVERT: 2 16 LYS cc_start: 0.8004 (tttp) cc_final: 0.7571 (tttt) REVERT: 2 19 LYS cc_start: 0.7747 (mtmt) cc_final: 0.7418 (mtmt) REVERT: 3 8 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7594 (ptmt) REVERT: 3 30 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6369 (tp30) REVERT: 3 36 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6653 (ttp-170) REVERT: 4 22 MET cc_start: 0.6840 (mtt) cc_final: 0.6051 (mtp) REVERT: 4 24 ILE cc_start: 0.6807 (pt) cc_final: 0.6588 (pt) REVERT: 4 33 ASN cc_start: 0.5475 (m-40) cc_final: 0.5037 (p0) REVERT: 4 59 ARG cc_start: 0.4195 (OUTLIER) cc_final: 0.3830 (ppt170) outliers start: 232 outliers final: 137 residues processed: 996 average time/residue: 2.2773 time to fit residues: 3183.5944 Evaluate side-chains 1036 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 855 time to evaluate : 6.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 119 ARG Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 85 CYS Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 10 GLU Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 97 LYS Chi-restraints excluded: chain N residue 98 LYS Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 68 ASP Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain S residue 18 LYS Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain U residue 45 ARG Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 197 THR Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 119 ILE Chi-restraints excluded: chain f residue 78 LYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 98 GLU Chi-restraints excluded: chain i residue 136 GLN Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 13 LYS Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 74 THR Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain l residue 136 MET Chi-restraints excluded: chain m residue 98 LEU Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 68 LYS Chi-restraints excluded: chain n residue 116 GLN Chi-restraints excluded: chain o residue 5 ILE Chi-restraints excluded: chain o residue 27 GLU Chi-restraints excluded: chain o residue 87 LYS Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 13 ARG Chi-restraints excluded: chain q residue 19 THR Chi-restraints excluded: chain q residue 49 ILE Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain q residue 101 ILE Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain s residue 27 SER Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 35 ILE Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain t residue 88 GLU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 42 LEU Chi-restraints excluded: chain u residue 59 GLU Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain v residue 44 LYS Chi-restraints excluded: chain v residue 66 LYS Chi-restraints excluded: chain w residue 2 SER Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain x residue 30 MET Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain x residue 58 ASN Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain z residue 46 ASP Chi-restraints excluded: chain 0 residue 27 LYS Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 54 ASP Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 30 GLU Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 59 ARG Chi-restraints excluded: chain 4 residue 66 ILE 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: 6.9990 chunk 569 optimal weight: 10.0000 chunk 287 optimal weight: 30.0000 chunk 187 optimal weight: 2.9990 chunk 184 optimal weight: 0.0000 chunk 606 optimal weight: 10.0000 chunk 650 optimal weight: 10.0000 chunk 471 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 750 optimal weight: 9.9990 overall best weight: 5.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN C 140 ASN D 116 GLN D 136 GLN E 78 ASN E 97 GLN F 55 HIS ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN K 64 GLN L 73 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS d 32 ASN d 94 GLN e 156 ASN g 64 GLN g 143 GLN n 38 GLN q 43 ASN u 24 ASN v 3 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 153997 Z= 0.286 Angle : 0.795 15.971 230462 Z= 0.425 Chirality : 0.041 0.363 29304 Planarity : 0.008 0.147 12266 Dihedral : 23.107 178.038 77231 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.22 % Favored : 95.71 % Rotamer: Outliers : 4.70 % Allowed : 18.19 % Favored : 77.11 % 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: -0.32 (0.11), residues: 5480 helix: 0.59 (0.11), residues: 1899 sheet: -0.27 (0.15), residues: 1089 loop : -0.72 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 248 HIS 0.008 0.001 HIS k 35 PHE 0.023 0.002 PHE B 50 TYR 0.029 0.002 TYR r 38 ARG 0.012 0.001 ARG T 60 *********************** 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 1058 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 843 time to evaluate : 6.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 LYS cc_start: 0.4532 (ttmm) cc_final: 0.3759 (tmtt) REVERT: B 115 LYS cc_start: 0.2729 (mttm) cc_final: 0.2381 (ttpt) REVERT: B 153 ASP cc_start: 0.2944 (m-30) cc_final: 0.2276 (t0) REVERT: B 161 LEU cc_start: 0.4605 (mp) cc_final: 0.4314 (mm) REVERT: B 174 LYS cc_start: 0.3103 (tptp) cc_final: 0.2612 (mmmm) REVERT: C 45 LYS cc_start: 0.6572 (tmtt) cc_final: 0.6159 (mptt) REVERT: C 72 ARG cc_start: 0.5498 (mtp85) cc_final: 0.4474 (mmt180) REVERT: C 86 LYS cc_start: 0.6449 (ttmm) cc_final: 0.5656 (tptp) REVERT: C 89 LYS cc_start: 0.6078 (mtmt) cc_final: 0.5862 (mppt) REVERT: C 108 LYS cc_start: 0.6661 (OUTLIER) cc_final: 0.6413 (ptmt) REVERT: C 134 MET cc_start: 0.7569 (mtp) cc_final: 0.7117 (mtm) REVERT: C 135 LYS cc_start: 0.7052 (mttt) cc_final: 0.6458 (tttm) REVERT: D 73 ARG cc_start: 0.6692 (tpt-90) cc_final: 0.6060 (ttp-170) REVERT: D 126 ASN cc_start: 0.5871 (m-40) cc_final: 0.5283 (t0) REVERT: D 159 LEU cc_start: 0.4256 (mt) cc_final: 0.3767 (mt) REVERT: D 179 GLU cc_start: 0.5150 (OUTLIER) cc_final: 0.4593 (tt0) REVERT: F 29 ILE cc_start: 0.5881 (OUTLIER) cc_final: 0.5659 (mm) REVERT: F 74 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6187 (tp) REVERT: F 102 MET cc_start: 0.5623 (OUTLIER) cc_final: 0.5214 (ptp) REVERT: G 40 GLU cc_start: 0.6450 (mm-30) cc_final: 0.6077 (mm-30) REVERT: G 92 ARG cc_start: 0.4567 (mtm110) cc_final: 0.4264 (ptp-170) REVERT: G 106 GLU cc_start: 0.6935 (pt0) cc_final: 0.6610 (pt0) REVERT: H 3 MET cc_start: 0.7145 (tpp) cc_final: 0.6493 (tpp) REVERT: H 5 ASP cc_start: 0.7515 (t0) cc_final: 0.7262 (t0) REVERT: H 26 THR cc_start: 0.6656 (OUTLIER) cc_final: 0.6367 (p) REVERT: H 69 LYS cc_start: 0.6389 (mtpp) cc_final: 0.6079 (mptp) REVERT: H 88 ARG cc_start: 0.6275 (mtm110) cc_final: 0.5646 (mtp85) REVERT: H 89 LYS cc_start: 0.6778 (ttpt) cc_final: 0.6248 (tptm) REVERT: H 90 ASP cc_start: 0.6018 (p0) cc_final: 0.5291 (t0) REVERT: H 114 ARG cc_start: 0.6561 (ttm110) cc_final: 0.6322 (ttt180) REVERT: I 41 ARG cc_start: 0.5528 (ttt90) cc_final: 0.5313 (ttt180) REVERT: I 46 MET cc_start: 0.5085 (tpp) cc_final: 0.4777 (tpp) REVERT: I 49 ARG cc_start: 0.6298 (mtm-85) cc_final: 0.5807 (mtt-85) REVERT: I 68 LYS cc_start: 0.6964 (mtpp) cc_final: 0.6413 (mtpt) REVERT: I 112 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6502 (mt-10) REVERT: J 11 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7759 (mttp) REVERT: J 15 HIS cc_start: 0.6934 (p-80) cc_final: 0.6443 (p-80) REVERT: J 102 LEU cc_start: 0.3719 (OUTLIER) cc_final: 0.3490 (mm) REVERT: K 80 LYS cc_start: 0.6283 (mptt) cc_final: 0.5923 (mmtm) REVERT: K 83 GLU cc_start: 0.6026 (mt-10) cc_final: 0.5723 (mt-10) REVERT: K 98 ARG cc_start: 0.5624 (ttm-80) cc_final: 0.5025 (ttm170) REVERT: L 88 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7219 (tmmt) REVERT: L 102 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.6200 (mt) REVERT: L 121 ARG cc_start: 0.6378 (ttt90) cc_final: 0.5905 (ttt-90) REVERT: M 21 SER cc_start: 0.7929 (m) cc_final: 0.7568 (p) REVERT: M 93 ARG cc_start: 0.5908 (mmp80) cc_final: 0.5348 (mpt-90) REVERT: M 104 THR cc_start: 0.6761 (OUTLIER) cc_final: 0.6316 (p) REVERT: N 6 MET cc_start: 0.7538 (mmm) cc_final: 0.7289 (mmp) REVERT: N 92 GLU cc_start: 0.6578 (mt-10) cc_final: 0.6104 (mm-30) REVERT: N 98 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7836 (mmtp) REVERT: O 58 ARG cc_start: 0.6834 (ttt180) cc_final: 0.6509 (ttp-170) REVERT: O 59 MET cc_start: 0.7909 (mtt) cc_final: 0.7437 (mtt) REVERT: O 71 LYS cc_start: 0.7417 (tttm) cc_final: 0.6957 (tptp) REVERT: O 82 ILE cc_start: 0.6797 (pt) cc_final: 0.6512 (pp) REVERT: Q 11 ARG cc_start: 0.5722 (mtp-110) cc_final: 0.4859 (mmm-85) REVERT: Q 41 THR cc_start: 0.7568 (m) cc_final: 0.7282 (p) REVERT: Q 61 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7174 (pt) REVERT: Q 67 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7646 (mt) REVERT: R 38 LYS cc_start: 0.7261 (mttm) cc_final: 0.6906 (mtpp) REVERT: S 18 LYS cc_start: 0.6802 (OUTLIER) cc_final: 0.6438 (mtmm) REVERT: U 39 GLU cc_start: 0.7101 (tt0) cc_final: 0.6665 (tt0) REVERT: U 45 ARG cc_start: 0.5754 (OUTLIER) cc_final: 0.5097 (mtm-85) REVERT: U 60 LEU cc_start: 0.3997 (OUTLIER) cc_final: 0.3299 (mp) REVERT: c 97 LYS cc_start: 0.7436 (mmmm) cc_final: 0.7189 (mptt) REVERT: c 111 LYS cc_start: 0.7173 (mtmm) cc_final: 0.6626 (mttt) REVERT: c 115 GLN cc_start: 0.7106 (mm-40) cc_final: 0.6597 (tt0) REVERT: c 183 LYS cc_start: 0.8131 (mtmm) cc_final: 0.7861 (mtmt) REVERT: c 187 ASP cc_start: 0.6959 (m-30) cc_final: 0.6533 (m-30) REVERT: c 269 ARG cc_start: 0.7137 (ttp-110) cc_final: 0.6596 (ttm170) REVERT: d 18 ASP cc_start: 0.5803 (OUTLIER) cc_final: 0.5567 (p0) REVERT: d 40 LEU cc_start: 0.7626 (mt) cc_final: 0.7262 (mm) REVERT: d 74 GLU cc_start: 0.6684 (mm-30) cc_final: 0.6029 (tp30) REVERT: d 128 ARG cc_start: 0.7297 (mmt180) cc_final: 0.6935 (mpt90) REVERT: d 181 ASP cc_start: 0.6026 (t0) cc_final: 0.5771 (t0) REVERT: e 1 MET cc_start: 0.3513 (OUTLIER) cc_final: 0.2156 (mpp) REVERT: e 22 ASP cc_start: 0.5607 (t0) cc_final: 0.5241 (p0) REVERT: e 140 ASP cc_start: 0.5480 (m-30) cc_final: 0.5113 (m-30) REVERT: f 42 GLU cc_start: 0.5788 (pm20) cc_final: 0.5486 (pm20) REVERT: f 81 GLN cc_start: 0.7750 (tt0) cc_final: 0.7538 (tt0) REVERT: f 96 MET cc_start: 0.7610 (ttp) cc_final: 0.7192 (ttp) REVERT: f 101 GLU cc_start: 0.6712 (tt0) cc_final: 0.6409 (tm-30) REVERT: g 10 VAL cc_start: 0.5236 (OUTLIER) cc_final: 0.4762 (t) REVERT: g 115 HIS cc_start: 0.6886 (t70) cc_final: 0.6613 (t-90) REVERT: g 155 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6014 (pp20) REVERT: h 1 MET cc_start: 0.4092 (OUTLIER) cc_final: 0.2187 (ttt) REVERT: h 12 LEU cc_start: 0.4586 (OUTLIER) cc_final: 0.3532 (mm) REVERT: i 49 ASP cc_start: 0.8131 (t0) cc_final: 0.7806 (t70) REVERT: i 96 ARG cc_start: 0.6404 (mmm160) cc_final: 0.5948 (ptt-90) REVERT: i 136 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7548 (mt0) REVERT: j 14 SER cc_start: 0.8455 (p) cc_final: 0.8206 (p) REVERT: j 53 LYS cc_start: 0.7145 (mmtm) cc_final: 0.6655 (mmtt) REVERT: k 2 ARG cc_start: 0.6250 (mmm-85) cc_final: 0.5240 (mmt-90) REVERT: l 53 MET cc_start: 0.7714 (ptp) cc_final: 0.7469 (ptm) REVERT: l 115 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6532 (tm-30) REVERT: l 133 LYS cc_start: 0.7523 (ttpt) cc_final: 0.7168 (ttpt) REVERT: m 65 LEU cc_start: 0.8172 (mt) cc_final: 0.7878 (mp) REVERT: m 98 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7639 (mp) REVERT: n 13 ARG cc_start: 0.6911 (ttp80) cc_final: 0.6398 (ttm-80) REVERT: n 19 GLN cc_start: 0.7147 (tt0) cc_final: 0.6645 (tp40) REVERT: n 24 THR cc_start: 0.7582 (m) cc_final: 0.7191 (p) REVERT: n 68 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7500 (mtmp) REVERT: n 98 GLN cc_start: 0.7934 (tp40) cc_final: 0.7199 (mm-40) REVERT: o 6 LYS cc_start: 0.6235 (ttpp) cc_final: 0.5835 (mtpt) REVERT: o 38 LYS cc_start: 0.6884 (ptmm) cc_final: 0.6209 (pttm) REVERT: o 44 GLU cc_start: 0.7766 (tt0) cc_final: 0.7478 (tt0) REVERT: o 87 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7346 (mmmt) REVERT: o 106 LYS cc_start: 0.7584 (mmtt) cc_final: 0.7195 (mmtp) REVERT: o 111 LYS cc_start: 0.6868 (ttpp) cc_final: 0.6499 (tmtt) REVERT: p 84 LYS cc_start: 0.7284 (mmtt) cc_final: 0.6273 (ttpm) REVERT: q 13 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7690 (ttt90) REVERT: q 18 GLN cc_start: 0.6922 (tt0) cc_final: 0.6518 (mt0) REVERT: q 97 LYS cc_start: 0.7385 (ttmm) cc_final: 0.7124 (ttpp) REVERT: q 101 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7249 (mp) REVERT: s 1 MET cc_start: 0.3574 (ttp) cc_final: 0.3280 (tmm) REVERT: s 4 GLU cc_start: 0.5591 (tt0) cc_final: 0.4988 (tp30) REVERT: s 18 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6786 (tm-30) REVERT: s 73 ARG cc_start: 0.6077 (ttm170) cc_final: 0.5634 (ttm-80) REVERT: t 10 GLU cc_start: 0.6632 (tp30) cc_final: 0.6379 (mm-30) REVERT: t 24 LYS cc_start: 0.7648 (ttmm) cc_final: 0.7390 (ttmt) REVERT: u 1 MET cc_start: 0.4454 (OUTLIER) cc_final: 0.4206 (ttm) REVERT: u 42 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7418 (mt) REVERT: u 48 MET cc_start: 0.7054 (tpt) cc_final: 0.6757 (tpt) REVERT: u 50 MET cc_start: 0.6226 (mtp) cc_final: 0.5812 (ttm) REVERT: u 59 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.5803 (mp0) REVERT: u 68 LYS cc_start: 0.5561 (mmtm) cc_final: 0.5099 (mttt) REVERT: u 71 LYS cc_start: 0.6846 (mmtp) cc_final: 0.6320 (mppt) REVERT: v 44 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7637 (ttmm) REVERT: v 66 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7635 (mtmt) REVERT: x 30 MET cc_start: 0.6292 (OUTLIER) cc_final: 0.5552 (mtm) REVERT: x 45 GLN cc_start: 0.7132 (mt0) cc_final: 0.6914 (mt0) REVERT: x 49 ASP cc_start: 0.6635 (m-30) cc_final: 0.6382 (m-30) REVERT: x 58 ASN cc_start: 0.7440 (OUTLIER) cc_final: 0.6943 (t0) REVERT: y 11 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7620 (mtt90) REVERT: y 49 ASN cc_start: 0.8087 (t0) cc_final: 0.7849 (t0) REVERT: y 58 GLU cc_start: 0.5639 (tp30) cc_final: 0.4946 (mp0) REVERT: z 46 ASP cc_start: 0.6366 (OUTLIER) cc_final: 0.6114 (m-30) REVERT: 0 27 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7065 (ptpp) REVERT: 1 29 GLN cc_start: 0.8017 (mt0) cc_final: 0.7771 (mt0) REVERT: 2 16 LYS cc_start: 0.7963 (tttp) cc_final: 0.7571 (tttt) REVERT: 2 19 LYS cc_start: 0.7737 (mtmt) cc_final: 0.7412 (mtmt) REVERT: 3 8 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7636 (ptmt) REVERT: 3 36 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6629 (ttp-170) REVERT: 4 22 MET cc_start: 0.6877 (mtt) cc_final: 0.6020 (mtp) REVERT: 4 24 ILE cc_start: 0.6844 (pt) cc_final: 0.6621 (pt) REVERT: 4 33 ASN cc_start: 0.5435 (m-40) cc_final: 0.5014 (p0) REVERT: 4 59 ARG cc_start: 0.4215 (OUTLIER) cc_final: 0.3869 (ppt170) outliers start: 215 outliers final: 132 residues processed: 962 average time/residue: 2.2667 time to fit residues: 3053.2925 Evaluate side-chains 1015 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 838 time to evaluate : 6.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 85 CYS Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 10 GLU Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 97 LYS Chi-restraints excluded: chain N residue 98 LYS Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 68 ASP Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain S residue 18 LYS Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain U residue 45 ARG Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 197 THR Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain f residue 78 LYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 98 GLU Chi-restraints excluded: chain i residue 136 GLN Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 13 LYS Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 74 THR Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain l residue 136 MET Chi-restraints excluded: chain m residue 98 LEU Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 68 LYS Chi-restraints excluded: chain n residue 116 GLN Chi-restraints excluded: chain o residue 27 GLU Chi-restraints excluded: chain o residue 87 LYS Chi-restraints excluded: chain q residue 13 ARG Chi-restraints excluded: chain q residue 19 THR Chi-restraints excluded: chain q residue 49 ILE Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain q residue 101 ILE Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain s residue 27 SER Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 35 ILE Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain t residue 88 GLU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 42 LEU Chi-restraints excluded: chain u residue 59 GLU Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain v residue 44 LYS Chi-restraints excluded: chain v residue 66 LYS Chi-restraints excluded: chain w residue 2 SER Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain x residue 30 MET Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain x residue 58 ASN Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain z residue 46 ASP Chi-restraints excluded: chain 0 residue 27 LYS Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 54 ASP Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 59 ARG Chi-restraints excluded: chain 4 residue 66 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 868 optimal weight: 5.9990 chunk 914 optimal weight: 1.9990 chunk 834 optimal weight: 9.9990 chunk 889 optimal weight: 5.9990 chunk 913 optimal weight: 2.9990 chunk 535 optimal weight: 20.0000 chunk 387 optimal weight: 10.0000 chunk 698 optimal weight: 4.9990 chunk 272 optimal weight: 8.9990 chunk 803 optimal weight: 10.0000 chunk 840 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN C 140 ASN D 116 GLN D 136 GLN E 78 ASN E 97 GLN F 55 HIS ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN I 75 GLN K 64 GLN L 73 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN d 94 GLN e 136 GLN e 156 ASN g 64 GLN n 38 GLN u 24 ASN v 3 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 153997 Z= 0.231 Angle : 0.744 15.191 230462 Z= 0.405 Chirality : 0.039 0.365 29304 Planarity : 0.008 0.144 12266 Dihedral : 23.087 178.411 77231 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 4.35 % Allowed : 18.69 % Favored : 76.96 % 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: 0.71 (0.11), residues: 1899 sheet: -0.25 (0.15), residues: 1090 loop : -0.69 (0.12), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP l 64 HIS 0.007 0.001 HIS k 35 PHE 0.020 0.002 PHE B 50 TYR 0.027 0.002 TYR C 42 ARG 0.012 0.001 ARG O 88 *********************** 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 1043 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 844 time to evaluate : 6.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 LYS cc_start: 0.4581 (ttmm) cc_final: 0.3796 (tmtt) REVERT: B 115 LYS cc_start: 0.2701 (mttm) cc_final: 0.2348 (ttpt) REVERT: B 153 ASP cc_start: 0.2930 (m-30) cc_final: 0.2270 (t0) REVERT: B 161 LEU cc_start: 0.4599 (mp) cc_final: 0.4313 (mm) REVERT: B 174 LYS cc_start: 0.3081 (tptp) cc_final: 0.2601 (mmmm) REVERT: C 45 LYS cc_start: 0.6528 (tmtt) cc_final: 0.6132 (mptt) REVERT: C 72 ARG cc_start: 0.5487 (mtp85) cc_final: 0.4472 (mmt180) REVERT: C 86 LYS cc_start: 0.6465 (ttmm) cc_final: 0.5607 (tptp) REVERT: C 89 LYS cc_start: 0.6130 (mtmt) cc_final: 0.5245 (ttmt) REVERT: C 108 LYS cc_start: 0.6654 (OUTLIER) cc_final: 0.6407 (ptmt) REVERT: C 134 MET cc_start: 0.7552 (mtp) cc_final: 0.6942 (mtm) REVERT: C 135 LYS cc_start: 0.7046 (mttt) cc_final: 0.6450 (tttm) REVERT: D 73 ARG cc_start: 0.6680 (tpt-90) cc_final: 0.6096 (ttp-170) REVERT: D 154 ARG cc_start: 0.5548 (OUTLIER) cc_final: 0.5221 (ptt180) REVERT: D 159 LEU cc_start: 0.4279 (mt) cc_final: 0.3790 (mt) REVERT: D 179 GLU cc_start: 0.5135 (OUTLIER) cc_final: 0.4579 (tt0) REVERT: F 29 ILE cc_start: 0.5863 (OUTLIER) cc_final: 0.5647 (mm) REVERT: F 74 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6162 (tp) REVERT: F 102 MET cc_start: 0.5616 (OUTLIER) cc_final: 0.5194 (ptp) REVERT: G 40 GLU cc_start: 0.6459 (mm-30) cc_final: 0.6029 (mm-30) REVERT: G 92 ARG cc_start: 0.4548 (mtm110) cc_final: 0.4239 (ptp-170) REVERT: G 106 GLU cc_start: 0.6934 (pt0) cc_final: 0.6610 (pt0) REVERT: H 3 MET cc_start: 0.7146 (tpp) cc_final: 0.6504 (tpp) REVERT: H 5 ASP cc_start: 0.7507 (t0) cc_final: 0.7252 (t0) REVERT: H 26 THR cc_start: 0.6685 (OUTLIER) cc_final: 0.6395 (p) REVERT: H 42 GLU cc_start: 0.6423 (mp0) cc_final: 0.6213 (mp0) REVERT: H 69 LYS cc_start: 0.6383 (mtpp) cc_final: 0.6076 (mptp) REVERT: H 88 ARG cc_start: 0.6276 (mtm110) cc_final: 0.5644 (mtp85) REVERT: H 89 LYS cc_start: 0.6762 (ttpt) cc_final: 0.6205 (tptm) REVERT: H 90 ASP cc_start: 0.5997 (p0) cc_final: 0.5280 (t0) REVERT: H 114 ARG cc_start: 0.6558 (ttm110) cc_final: 0.6322 (ttt180) REVERT: I 46 MET cc_start: 0.5095 (tpp) cc_final: 0.4794 (tpp) REVERT: I 49 ARG cc_start: 0.6303 (mtm-85) cc_final: 0.5809 (mtt-85) REVERT: I 68 LYS cc_start: 0.6932 (mtpp) cc_final: 0.6382 (mtpt) REVERT: I 112 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6490 (mt-10) REVERT: I 119 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.6317 (ptm160) REVERT: J 11 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7781 (mttp) REVERT: J 15 HIS cc_start: 0.6959 (p-80) cc_final: 0.6466 (p-80) REVERT: K 32 VAL cc_start: 0.7516 (t) cc_final: 0.7269 (t) REVERT: K 80 LYS cc_start: 0.6285 (mptt) cc_final: 0.5927 (mmtm) REVERT: K 83 GLU cc_start: 0.6022 (mt-10) cc_final: 0.5714 (mt-10) REVERT: K 98 ARG cc_start: 0.5630 (ttm-80) cc_final: 0.5032 (ttm170) REVERT: L 88 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7222 (tmmt) REVERT: L 102 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6219 (mt) REVERT: L 121 ARG cc_start: 0.6395 (ttt90) cc_final: 0.5923 (ttt-90) REVERT: M 21 SER cc_start: 0.7923 (m) cc_final: 0.7573 (p) REVERT: M 93 ARG cc_start: 0.5909 (mmp80) cc_final: 0.5346 (mpt-90) REVERT: M 104 THR cc_start: 0.6722 (OUTLIER) cc_final: 0.6287 (p) REVERT: N 6 MET cc_start: 0.7516 (mmm) cc_final: 0.7256 (mmp) REVERT: N 92 GLU cc_start: 0.6576 (mt-10) cc_final: 0.6100 (mm-30) REVERT: N 98 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7799 (mmtp) REVERT: O 14 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.5825 (tm-30) REVERT: O 58 ARG cc_start: 0.6833 (ttt180) cc_final: 0.6504 (ttp-170) REVERT: O 59 MET cc_start: 0.7901 (mtt) cc_final: 0.7427 (mtt) REVERT: O 71 LYS cc_start: 0.7367 (tttm) cc_final: 0.6980 (tptp) REVERT: O 82 ILE cc_start: 0.6788 (pt) cc_final: 0.6472 (pp) REVERT: Q 11 ARG cc_start: 0.5708 (mtp-110) cc_final: 0.4856 (mmm-85) REVERT: Q 41 THR cc_start: 0.7575 (m) cc_final: 0.7280 (p) REVERT: Q 61 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7172 (pt) REVERT: Q 67 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7646 (mt) REVERT: R 38 LYS cc_start: 0.7252 (mttm) cc_final: 0.6891 (mtpp) REVERT: T 27 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7082 (tmt) REVERT: U 39 GLU cc_start: 0.7118 (tt0) cc_final: 0.6661 (tt0) REVERT: U 60 LEU cc_start: 0.4005 (OUTLIER) cc_final: 0.3271 (mp) REVERT: c 97 LYS cc_start: 0.7433 (mmmm) cc_final: 0.7186 (mptt) REVERT: c 111 LYS cc_start: 0.7182 (mtmm) cc_final: 0.6661 (mttt) REVERT: c 115 GLN cc_start: 0.7102 (mm-40) cc_final: 0.6592 (tt0) REVERT: c 183 LYS cc_start: 0.8133 (mtmm) cc_final: 0.7846 (mtmt) REVERT: c 187 ASP cc_start: 0.6959 (m-30) cc_final: 0.6535 (m-30) REVERT: c 269 ARG cc_start: 0.7118 (ttp-110) cc_final: 0.6585 (ttm170) REVERT: d 18 ASP cc_start: 0.5810 (OUTLIER) cc_final: 0.5573 (p0) REVERT: d 40 LEU cc_start: 0.7618 (mt) cc_final: 0.7249 (mm) REVERT: d 74 GLU cc_start: 0.6682 (mm-30) cc_final: 0.6025 (tp30) REVERT: d 128 ARG cc_start: 0.7308 (mmt180) cc_final: 0.6945 (mpt90) REVERT: d 181 ASP cc_start: 0.6005 (t0) cc_final: 0.5752 (t0) REVERT: e 1 MET cc_start: 0.3529 (OUTLIER) cc_final: 0.2140 (mpp) REVERT: e 22 ASP cc_start: 0.5602 (t0) cc_final: 0.5242 (p0) REVERT: e 140 ASP cc_start: 0.5512 (m-30) cc_final: 0.5136 (m-30) REVERT: f 42 GLU cc_start: 0.5786 (pm20) cc_final: 0.5482 (pm20) REVERT: f 81 GLN cc_start: 0.7745 (tt0) cc_final: 0.7537 (tt0) REVERT: f 96 MET cc_start: 0.7629 (ttp) cc_final: 0.7207 (ttp) REVERT: f 101 GLU cc_start: 0.6716 (tt0) cc_final: 0.6360 (tm-30) REVERT: g 10 VAL cc_start: 0.5220 (OUTLIER) cc_final: 0.4758 (t) REVERT: g 95 ARG cc_start: 0.6250 (ptp-110) cc_final: 0.5727 (ptp90) REVERT: g 115 HIS cc_start: 0.6869 (t70) cc_final: 0.6596 (t-90) REVERT: g 155 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.6020 (pp20) REVERT: h 1 MET cc_start: 0.4091 (OUTLIER) cc_final: 0.2180 (ttt) REVERT: h 12 LEU cc_start: 0.4630 (OUTLIER) cc_final: 0.3480 (mm) REVERT: i 49 ASP cc_start: 0.8051 (t0) cc_final: 0.7814 (t70) REVERT: i 96 ARG cc_start: 0.6407 (mmm160) cc_final: 0.5940 (ptt-90) REVERT: i 136 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7538 (mt0) REVERT: j 14 SER cc_start: 0.8452 (p) cc_final: 0.8209 (p) REVERT: j 53 LYS cc_start: 0.7146 (mmtm) cc_final: 0.6662 (mmtt) REVERT: k 2 ARG cc_start: 0.6221 (mmm-85) cc_final: 0.5220 (mmt-90) REVERT: k 91 ASP cc_start: 0.6384 (t70) cc_final: 0.5994 (m-30) REVERT: l 53 MET cc_start: 0.7678 (ptp) cc_final: 0.7443 (ptm) REVERT: l 106 ASP cc_start: 0.7814 (t0) cc_final: 0.7277 (t70) REVERT: l 115 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6506 (tm-30) REVERT: l 133 LYS cc_start: 0.7527 (ttpt) cc_final: 0.7188 (ttpt) REVERT: m 65 LEU cc_start: 0.8154 (mt) cc_final: 0.7869 (mp) REVERT: m 98 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7626 (mp) REVERT: n 13 ARG cc_start: 0.6916 (ttp80) cc_final: 0.6398 (ttm-80) REVERT: n 19 GLN cc_start: 0.7130 (tt0) cc_final: 0.6641 (tp40) REVERT: n 24 THR cc_start: 0.7570 (m) cc_final: 0.7173 (p) REVERT: n 68 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7474 (mtmp) REVERT: n 98 GLN cc_start: 0.7918 (tp40) cc_final: 0.7122 (mm-40) REVERT: o 6 LYS cc_start: 0.6187 (ttpp) cc_final: 0.5761 (mtpt) REVERT: o 38 LYS cc_start: 0.6903 (ptmm) cc_final: 0.6222 (pttm) REVERT: o 44 GLU cc_start: 0.7760 (tt0) cc_final: 0.7475 (tt0) REVERT: o 87 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7350 (mmmt) REVERT: o 106 LYS cc_start: 0.7580 (mmtt) cc_final: 0.7190 (mmtp) REVERT: o 111 LYS cc_start: 0.6874 (ttpp) cc_final: 0.6509 (tmtt) REVERT: p 84 LYS cc_start: 0.7304 (mmtt) cc_final: 0.6300 (ttpm) REVERT: q 13 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7693 (ttt90) REVERT: q 18 GLN cc_start: 0.6917 (tt0) cc_final: 0.6576 (mt0) REVERT: q 97 LYS cc_start: 0.7396 (ttmm) cc_final: 0.7088 (tttp) REVERT: s 1 MET cc_start: 0.3573 (ttp) cc_final: 0.3278 (tmm) REVERT: s 4 GLU cc_start: 0.5603 (tt0) cc_final: 0.4986 (tp30) REVERT: s 73 ARG cc_start: 0.6078 (ttm170) cc_final: 0.5638 (ttm-80) REVERT: t 10 GLU cc_start: 0.6629 (tp30) cc_final: 0.6375 (mm-30) REVERT: t 24 LYS cc_start: 0.7648 (ttmm) cc_final: 0.7390 (ttmt) REVERT: u 1 MET cc_start: 0.4452 (OUTLIER) cc_final: 0.4207 (ttm) REVERT: u 42 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7425 (mt) REVERT: u 48 MET cc_start: 0.7074 (tpt) cc_final: 0.6853 (tpt) REVERT: u 50 MET cc_start: 0.6238 (mtp) cc_final: 0.5852 (ttm) REVERT: u 59 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.5798 (mp0) REVERT: u 68 LYS cc_start: 0.5579 (mmtm) cc_final: 0.5110 (mttt) REVERT: u 71 LYS cc_start: 0.6861 (mmtp) cc_final: 0.6340 (mppt) REVERT: v 44 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7604 (ttmm) REVERT: v 66 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7636 (mtmt) REVERT: x 30 MET cc_start: 0.6242 (OUTLIER) cc_final: 0.5583 (mtm) REVERT: x 45 GLN cc_start: 0.7121 (mt0) cc_final: 0.6893 (mt0) REVERT: x 49 ASP cc_start: 0.6631 (m-30) cc_final: 0.6373 (m-30) REVERT: x 58 ASN cc_start: 0.7438 (OUTLIER) cc_final: 0.6949 (t0) REVERT: y 11 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7598 (mtt90) REVERT: y 49 ASN cc_start: 0.8086 (t0) cc_final: 0.7846 (t0) REVERT: y 58 GLU cc_start: 0.5593 (tp30) cc_final: 0.4981 (mp0) REVERT: z 46 ASP cc_start: 0.6376 (OUTLIER) cc_final: 0.6136 (m-30) REVERT: 1 29 GLN cc_start: 0.8001 (mt0) cc_final: 0.7755 (mt0) REVERT: 2 16 LYS cc_start: 0.7963 (tttp) cc_final: 0.7563 (tttt) REVERT: 2 19 LYS cc_start: 0.7736 (mtmt) cc_final: 0.7407 (mtmt) REVERT: 3 8 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7685 (ptmt) REVERT: 3 36 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6599 (ttp-170) REVERT: 4 22 MET cc_start: 0.6891 (mtt) cc_final: 0.6002 (mtp) REVERT: 4 33 ASN cc_start: 0.5420 (m-40) cc_final: 0.5002 (p0) REVERT: 4 59 ARG cc_start: 0.4215 (OUTLIER) cc_final: 0.3874 (ppt170) outliers start: 199 outliers final: 131 residues processed: 956 average time/residue: 2.2926 time to fit residues: 3070.0619 Evaluate side-chains 1011 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 837 time to evaluate : 6.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 119 ARG Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 85 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 97 LYS Chi-restraints excluded: chain N residue 98 LYS Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 68 ASP Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 197 THR Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain f residue 78 LYS Chi-restraints excluded: chain f residue 111 ILE Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 98 GLU Chi-restraints excluded: chain i residue 136 GLN Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 13 LYS Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 74 THR Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain l residue 136 MET Chi-restraints excluded: chain m residue 98 LEU Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 68 LYS Chi-restraints excluded: chain n residue 116 GLN Chi-restraints excluded: chain o residue 27 GLU Chi-restraints excluded: chain o residue 87 LYS Chi-restraints excluded: chain q residue 13 ARG Chi-restraints excluded: chain q residue 19 THR Chi-restraints excluded: chain q residue 49 ILE Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 27 SER Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain t residue 88 GLU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 42 LEU Chi-restraints excluded: chain u residue 59 GLU Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain v residue 44 LYS Chi-restraints excluded: chain v residue 66 LYS Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain x residue 30 MET Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain x residue 58 ASN Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain z residue 46 ASP Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 54 ASP Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 59 ARG Chi-restraints excluded: chain 4 residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 886 optimal weight: 9.9990 chunk 583 optimal weight: 10.0000 chunk 940 optimal weight: 0.7980 chunk 573 optimal weight: 9.9990 chunk 446 optimal weight: 10.0000 chunk 653 optimal weight: 10.0000 chunk 986 optimal weight: 10.0000 chunk 907 optimal weight: 10.0000 chunk 785 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 606 optimal weight: 10.0000 overall best weight: 6.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN C 140 ASN D 116 GLN D 136 GLN E 78 ASN E 97 GLN F 55 HIS ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN K 64 GLN L 73 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN d 94 GLN e 156 ASN g 64 GLN n 38 GLN u 24 ASN v 3 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 153997 Z= 0.303 Angle : 0.812 16.462 230462 Z= 0.432 Chirality : 0.042 0.359 29304 Planarity : 0.008 0.149 12266 Dihedral : 23.113 178.022 77231 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.49 % Favored : 95.44 % Rotamer: Outliers : 4.35 % Allowed : 18.73 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.11), residues: 5480 helix: 0.60 (0.11), residues: 1899 sheet: -0.29 (0.15), residues: 1090 loop : -0.72 (0.12), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 248 HIS 0.010 0.001 HIS k 35 PHE 0.024 0.002 PHE B 50 TYR 0.029 0.003 TYR r 38 ARG 0.013 0.001 ARG T 60 ********************** 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 1045 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 846 time to evaluate : 6.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 LYS cc_start: 0.4536 (ttmm) cc_final: 0.3760 (tmtt) REVERT: B 115 LYS cc_start: 0.2708 (mttm) cc_final: 0.2359 (ttpt) REVERT: B 153 ASP cc_start: 0.2939 (m-30) cc_final: 0.2259 (t0) REVERT: B 161 LEU cc_start: 0.4664 (mp) cc_final: 0.4363 (mm) REVERT: B 174 LYS cc_start: 0.3108 (tptp) cc_final: 0.2611 (mmmm) REVERT: C 38 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.5621 (mptp) REVERT: C 45 LYS cc_start: 0.6572 (tmtt) cc_final: 0.6132 (mptt) REVERT: C 72 ARG cc_start: 0.5480 (mtp85) cc_final: 0.4466 (mmt180) REVERT: C 86 LYS cc_start: 0.6440 (ttmm) cc_final: 0.5577 (tptp) REVERT: C 89 LYS cc_start: 0.6083 (mtmt) cc_final: 0.5254 (ttmt) REVERT: C 108 LYS cc_start: 0.6654 (OUTLIER) cc_final: 0.6410 (ptmt) REVERT: C 134 MET cc_start: 0.7567 (mtp) cc_final: 0.7122 (mtm) REVERT: C 135 LYS cc_start: 0.7050 (mttt) cc_final: 0.6455 (tttm) REVERT: D 73 ARG cc_start: 0.6673 (tpt-90) cc_final: 0.6090 (ttp-170) REVERT: D 126 ASN cc_start: 0.5905 (m-40) cc_final: 0.5327 (t0) REVERT: D 128 ARG cc_start: 0.5131 (ttt90) cc_final: 0.4910 (mmm-85) REVERT: D 159 LEU cc_start: 0.4287 (mt) cc_final: 0.3792 (mt) REVERT: D 179 GLU cc_start: 0.5059 (OUTLIER) cc_final: 0.4612 (tt0) REVERT: F 29 ILE cc_start: 0.5854 (OUTLIER) cc_final: 0.5641 (mm) REVERT: F 74 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6185 (tp) REVERT: F 102 MET cc_start: 0.5615 (OUTLIER) cc_final: 0.5228 (ptp) REVERT: G 40 GLU cc_start: 0.6453 (mm-30) cc_final: 0.6038 (mm-30) REVERT: G 92 ARG cc_start: 0.4569 (mtm110) cc_final: 0.4263 (ptp-170) REVERT: G 106 GLU cc_start: 0.6932 (pt0) cc_final: 0.6606 (pt0) REVERT: H 3 MET cc_start: 0.7150 (tpp) cc_final: 0.6591 (tpp) REVERT: H 5 ASP cc_start: 0.7517 (t0) cc_final: 0.7241 (t0) REVERT: H 26 THR cc_start: 0.6658 (OUTLIER) cc_final: 0.6370 (p) REVERT: H 69 LYS cc_start: 0.6409 (mtpp) cc_final: 0.6081 (mptp) REVERT: H 88 ARG cc_start: 0.6263 (mtm110) cc_final: 0.5635 (mtp85) REVERT: H 89 LYS cc_start: 0.6766 (ttpt) cc_final: 0.6205 (tptm) REVERT: H 90 ASP cc_start: 0.6017 (p0) cc_final: 0.5308 (t0) REVERT: H 114 ARG cc_start: 0.6542 (ttm110) cc_final: 0.6316 (ttt180) REVERT: I 46 MET cc_start: 0.5219 (tpp) cc_final: 0.4874 (tpp) REVERT: I 49 ARG cc_start: 0.6300 (mtm-85) cc_final: 0.5812 (mtt-85) REVERT: I 68 LYS cc_start: 0.6963 (mtpp) cc_final: 0.6398 (mtpt) REVERT: I 119 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.6385 (ptm160) REVERT: J 11 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7798 (mttp) REVERT: J 15 HIS cc_start: 0.6924 (p-80) cc_final: 0.6423 (p-80) REVERT: J 102 LEU cc_start: 0.3909 (OUTLIER) cc_final: 0.3666 (mm) REVERT: K 32 VAL cc_start: 0.7518 (t) cc_final: 0.7270 (t) REVERT: K 80 LYS cc_start: 0.6286 (mptt) cc_final: 0.5929 (mmtm) REVERT: K 83 GLU cc_start: 0.6021 (mt-10) cc_final: 0.5716 (mt-10) REVERT: K 98 ARG cc_start: 0.5602 (ttm-80) cc_final: 0.5013 (ttm170) REVERT: L 88 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7223 (tmmt) REVERT: L 102 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.6204 (mt) REVERT: L 108 LYS cc_start: 0.5521 (mmtt) cc_final: 0.5283 (mmtp) REVERT: L 121 ARG cc_start: 0.6388 (ttt90) cc_final: 0.5907 (ttt-90) REVERT: M 21 SER cc_start: 0.7929 (m) cc_final: 0.7569 (p) REVERT: M 93 ARG cc_start: 0.5906 (mmp80) cc_final: 0.5364 (mpt-90) REVERT: M 104 THR cc_start: 0.6733 (OUTLIER) cc_final: 0.6280 (p) REVERT: N 6 MET cc_start: 0.7549 (mmm) cc_final: 0.7285 (mmp) REVERT: N 92 GLU cc_start: 0.6578 (mt-10) cc_final: 0.6106 (mm-30) REVERT: N 98 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7839 (mmtp) REVERT: O 58 ARG cc_start: 0.6835 (ttt180) cc_final: 0.6501 (ttp-170) REVERT: O 59 MET cc_start: 0.7911 (mtt) cc_final: 0.7438 (mtt) REVERT: O 71 LYS cc_start: 0.7392 (tttm) cc_final: 0.6933 (tptp) REVERT: O 82 ILE cc_start: 0.6830 (pt) cc_final: 0.6537 (pp) REVERT: Q 11 ARG cc_start: 0.5716 (mtp-110) cc_final: 0.4867 (mmm-85) REVERT: Q 41 THR cc_start: 0.7590 (m) cc_final: 0.7320 (p) REVERT: Q 61 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7169 (pt) REVERT: R 38 LYS cc_start: 0.7267 (mttm) cc_final: 0.6913 (mtpp) REVERT: T 27 MET cc_start: 0.7484 (tmt) cc_final: 0.7079 (tmt) REVERT: U 39 GLU cc_start: 0.7110 (tt0) cc_final: 0.6632 (tt0) REVERT: U 45 ARG cc_start: 0.5705 (OUTLIER) cc_final: 0.5042 (mtm-85) REVERT: U 60 LEU cc_start: 0.3996 (OUTLIER) cc_final: 0.3268 (mp) REVERT: c 97 LYS cc_start: 0.7438 (mmmm) cc_final: 0.7194 (mptt) REVERT: c 111 LYS cc_start: 0.7183 (mtmm) cc_final: 0.6617 (mttt) REVERT: c 115 GLN cc_start: 0.7105 (mm-40) cc_final: 0.6607 (tt0) REVERT: c 183 LYS cc_start: 0.8133 (mtmm) cc_final: 0.7863 (mtmt) REVERT: c 187 ASP cc_start: 0.6958 (m-30) cc_final: 0.6531 (m-30) REVERT: c 269 ARG cc_start: 0.7149 (ttp-110) cc_final: 0.6559 (ttm170) REVERT: d 18 ASP cc_start: 0.5788 (OUTLIER) cc_final: 0.5549 (p0) REVERT: d 40 LEU cc_start: 0.7646 (mt) cc_final: 0.7383 (mt) REVERT: d 74 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6052 (tp30) REVERT: d 128 ARG cc_start: 0.7307 (mmt180) cc_final: 0.6946 (mpt90) REVERT: d 181 ASP cc_start: 0.6018 (t0) cc_final: 0.5758 (t0) REVERT: e 1 MET cc_start: 0.3497 (OUTLIER) cc_final: 0.2127 (mpp) REVERT: e 22 ASP cc_start: 0.5583 (t0) cc_final: 0.5227 (p0) REVERT: e 140 ASP cc_start: 0.5496 (m-30) cc_final: 0.5116 (m-30) REVERT: f 11 GLU cc_start: 0.5540 (OUTLIER) cc_final: 0.5244 (mp0) REVERT: f 42 GLU cc_start: 0.5787 (pm20) cc_final: 0.5482 (pm20) REVERT: f 81 GLN cc_start: 0.7755 (tt0) cc_final: 0.7547 (tt0) REVERT: f 96 MET cc_start: 0.7619 (ttp) cc_final: 0.7190 (ttp) REVERT: f 101 GLU cc_start: 0.6702 (tt0) cc_final: 0.6396 (tm-30) REVERT: g 10 VAL cc_start: 0.5255 (OUTLIER) cc_final: 0.4790 (t) REVERT: g 115 HIS cc_start: 0.6873 (t70) cc_final: 0.6598 (t-90) REVERT: g 155 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6025 (pp20) REVERT: h 1 MET cc_start: 0.4103 (OUTLIER) cc_final: 0.2186 (ttt) REVERT: h 12 LEU cc_start: 0.4570 (OUTLIER) cc_final: 0.3453 (mm) REVERT: i 49 ASP cc_start: 0.8089 (t0) cc_final: 0.7855 (t70) REVERT: i 96 ARG cc_start: 0.6400 (mmm160) cc_final: 0.5944 (ptt-90) REVERT: i 136 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7557 (mt0) REVERT: j 14 SER cc_start: 0.8453 (p) cc_final: 0.8204 (p) REVERT: j 53 LYS cc_start: 0.7138 (mmtm) cc_final: 0.6716 (mmtt) REVERT: j 58 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7951 (pt) REVERT: k 2 ARG cc_start: 0.6130 (mmm-85) cc_final: 0.5150 (mmt-90) REVERT: l 53 MET cc_start: 0.7774 (ptp) cc_final: 0.7559 (ptm) REVERT: l 115 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6536 (tm-30) REVERT: l 133 LYS cc_start: 0.7502 (ttpt) cc_final: 0.7172 (ttpt) REVERT: m 65 LEU cc_start: 0.8172 (mt) cc_final: 0.7875 (mp) REVERT: m 98 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7645 (mp) REVERT: n 13 ARG cc_start: 0.6910 (ttp80) cc_final: 0.6400 (ttm-80) REVERT: n 19 GLN cc_start: 0.7146 (tt0) cc_final: 0.6641 (tp40) REVERT: n 24 THR cc_start: 0.7586 (m) cc_final: 0.7201 (p) REVERT: n 68 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7505 (mtmp) REVERT: n 98 GLN cc_start: 0.7955 (tp40) cc_final: 0.7137 (mm-40) REVERT: o 6 LYS cc_start: 0.6225 (ttpp) cc_final: 0.5793 (mtpt) REVERT: o 38 LYS cc_start: 0.6886 (ptmm) cc_final: 0.6210 (pttm) REVERT: o 44 GLU cc_start: 0.7762 (tt0) cc_final: 0.7473 (tt0) REVERT: o 87 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7348 (mmmt) REVERT: o 106 LYS cc_start: 0.7615 (mmtt) cc_final: 0.7224 (mmtp) REVERT: o 111 LYS cc_start: 0.6869 (ttpp) cc_final: 0.6503 (tmtt) REVERT: p 84 LYS cc_start: 0.7299 (mmtt) cc_final: 0.6287 (ttpm) REVERT: q 13 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7689 (ttt90) REVERT: q 18 GLN cc_start: 0.6914 (tt0) cc_final: 0.6516 (mt0) REVERT: q 97 LYS cc_start: 0.7410 (ttmm) cc_final: 0.7132 (ttpp) REVERT: s 1 MET cc_start: 0.3533 (ttp) cc_final: 0.2908 (tpt) REVERT: s 4 GLU cc_start: 0.5628 (tt0) cc_final: 0.5009 (tp30) REVERT: s 73 ARG cc_start: 0.6077 (ttm170) cc_final: 0.5637 (ttm-80) REVERT: t 10 GLU cc_start: 0.6628 (tp30) cc_final: 0.6368 (mm-30) REVERT: t 24 LYS cc_start: 0.7644 (ttmm) cc_final: 0.7387 (ttmt) REVERT: u 1 MET cc_start: 0.4459 (OUTLIER) cc_final: 0.4213 (ttm) REVERT: u 42 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7414 (mt) REVERT: u 48 MET cc_start: 0.7057 (tpt) cc_final: 0.6789 (tpt) REVERT: u 50 MET cc_start: 0.6210 (mtp) cc_final: 0.5832 (ttm) REVERT: u 59 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.5805 (mp0) REVERT: u 68 LYS cc_start: 0.5561 (mmtm) cc_final: 0.5087 (mttt) REVERT: u 71 LYS cc_start: 0.6911 (mmtp) cc_final: 0.6360 (mppt) REVERT: v 44 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7642 (ttmm) REVERT: v 66 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7683 (mtmt) REVERT: x 30 MET cc_start: 0.6269 (OUTLIER) cc_final: 0.5564 (mtm) REVERT: x 45 GLN cc_start: 0.7177 (mt0) cc_final: 0.6948 (mt0) REVERT: x 49 ASP cc_start: 0.6634 (m-30) cc_final: 0.6375 (m-30) REVERT: x 58 ASN cc_start: 0.7437 (OUTLIER) cc_final: 0.6945 (t0) REVERT: y 11 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7612 (mtt90) REVERT: y 49 ASN cc_start: 0.8082 (t0) cc_final: 0.7858 (t0) REVERT: y 58 GLU cc_start: 0.5618 (tp30) cc_final: 0.4968 (mp0) REVERT: z 46 ASP cc_start: 0.6371 (OUTLIER) cc_final: 0.6108 (m-30) REVERT: 1 29 GLN cc_start: 0.8019 (mt0) cc_final: 0.7772 (mt0) REVERT: 2 16 LYS cc_start: 0.7964 (tttp) cc_final: 0.7566 (tttt) REVERT: 2 19 LYS cc_start: 0.7741 (mtmt) cc_final: 0.7414 (mtmt) REVERT: 3 8 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7612 (ptmt) REVERT: 3 36 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6633 (ttp-170) REVERT: 4 22 MET cc_start: 0.6883 (mtt) cc_final: 0.6028 (mtp) REVERT: 4 24 ILE cc_start: 0.6842 (pt) cc_final: 0.6621 (pt) REVERT: 4 33 ASN cc_start: 0.5452 (m-40) cc_final: 0.5012 (p0) REVERT: 4 59 ARG cc_start: 0.4240 (OUTLIER) cc_final: 0.3893 (ppt170) outliers start: 199 outliers final: 133 residues processed: 962 average time/residue: 2.2973 time to fit residues: 3094.7269 Evaluate side-chains 1017 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 841 time to evaluate : 5.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 119 ARG Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 85 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 33 ASP Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 97 LYS Chi-restraints excluded: chain N residue 98 LYS Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 68 ASP Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain S residue 18 LYS Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain U residue 45 ARG Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 170 VAL Chi-restraints excluded: chain d residue 197 THR Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain f residue 11 GLU Chi-restraints excluded: chain f residue 78 LYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 98 GLU Chi-restraints excluded: chain i residue 136 GLN Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 114 LYS Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 13 LYS Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 74 THR Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain l residue 136 MET Chi-restraints excluded: chain m residue 98 LEU Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 43 ASN Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 68 LYS Chi-restraints excluded: chain n residue 116 GLN Chi-restraints excluded: chain o residue 27 GLU Chi-restraints excluded: chain o residue 87 LYS Chi-restraints excluded: chain q residue 13 ARG Chi-restraints excluded: chain q residue 19 THR Chi-restraints excluded: chain q residue 49 ILE Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 27 SER Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain t residue 88 GLU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 42 LEU Chi-restraints excluded: chain u residue 59 GLU Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain v residue 44 LYS Chi-restraints excluded: chain v residue 66 LYS Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain x residue 30 MET Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain x residue 58 ASN Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 10 THR Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain y residue 57 VAL Chi-restraints excluded: chain z residue 46 ASP Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 54 ASP Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 59 ARG Chi-restraints excluded: chain 4 residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 481 optimal weight: 10.0000 chunk 623 optimal weight: 10.0000 chunk 836 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 724 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 786 optimal weight: 7.9990 chunk 329 optimal weight: 0.7980 chunk 807 optimal weight: 7.9990 chunk 99 optimal weight: 30.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN C 140 ASN D 116 GLN D 136 GLN E 78 ASN E 97 GLN F 55 HIS ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN I 75 GLN K 64 GLN L 73 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS d 32 ASN d 94 GLN e 156 ASN g 64 GLN n 38 GLN u 24 ASN v 3 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.161093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.140085 restraints weight = 132634.982| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 0.33 r_work: 0.3321 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work: 0.3143 rms_B_bonded: 4.67 restraints_weight: 0.1250 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 153997 Z= 0.303 Angle : 0.812 16.373 230462 Z= 0.432 Chirality : 0.042 0.359 29304 Planarity : 0.008 0.149 12266 Dihedral : 23.111 178.009 77231 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.53 % Favored : 95.40 % Rotamer: Outliers : 4.31 % Allowed : 18.91 % Favored : 76.79 % 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: -0.33 (0.11), residues: 5480 helix: 0.59 (0.11), residues: 1899 sheet: -0.30 (0.15), residues: 1091 loop : -0.72 (0.12), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 248 HIS 0.009 0.001 HIS k 35 PHE 0.024 0.002 PHE B 50 TYR 0.031 0.003 TYR C 42 ARG 0.012 0.001 ARG O 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44956.62 seconds wall clock time: 780 minutes 5.00 seconds (46805.00 seconds total)