Starting phenix.real_space_refine on Fri Mar 22 14:36:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6w_29786/03_2024/8g6w_29786_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6w_29786/03_2024/8g6w_29786.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6w_29786/03_2024/8g6w_29786_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6w_29786/03_2024/8g6w_29786_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6w_29786/03_2024/8g6w_29786_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6w_29786/03_2024/8g6w_29786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6w_29786/03_2024/8g6w_29786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6w_29786/03_2024/8g6w_29786_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6w_29786/03_2024/8g6w_29786_updated.pdb" } resolution = 2.02 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= 0.005 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: 8 Type Number sf(0) Gaussians K 14 8.98 5 Zn 2 6.06 5 P 4557 5.49 5 Mg 320 5.21 5 S 150 5.16 5 C 71161 2.51 5 N 26456 2.21 5 O 43089 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 32": "OE1" <-> "OE2" 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 10": "OE1" <-> "OE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F GLU 65": "OE1" <-> "OE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "I GLU 53": "OE1" <-> "OE2" Residue "I GLU 97": "OE1" <-> "OE2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "J GLU 24": "OE1" <-> "OE2" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "M TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M GLU 59": "OE1" <-> "OE2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "N GLU 26": "OE1" <-> "OE2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O GLU 45": "OE1" <-> "OE2" Residue "Q GLU 18": "OE1" <-> "OE2" Residue "Q GLU 26": "OE1" <-> "OE2" Residue "Q GLU 60": "OE1" <-> "OE2" Residue "Q GLU 80": "OE1" <-> "OE2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R GLU 20": "OE1" <-> "OE2" Residue "S GLU 20": "OE1" <-> "OE2" Residue "S GLU 73": "OE1" <-> "OE2" Residue "T GLU 15": "OE1" <-> "OE2" Residue "T GLU 40": "OE1" <-> "OE2" Residue "U GLU 8": "OE1" <-> "OE2" Residue "U GLU 10": "OE1" <-> "OE2" Residue "U GLU 24": "OE1" <-> "OE2" Residue "U GLU 31": "OE1" <-> "OE2" Residue "U GLU 39": "OE1" <-> "OE2" Residue "U GLU 44": "OE1" <-> "OE2" Residue "U GLU 63": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d GLU 17": "OE1" <-> "OE2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d GLU 81": "OE1" <-> "OE2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d GLU 86": "OE1" <-> "OE2" Residue "d ARG 128": "NH1" <-> "NH2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d GLU 183": "OE1" <-> "OE2" Residue "e GLU 16": "OE1" <-> "OE2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ASP 168": "OD1" <-> "OD2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "e GLU 198": "OE1" <-> "OE2" Residue "f GLU 11": "OE1" <-> "OE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f ARG 102": "NH1" <-> "NH2" Residue "f ARG 110": "NH1" <-> "NH2" Residue "f ARG 112": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "f TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 164": "OE1" <-> "OE2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g GLU 32": "OE1" <-> "OE2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g GLU 155": "OE1" <-> "OE2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "g GLU 173": "OE1" <-> "OE2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "i PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i ARG 37": "NH1" <-> "NH2" Residue "i ARG 96": "NH1" <-> "NH2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "k ARG 21": "NH1" <-> "NH2" Residue "k ARG 33": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k ARG 47": "NH1" <-> "NH2" Residue "k ARG 60": "NH1" <-> "NH2" Residue "k ARG 78": "NH1" <-> "NH2" Residue "k GLU 86": "OE1" <-> "OE2" Residue "k GLU 115": "OE1" <-> "OE2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "l ARG 10": "NH1" <-> "NH2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ARG 40": "NH1" <-> "NH2" Residue "l ARG 44": "NH1" <-> "NH2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "l GLU 115": "OE1" <-> "OE2" Residue "m ARG 12": "NH1" <-> "NH2" Residue "m ARG 17": "NH1" <-> "NH2" Residue "m ARG 22": "NH1" <-> "NH2" Residue "m ARG 46": "NH1" <-> "NH2" 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 GLU 74": "OE1" <-> "OE2" 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 GLU 60": "OE1" <-> "OE2" Residue "n ARG 81": "NH1" <-> "NH2" Residue "n ARG 94": "NH1" <-> "NH2" Residue "n ARG 102": "NH1" <-> "NH2" Residue "n ARG 111": "NH1" <-> "NH2" Residue "n GLU 112": "OE1" <-> "OE2" Residue "o ARG 21": "NH1" <-> "NH2" 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 GLU 89": "OE1" <-> "OE2" Residue "p GLU 111": "OE1" <-> "OE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q GLU 34": "OE1" <-> "OE2" Residue "q GLU 45": "OE1" <-> "OE2" Residue "q ARG 68": "NH1" <-> "NH2" Residue "q GLU 70": "OE1" <-> "OE2" Residue "q ARG 79": "NH1" <-> "NH2" Residue "q ARG 84": "NH1" <-> "NH2" Residue "r GLU 2": "OE1" <-> "OE2" Residue "r 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 25": "OE1" <-> "OE2" Residue "s GLU 54": "OE1" <-> "OE2" Residue "s GLU 56": "OE1" <-> "OE2" Residue "s ARG 73": "NH1" <-> "NH2" Residue "s GLU 89": "OE1" <-> "OE2" Residue "t ARG 6": "NH1" <-> "NH2" Residue "t ARG 7": "NH1" <-> "NH2" Residue "t ARG 82": "NH1" <-> "NH2" Residue "t ARG 86": "NH1" <-> "NH2" Residue "t ARG 94": "NH1" <-> "NH2" Residue "u GLU 55": "OE1" <-> "OE2" Residue "u GLU 59": "OE1" <-> "OE2" Residue "u GLU 69": "OE1" <-> "OE2" Residue "v GLU 17": "OE1" <-> "OE2" Residue "w ARG 3": "NH1" <-> "NH2" Residue "w ARG 11": "NH1" <-> "NH2" Residue "w ARG 37": "NH1" <-> "NH2" Residue "w ARG 50": "NH1" <-> "NH2" Residue "w ARG 57": "NH1" <-> "NH2" Residue "w ARG 74": "NH1" <-> "NH2" Residue "x GLU 8": "OE1" <-> "OE2" Residue "x GLU 12": "OE1" <-> "OE2" Residue "x GLU 13": "OE1" <-> "OE2" Residue "x ARG 29": "NH1" <-> "NH2" Residue "x ARG 47": "NH1" <-> "NH2" Residue "x ARG 52": "NH1" <-> "NH2" Residue "y ARG 11": "NH1" <-> "NH2" Residue "y ARG 30": "NH1" <-> "NH2" Residue "y GLU 37": "OE1" <-> "OE2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "z ARG 52": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 145749 Number of models: 1 Model: "" Number of chains: 97 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: "A" Number of atoms: 32612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32612 Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 120, 'rna2p_pyr': 81, 'rna3p': 10, 'rna3p_pur': 742, 'rna3p_pyr': 565} Link IDs: {'rna2p': 202, 'rna3p': 1316} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 839 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "G" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1203 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 785 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 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: "X" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 317 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 5, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 12} Chain: "Y" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1578 Classifications: {'RNA': 74} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 32, 'rna3p_pyr': 28} Link IDs: {'rna2p': 13, 'rna3p': 60} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1601 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'rna2p': 9, 'rna3p': 65} Chain: "a" Number of atoms: 59170 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2753, 59130 Classifications: {'RNA': 2753} Modifications used: {'rna2p': 6, 'rna2p_pur': 266, 'rna2p_pyr': 141, 'rna3p': 17, 'rna3p_pur': 1319, 'rna3p_pyr': 1004} Link IDs: {'rna2p': 412, 'rna3p': 2340} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Conformer: "B" Number of residues, atoms: 2753, 59130 Classifications: {'RNA': 2753} Modifications used: {'rna2p': 6, 'rna2p_pur': 266, 'rna2p_pyr': 141, 'rna3p': 17, 'rna3p_pur': 1319, 'rna3p_pyr': 1004} Link IDs: {'rna2p': 412, 'rna3p': 2340} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 bond proxies already assigned to first conformer: 66180 Chain: "b" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 58, 'rna3p_pyr': 49} Link IDs: {'rna2p': 12, 'rna3p': 106} 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: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 582 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} 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: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 131 Unusual residues: {' MG': 89, 'PAR': 1} Classifications: {'undetermined': 90} Link IDs: {None: 89} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'2AE': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' MG': 1, '8AN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "a" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 310 Unusual residues: {' K': 13, ' MG': 217, 'SPD': 7} Classifications: {'peptide': 1, 'undetermined': 237} Link IDs: {None: 237} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "c" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' MG': 1, 'SPD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "p" 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: "1" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "2" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "a" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3197, 3197 Classifications: {'water': 3197} Link IDs: {None: 3196} Chain: "b" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "c" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "d" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "e" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "j" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "k" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "l" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "m" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "o" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "p" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "q" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "r" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "s" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "u" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "v" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "w" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "z" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1383 SG CYS 3 11 156.010 84.869 164.087 1.00 14.19 S ATOM 1408 SG CYS 3 14 153.617 82.974 161.682 1.00 11.35 S ATOM 1511 SG CYS 3 27 152.789 83.404 165.293 1.00 10.81 S ATOM 1730 SG CYS 4 16 208.205 153.172 92.470 1.00 19.15 S ATOM 1742 SG CYS 4 18 211.106 154.100 94.854 1.00 22.59 S ATOM 1884 SG CYS 4 37 209.818 150.197 94.429 1.00 22.01 S ATOM 1905 SG CYS 4 40 208.620 153.002 96.396 1.00 24.60 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A U a2491 " occ=0.50 ... (38 atoms not shown) pdb=" C6 B U a2491 " occ=0.50 residue: pdb=" P A U a2492 " occ=0.50 ... (38 atoms not shown) pdb=" C6 B U a2492 " occ=0.50 Time building chain proxies: 80.27, per 1000 atoms: 0.55 Number of scatterers: 145749 At special positions: 0 Unit cell: (232.142, 256.838, 269.186, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 K 14 19.00 S 150 16.00 P 4557 15.00 Mg 320 11.99 O 43089 8.00 N 26456 7.00 C 71161 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 69.18 Conformation dependent library (CDL) restraints added in 8.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 40 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 18 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 16 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 37 " Number of angles added : 9 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10262 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: 175 helices and 66 sheets defined 39.4% alpha, 19.8% beta 1568 base pairs and 2262 stacking pairs defined. Time for finding SS restraints: 87.82 Creating SS restraints... Processing helix chain '0' and resid 26 through 31 Proline residue: 0 31 - end of helix No H-bonds generated for 'chain '0' and resid 26 through 31' Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.136A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 removed outlier: 3.620A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 32 through 37 removed outlier: 4.945A pdb=" N LYS 2 36 " --> pdb=" O ILE 2 32 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ALA 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 32 through 37' Processing helix chain '2' and resid 38 through 46 Proline residue: 2 46 - end of helix Processing helix chain '2' and resid 51 through 63 removed outlier: 4.312A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 5.092A 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 removed outlier: 3.516A pdb=" N THR 4 45 " --> pdb=" O HIS 4 41 " (cutoff:3.500A) Processing helix chain '4' and resid 55 through 64 removed outlier: 3.687A pdb=" N ARG 4 59 " --> pdb=" O GLY 4 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.943A pdb=" N LYS B 28 " --> pdb=" O ASN B 24 " (cutoff:3.500A) Proline residue: B 29 - end of helix No H-bonds generated for 'chain 'B' and resid 24 through 29' Processing helix chain 'B' and resid 42 through 64 Proline residue: B 48 - end of helix removed outlier: 3.636A pdb=" N ALA B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 removed outlier: 3.641A pdb=" N SER B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 124 removed outlier: 4.783A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLY B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 148 removed outlier: 6.597A pdb=" N ALA B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU B 135 " --> pdb=" O LYS B 131 " (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 13 removed outlier: 3.872A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLY C 13 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 48 Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.625A pdb=" N VAL C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 78 " --> pdb=" O GLY C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 108 through 113 removed outlier: 4.061A pdb=" N ASP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 5.767A 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: 3.635A pdb=" N ARG C 127 " --> pdb=" O GLN C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 145 removed outlier: 3.600A pdb=" N ALA C 133 " --> pdb=" O MET C 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.400A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.861A 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 82 Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.912A pdb=" N ARG D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 110 through 121 removed outlier: 3.999A pdb=" N LYS D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 removed outlier: 5.118A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 3.722A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.632A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.518A pdb=" N MET E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 147 removed outlier: 3.706A pdb=" N MET E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 14 through 33 removed outlier: 3.745A pdb=" N VAL F 18 " --> pdb=" O GLN F 14 " (cutoff:3.500A) Proline residue: F 19 - end of helix 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 Processing helix chain 'G' and resid 92 through 111 removed outlier: 3.864A pdb=" N ARG G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.729A pdb=" N ARG G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 153 removed outlier: 3.605A pdb=" N ASN G 148 " --> pdb=" O MET G 144 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ALA G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 5.557A 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 94 through 99 removed outlier: 5.412A pdb=" N GLY H 98 " --> pdb=" O LYS H 94 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 94 through 99' Processing helix chain 'H' and resid 112 through 120 removed outlier: 3.579A pdb=" N GLY H 120 " --> pdb=" O ALA H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 41 through 56 Proline residue: I 51 - end of helix removed outlier: 3.790A pdb=" N LEU I 54 " --> pdb=" O GLN I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 91 Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'J' and resid 14 through 33 removed outlier: 3.639A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 91 removed outlier: 3.753A pdb=" N VAL J 84 " --> pdb=" O THR J 80 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASP J 91 " --> pdb=" O LEU J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 51 removed outlier: 3.532A pdb=" N SER K 50 " --> pdb=" O THR K 46 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 46 through 51' Processing helix chain 'K' and resid 54 through 60 removed outlier: 3.844A pdb=" N THR K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix Processing helix chain 'K' and resid 61 through 76 removed outlier: 5.186A pdb=" N GLU K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 104 removed outlier: 3.872A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 4.003A 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 Processing helix chain 'M' and resid 14 through 21 removed outlier: 3.756A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 44 through 49 removed outlier: 4.343A pdb=" N LEU M 48 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER M 49 " --> pdb=" O ILE M 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 44 through 49' Processing helix chain 'M' and resid 50 through 63 removed outlier: 3.796A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.821A pdb=" N GLY M 84 " --> pdb=" O LEU M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 94 removed outlier: 3.631A pdb=" N GLY M 94 " --> pdb=" O ARG M 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 21 Processing helix chain 'N' and resid 22 through 33 removed outlier: 3.709A pdb=" N ASP N 33 " --> pdb=" O ALA N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 52 Proline residue: N 52 - end of helix Processing helix chain 'N' and resid 56 through 61 removed outlier: 3.947A pdb=" N GLN N 60 " --> pdb=" O SER N 56 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ARG N 61 " --> pdb=" O PRO N 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 56 through 61' Processing helix chain 'N' and resid 80 through 91 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 44 removed outlier: 4.344A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 74 removed outlier: 4.081A 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: 3.718A pdb=" N GLY P 64 " --> pdb=" O TRP P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 80 removed outlier: 4.081A pdb=" N LYS P 80 " --> pdb=" O LYS P 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.833A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 34 removed outlier: 3.905A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 5.448A 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 removed outlier: 3.816A pdb=" N SER S 25 " --> pdb=" O LYS S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 76 removed outlier: 4.718A 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 71 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: 3.832A pdb=" N LEU T 86 " --> pdb=" O GLN T 82 " (cutoff:3.500A) removed outlier: 3.672A 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 36 Processing helix chain 'U' and resid 40 through 69 removed outlier: 3.528A pdb=" N ARG U 66 " --> pdb=" O ARG U 62 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ARG U 67 " --> pdb=" O GLU U 63 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR U 68 " --> pdb=" O ASN U 64 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ARG U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 17 removed outlier: 4.924A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N VAL c 16 " --> pdb=" O GLY c 12 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL c 17 " --> pdb=" O ARG c 13 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 4.072A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.766A 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 Proline residue: c 136 - end of helix Processing helix chain 'c' and resid 207 through 215 removed outlier: 3.953A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 3.991A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.307A 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: 4.776A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 4.008A 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) Processing helix chain 'd' and resid 56 through 61 removed outlier: 3.509A pdb=" N VAL d 60 " --> pdb=" O LYS d 56 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N THR d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 56 through 61' Processing helix chain 'd' and resid 62 through 72 removed outlier: 3.680A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 103 removed outlier: 4.252A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 5.184A 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 24 through 40 removed outlier: 3.675A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 53 removed outlier: 6.416A 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: 3.517A pdb=" N LEU e 134 " --> pdb=" O LYS e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 163 removed outlier: 3.726A pdb=" N PHE e 158 " --> pdb=" O ASP e 154 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 removed outlier: 3.571A pdb=" N ILE e 181 " --> pdb=" O PRO e 177 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE e 183 " --> pdb=" O SER e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'e' and resid 16 through 21 Processing helix chain 'f' and resid 2 through 21 removed outlier: 5.643A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE f 20 " --> pdb=" O LEU f 16 " (cutoff:3.500A) Processing helix chain 'f' and resid 24 through 29 removed outlier: 4.061A pdb=" N VAL f 28 " --> pdb=" O SER f 24 " (cutoff:3.500A) Proline residue: f 29 - end of helix No H-bonds generated for 'chain 'f' and resid 24 through 29' Processing helix chain 'f' and resid 42 through 47 removed outlier: 4.155A pdb=" N ASP f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) removed outlier: 4.048A 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 removed outlier: 3.897A pdb=" N ALA f 55 " --> pdb=" O ASP f 51 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU f 57 " --> pdb=" O ALA f 53 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA f 59 " --> pdb=" O ALA f 55 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 111 removed outlier: 3.734A pdb=" N ALA f 107 " --> pdb=" O LEU f 103 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 removed outlier: 3.812A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP f 174 " --> pdb=" O LEU f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 134 through 139 removed outlier: 3.642A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE f 138 " --> pdb=" O GLN f 135 " (cutoff:3.500A) Proline residue: f 139 - end of helix No H-bonds generated for 'chain 'f' and resid 134 through 139' Processing helix chain 'g' and resid 2 through 8 removed outlier: 4.514A 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: 5.214A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL g 79 " --> pdb=" O MET g 75 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU g 81 " --> pdb=" O ILE g 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 4.432A 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: 3.696A pdb=" N GLY h 34 " --> pdb=" O LEU h 30 " (cutoff:3.500A) Processing helix chain 'i' and resid 24 through 38 removed outlier: 3.954A 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: 4.372A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 3.690A 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 123 removed outlier: 4.004A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LYS i 123 " --> pdb=" O PHE i 119 " (cutoff:3.500A) Processing helix chain 'j' and resid 104 through 109 removed outlier: 4.528A pdb=" N ARG j 108 " --> pdb=" O THR j 104 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N SER j 109 " --> pdb=" O ARG j 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 104 through 109' Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'k' and resid 56 through 62 Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 3.910A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 78 through 85 removed outlier: 3.817A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 3.828A 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 removed outlier: 3.507A pdb=" N ALA k 138 " --> pdb=" O ALA k 134 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY k 139 " --> pdb=" O ILE k 135 " (cutoff:3.500A) Processing helix chain 'l' and resid 42 through 58 Processing helix chain 'l' and resid 109 through 125 removed outlier: 4.203A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 3.840A 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: 4.174A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 4.454A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP m 58 " --> pdb=" O LEU m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 4.019A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 4.841A 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: 3.747A pdb=" N ALA n 6 " --> pdb=" O ASP n 2 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 3.737A pdb=" N GLU n 60 " --> pdb=" O LYS n 56 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 6.178A 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: 3.520A pdb=" N GLY n 114 " --> pdb=" O ALA n 110 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 13 removed outlier: 3.827A pdb=" N GLU o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.470A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.292A 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: 3.568A pdb=" N LYS p 22 " --> pdb=" O LEU p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.668A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 32 through 37 removed outlier: 3.694A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 73 removed outlier: 3.822A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 87 Processing helix chain 'p' and resid 91 through 102 Processing helix chain 'p' and resid 103 through 118 Processing helix chain 'r' and resid 13 through 25 removed outlier: 3.879A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 40 removed outlier: 3.508A pdb=" N TYR r 38 " --> pdb=" O ASP r 34 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASN r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 61 removed outlier: 3.595A pdb=" N VAL r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 65 through 70 removed outlier: 3.918A pdb=" N LEU r 69 " --> pdb=" O ASP r 65 " (cutoff:3.500A) removed outlier: 5.720A 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: 3.741A pdb=" N LYS s 9 " --> pdb=" O GLU s 5 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL s 10 " --> pdb=" O ARG s 6 " (cutoff:3.500A) removed outlier: 4.443A 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 50 Processing helix chain 't' and resid 66 through 71 removed outlier: 3.964A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.391A 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: 3.520A pdb=" N ASN u 24 " --> pdb=" O LEU u 20 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 53 removed outlier: 3.589A pdb=" N ALA u 52 " --> pdb=" O MET u 48 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 3.702A 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: 3.944A pdb=" N GLU x 8 " --> pdb=" O LYS x 4 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N SER x 10 " --> pdb=" O LEU x 6 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 35 removed outlier: 3.569A pdb=" N GLY x 35 " --> pdb=" O GLN x 31 " (cutoff:3.500A) Processing helix chain 'x' and resid 40 through 62 removed outlier: 4.411A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (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: 4.905A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 19 through 24 removed outlier: 6.104A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE 0 48 " --> pdb=" O SER 0 14 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '2' and resid 22 through 25 removed outlier: 5.637A pdb=" N PHE 2 22 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '3' and resid 1 through 5 removed outlier: 7.325A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER 3 28 " --> pdb=" O ASN 3 13 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N ASN 3 13 " --> pdb=" O SER 3 28 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '4' and resid 20 through 25 removed outlier: 4.131A pdb=" N ASN 4 20 " --> pdb=" O CYS 4 16 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 67 through 71 Processing sheet with id= 6, first strand: chain 'C' and resid 53 through 59 removed outlier: 3.798A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 164 through 169 removed outlier: 6.469A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 141 through 145 removed outlier: 3.676A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 180 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET D 178 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU D 179 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 12 through 16 removed outlier: 6.453A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 84 through 88 removed outlier: 3.690A pdb=" N GLY E 87 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 33 through 40 Processing sheet with id= 12, first strand: chain 'F' and resid 38 through 43 removed outlier: 5.805A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 44 through 47 removed outlier: 6.405A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 73 through 79 Processing sheet with id= 15, first strand: chain 'H' and resid 24 through 27 removed outlier: 3.558A pdb=" N GLU H 58 " --> pdb=" O GLU H 52 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 74 through 77 removed outlier: 4.378A pdb=" N SER H 74 " --> pdb=" O ALA H 130 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'I' and resid 5 through 11 removed outlier: 4.347A pdb=" N ALA I 16 " --> pdb=" O GLY I 69 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLY I 69 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ARG I 18 " --> pdb=" O VAL I 67 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL I 67 " --> pdb=" O ARG I 18 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N PHE I 20 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE I 65 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LYS I 22 " --> pdb=" O LEU I 63 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU I 63 " --> pdb=" O LYS I 22 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY I 24 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS I 27 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL I 29 " --> pdb=" O LEU I 63 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'J' and resid 42 through 52 removed outlier: 5.086A pdb=" N LEU J 71 " --> pdb=" O PRO J 43 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU J 47 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE J 67 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL J 74 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS J 11 " --> pdb=" O ASP J 97 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'K' and resid 42 through 45 removed outlier: 3.518A pdb=" N VAL K 20 " --> pdb=" O THR K 35 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 83 through 88 removed outlier: 5.936A pdb=" N GLY K 88 " --> pdb=" O VAL K 113 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'L' and resid 29 through 33 removed outlier: 5.201A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'L' and resid 35 through 41 removed outlier: 3.693A pdb=" N ARG L 36 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'P' and resid 4 through 10 removed outlier: 6.567A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Q' and resid 7 through 11 removed outlier: 7.237A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Q' and resid 19 through 30 No H-bonds generated for sheet with id= 25 Processing sheet with id= 26, first strand: chain 'S' and resid 30 through 34 removed outlier: 3.537A pdb=" N ALA S 50 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS S 52 " --> pdb=" O THR S 33 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU S 47 " --> pdb=" O VAL S 62 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL S 51 " --> pdb=" O VAL S 58 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'c' and resid 73 through 78 removed outlier: 4.762A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'c' and resid 80 through 83 removed outlier: 5.313A pdb=" N ASN c 90 " --> pdb=" O ALA c 106 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'c' and resid 138 through 142 removed outlier: 4.220A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'd' and resid 3 through 6 removed outlier: 4.117A pdb=" N GLU d 168 " --> pdb=" O SER d 113 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'd' and resid 10 through 16 removed outlier: 3.654A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'd' and resid 79 through 84 removed outlier: 5.883A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'd' and resid 105 through 108 removed outlier: 6.374A 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: 4.444A pdb=" N MET e 1 " --> pdb=" O VAL e 14 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'e' and resid 44 through 47 No H-bonds generated for sheet with id= 35 Processing sheet with id= 36, first strand: chain 'e' and resid 117 through 120 removed outlier: 5.762A pdb=" N ARG e 117 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'f' and resid 65 through 69 removed outlier: 6.420A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS f 33 " --> pdb=" O THR f 157 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'g' and resid 15 through 20 removed outlier: 5.723A pdb=" N GLN g 22 " --> pdb=" O LEU g 37 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY g 31 " --> pdb=" O GLY g 28 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'g' and resid 94 through 99 removed outlier: 6.508A pdb=" N ASN g 101 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'g' and resid 121 through 125 removed outlier: 6.077A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL g 90 " --> pdb=" O GLY g 161 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY g 161 " --> pdb=" O VAL g 90 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'h' and resid 1 through 5 removed outlier: 3.772A pdb=" N LEU h 5 " --> pdb=" O ASP h 17 " (cutoff:3.500A) removed outlier: 4.783A 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: 4.861A 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: 7.345A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'j' and resid 17 through 21 removed outlier: 6.347A pdb=" N ARG j 17 " --> pdb=" O VAL j 10 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL j 10 " --> pdb=" O ARG j 17 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ASN j 82 " --> pdb=" O MET j 7 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'l' and resid 37 through 40 No H-bonds generated for sheet with id= 45 Processing sheet with id= 46, first strand: chain 'l' and resid 62 through 65 removed outlier: 3.506A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU l 33 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS l 100 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'l' and resid 73 through 76 removed outlier: 6.924A pdb=" N ILE l 73 " --> pdb=" O GLU l 90 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'l' and resid 30 through 36 removed outlier: 7.719A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'm' and resid 33 through 37 removed outlier: 5.790A pdb=" N ALA m 108 " --> pdb=" O PHE m 102 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE m 102 " --> pdb=" O ALA m 108 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N MET m 110 " --> pdb=" O CYS m 100 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'n' and resid 49 through 52 removed outlier: 3.794A pdb=" N VAL n 49 " --> pdb=" O VAL n 39 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'o' and resid 49 through 53 removed outlier: 3.728A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG o 53 " --> pdb=" O HIS o 56 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR o 60 " --> pdb=" O ILE o 48 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'o' and resid 57 through 64 removed outlier: 7.607A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'q' and resid 11 through 15 removed outlier: 3.702A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU q 39 " --> pdb=" O GLY q 50 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU q 46 " --> pdb=" O ASN q 43 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'q' and resid 18 through 23 removed outlier: 4.098A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU q 31 " --> pdb=" O VAL q 63 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 56, first strand: chain 'q' and resid 65 through 68 removed outlier: 3.554A pdb=" N ALA q 65 " --> pdb=" O ASP q 95 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.262A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'r' and resid 2 through 8 Processing sheet with id= 59, first strand: chain 's' and resid 12 through 15 removed outlier: 5.288A pdb=" N VAL s 31 " --> pdb=" O HIS s 15 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS s 81 " --> pdb=" O VAL s 34 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 't' and resid 83 through 87 Processing sheet with id= 61, first strand: chain 'u' and resid 69 through 72 removed outlier: 3.728A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'v' and resid 51 through 54 removed outlier: 4.270A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'v' and resid 65 through 71 Processing sheet with id= 64, first strand: chain 'w' and resid 11 through 19 No H-bonds generated for sheet with id= 64 Processing sheet with id= 65, first strand: chain 'w' and resid 35 through 41 removed outlier: 3.549A pdb=" N ARG w 45 " --> pdb=" O VAL w 40 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.252A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) 1837 hydrogen bonds defined for protein. 5448 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3949 hydrogen bonds 6178 hydrogen bond angles 0 basepair planarities 1568 basepair parallelities 2263 stacking parallelities Total time for adding SS restraints: 610.74 Time building geometry restraints manager: 74.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 22103 1.33 - 1.46: 68862 1.46 - 1.59: 54251 1.59 - 1.72: 8593 1.72 - 1.84: 266 Bond restraints: 154075 Sorted by residual: bond pdb=" C4 5MU a1939 " pdb=" C5 5MU a1939 " ideal model delta sigma weight residual 1.802 1.480 0.322 2.00e-02 2.50e+03 2.60e+02 bond pdb=" C4 5MU a 747 " pdb=" C5 5MU a 747 " ideal model delta sigma weight residual 1.802 1.482 0.320 2.00e-02 2.50e+03 2.56e+02 bond pdb=" N1 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.635 1.327 0.308 2.00e-02 2.50e+03 2.37e+02 bond pdb=" N1 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.635 1.338 0.297 2.00e-02 2.50e+03 2.21e+02 bond pdb=" N ARG J 31 " pdb=" CA ARG J 31 " ideal model delta sigma weight residual 1.458 1.294 0.164 1.30e-02 5.92e+03 1.59e+02 ... (remaining 154070 not shown) Histogram of bond angle deviations from ideal: 81.64 - 92.92: 1 92.92 - 104.20: 16917 104.20 - 115.48: 114387 115.48 - 126.75: 86910 126.75 - 138.03: 12320 Bond angle restraints: 230535 Sorted by residual: angle pdb=" O3' G a2490 " pdb=" P B U a2491 " pdb=" O5'B U a2491 " ideal model delta sigma weight residual 104.00 81.64 22.36 1.50e+00 4.44e-01 2.22e+02 angle pdb=" C3' G a2490 " pdb=" O3' G a2490 " pdb=" P B U a2491 " ideal model delta sigma weight residual 120.20 103.85 16.35 1.50e+00 4.44e-01 1.19e+02 angle pdb=" C VAL l 80 " pdb=" N 4D4 l 81 " pdb=" CA 4D4 l 81 " ideal model delta sigma weight residual 121.70 106.76 14.94 1.80e+00 3.09e-01 6.89e+01 angle pdb=" C3' A Z 72 " pdb=" O3' A Z 72 " pdb=" P A Z 73 " ideal model delta sigma weight residual 120.20 108.13 12.07 1.50e+00 4.44e-01 6.47e+01 angle pdb=" C3'A U a2491 " pdb=" O3'A U a2491 " pdb=" P A U a2492 " ideal model delta sigma weight residual 120.20 109.41 10.79 1.50e+00 4.44e-01 5.17e+01 ... (remaining 230530 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 86477 35.84 - 71.69: 10967 71.69 - 107.53: 1211 107.53 - 143.38: 14 143.38 - 179.22: 13 Dihedral angle restraints: 98682 sinusoidal: 82776 harmonic: 15906 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 -128.48 -51.52 0 5.00e+00 4.00e-02 1.06e+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 -128.52 -51.48 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA ASN g 48 " pdb=" C ASN g 48 " pdb=" N THR g 49 " pdb=" CA THR g 49 " ideal model delta harmonic sigma weight residual 180.00 133.39 46.61 0 5.00e+00 4.00e-02 8.69e+01 ... (remaining 98679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 28628 0.110 - 0.219: 689 0.219 - 0.329: 21 0.329 - 0.439: 29 0.439 - 0.548: 13 Chirality restraints: 29380 Sorted by residual: chirality pdb=" CA ARG J 31 " pdb=" N ARG J 31 " pdb=" C ARG J 31 " pdb=" CB ARG J 31 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.51e+00 chirality pdb=" P U X 19 " pdb=" OP1 U X 19 " pdb=" OP2 U X 19 " pdb=" O5' U X 19 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CB D2T L 89 " pdb=" CA D2T L 89 " pdb=" SB D2T L 89 " pdb=" CG D2T L 89 " both_signs ideal model delta sigma weight residual False -3.02 -3.51 0.49 2.00e-01 2.50e+01 5.90e+00 ... (remaining 29377 not shown) Planarity restraints: 12250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " -0.089 2.00e-02 2.50e+03 6.14e-01 8.49e+03 pdb=" C4' 5MC A1407 " -0.435 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " -0.572 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " 0.598 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " 0.702 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " 0.137 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " -1.044 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " -0.226 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " 0.928 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a2445 " -0.060 2.00e-02 2.50e+03 6.12e-01 8.43e+03 pdb=" C4' 2MG a2445 " -0.443 2.00e-02 2.50e+03 pdb=" O4' 2MG a2445 " -0.716 2.00e-02 2.50e+03 pdb=" C3' 2MG a2445 " 0.608 2.00e-02 2.50e+03 pdb=" O3' 2MG a2445 " 0.623 2.00e-02 2.50e+03 pdb=" C2' 2MG a2445 " 0.201 2.00e-02 2.50e+03 pdb=" O2' 2MG a2445 " -0.959 2.00e-02 2.50e+03 pdb=" C1' 2MG a2445 " -0.203 2.00e-02 2.50e+03 pdb=" N9 2MG a2445 " 0.950 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC a2498 " -0.069 2.00e-02 2.50e+03 5.97e-01 8.01e+03 pdb=" C4' OMC a2498 " -0.433 2.00e-02 2.50e+03 pdb=" O4' OMC a2498 " -0.586 2.00e-02 2.50e+03 pdb=" C3' OMC a2498 " 0.604 2.00e-02 2.50e+03 pdb=" O3' OMC a2498 " 0.654 2.00e-02 2.50e+03 pdb=" C2' OMC a2498 " 0.164 2.00e-02 2.50e+03 pdb=" O2' OMC a2498 " -0.999 2.00e-02 2.50e+03 pdb=" C1' OMC a2498 " -0.229 2.00e-02 2.50e+03 pdb=" N1 OMC a2498 " 0.895 2.00e-02 2.50e+03 ... (remaining 12247 not shown) Histogram of nonbonded interaction distances: 1.22 - 2.01: 227 2.01 - 2.79: 36022 2.79 - 3.57: 263484 3.57 - 4.36: 591502 4.36 - 5.14: 791697 Nonbonded interactions: 1682932 Sorted by model distance: nonbonded pdb=" N10 SPD a6211 " pdb=" O HOH a6301 " model vdw 1.223 2.520 nonbonded pdb="MG MG a6165 " pdb=" O HOH a9102 " model vdw 1.614 2.170 nonbonded pdb=" K K a6214 " pdb=" O HOH a9425 " model vdw 1.651 2.850 nonbonded pdb="MG MG a6234 " pdb=" O HOH a9242 " model vdw 1.686 2.170 nonbonded pdb="MG MG a6138 " pdb=" O HOH a9341 " model vdw 1.709 2.170 ... (remaining 1682927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 4.660 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: 0.120 Extract box with map and model: 25.150 Check model and map are aligned: 1.660 Set scattering table: 1.020 Process input model: 982.160 Find NCS groups from input model: 3.200 Set up NCS constraints: 0.490 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:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 1029.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.006 0.322 154075 Z= 0.361 Angle : 0.813 22.360 230535 Z= 0.425 Chirality : 0.045 0.548 29380 Planarity : 0.018 0.614 12250 Dihedral : 23.384 179.223 88420 Min Nonbonded Distance : 1.223 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 6.74 % Allowed : 21.00 % Favored : 72.27 % 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: -2.71 (0.10), residues: 5473 helix: -2.15 (0.09), residues: 1842 sheet: -1.21 (0.15), residues: 1027 loop : -1.66 (0.11), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP l 64 HIS 0.011 0.002 HIS k 35 PHE 0.025 0.002 PHE d 118 TYR 0.024 0.002 TYR r 38 ARG 0.008 0.001 ARG p 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1420 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 1112 time to evaluate : 6.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 1 MET cc_start: 0.8310 (tpp) cc_final: 0.7957 (tpp) REVERT: B 63 ARG cc_start: 0.3343 (OUTLIER) cc_final: 0.3014 (ttp-110) REVERT: C 88 ARG cc_start: 0.4237 (tmt90) cc_final: 0.3945 (tmt90) REVERT: D 3 ARG cc_start: 0.5131 (mtp-110) cc_final: 0.4851 (ttm-80) REVERT: D 156 LYS cc_start: 0.3892 (mtmm) cc_final: 0.3636 (pttm) REVERT: E 20 ARG cc_start: 0.7455 (ttp-170) cc_final: 0.7176 (ttp-170) REVERT: H 5 ASP cc_start: 0.6917 (t0) cc_final: 0.6698 (t0) REVERT: K 55 SER cc_start: 0.6250 (OUTLIER) cc_final: 0.5941 (t) REVERT: L 77 HIS cc_start: 0.5298 (m90) cc_final: 0.5076 (m90) REVERT: P 24 SER cc_start: 0.7031 (OUTLIER) cc_final: 0.6800 (m) REVERT: R 14 THR cc_start: 0.4094 (OUTLIER) cc_final: 0.3757 (p) REVERT: S 14 HIS cc_start: 0.3994 (OUTLIER) cc_final: 0.3603 (p90) REVERT: T 8 LYS cc_start: 0.5770 (mttm) cc_final: 0.5549 (mtmm) REVERT: U 35 ARG cc_start: 0.8056 (mtt-85) cc_final: 0.7792 (mtt90) REVERT: d 202 ILE cc_start: 0.8501 (mp) cc_final: 0.8256 (mp) REVERT: g 149 ARG cc_start: 0.7377 (ttt-90) cc_final: 0.7083 (ttp80) REVERT: k 115 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.5987 (tm-30) REVERT: l 7 THR cc_start: 0.7580 (p) cc_final: 0.7377 (p) REVERT: l 53 MET cc_start: 0.7561 (ttm) cc_final: 0.7348 (ttm) REVERT: m 18 GLN cc_start: 0.8244 (tt0) cc_final: 0.8027 (tt0) REVERT: m 110 MET cc_start: 0.8890 (mmm) cc_final: 0.8420 (mmm) REVERT: t 33 LYS cc_start: 0.7801 (mttt) cc_final: 0.7574 (mttm) outliers start: 308 outliers final: 45 residues processed: 1345 average time/residue: 2.4507 time to fit residues: 4578.3754 Evaluate side-chains 861 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 810 time to evaluate : 6.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 57 ARG Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain S residue 14 HIS Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain k residue 115 GLU Chi-restraints excluded: chain m residue 6 SER Chi-restraints excluded: chain o residue 80 VAL Chi-restraints excluded: chain p residue 87 SER Chi-restraints excluded: chain s residue 27 SER Chi-restraints excluded: chain s residue 53 VAL Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain w residue 22 LEU Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain y residue 59 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 834 optimal weight: 4.9990 chunk 748 optimal weight: 5.9990 chunk 415 optimal weight: 20.0000 chunk 255 optimal weight: 6.9990 chunk 505 optimal weight: 9.9990 chunk 400 optimal weight: 1.9990 chunk 774 optimal weight: 8.9990 chunk 299 optimal weight: 8.9990 chunk 470 optimal weight: 10.0000 chunk 576 optimal weight: 9.9990 chunk 897 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 20 ASN 4 48 GLN B 122 GLN C 3 GLN ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN E 77 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 ASN I 4 ASN I 110 GLN O 62 GLN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN R 54 GLN ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN c 86 ASN d 185 ASN e 195 GLN ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 ASN j 93 GLN k 93 ASN k 104 GLN o 3 ASN p 81 ASN r 31 GLN s 92 ASN u 12 GLN x 20 ASN z 42 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 154075 Z= 0.352 Angle : 0.900 18.977 230535 Z= 0.457 Chirality : 0.046 0.471 29380 Planarity : 0.009 0.147 12250 Dihedral : 23.370 179.544 77478 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.93 % Favored : 95.98 % Rotamer: Outliers : 5.53 % Allowed : 21.72 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.11), residues: 5473 helix: -0.39 (0.11), residues: 1892 sheet: -0.73 (0.15), residues: 1070 loop : -0.78 (0.12), residues: 2511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP c 248 HIS 0.014 0.003 HIS C 176 PHE 0.021 0.003 PHE E 33 TYR 0.037 0.003 TYR g 164 ARG 0.016 0.001 ARG l 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 873 time to evaluate : 6.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 ARG cc_start: 0.3729 (OUTLIER) cc_final: 0.3401 (ttp-170) REVERT: B 111 ILE cc_start: 0.5834 (OUTLIER) cc_final: 0.5202 (mp) REVERT: C 53 SER cc_start: 0.4210 (OUTLIER) cc_final: 0.3837 (m) REVERT: C 62 LYS cc_start: 0.2519 (OUTLIER) cc_final: 0.1821 (tptp) REVERT: C 88 ARG cc_start: 0.4344 (tmt90) cc_final: 0.3955 (tmt90) REVERT: C 107 ARG cc_start: 0.3379 (OUTLIER) cc_final: 0.3055 (tpp-160) REVERT: C 132 ARG cc_start: 0.4411 (OUTLIER) cc_final: 0.4042 (tmm160) REVERT: D 3 ARG cc_start: 0.5501 (mtp-110) cc_final: 0.5065 (ttm-80) REVERT: D 177 LYS cc_start: 0.3366 (OUTLIER) cc_final: 0.2275 (mmtt) REVERT: F 21 MET cc_start: 0.6065 (mtp) cc_final: 0.5776 (mtp) REVERT: G 78 ARG cc_start: 0.2932 (tpt170) cc_final: 0.2699 (tpt-90) REVERT: G 111 ARG cc_start: 0.4304 (OUTLIER) cc_final: 0.3986 (mmt90) REVERT: G 123 GLU cc_start: 0.5031 (tm-30) cc_final: 0.4700 (mm-30) REVERT: G 143 ARG cc_start: 0.4624 (OUTLIER) cc_final: 0.4279 (ptm-80) REVERT: H 27 MET cc_start: 0.6637 (mtm) cc_final: 0.6330 (mtm) REVERT: H 31 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6163 (pttt) REVERT: I 85 ARG cc_start: 0.6027 (OUTLIER) cc_final: 0.4906 (mpt-90) REVERT: J 14 ASP cc_start: 0.5965 (OUTLIER) cc_final: 0.5064 (p0) REVERT: J 32 THR cc_start: 0.3302 (OUTLIER) cc_final: 0.3027 (t) REVERT: J 45 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.6197 (tmt170) REVERT: K 56 ARG cc_start: 0.5717 (OUTLIER) cc_final: 0.5349 (mtp180) REVERT: K 116 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7786 (mp) REVERT: L 111 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6245 (mptt) REVERT: M 44 LYS cc_start: 0.5245 (OUTLIER) cc_final: 0.5033 (pttm) REVERT: P 24 SER cc_start: 0.7513 (OUTLIER) cc_final: 0.7155 (m) REVERT: R 25 ASP cc_start: 0.5367 (OUTLIER) cc_final: 0.4958 (p0) REVERT: T 27 MET cc_start: 0.6204 (ttp) cc_final: 0.5716 (tmm) REVERT: U 21 ARG cc_start: 0.5598 (mmt90) cc_final: 0.5319 (mtt90) REVERT: U 35 ARG cc_start: 0.8236 (mtt-85) cc_final: 0.7961 (mtt90) REVERT: c 189 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8004 (mtt90) REVERT: f 17 MET cc_start: 0.4630 (tpt) cc_final: 0.4193 (tpt) REVERT: f 113 ASP cc_start: 0.4284 (m-30) cc_final: 0.3940 (m-30) REVERT: f 142 ASP cc_start: 0.3684 (t70) cc_final: 0.3250 (t70) REVERT: g 149 ARG cc_start: 0.7430 (ttt-90) cc_final: 0.7081 (ttt-90) REVERT: g 151 TYR cc_start: 0.6499 (m-80) cc_final: 0.5360 (m-10) REVERT: k 115 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6542 (mm-30) REVERT: l 8 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7161 (pttt) REVERT: m 110 MET cc_start: 0.9165 (mmm) cc_final: 0.8818 (mmm) REVERT: n 19 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6803 (tm-30) REVERT: q 43 ASN cc_start: 0.6899 (t0) cc_final: 0.6580 (t0) REVERT: t 22 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.6895 (mtm-85) REVERT: t 47 LYS cc_start: 0.6859 (tptt) cc_final: 0.6458 (mttm) REVERT: t 97 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7373 (mttm) REVERT: u 85 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7645 (mttm) REVERT: x 52 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7778 (mtt90) REVERT: y 39 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7112 (pt0) outliers start: 253 outliers final: 72 residues processed: 1054 average time/residue: 2.5285 time to fit residues: 3690.0031 Evaluate side-chains 912 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 811 time to evaluate : 6.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 22 LYS Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 56 ARG Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 44 LYS Chi-restraints excluded: chain M residue 65 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 19 LYS Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 25 ASP Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain c residue 189 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain e residue 2 GLU Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 55 SER Chi-restraints excluded: chain e residue 107 SER Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 91 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 48 ASN Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 92 LEU Chi-restraints excluded: chain k residue 115 GLU Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain o residue 80 VAL Chi-restraints excluded: chain q residue 46 GLU Chi-restraints excluded: chain s residue 27 SER Chi-restraints excluded: chain t residue 22 ARG Chi-restraints excluded: chain t residue 97 LYS Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 85 LYS Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain w residue 22 LEU Chi-restraints excluded: chain x residue 52 ARG Chi-restraints excluded: chain y residue 39 GLU Chi-restraints excluded: chain y residue 59 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 498 optimal weight: 8.9990 chunk 278 optimal weight: 8.9990 chunk 746 optimal weight: 0.5980 chunk 610 optimal weight: 10.0000 chunk 247 optimal weight: 6.9990 chunk 898 optimal weight: 0.5980 chunk 970 optimal weight: 5.9990 chunk 800 optimal weight: 0.3980 chunk 891 optimal weight: 4.9990 chunk 306 optimal weight: 0.0170 chunk 721 optimal weight: 0.7980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 177 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 54 GLN E 132 ASN F 3 HIS ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 ASN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN J 58 ASN O 62 GLN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 83 HIS ** T 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 HIS T 84 ASN c 115 GLN d 32 ASN e 115 GLN e 195 GLN f 27 GLN i 136 GLN j 29 HIS j 93 GLN k 93 ASN m 18 GLN o 3 ASN p 20 GLN q 12 HIS r 31 GLN t 40 ASN u 12 GLN x 20 ASN x 39 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 154075 Z= 0.122 Angle : 0.595 13.310 230535 Z= 0.326 Chirality : 0.034 0.409 29380 Planarity : 0.006 0.125 12250 Dihedral : 23.107 178.511 77438 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.12 % Favored : 96.82 % Rotamer: Outliers : 3.28 % Allowed : 24.08 % Favored : 72.64 % 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: -0.12 (0.11), residues: 5473 helix: 0.70 (0.12), residues: 1899 sheet: -0.33 (0.15), residues: 1103 loop : -0.45 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 42 HIS 0.005 0.001 HIS E 89 PHE 0.018 0.001 PHE F 8 TYR 0.015 0.001 TYR r 38 ARG 0.007 0.000 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 863 time to evaluate : 6.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 ILE cc_start: 0.5557 (OUTLIER) cc_final: 0.4935 (mp) REVERT: B 116 ASP cc_start: 0.4175 (OUTLIER) cc_final: 0.3531 (t0) REVERT: G 111 ARG cc_start: 0.3931 (mtp85) cc_final: 0.3701 (mmm160) REVERT: G 143 ARG cc_start: 0.4587 (OUTLIER) cc_final: 0.4309 (ptm-80) REVERT: I 85 ARG cc_start: 0.5920 (OUTLIER) cc_final: 0.5594 (ttm170) REVERT: O 87 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6557 (mt) REVERT: R 25 ASP cc_start: 0.5120 (OUTLIER) cc_final: 0.4725 (p0) REVERT: S 66 MET cc_start: 0.4310 (OUTLIER) cc_final: 0.3886 (mtt) REVERT: T 27 MET cc_start: 0.6088 (ttp) cc_final: 0.5610 (tmm) REVERT: U 21 ARG cc_start: 0.5388 (mmt90) cc_final: 0.5170 (mtt90) REVERT: U 45 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7144 (ptp-110) REVERT: c 189 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7946 (mtt90) REVERT: d 161 MET cc_start: 0.9163 (mtt) cc_final: 0.8697 (mtp) REVERT: f 17 MET cc_start: 0.4589 (tpt) cc_final: 0.4297 (tpt) REVERT: g 155 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6915 (pp20) REVERT: k 115 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6227 (mm-30) REVERT: m 110 MET cc_start: 0.9054 (mmm) cc_final: 0.8708 (mmm) REVERT: n 98 GLN cc_start: 0.7430 (mm-40) cc_final: 0.7139 (tp40) REVERT: o 18 PRO cc_start: 0.8468 (Cg_endo) cc_final: 0.8239 (Cg_exo) REVERT: q 43 ASN cc_start: 0.6617 (t0) cc_final: 0.6404 (t0) outliers start: 150 outliers final: 30 residues processed: 958 average time/residue: 2.5060 time to fit residues: 3340.9077 Evaluate side-chains 831 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 790 time to evaluate : 6.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 5 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 25 ASP Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain U residue 45 ARG Chi-restraints excluded: chain c residue 189 ARG Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain k residue 115 GLU Chi-restraints excluded: chain o residue 80 VAL Chi-restraints excluded: chain x residue 54 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 888 optimal weight: 2.9990 chunk 675 optimal weight: 10.0000 chunk 466 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 428 optimal weight: 10.0000 chunk 603 optimal weight: 10.0000 chunk 902 optimal weight: 20.0000 chunk 955 optimal weight: 3.9990 chunk 471 optimal weight: 10.0000 chunk 854 optimal weight: 10.0000 chunk 257 optimal weight: 20.0000 overall best weight: 7.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN C 139 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN E 19 ASN E 61 GLN E 148 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 ASN G 86 GLN K 40 ASN O 62 GLN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN ** T 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 163 GLN d 32 ASN e 115 GLN e 195 GLN f 27 GLN ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 ASN o 7 GLN o 66 ASN ** r 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 61 ASN s 28 ASN t 40 ASN u 12 GLN ** x 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 154075 Z= 0.431 Angle : 0.984 22.372 230535 Z= 0.488 Chirality : 0.049 0.425 29380 Planarity : 0.009 0.158 12250 Dihedral : 23.314 179.140 77410 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.02 % Favored : 95.85 % Rotamer: Outliers : 5.10 % Allowed : 22.51 % Favored : 72.40 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.11), residues: 5473 helix: 0.16 (0.11), residues: 1902 sheet: -0.37 (0.15), residues: 1086 loop : -0.51 (0.12), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP c 248 HIS 0.011 0.003 HIS M 12 PHE 0.026 0.003 PHE F 8 TYR 0.025 0.004 TYR L 117 ARG 0.016 0.001 ARG O 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 843 time to evaluate : 6.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 ILE cc_start: 0.5910 (OUTLIER) cc_final: 0.5290 (mp) REVERT: B 116 ASP cc_start: 0.4532 (OUTLIER) cc_final: 0.3752 (t70) REVERT: B 222 ARG cc_start: 0.5169 (OUTLIER) cc_final: 0.4910 (mtm-85) REVERT: C 43 LEU cc_start: 0.1908 (OUTLIER) cc_final: 0.1703 (mp) REVERT: C 62 LYS cc_start: 0.2477 (OUTLIER) cc_final: 0.1968 (tptt) REVERT: F 39 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6152 (mt) REVERT: G 97 ASN cc_start: 0.4964 (OUTLIER) cc_final: 0.4661 (p0) REVERT: G 111 ARG cc_start: 0.4516 (OUTLIER) cc_final: 0.4165 (mmm160) REVERT: G 143 ARG cc_start: 0.4791 (OUTLIER) cc_final: 0.4565 (ptm-80) REVERT: H 31 LYS cc_start: 0.6749 (OUTLIER) cc_final: 0.6177 (pttt) REVERT: I 41 ARG cc_start: 0.5189 (ttp-170) cc_final: 0.4984 (ttp-170) REVERT: I 85 ARG cc_start: 0.6058 (OUTLIER) cc_final: 0.5073 (mpt-90) REVERT: K 116 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7743 (mp) REVERT: L 77 HIS cc_start: 0.5887 (m90) cc_final: 0.5501 (m90) REVERT: O 59 MET cc_start: 0.8402 (mtt) cc_final: 0.8130 (mtt) REVERT: P 57 ILE cc_start: 0.6752 (OUTLIER) cc_final: 0.6305 (mt) REVERT: R 25 ASP cc_start: 0.5368 (OUTLIER) cc_final: 0.4915 (p0) REVERT: T 28 MET cc_start: 0.6423 (ttp) cc_final: 0.6154 (ttp) REVERT: U 21 ARG cc_start: 0.5693 (mmt90) cc_final: 0.5334 (mtt90) REVERT: c 189 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8045 (mtt90) REVERT: e 191 ASP cc_start: 0.6116 (OUTLIER) cc_final: 0.5903 (m-30) REVERT: f 17 MET cc_start: 0.4663 (tpt) cc_final: 0.4308 (tpt) REVERT: f 19 GLU cc_start: 0.5303 (tt0) cc_final: 0.4778 (tt0) REVERT: f 164 GLU cc_start: 0.5341 (OUTLIER) cc_final: 0.5034 (mp0) REVERT: g 151 TYR cc_start: 0.6433 (m-80) cc_final: 0.5072 (m-10) REVERT: i 91 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8194 (mt-10) REVERT: j 66 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8263 (mtmm) REVERT: k 115 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6617 (mm-30) REVERT: l 8 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7161 (pttt) REVERT: m 110 MET cc_start: 0.9162 (mmm) cc_final: 0.8708 (mmm) REVERT: n 19 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6559 (tm-30) REVERT: n 46 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6247 (mt-10) REVERT: o 64 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7700 (mm) REVERT: t 22 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.6884 (mtm-85) REVERT: t 97 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7464 (mttm) REVERT: u 53 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6648 (mttp) REVERT: x 52 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7811 (mtt90) REVERT: y 39 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7174 (pt0) outliers start: 233 outliers final: 97 residues processed: 997 average time/residue: 2.4437 time to fit residues: 3383.7054 Evaluate side-chains 938 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 813 time to evaluate : 6.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 5 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 97 ASN Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 25 ASP Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 189 ARG Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 55 SER Chi-restraints excluded: chain e residue 107 SER Chi-restraints excluded: chain e residue 132 LYS Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 91 LEU Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 48 ASN Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain j residue 66 LYS Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 115 GLU Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 7 THR Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain o residue 32 VAL Chi-restraints excluded: chain o residue 64 ILE Chi-restraints excluded: chain o residue 80 VAL Chi-restraints excluded: chain p residue 87 SER Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain s residue 93 LEU Chi-restraints excluded: chain t residue 22 ARG Chi-restraints excluded: chain t residue 97 LYS Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 46 LYS Chi-restraints excluded: chain u residue 53 LYS Chi-restraints excluded: chain u residue 76 ASP Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain x residue 34 SER Chi-restraints excluded: chain x residue 52 ARG Chi-restraints excluded: chain y residue 39 GLU Chi-restraints excluded: chain y residue 59 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 795 optimal weight: 20.0000 chunk 542 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 711 optimal weight: 0.7980 chunk 394 optimal weight: 6.9990 chunk 814 optimal weight: 2.9990 chunk 660 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 487 optimal weight: 8.9990 chunk 857 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 20 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 43 ASN E 61 GLN E 148 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN M 12 HIS O 62 GLN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN S 83 HIS ** T 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN e 115 GLN e 195 GLN f 27 GLN g 111 HIS j 93 GLN k 93 ASN o 3 ASN o 7 GLN q 43 ASN r 31 GLN r 61 ASN t 40 ASN u 12 GLN x 25 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 154075 Z= 0.152 Angle : 0.630 13.435 230535 Z= 0.341 Chirality : 0.035 0.403 29380 Planarity : 0.006 0.132 12250 Dihedral : 23.103 179.102 77410 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.22 % Favored : 96.71 % Rotamer: Outliers : 3.57 % Allowed : 23.99 % Favored : 72.44 % 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: 0.07 (0.11), residues: 5473 helix: 0.83 (0.12), residues: 1917 sheet: -0.23 (0.15), residues: 1103 loop : -0.33 (0.12), residues: 2453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 201 HIS 0.005 0.001 HIS E 89 PHE 0.020 0.001 PHE F 8 TYR 0.016 0.002 TYR r 38 ARG 0.008 0.001 ARG U 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 828 time to evaluate : 6.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 ARG cc_start: 0.5205 (OUTLIER) cc_final: 0.4903 (ttm110) REVERT: C 62 LYS cc_start: 0.2426 (OUTLIER) cc_final: 0.2013 (tptp) REVERT: D 95 GLU cc_start: 0.4798 (mm-30) cc_final: 0.4562 (mm-30) REVERT: E 48 PHE cc_start: 0.7846 (p90) cc_final: 0.7616 (p90) REVERT: E 97 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6707 (tt0) REVERT: G 28 ASN cc_start: 0.7231 (m-40) cc_final: 0.6839 (m110) REVERT: G 111 ARG cc_start: 0.4224 (mtp85) cc_final: 0.3977 (mmm160) REVERT: H 21 ASN cc_start: 0.7335 (OUTLIER) cc_final: 0.6912 (m-40) REVERT: I 85 ARG cc_start: 0.5925 (OUTLIER) cc_final: 0.5602 (ttm170) REVERT: K 116 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7738 (mp) REVERT: L 29 GLN cc_start: 0.7539 (mp10) cc_final: 0.7297 (mp10) REVERT: L 36 ARG cc_start: 0.5887 (ttp80) cc_final: 0.5551 (ttp-110) REVERT: L 77 HIS cc_start: 0.5838 (m90) cc_final: 0.5497 (m90) REVERT: O 87 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6531 (mt) REVERT: R 25 ASP cc_start: 0.5166 (OUTLIER) cc_final: 0.4734 (p0) REVERT: S 66 MET cc_start: 0.4522 (OUTLIER) cc_final: 0.3912 (ptp) REVERT: U 17 ARG cc_start: 0.5667 (OUTLIER) cc_final: 0.5421 (mtp180) REVERT: U 21 ARG cc_start: 0.5498 (mmt90) cc_final: 0.5176 (mtt90) REVERT: U 33 ARG cc_start: 0.6396 (ttm170) cc_final: 0.6064 (mtt180) REVERT: U 35 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7784 (mtt90) REVERT: c 189 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8010 (mtt90) REVERT: e 168 ASP cc_start: 0.7172 (t0) cc_final: 0.6869 (t70) REVERT: f 17 MET cc_start: 0.4654 (tpt) cc_final: 0.4361 (tpt) REVERT: f 164 GLU cc_start: 0.5384 (OUTLIER) cc_final: 0.5076 (mp0) REVERT: g 151 TYR cc_start: 0.6164 (m-80) cc_final: 0.5867 (m-80) REVERT: g 155 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6981 (pp20) REVERT: i 91 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8170 (mt-10) REVERT: k 115 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6311 (mm-30) REVERT: m 110 MET cc_start: 0.9118 (mmm) cc_final: 0.8627 (mmm) REVERT: n 19 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6522 (tm-30) REVERT: o 66 ASN cc_start: 0.8265 (m110) cc_final: 0.7998 (m-40) REVERT: s 4 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6559 (tt0) REVERT: t 97 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7356 (mttm) REVERT: u 24 ASN cc_start: 0.6996 (OUTLIER) cc_final: 0.6714 (m110) REVERT: u 85 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7258 (mtmm) REVERT: y 39 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7006 (pt0) outliers start: 163 outliers final: 57 residues processed: 931 average time/residue: 2.5340 time to fit residues: 3276.2869 Evaluate side-chains 873 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 796 time to evaluate : 6.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 5 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 56 ARG Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 25 ASP Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain U residue 17 ARG Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 189 ARG Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 155 GLU Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 115 GLU Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain o residue 80 VAL Chi-restraints excluded: chain p residue 87 SER Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain s residue 4 GLU Chi-restraints excluded: chain t residue 97 LYS Chi-restraints excluded: chain u residue 24 ASN Chi-restraints excluded: chain u residue 76 ASP Chi-restraints excluded: chain u residue 85 LYS Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain y residue 39 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 321 optimal weight: 6.9990 chunk 860 optimal weight: 9.9990 chunk 188 optimal weight: 1.9990 chunk 560 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 chunk 955 optimal weight: 4.9990 chunk 793 optimal weight: 0.8980 chunk 442 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 316 optimal weight: 2.9990 chunk 501 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 20 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 ASN E 19 ASN E 61 GLN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN H 118 GLN J 58 ASN K 40 ASN L 72 HIS O 62 GLN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN ** T 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 163 GLN d 32 ASN e 115 GLN e 195 GLN f 27 GLN ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 HIS k 93 ASN o 3 ASN o 7 GLN o 15 GLN ** r 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 61 ASN x 20 ASN x 25 GLN x 39 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 154075 Z= 0.233 Angle : 0.720 16.004 230535 Z= 0.379 Chirality : 0.039 0.399 29380 Planarity : 0.007 0.143 12250 Dihedral : 23.129 179.746 77408 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.82 % Favored : 96.09 % Rotamer: Outliers : 3.52 % Allowed : 24.17 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.11), residues: 5473 helix: 0.76 (0.12), residues: 1921 sheet: -0.23 (0.15), residues: 1091 loop : -0.34 (0.12), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 248 HIS 0.006 0.001 HIS u 44 PHE 0.022 0.002 PHE F 8 TYR 0.021 0.002 TYR p 32 ARG 0.008 0.001 ARG R 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 811 time to evaluate : 6.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 VAL cc_start: 0.4661 (OUTLIER) cc_final: 0.4144 (t) REVERT: C 53 SER cc_start: 0.3990 (OUTLIER) cc_final: 0.3709 (m) REVERT: C 161 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5798 (tt0) REVERT: E 48 PHE cc_start: 0.7901 (p90) cc_final: 0.7665 (p90) REVERT: E 97 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6777 (tt0) REVERT: F 39 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6226 (mt) REVERT: G 28 ASN cc_start: 0.7242 (m-40) cc_final: 0.6847 (m110) REVERT: G 111 ARG cc_start: 0.4374 (mtp85) cc_final: 0.4067 (mmm160) REVERT: H 31 LYS cc_start: 0.6669 (OUTLIER) cc_final: 0.6147 (pttt) REVERT: I 85 ARG cc_start: 0.5996 (OUTLIER) cc_final: 0.5634 (ttm170) REVERT: K 116 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7695 (mp) REVERT: L 36 ARG cc_start: 0.5954 (ttp80) cc_final: 0.5605 (ttp-110) REVERT: L 77 HIS cc_start: 0.5874 (m90) cc_final: 0.5512 (m90) REVERT: O 87 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6566 (mt) REVERT: P 57 ILE cc_start: 0.6533 (OUTLIER) cc_final: 0.6122 (mt) REVERT: R 25 ASP cc_start: 0.5230 (OUTLIER) cc_final: 0.4785 (p0) REVERT: S 66 MET cc_start: 0.4506 (OUTLIER) cc_final: 0.3906 (ptp) REVERT: U 21 ARG cc_start: 0.5490 (mmt90) cc_final: 0.5165 (mtt90) REVERT: U 25 LYS cc_start: 0.5067 (OUTLIER) cc_final: 0.4746 (tptt) REVERT: U 62 ARG cc_start: 0.3061 (OUTLIER) cc_final: 0.2555 (ptp-170) REVERT: c 189 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8043 (mtt90) REVERT: e 168 ASP cc_start: 0.7160 (t0) cc_final: 0.6851 (t70) REVERT: f 17 MET cc_start: 0.4629 (tpt) cc_final: 0.4319 (tpt) REVERT: f 19 GLU cc_start: 0.5287 (tt0) cc_final: 0.4827 (tt0) REVERT: f 95 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6526 (mtp85) REVERT: f 164 GLU cc_start: 0.5328 (OUTLIER) cc_final: 0.5005 (mp0) REVERT: g 151 TYR cc_start: 0.6228 (m-80) cc_final: 0.5849 (m-80) REVERT: i 91 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8201 (mt-10) REVERT: k 115 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6554 (mm-30) REVERT: m 110 MET cc_start: 0.9147 (mmm) cc_final: 0.8658 (mmm) REVERT: n 19 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6498 (tm-30) REVERT: s 4 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6600 (tt0) REVERT: t 22 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.6840 (mtm-85) REVERT: t 97 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7375 (mttm) REVERT: u 85 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7274 (mtmm) REVERT: w 45 ARG cc_start: 0.6943 (ptt180) cc_final: 0.6553 (ppt170) REVERT: x 52 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7726 (mtt90) REVERT: y 39 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7089 (pt0) outliers start: 161 outliers final: 77 residues processed: 921 average time/residue: 2.5296 time to fit residues: 3229.4601 Evaluate side-chains 898 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 796 time to evaluate : 6.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 5 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 56 ARG Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 25 ASP Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 62 ARG Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 189 ARG Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 55 SER Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 95 ARG Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 115 GLU Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain o residue 32 VAL Chi-restraints excluded: chain o residue 80 VAL Chi-restraints excluded: chain p residue 87 SER Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain s residue 4 GLU Chi-restraints excluded: chain t residue 22 ARG Chi-restraints excluded: chain t residue 97 LYS Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 85 LYS Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain w residue 44 LYS Chi-restraints excluded: chain x residue 52 ARG Chi-restraints excluded: chain y residue 39 GLU Chi-restraints excluded: chain y residue 59 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 921 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 544 optimal weight: 10.0000 chunk 698 optimal weight: 20.0000 chunk 540 optimal weight: 10.0000 chunk 804 optimal weight: 9.9990 chunk 533 optimal weight: 9.9990 chunk 952 optimal weight: 7.9990 chunk 595 optimal weight: 10.0000 chunk 580 optimal weight: 9.9990 chunk 439 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 20 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 61 GLN E 148 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS J 58 ASN K 40 ASN O 62 GLN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN ** T 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 163 GLN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN f 27 GLN ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 HIS k 93 ASN o 7 GLN o 15 GLN ** r 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 20 ASN x 25 GLN x 39 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 154075 Z= 0.466 Angle : 1.026 23.512 230535 Z= 0.507 Chirality : 0.051 0.427 29380 Planarity : 0.009 0.164 12250 Dihedral : 23.361 178.691 77408 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.31 % Favored : 95.58 % Rotamer: Outliers : 4.16 % Allowed : 23.64 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.11), residues: 5473 helix: 0.05 (0.11), residues: 1902 sheet: -0.43 (0.15), residues: 1092 loop : -0.59 (0.12), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP C 167 HIS 0.011 0.003 HIS c 53 PHE 0.028 0.004 PHE F 8 TYR 0.025 0.004 TYR g 164 ARG 0.017 0.001 ARG R 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 812 time to evaluate : 6.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 37 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7930 (mttt) REVERT: 4 62 LYS cc_start: 0.4731 (OUTLIER) cc_final: 0.4170 (pttp) REVERT: C 53 SER cc_start: 0.4077 (OUTLIER) cc_final: 0.3671 (m) REVERT: C 62 LYS cc_start: 0.2797 (OUTLIER) cc_final: 0.2106 (tptt) REVERT: C 161 GLU cc_start: 0.6296 (OUTLIER) cc_final: 0.5766 (tt0) REVERT: D 44 ARG cc_start: 0.3034 (OUTLIER) cc_final: 0.2687 (ttm170) REVERT: D 147 GLU cc_start: 0.4551 (mp0) cc_final: 0.4235 (pm20) REVERT: F 16 GLU cc_start: 0.4608 (OUTLIER) cc_final: 0.4100 (mp0) REVERT: F 39 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6329 (mt) REVERT: G 78 ARG cc_start: 0.4668 (ttt-90) cc_final: 0.3923 (mmt180) REVERT: H 31 LYS cc_start: 0.6702 (OUTLIER) cc_final: 0.6182 (pttt) REVERT: I 85 ARG cc_start: 0.6080 (OUTLIER) cc_final: 0.5081 (mpt-90) REVERT: K 116 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7738 (mp) REVERT: R 25 ASP cc_start: 0.5359 (OUTLIER) cc_final: 0.4864 (p0) REVERT: S 44 MET cc_start: 0.3560 (OUTLIER) cc_final: 0.2841 (ttm) REVERT: S 66 MET cc_start: 0.4704 (OUTLIER) cc_final: 0.4149 (ptp) REVERT: U 25 LYS cc_start: 0.5180 (OUTLIER) cc_final: 0.4881 (tptt) REVERT: U 62 ARG cc_start: 0.3151 (OUTLIER) cc_final: 0.2642 (ptp-170) REVERT: c 189 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8067 (mtt90) REVERT: e 191 ASP cc_start: 0.6205 (OUTLIER) cc_final: 0.5905 (m-30) REVERT: f 17 MET cc_start: 0.4651 (tpt) cc_final: 0.4328 (tpt) REVERT: f 19 GLU cc_start: 0.5462 (tt0) cc_final: 0.4882 (tt0) REVERT: f 95 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6536 (mtp85) REVERT: i 2 LYS cc_start: 0.7766 (mtpt) cc_final: 0.7518 (tttp) REVERT: i 91 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8194 (mt-10) REVERT: k 115 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6593 (mm-30) REVERT: l 8 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7212 (pttt) REVERT: m 110 MET cc_start: 0.9161 (mmm) cc_final: 0.8671 (mmm) REVERT: n 19 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.6563 (tm-30) REVERT: n 46 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.6148 (mt-10) REVERT: o 64 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7667 (mm) REVERT: s 4 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6784 (tt0) REVERT: t 22 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.6894 (mtm-85) REVERT: t 97 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7441 (mttm) REVERT: u 24 ASN cc_start: 0.7112 (OUTLIER) cc_final: 0.6863 (m110) REVERT: u 85 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7340 (mtmm) REVERT: x 52 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7792 (mtt90) REVERT: y 39 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6952 (pt0) REVERT: z 12 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8472 (mmpt) outliers start: 190 outliers final: 97 residues processed: 941 average time/residue: 2.5556 time to fit residues: 3342.9236 Evaluate side-chains 923 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 794 time to evaluate : 5.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain 4 residue 62 LYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 25 ASP Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 62 ARG Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 189 ARG Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 55 SER Chi-restraints excluded: chain e residue 107 SER Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 95 ARG Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain i residue 12 LYS Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 92 LEU Chi-restraints excluded: chain k residue 115 GLU Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 7 THR Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain o residue 32 VAL Chi-restraints excluded: chain o residue 64 ILE Chi-restraints excluded: chain o residue 80 VAL Chi-restraints excluded: chain p residue 87 SER Chi-restraints excluded: chain q residue 59 ILE Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain s residue 4 GLU Chi-restraints excluded: chain t residue 22 ARG Chi-restraints excluded: chain t residue 97 LYS Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 24 ASN Chi-restraints excluded: chain u residue 76 ASP Chi-restraints excluded: chain u residue 85 LYS Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain x residue 52 ARG Chi-restraints excluded: chain y residue 39 GLU Chi-restraints excluded: chain y residue 59 GLU Chi-restraints excluded: chain z residue 12 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 589 optimal weight: 10.0000 chunk 380 optimal weight: 7.9990 chunk 568 optimal weight: 20.0000 chunk 286 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 184 optimal weight: 0.9980 chunk 605 optimal weight: 8.9990 chunk 648 optimal weight: 8.9990 chunk 470 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 748 optimal weight: 0.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 20 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 61 GLN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN O 62 GLN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN S 83 HIS ** T 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 163 GLN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN f 27 GLN g 111 HIS k 93 ASN o 3 ASN o 7 GLN ** r 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 20 ASN x 25 GLN x 39 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 154075 Z= 0.245 Angle : 0.749 16.024 230535 Z= 0.392 Chirality : 0.040 0.396 29380 Planarity : 0.007 0.144 12250 Dihedral : 23.190 179.777 77407 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.62 % Favored : 96.27 % Rotamer: Outliers : 3.52 % Allowed : 24.32 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.11), residues: 5473 helix: 0.52 (0.11), residues: 1907 sheet: -0.34 (0.15), residues: 1092 loop : -0.50 (0.12), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 248 HIS 0.006 0.002 HIS u 44 PHE 0.022 0.002 PHE F 8 TYR 0.020 0.002 TYR p 32 ARG 0.007 0.001 ARG R 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 812 time to evaluate : 6.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 VAL cc_start: 0.4214 (OUTLIER) cc_final: 0.3685 (t) REVERT: B 116 ASP cc_start: 0.4458 (OUTLIER) cc_final: 0.3765 (t70) REVERT: C 53 SER cc_start: 0.4067 (OUTLIER) cc_final: 0.3767 (m) REVERT: C 62 LYS cc_start: 0.2720 (OUTLIER) cc_final: 0.1974 (tptt) REVERT: C 161 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5726 (tt0) REVERT: D 15 GLU cc_start: 0.5382 (mm-30) cc_final: 0.5162 (tp30) REVERT: D 147 GLU cc_start: 0.4476 (mp0) cc_final: 0.4071 (pm20) REVERT: D 148 LYS cc_start: 0.4808 (OUTLIER) cc_final: 0.4206 (pptt) REVERT: D 182 PHE cc_start: 0.5305 (OUTLIER) cc_final: 0.3971 (m-80) REVERT: E 48 PHE cc_start: 0.7915 (p90) cc_final: 0.7670 (p90) REVERT: F 16 GLU cc_start: 0.4592 (OUTLIER) cc_final: 0.4174 (mp0) REVERT: F 39 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6226 (mt) REVERT: G 78 ARG cc_start: 0.4531 (ttt-90) cc_final: 0.3800 (mmt180) REVERT: G 111 ARG cc_start: 0.4297 (mtt180) cc_final: 0.3987 (mmt90) REVERT: H 31 LYS cc_start: 0.6707 (OUTLIER) cc_final: 0.6165 (pttt) REVERT: I 85 ARG cc_start: 0.6010 (OUTLIER) cc_final: 0.5031 (mpt-90) REVERT: K 116 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7630 (mp) REVERT: L 77 HIS cc_start: 0.6015 (m90) cc_final: 0.5684 (m90) REVERT: N 3 LYS cc_start: 0.6591 (OUTLIER) cc_final: 0.6308 (mmmt) REVERT: O 87 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6529 (mt) REVERT: P 57 ILE cc_start: 0.6608 (OUTLIER) cc_final: 0.6259 (mt) REVERT: R 25 ASP cc_start: 0.5193 (OUTLIER) cc_final: 0.4761 (p0) REVERT: S 66 MET cc_start: 0.4640 (OUTLIER) cc_final: 0.4098 (ptp) REVERT: U 25 LYS cc_start: 0.5114 (OUTLIER) cc_final: 0.4791 (tptt) REVERT: c 189 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8083 (mtt90) REVERT: e 168 ASP cc_start: 0.7143 (t0) cc_final: 0.6885 (t70) REVERT: f 17 MET cc_start: 0.4690 (tpt) cc_final: 0.4416 (tpt) REVERT: f 19 GLU cc_start: 0.5392 (tt0) cc_final: 0.4925 (tt0) REVERT: f 95 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.6556 (mtp85) REVERT: f 178 ARG cc_start: 0.3749 (OUTLIER) cc_final: 0.3422 (ptt-90) REVERT: g 151 TYR cc_start: 0.6311 (m-80) cc_final: 0.5401 (m-10) REVERT: i 91 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8175 (mt-10) REVERT: k 115 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6569 (mm-30) REVERT: m 110 MET cc_start: 0.9147 (mmm) cc_final: 0.8641 (mmm) REVERT: n 19 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6531 (tm-30) REVERT: n 46 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6204 (mt-10) REVERT: t 22 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.6844 (mtm-85) REVERT: t 97 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7389 (mttm) REVERT: u 24 ASN cc_start: 0.7054 (OUTLIER) cc_final: 0.6842 (m110) REVERT: u 85 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7280 (mtmm) REVERT: x 52 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7739 (mtt90) REVERT: y 39 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7080 (pt0) outliers start: 161 outliers final: 83 residues processed: 921 average time/residue: 2.4989 time to fit residues: 3187.6806 Evaluate side-chains 907 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 794 time to evaluate : 6.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 182 PHE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 3 LYS Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 25 ASP Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 189 ARG Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 55 SER Chi-restraints excluded: chain e residue 107 SER Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 95 ARG Chi-restraints excluded: chain f residue 178 ARG Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 115 GLU Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain o residue 32 VAL Chi-restraints excluded: chain o residue 80 VAL Chi-restraints excluded: chain p residue 87 SER Chi-restraints excluded: chain q residue 19 THR Chi-restraints excluded: chain q residue 59 ILE Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain t residue 22 ARG Chi-restraints excluded: chain t residue 97 LYS Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 24 ASN Chi-restraints excluded: chain u residue 85 LYS Chi-restraints excluded: chain x residue 52 ARG Chi-restraints excluded: chain y residue 39 GLU Chi-restraints excluded: chain y residue 59 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 866 optimal weight: 4.9990 chunk 912 optimal weight: 10.0000 chunk 832 optimal weight: 10.0000 chunk 887 optimal weight: 0.7980 chunk 534 optimal weight: 9.9990 chunk 386 optimal weight: 8.9990 chunk 696 optimal weight: 9.9990 chunk 272 optimal weight: 6.9990 chunk 801 optimal weight: 5.9990 chunk 839 optimal weight: 10.0000 chunk 884 optimal weight: 8.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 20 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN C 139 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN K 40 ASN O 62 GLN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN ** T 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 HIS k 93 ASN o 7 GLN o 15 GLN ** r 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 20 ASN x 25 GLN x 39 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 154075 Z= 0.339 Angle : 0.866 20.344 230535 Z= 0.441 Chirality : 0.045 0.412 29380 Planarity : 0.008 0.153 12250 Dihedral : 23.255 179.056 77407 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 3.30 % Allowed : 24.83 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.11), residues: 5473 helix: 0.29 (0.11), residues: 1908 sheet: -0.41 (0.15), residues: 1075 loop : -0.55 (0.12), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP c 248 HIS 0.008 0.002 HIS u 44 PHE 0.025 0.003 PHE F 8 TYR 0.022 0.003 TYR p 32 ARG 0.015 0.001 ARG T 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 793 time to evaluate : 6.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 LEU cc_start: 0.5140 (tp) cc_final: 0.4790 (pp) REVERT: C 53 SER cc_start: 0.4166 (OUTLIER) cc_final: 0.3738 (m) REVERT: C 62 LYS cc_start: 0.2872 (OUTLIER) cc_final: 0.2127 (tptt) REVERT: C 139 GLN cc_start: 0.6068 (OUTLIER) cc_final: 0.5749 (tm130) REVERT: C 161 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5641 (tt0) REVERT: D 15 GLU cc_start: 0.5494 (mm-30) cc_final: 0.5282 (tp30) REVERT: D 148 LYS cc_start: 0.4808 (OUTLIER) cc_final: 0.4245 (pptt) REVERT: D 182 PHE cc_start: 0.5394 (OUTLIER) cc_final: 0.3979 (m-80) REVERT: F 16 GLU cc_start: 0.4539 (OUTLIER) cc_final: 0.4194 (mp0) REVERT: F 39 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6172 (mt) REVERT: G 78 ARG cc_start: 0.4551 (ttt-90) cc_final: 0.3858 (mmt180) REVERT: H 31 LYS cc_start: 0.6718 (OUTLIER) cc_final: 0.6169 (pttt) REVERT: I 11 ARG cc_start: 0.6354 (OUTLIER) cc_final: 0.6065 (mtt90) REVERT: I 85 ARG cc_start: 0.6004 (OUTLIER) cc_final: 0.5029 (mpt-90) REVERT: K 116 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7632 (mp) REVERT: L 29 GLN cc_start: 0.7512 (mp10) cc_final: 0.7252 (mp10) REVERT: N 3 LYS cc_start: 0.6691 (OUTLIER) cc_final: 0.6391 (mmmt) REVERT: P 57 ILE cc_start: 0.6614 (OUTLIER) cc_final: 0.6269 (mt) REVERT: R 25 ASP cc_start: 0.5278 (OUTLIER) cc_final: 0.4802 (p0) REVERT: S 66 MET cc_start: 0.4774 (OUTLIER) cc_final: 0.4226 (ptp) REVERT: U 25 LYS cc_start: 0.5116 (OUTLIER) cc_final: 0.4808 (tptt) REVERT: c 189 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8069 (mtt90) REVERT: f 17 MET cc_start: 0.4666 (tpt) cc_final: 0.4383 (tpt) REVERT: f 19 GLU cc_start: 0.5474 (tt0) cc_final: 0.4959 (tt0) REVERT: f 95 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6567 (mtp85) REVERT: f 178 ARG cc_start: 0.3822 (OUTLIER) cc_final: 0.3486 (ptt-90) REVERT: g 151 TYR cc_start: 0.6385 (m-80) cc_final: 0.5331 (m-10) REVERT: i 2 LYS cc_start: 0.7721 (mtpt) cc_final: 0.7517 (tttp) REVERT: i 91 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8169 (mt-10) REVERT: k 115 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6601 (mm-30) REVERT: m 110 MET cc_start: 0.9153 (mmm) cc_final: 0.8653 (mmm) REVERT: n 19 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.6532 (tm-30) REVERT: n 46 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.6202 (mt-10) REVERT: t 22 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.6860 (mtm-85) REVERT: t 97 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7456 (mttm) REVERT: u 24 ASN cc_start: 0.7053 (OUTLIER) cc_final: 0.6823 (m110) REVERT: u 85 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7320 (mtmm) REVERT: x 52 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7726 (mtt90) REVERT: y 39 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7144 (pt0) outliers start: 151 outliers final: 94 residues processed: 897 average time/residue: 2.4968 time to fit residues: 3115.4206 Evaluate side-chains 916 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 793 time to evaluate : 6.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 136 ARG Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 182 PHE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 11 ARG Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 3 LYS Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 25 ASP Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 189 ARG Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 55 SER Chi-restraints excluded: chain e residue 107 SER Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 95 ARG Chi-restraints excluded: chain f residue 178 ARG Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 12 LYS Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 115 GLU Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain o residue 32 VAL Chi-restraints excluded: chain o residue 80 VAL Chi-restraints excluded: chain p residue 87 SER Chi-restraints excluded: chain q residue 19 THR Chi-restraints excluded: chain q residue 59 ILE Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain t residue 22 ARG Chi-restraints excluded: chain t residue 97 LYS Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 24 ASN Chi-restraints excluded: chain u residue 76 ASP Chi-restraints excluded: chain u residue 85 LYS Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain x residue 52 ARG Chi-restraints excluded: chain y residue 39 GLU Chi-restraints excluded: chain y residue 59 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 582 optimal weight: 7.9990 chunk 938 optimal weight: 2.9990 chunk 572 optimal weight: 10.0000 chunk 445 optimal weight: 9.9990 chunk 652 optimal weight: 10.0000 chunk 984 optimal weight: 0.7980 chunk 905 optimal weight: 0.2980 chunk 783 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 605 optimal weight: 10.0000 chunk 480 optimal weight: 8.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 20 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN O 62 GLN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN ** T 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 163 GLN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN e 195 GLN g 111 HIS k 93 ASN o 7 GLN ** r 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 20 ASN x 25 GLN x 39 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 154075 Z= 0.260 Angle : 0.763 16.908 230535 Z= 0.398 Chirality : 0.041 0.397 29380 Planarity : 0.007 0.145 12250 Dihedral : 23.199 179.894 77407 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.76 % Favored : 96.14 % Rotamer: Outliers : 2.93 % Allowed : 25.15 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.11), residues: 5473 helix: 0.52 (0.11), residues: 1907 sheet: -0.40 (0.15), residues: 1084 loop : -0.49 (0.12), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 248 HIS 0.007 0.002 HIS k 35 PHE 0.024 0.002 PHE E 48 TYR 0.021 0.002 TYR p 32 ARG 0.011 0.001 ARG K 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 798 time to evaluate : 6.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 LEU cc_start: 0.5012 (tp) cc_final: 0.4674 (pp) REVERT: C 53 SER cc_start: 0.4126 (OUTLIER) cc_final: 0.3764 (m) REVERT: C 161 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5566 (tt0) REVERT: D 15 GLU cc_start: 0.5488 (mm-30) cc_final: 0.5276 (tp30) REVERT: D 147 GLU cc_start: 0.4383 (mp0) cc_final: 0.4097 (pm20) REVERT: D 148 LYS cc_start: 0.4796 (OUTLIER) cc_final: 0.4208 (pptt) REVERT: D 177 LYS cc_start: 0.3672 (OUTLIER) cc_final: 0.3361 (tmtt) REVERT: D 182 PHE cc_start: 0.5281 (OUTLIER) cc_final: 0.3881 (m-80) REVERT: E 48 PHE cc_start: 0.7931 (p90) cc_final: 0.7731 (p90) REVERT: F 16 GLU cc_start: 0.4597 (OUTLIER) cc_final: 0.4221 (mp0) REVERT: G 78 ARG cc_start: 0.4564 (ttt-90) cc_final: 0.3940 (mmt180) REVERT: H 31 LYS cc_start: 0.6716 (OUTLIER) cc_final: 0.6179 (pttt) REVERT: I 11 ARG cc_start: 0.6296 (OUTLIER) cc_final: 0.6032 (mtt90) REVERT: I 85 ARG cc_start: 0.5972 (OUTLIER) cc_final: 0.4985 (mpt-90) REVERT: K 116 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7631 (mp) REVERT: L 29 GLN cc_start: 0.7510 (mp10) cc_final: 0.7246 (mp10) REVERT: L 77 HIS cc_start: 0.5963 (m90) cc_final: 0.5660 (m90) REVERT: N 3 LYS cc_start: 0.6562 (OUTLIER) cc_final: 0.6287 (mmmt) REVERT: O 14 GLU cc_start: 0.5567 (OUTLIER) cc_final: 0.5287 (tt0) REVERT: P 57 ILE cc_start: 0.6599 (OUTLIER) cc_final: 0.6254 (mt) REVERT: R 14 THR cc_start: 0.4132 (OUTLIER) cc_final: 0.3545 (m) REVERT: R 25 ASP cc_start: 0.5240 (OUTLIER) cc_final: 0.4789 (p0) REVERT: S 66 MET cc_start: 0.4650 (OUTLIER) cc_final: 0.4048 (ptp) REVERT: U 25 LYS cc_start: 0.5089 (OUTLIER) cc_final: 0.4768 (tptt) REVERT: c 189 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8080 (mtt90) REVERT: f 17 MET cc_start: 0.4655 (tpt) cc_final: 0.4384 (tpt) REVERT: f 19 GLU cc_start: 0.5449 (tt0) cc_final: 0.5041 (tt0) REVERT: f 95 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.6593 (mtp85) REVERT: f 178 ARG cc_start: 0.3812 (OUTLIER) cc_final: 0.3484 (ptt-90) REVERT: g 151 TYR cc_start: 0.6300 (m-80) cc_final: 0.5399 (m-10) REVERT: i 2 LYS cc_start: 0.7719 (mtpt) cc_final: 0.7499 (tttp) REVERT: i 91 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8178 (mt-10) REVERT: k 115 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6569 (mm-30) REVERT: m 110 MET cc_start: 0.9149 (mmm) cc_final: 0.8643 (mmm) REVERT: n 19 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6476 (tm-30) REVERT: n 46 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6203 (mt-10) REVERT: t 22 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6844 (mtm-85) REVERT: t 97 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7391 (mttm) REVERT: u 24 ASN cc_start: 0.7057 (OUTLIER) cc_final: 0.6829 (m110) REVERT: u 85 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7325 (mtmm) REVERT: w 45 ARG cc_start: 0.6945 (ptt180) cc_final: 0.6484 (ppt170) REVERT: x 52 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7735 (mtt90) REVERT: y 39 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7103 (pt0) outliers start: 134 outliers final: 87 residues processed: 886 average time/residue: 2.5606 time to fit residues: 3141.0026 Evaluate side-chains 900 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 784 time to evaluate : 6.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 182 PHE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 11 ARG Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 3 LYS Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 25 ASP Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 189 ARG Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 55 SER Chi-restraints excluded: chain e residue 107 SER Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 95 ARG Chi-restraints excluded: chain f residue 178 ARG Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 115 GLU Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain o residue 32 VAL Chi-restraints excluded: chain o residue 80 VAL Chi-restraints excluded: chain p residue 77 SER Chi-restraints excluded: chain p residue 87 SER Chi-restraints excluded: chain q residue 19 THR Chi-restraints excluded: chain q residue 59 ILE Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain t residue 22 ARG Chi-restraints excluded: chain t residue 97 LYS Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 24 ASN Chi-restraints excluded: chain u residue 76 ASP Chi-restraints excluded: chain u residue 85 LYS Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain x residue 52 ARG Chi-restraints excluded: chain y residue 39 GLU Chi-restraints excluded: chain y residue 59 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 622 optimal weight: 10.0000 chunk 834 optimal weight: 8.9990 chunk 240 optimal weight: 7.9990 chunk 722 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 217 optimal weight: 8.9990 chunk 785 optimal weight: 4.9990 chunk 328 optimal weight: 20.0000 chunk 806 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 20 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 61 GLN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN O 62 GLN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN ** T 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 163 GLN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN e 195 GLN g 111 HIS ** j 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 ASN o 7 GLN o 15 GLN ** r 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 20 ASN x 25 GLN x 39 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.193771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.154846 restraints weight = 126785.267| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.74 r_work: 0.3271 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work: 0.3098 rms_B_bonded: 4.72 restraints_weight: 0.1250 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 154075 Z= 0.360 Angle : 0.895 20.925 230535 Z= 0.453 Chirality : 0.046 0.412 29380 Planarity : 0.008 0.155 12250 Dihedral : 23.260 178.875 77407 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 2.97 % Allowed : 25.15 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.11), residues: 5473 helix: 0.26 (0.11), residues: 1899 sheet: -0.42 (0.15), residues: 1074 loop : -0.57 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP c 248 HIS 0.008 0.002 HIS L 77 PHE 0.025 0.003 PHE F 8 TYR 0.021 0.003 TYR I 90 ARG 0.012 0.001 ARG O 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 55573.83 seconds wall clock time: 962 minutes 38.94 seconds (57758.94 seconds total)