Starting phenix.real_space_refine on Sun Feb 25 05:12:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ost_20188/02_2024/6ost_20188_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ost_20188/02_2024/6ost_20188.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ost_20188/02_2024/6ost_20188_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ost_20188/02_2024/6ost_20188_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ost_20188/02_2024/6ost_20188_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ost_20188/02_2024/6ost_20188.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ost_20188/02_2024/6ost_20188.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ost_20188/02_2024/6ost_20188_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ost_20188/02_2024/6ost_20188_updated.pdb" } resolution = 4.2 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4642 5.49 5 Mg 12 5.21 5 S 154 5.16 5 C 73851 2.51 5 N 27289 2.21 5 O 40671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X ARG 45": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c ARG 28": "NH1" <-> "NH2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "g ARG 63": "NH1" <-> "NH2" Residue "g ARG 74": "NH1" <-> "NH2" Residue "g ARG 208": "NH1" <-> "NH2" Residue "g ARG 225": "NH1" <-> "NH2" Residue "h ARG 54": "NH1" <-> "NH2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "h ARG 127": "NH1" <-> "NH2" Residue "h ARG 131": "NH1" <-> "NH2" Residue "h ARG 132": "NH1" <-> "NH2" Residue "h ARG 164": "NH1" <-> "NH2" Residue "i ARG 73": "NH1" <-> "NH2" Residue "i ARG 81": "NH1" <-> "NH2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 68": "NH1" <-> "NH2" Residue "j ARG 69": "NH1" <-> "NH2" Residue "j ARG 93": "NH1" <-> "NH2" Residue "j ARG 157": "NH1" <-> "NH2" Residue "k ARG 45": "NH1" <-> "NH2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "l ARG 4": "NH1" <-> "NH2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 79": "NH1" <-> "NH2" Residue "l ARG 92": "NH1" <-> "NH2" Residue "n ARG 11": "NH1" <-> "NH2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "n ARG 130": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 45": "NH1" <-> "NH2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p ARG 37": "NH1" <-> "NH2" Residue "p ARG 69": "NH1" <-> "NH2" Residue "p ARG 93": "NH1" <-> "NH2" Residue "p ARG 106": "NH1" <-> "NH2" Residue "q ARG 9": "NH1" <-> "NH2" Residue "q ARG 14": "NH1" <-> "NH2" Residue "q ARG 50": "NH1" <-> "NH2" Residue "q ARG 83": "NH1" <-> "NH2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "r ARG 87": "NH1" <-> "NH2" Residue "r ARG 109": "NH1" <-> "NH2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s ARG 63": "NH1" <-> "NH2" Residue "s ARG 65": "NH1" <-> "NH2" Residue "s ARG 69": "NH1" <-> "NH2" Residue "s ARG 85": "NH1" <-> "NH2" Residue "t ARG 72": "NH1" <-> "NH2" Residue "t ARG 89": "NH1" <-> "NH2" Residue "u ARG 28": "NH1" <-> "NH2" Residue "u PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 51": "NH1" <-> "NH2" Residue "v ARG 11": "NH1" <-> "NH2" Residue "v ARG 27": "NH1" <-> "NH2" Residue "v ARG 65": "NH1" <-> "NH2" Residue "v ARG 77": "NH1" <-> "NH2" Residue "w ARG 61": "NH1" <-> "NH2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "y ARG 60": "NH1" <-> "NH2" Residue "y ARG 74": "NH1" <-> "NH2" Residue "z ARG 33": "NH1" <-> "NH2" Residue "z ARG 45": "NH1" <-> "NH2" Residue "z ARG 55": "NH1" <-> "NH2" Residue "z ARG 62": "NH1" <-> "NH2" Residue "z ARG 67": "NH1" <-> "NH2" Residue "z ARG 69": "NH1" <-> "NH2" Residue "7 ARG 150": "NH1" <-> "NH2" Residue "7 ARG 159": "NH1" <-> "NH2" Residue "7 ARG 200": "NH1" <-> "NH2" Residue "7 ARG 203": "NH1" <-> "NH2" Residue "7 ARG 212": "NH1" <-> "NH2" Residue "7 ARG 213": "NH1" <-> "NH2" Residue "7 ARG 240": "NH1" <-> "NH2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 146620 Number of models: 1 Model: "" Number of chains: 61 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 6, 'rna2p_pur': 289, 'rna2p_pyr': 166, 'rna3p': 16, 'rna3p_pur': 1378, 'rna3p_pyr': 1048} Link IDs: {'rna2p': 460, 'rna3p': 2442} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 32929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32929 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 1, 'rna2p_pur': 120, 'rna2p_pyr': 89, 'rna3p': 10, 'rna3p_pur': 749, 'rna3p_pyr': 564} Link IDs: {'rna2p': 209, 'rna3p': 1324} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "B" 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: "C" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "D" 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: "E" 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: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "J" 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: "K" 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: "L" 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: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "O" 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: "P" 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: "Q" 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: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" 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: "T" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "U" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "V" 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: "W" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 582 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "X" 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: "Y" 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: "Z" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "b" 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: "c" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "d" 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: "e" 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: "f" 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: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "h" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "i" 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: "j" 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: "k" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "l" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "m" 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: "n" 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: "o" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "p" 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: "q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "s" 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: "t" 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: "u" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "v" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" 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: "x" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "y" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "z" 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: "4" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 7} Chain: "7" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2793 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 1 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: "5" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1627 Classifications: {'RNA': 76} Modifications used: {'rna2p': 2, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p': 3, 'rna3p_pur': 34, 'rna3p_pyr': 25} Link IDs: {'rna2p': 13, 'rna3p': 62} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "6" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} 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: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0HJC SG CYS f 11 137.780 161.582 57.853 1.00254.68 S ATOM A0HK1 SG CYS f 14 140.494 159.271 58.195 1.00256.62 S ATOM A0HMW SG CYS f 27 140.531 163.582 58.755 1.00266.87 S Time building chain proxies: 55.47, per 1000 atoms: 0.38 Number of scatterers: 146620 At special positions: 0 Unit cell: (284.585, 268.135, 227.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 154 16.00 P 4642 15.00 Mg 12 11.99 O 40671 8.00 N 27289 7.00 C 73851 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=0, symmetry=0 Time building additional restraints: 78.46 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " Number of angles added : 3 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11028 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: 184 helices and 73 sheets defined 40.3% alpha, 19.8% beta 1282 base pairs and 2458 stacking pairs defined. Time for finding SS restraints: 81.78 Creating SS restraints... Processing helix chain 'B' and resid 10 through 17 removed outlier: 7.658A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 4.132A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLU B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 35' Processing helix chain 'B' and resid 131 through 136 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.722A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 268 removed outlier: 3.538A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 6.112A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.532A pdb=" N HIS C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 removed outlier: 4.211A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ASP C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 103' Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'D' and resid 24 through 41 removed outlier: 3.550A pdb=" N VAL D 28 " --> pdb=" O ASN D 24 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 33 " --> pdb=" O HIS D 29 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 39 " --> pdb=" O TYR D 35 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 removed outlier: 3.829A pdb=" N ARG D 102 " --> pdb=" O LYS D 98 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 154 through 163 removed outlier: 4.304A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 removed outlier: 4.919A pdb=" N LEU D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASP D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 Processing helix chain 'D' and resid 15 through 21 removed outlier: 3.829A pdb=" N GLY D 20 " --> pdb=" O SER D 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 removed outlier: 3.726A pdb=" N GLU E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 62 removed outlier: 4.286A pdb=" N LEU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 3.631A pdb=" N ILE E 106 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Proline residue: E 109 - end of helix Processing helix chain 'E' and resid 162 through 174 removed outlier: 4.476A pdb=" N GLY E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG E 167 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.725A pdb=" N ILE E 44 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA E 45 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 123 removed outlier: 4.408A pdb=" N SER E 121 " --> pdb=" O SER E 118 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N PHE E 122 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP E 123 " --> pdb=" O LYS E 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 118 through 123' Processing helix chain 'E' and resid 134 through 139 removed outlier: 4.337A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Proline residue: E 139 - end of helix Processing helix chain 'F' and resid 2 through 7 removed outlier: 3.568A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 81 removed outlier: 3.754A pdb=" N ILE F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL F 79 " --> pdb=" O MET F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 4.241A pdb=" N ARG F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 27 Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 40 through 48 Processing helix chain 'G' and resid 51 through 74 removed outlier: 4.795A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS G 57 " --> pdb=" O GLU G 53 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU G 70 " --> pdb=" O ASN G 66 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'J' and resid 24 through 38 removed outlier: 6.008A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.691A pdb=" N MET J 92 " --> pdb=" O THR J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 110 removed outlier: 3.942A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 4.008A pdb=" N PHE J 119 " --> pdb=" O GLY J 115 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 109 removed outlier: 4.132A pdb=" N ARG K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N SER K 109 " --> pdb=" O ARG K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 109' Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 3.830A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.657A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.720A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.509A pdb=" N ARG N 30 " --> pdb=" O GLY N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 58 removed outlier: 3.853A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.657A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASP N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 3.768A pdb=" N PHE N 67 " --> pdb=" O ARG N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.438A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.454A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.762A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.528A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.563A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 13 removed outlier: 4.100A pdb=" N GLN P 7 " --> pdb=" O ASN P 3 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.134A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.550A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.612A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 72 removed outlier: 3.627A pdb=" N LYS Q 41 " --> pdb=" O GLN Q 37 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR Q 47 " --> pdb=" O GLY Q 43 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG Q 70 " --> pdb=" O ASN Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 4.085A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 removed outlier: 4.336A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 5.699A pdb=" N LYS S 70 " --> pdb=" O ILE S 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 4.244A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 3.614A pdb=" N MET T 24 " --> pdb=" O ALA T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 50 removed outlier: 3.566A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.798A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.509A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 52 removed outlier: 3.764A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 removed outlier: 3.857A pdb=" N TYR V 57 " --> pdb=" O LYS V 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 removed outlier: 3.755A pdb=" N MET X 56 " --> pdb=" O SER X 52 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG X 57 " --> pdb=" O ALA X 53 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL X 58 " --> pdb=" O LYS X 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 75 Processing helix chain 'Y' and resid 2 through 10 removed outlier: 4.008A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N SER Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 35 removed outlier: 4.192A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 61 removed outlier: 4.634A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL Y 53 " --> pdb=" O ASP Y 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 removed outlier: 3.840A pdb=" N LEU Z 25 " --> pdb=" O LYS Z 21 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 52 Processing helix chain 'b' and resid 9 through 18 Processing helix chain 'c' and resid 26 through 31 Proline residue: c 31 - end of helix Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 24 removed outlier: 3.820A pdb=" N ALA d 23 " --> pdb=" O ARG d 19 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 38 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.550A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 37 removed outlier: 5.171A pdb=" N LYS e 36 " --> pdb=" O ILE e 32 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ALA e 37 " --> pdb=" O LEU e 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 32 through 37' Processing helix chain 'e' and resid 38 through 46 removed outlier: 3.509A pdb=" N LEU e 44 " --> pdb=" O ARG e 40 " (cutoff:3.500A) Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 54 through 63 removed outlier: 3.646A pdb=" N VAL e 58 " --> pdb=" O ASP e 54 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'g' and resid 5 through 13 Processing helix chain 'g' and resid 24 through 29 removed outlier: 4.163A pdb=" N LYS g 28 " --> pdb=" O ASN g 24 " (cutoff:3.500A) Proline residue: g 29 - end of helix No H-bonds generated for 'chain 'g' and resid 24 through 29' Processing helix chain 'g' and resid 43 through 64 Proline residue: g 48 - end of helix removed outlier: 3.571A pdb=" N ALA g 55 " --> pdb=" O ASN g 51 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU g 56 " --> pdb=" O GLU g 52 " (cutoff:3.500A) Processing helix chain 'g' and resid 73 through 88 removed outlier: 5.556A pdb=" N SER g 77 " --> pdb=" O LYS g 73 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL g 80 " --> pdb=" O ALA g 76 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA g 84 " --> pdb=" O VAL g 80 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 121 removed outlier: 3.649A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER g 110 " --> pdb=" O THR g 106 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER g 121 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 Processing helix chain 'g' and resid 165 through 170 Processing helix chain 'g' and resid 171 through 180 Processing helix chain 'g' and resid 206 through 227 removed outlier: 3.807A pdb=" N VAL g 210 " --> pdb=" O ALA g 206 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA g 219 " --> pdb=" O GLY g 215 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR g 220 " --> pdb=" O ALA g 216 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY g 224 " --> pdb=" O THR g 220 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN g 227 " --> pdb=" O GLU g 223 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 13 removed outlier: 4.581A pdb=" N GLY h 13 " --> pdb=" O GLY h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 25 through 48 removed outlier: 4.534A pdb=" N ALA h 30 " --> pdb=" O THR h 26 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ASP h 31 " --> pdb=" O LYS h 27 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN h 32 " --> pdb=" O GLU h 28 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU h 43 " --> pdb=" O VAL h 39 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA h 48 " --> pdb=" O THR h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 removed outlier: 4.505A pdb=" N VAL h 76 " --> pdb=" O ARG h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 96 removed outlier: 3.608A pdb=" N LYS h 86 " --> pdb=" O GLU h 82 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA h 92 " --> pdb=" O ARG h 88 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 3.864A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ALA h 113 " --> pdb=" O PRO h 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 108 through 113' Processing helix chain 'h' and resid 114 through 127 removed outlier: 3.537A pdb=" N ARG h 126 " --> pdb=" O SER h 122 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 145 removed outlier: 3.600A pdb=" N ARG h 136 " --> pdb=" O ARG h 132 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA h 137 " --> pdb=" O ALA h 133 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 16 Processing helix chain 'i' and resid 27 through 32 removed outlier: 3.516A pdb=" N LYS i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS i 32 " --> pdb=" O ILE i 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 27 through 32' Processing helix chain 'i' and resid 49 through 66 removed outlier: 3.858A pdb=" N TYR i 65 " --> pdb=" O VAL i 61 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 83 removed outlier: 3.627A pdb=" N ARG i 81 " --> pdb=" O LYS i 77 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 3.660A pdb=" N ARG i 97 " --> pdb=" O LEU i 93 " (cutoff:3.500A) Processing helix chain 'i' and resid 98 through 106 Processing helix chain 'i' and resid 110 through 121 removed outlier: 3.714A pdb=" N GLN i 116 " --> pdb=" O ALA i 112 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU i 117 " --> pdb=" O GLU i 113 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL i 118 " --> pdb=" O ALA i 114 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 151 removed outlier: 6.483A pdb=" N LYS i 150 " --> pdb=" O ARG i 146 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 146 through 151' Processing helix chain 'i' and resid 152 through 166 removed outlier: 3.782A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA i 157 " --> pdb=" O SER i 153 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU i 163 " --> pdb=" O LEU i 159 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLN i 164 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG i 165 " --> pdb=" O LEU i 161 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 4.358A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) Processing helix chain 'i' and resid 196 through 206 removed outlier: 4.179A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS i 206 " --> pdb=" O GLU i 202 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 4.028A pdb=" N ILE j 60 " --> pdb=" O VAL j 56 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN j 61 " --> pdb=" O PRO j 57 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS j 62 " --> pdb=" O ALA j 58 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 3.583A pdb=" N GLU j 116 " --> pdb=" O ARG j 112 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 147 removed outlier: 3.925A pdb=" N VAL j 137 " --> pdb=" O PRO j 133 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN j 146 " --> pdb=" O ASP j 142 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N MET j 147 " --> pdb=" O GLY j 143 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 Processing helix chain 'j' and resid 160 through 165 removed outlier: 3.548A pdb=" N ILE j 164 " --> pdb=" O SER j 160 " (cutoff:3.500A) Processing helix chain 'k' and resid 17 through 33 removed outlier: 3.834A pdb=" N ILE k 29 " --> pdb=" O TYR k 25 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 82 removed outlier: 3.795A pdb=" N ILE k 71 " --> pdb=" O PRO k 67 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR k 76 " --> pdb=" O ASP k 72 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ASP k 82 " --> pdb=" O PHE k 78 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 32 removed outlier: 5.455A pdb=" N VAL l 32 " --> pdb=" O ASN l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 Processing helix chain 'l' and resid 57 through 70 removed outlier: 3.532A pdb=" N GLU l 63 " --> pdb=" O LEU l 59 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 3.920A pdb=" N ASN l 97 " --> pdb=" O PRO l 93 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA l 98 " --> pdb=" O VAL l 94 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE l 104 " --> pdb=" O ALA l 100 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL l 105 " --> pdb=" O MET l 101 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU l 106 " --> pdb=" O ARG l 102 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA l 107 " --> pdb=" O TRP l 103 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS l 110 " --> pdb=" O GLU l 106 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 removed outlier: 3.826A pdb=" N ASN l 122 " --> pdb=" O LEU l 118 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 149 removed outlier: 3.939A pdb=" N HIS l 142 " --> pdb=" O ARG l 138 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET l 144 " --> pdb=" O ASP l 140 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU l 146 " --> pdb=" O HIS l 142 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA l 147 " --> pdb=" O ARG l 143 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 removed outlier: 3.760A pdb=" N ASP m 9 " --> pdb=" O ASP m 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA m 19 " --> pdb=" O ARG m 15 " (cutoff:3.500A) Processing helix chain 'm' and resid 30 through 44 removed outlier: 4.129A pdb=" N VAL m 39 " --> pdb=" O ALA m 35 " (cutoff:3.500A) Processing helix chain 'm' and resid 112 through 120 Processing helix chain 'n' and resid 34 through 39 removed outlier: 3.599A pdb=" N PHE n 39 " --> pdb=" O LEU n 35 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 53 removed outlier: 4.216A pdb=" N VAL n 48 " --> pdb=" O ALA n 44 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 51 - end of helix Processing helix chain 'n' and resid 71 through 92 removed outlier: 3.502A pdb=" N HIS n 81 " --> pdb=" O GLY n 77 " (cutoff:3.500A) Processing helix chain 'n' and resid 94 through 102 removed outlier: 3.538A pdb=" N LEU n 98 " --> pdb=" O LEU n 94 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS n 100 " --> pdb=" O SER n 96 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 33 removed outlier: 3.971A pdb=" N ASP o 19 " --> pdb=" O HIS o 15 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU o 24 " --> pdb=" O GLN o 20 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE o 25 " --> pdb=" O ALA o 21 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA o 29 " --> pdb=" O ILE o 25 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG o 31 " --> pdb=" O GLU o 27 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR o 32 " --> pdb=" O THR o 28 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY o 33 " --> pdb=" O ALA o 29 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 91 removed outlier: 3.520A pdb=" N VAL o 84 " --> pdb=" O THR o 80 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP o 85 " --> pdb=" O GLU o 81 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU o 87 " --> pdb=" O THR o 83 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N MET o 88 " --> pdb=" O VAL o 84 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 4.400A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 3.984A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 54 through 59' Processing helix chain 'p' and resid 60 through 75 removed outlier: 3.524A pdb=" N GLU p 68 " --> pdb=" O GLN p 64 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP p 72 " --> pdb=" O GLU p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 92 through 104 removed outlier: 3.638A pdb=" N THR p 96 " --> pdb=" O GLY p 92 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN p 101 " --> pdb=" O ILE p 97 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 10 Processing helix chain 'q' and resid 113 through 118 removed outlier: 3.704A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 22 removed outlier: 3.591A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 Processing helix chain 'r' and resid 49 through 64 removed outlier: 3.639A pdb=" N ALA r 61 " --> pdb=" O ARG r 57 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 5.781A pdb=" N ARG r 70 " --> pdb=" O GLU r 66 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY r 84 " --> pdb=" O LEU r 80 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 Processing helix chain 'r' and resid 106 through 111 Processing helix chain 's' and resid 3 through 21 removed outlier: 3.579A pdb=" N ALA s 17 " --> pdb=" O ARG s 13 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR s 20 " --> pdb=" O LEU s 16 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE s 21 " --> pdb=" O ALA s 17 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 34 removed outlier: 5.273A pdb=" N VAL s 34 " --> pdb=" O ILE s 30 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 52 removed outlier: 3.507A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) Proline residue: s 52 - end of helix Processing helix chain 's' and resid 80 through 91 Processing helix chain 't' and resid 4 through 16 Processing helix chain 't' and resid 24 through 47 removed outlier: 3.567A pdb=" N ALA t 30 " --> pdb=" O GLU t 26 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE t 43 " --> pdb=" O LEU t 39 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS t 47 " --> pdb=" O PHE t 43 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 3.646A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU t 70 " --> pdb=" O LEU t 66 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 Processing helix chain 'u' and resid 53 through 64 Processing helix chain 'u' and resid 68 through 81 removed outlier: 3.628A pdb=" N ALA u 81 " --> pdb=" O GLU u 77 " (cutoff:3.500A) Processing helix chain 'w' and resid 11 through 17 removed outlier: 5.006A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 34 removed outlier: 3.567A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 removed outlier: 3.656A pdb=" N THR w 45 " --> pdb=" O PRO w 41 " (cutoff:3.500A) Processing helix chain 'w' and resid 48 through 66 removed outlier: 3.565A pdb=" N TYR w 64 " --> pdb=" O LYS w 60 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU w 65 " --> pdb=" O ARG w 61 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER w 66 " --> pdb=" O ALA w 62 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 removed outlier: 3.629A pdb=" N GLU x 24 " --> pdb=" O GLU x 20 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY x 26 " --> pdb=" O ALA x 22 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.881A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 70 through 76' Processing helix chain 'x' and resid 64 through 69 removed outlier: 3.955A pdb=" N GLY x 68 " --> pdb=" O GLU x 65 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS x 69 " --> pdb=" O MET x 66 " (cutoff:3.500A) Processing helix chain 'y' and resid 4 through 42 removed outlier: 3.783A pdb=" N SER y 23 " --> pdb=" O LYS y 19 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG y 24 " --> pdb=" O HIS y 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE y 31 " --> pdb=" O MET y 27 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE y 32 " --> pdb=" O MET y 28 " (cutoff:3.500A) Processing helix chain 'y' and resid 43 through 65 removed outlier: 3.525A pdb=" N GLN y 55 " --> pdb=" O PHE y 51 " (cutoff:3.500A) Proline residue: y 56 - end of helix removed outlier: 3.576A pdb=" N ARG y 60 " --> pdb=" O PRO y 56 " (cutoff:3.500A) Processing helix chain 'y' and resid 68 through 87 removed outlier: 3.513A pdb=" N ASN y 78 " --> pdb=" O ARG y 74 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU y 79 " --> pdb=" O HIS y 75 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS y 85 " --> pdb=" O ALA y 81 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA y 87 " --> pdb=" O ILE y 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 Processing helix chain 'z' and resid 28 through 37 removed outlier: 4.744A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 67 removed outlier: 3.589A pdb=" N ALA z 50 " --> pdb=" O LYS z 46 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER z 51 " --> pdb=" O ARG z 47 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA z 52 " --> pdb=" O ALA z 48 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU z 60 " --> pdb=" O HIS z 56 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG z 66 " --> pdb=" O ARG z 62 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ARG z 67 " --> pdb=" O GLU z 63 " (cutoff:3.500A) Processing helix chain '7' and resid 4 through 26 removed outlier: 3.662A pdb=" N ASN 7 9 " --> pdb=" O ASN 7 5 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU 7 14 " --> pdb=" O ARG 7 10 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP 7 19 " --> pdb=" O THR 7 15 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL 7 20 " --> pdb=" O GLU 7 16 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY 7 23 " --> pdb=" O ASP 7 19 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR 7 24 " --> pdb=" O VAL 7 20 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP 7 26 " --> pdb=" O ARG 7 22 " (cutoff:3.500A) Processing helix chain '7' and resid 27 through 44 removed outlier: 3.646A pdb=" N ARG 7 33 " --> pdb=" O ALA 7 29 " (cutoff:3.500A) Proline residue: 7 44 - end of helix Processing helix chain '7' and resid 45 through 50 removed outlier: 4.256A pdb=" N GLU 7 49 " --> pdb=" O ASP 7 45 " (cutoff:3.500A) Proline residue: 7 50 - end of helix No H-bonds generated for 'chain '7' and resid 45 through 50' Processing helix chain '7' and resid 51 through 60 removed outlier: 4.314A pdb=" N GLU 7 59 " --> pdb=" O ALA 7 55 " (cutoff:3.500A) Processing helix chain '7' and resid 62 through 90 removed outlier: 4.159A pdb=" N VAL 7 66 " --> pdb=" O SER 7 62 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL 7 67 " --> pdb=" O LEU 7 63 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU 7 70 " --> pdb=" O VAL 7 66 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP 7 79 " --> pdb=" O GLN 7 75 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA 7 90 " --> pdb=" O LEU 7 86 " (cutoff:3.500A) Processing helix chain '7' and resid 92 through 120 removed outlier: 4.154A pdb=" N LEU 7 103 " --> pdb=" O ALA 7 99 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP 7 104 " --> pdb=" O VAL 7 100 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA 7 105 " --> pdb=" O ALA 7 101 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU 7 106 " --> pdb=" O GLU 7 102 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU 7 107 " --> pdb=" O LEU 7 103 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU 7 108 " --> pdb=" O ASP 7 104 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS 7 109 " --> pdb=" O ALA 7 105 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU 7 110 " --> pdb=" O LEU 7 106 " (cutoff:3.500A) Processing helix chain '7' and resid 138 through 160 removed outlier: 3.532A pdb=" N ASP 7 143 " --> pdb=" O THR 7 139 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR 7 152 " --> pdb=" O LEU 7 148 " (cutoff:3.500A) Processing helix chain '7' and resid 187 through 196 removed outlier: 5.443A pdb=" N THR 7 194 " --> pdb=" O GLY 7 190 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU 7 195 " --> pdb=" O TRP 7 191 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR 7 196 " --> pdb=" O LEU 7 192 " (cutoff:3.500A) Processing helix chain '7' and resid 235 through 240 removed outlier: 4.924A pdb=" N ARG 7 240 " --> pdb=" O PRO 7 236 " (cutoff:3.500A) Processing helix chain '7' and resid 279 through 309 removed outlier: 3.585A pdb=" N ASN 7 283 " --> pdb=" O SER 7 279 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS 7 289 " --> pdb=" O ASP 7 285 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS 7 302 " --> pdb=" O LEU 7 298 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLN 7 308 " --> pdb=" O ASN 7 304 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA 7 309 " --> pdb=" O ALA 7 305 " (cutoff:3.500A) Processing helix chain '7' and resid 344 through 351 Processing helix chain '7' and resid 352 through 364 removed outlier: 5.044A pdb=" N PHE 7 356 " --> pdb=" O SER 7 352 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 80 through 83 removed outlier: 6.608A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.766A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE B 164 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 90 through 97 No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain 'C' and resid 3 through 8 removed outlier: 4.389A pdb=" N SER C 199 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASP C 200 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N THR C 112 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU C 168 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 11 through 16 removed outlier: 4.793A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 36 through 40 removed outlier: 4.679A pdb=" N LEU C 40 " --> pdb=" O TYR C 45 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR C 45 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLN C 94 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.413A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 105 through 108 removed outlier: 6.227A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 1 through 5 removed outlier: 4.184A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 117 through 120 removed outlier: 3.873A pdb=" N VAL D 146 " --> pdb=" O LYS D 166 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 65 through 69 removed outlier: 3.504A pdb=" N CYS E 87 " --> pdb=" O MET E 38 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL E 89 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 36 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= 13, first strand: chain 'F' and resid 95 through 98 removed outlier: 3.697A pdb=" N VAL F 113 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 121 through 125 removed outlier: 5.542A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 7 through 10 removed outlier: 6.483A pdb=" N ASP G 7 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU G 15 " --> pdb=" O ASP G 7 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 17 through 21 removed outlier: 4.198A pdb=" N ASP G 17 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS G 35 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 78 through 83 removed outlier: 4.537A pdb=" N VAL G 78 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA G 140 " --> pdb=" O PHE G 132 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU G 114 " --> pdb=" O GLN G 133 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'J' and resid 14 through 19 Processing sheet with id= 19, first strand: chain 'J' and resid 74 through 78 removed outlier: 3.607A pdb=" N HIS J 76 " --> pdb=" O LYS J 85 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 56 through 60 removed outlier: 4.333A pdb=" N ASP K 56 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET K 20 " --> pdb=" O THR K 42 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL K 19 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.635A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'L' and resid 119 through 123 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 'M' and resid 62 through 66 removed outlier: 3.552A pdb=" N LYS M 62 " --> pdb=" O ASP M 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU M 102 " --> pdb=" O ARG M 66 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'M' and resid 71 through 74 Processing sheet with id= 25, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.296A pdb=" N ARG N 103 " --> pdb=" O ASN N 107 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY N 101 " --> pdb=" O PRO N 109 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA N 111 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS N 99 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE N 113 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE N 97 " --> pdb=" O ILE N 113 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU N 115 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR N 95 " --> pdb=" O LEU N 115 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.598A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS O 29 " --> pdb=" O TYR O 36 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE O 40 " --> pdb=" O ARG O 25 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG O 25 " --> pdb=" O ILE O 40 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'P' and resid 49 through 53 removed outlier: 3.907A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR P 60 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL P 47 " --> pdb=" O ASP P 24 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP P 24 " --> pdb=" O VAL P 47 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'P' and resid 57 through 64 removed outlier: 7.656A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'R' and resid 11 through 14 removed outlier: 5.974A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN R 43 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU R 46 " --> pdb=" O ASN R 43 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.000A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 57 through 60 Processing sheet with id= 32, first strand: chain 'R' and resid 65 through 68 Processing sheet with id= 33, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.259A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'S' and resid 2 through 8 Processing sheet with id= 35, first strand: chain 'T' and resid 12 through 15 removed outlier: 4.610A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA T 83 " --> pdb=" O LEU T 32 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL T 34 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'U' and resid 40 through 45 No H-bonds generated for sheet with id= 36 Processing sheet with id= 37, first strand: chain 'U' and resid 83 through 86 Processing sheet with id= 38, first strand: chain 'V' and resid 2 through 5 Processing sheet with id= 39, first strand: chain 'V' and resid 37 through 42 Processing sheet with id= 40, first strand: chain 'W' and resid 37 through 40 removed outlier: 3.719A pdb=" N VAL W 38 " --> pdb=" O LEU W 59 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN W 40 " --> pdb=" O HIS W 57 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N HIS W 57 " --> pdb=" O GLN W 40 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'W' and resid 66 through 71 Processing sheet with id= 42, first strand: chain 'X' and resid 12 through 19 removed outlier: 4.058A pdb=" N SER X 19 " --> pdb=" O ASN X 23 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'X' and resid 35 through 40 Processing sheet with id= 44, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.007A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'c' and resid 19 through 25 removed outlier: 5.740A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS c 10 " --> pdb=" O ALA c 52 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU c 36 " --> pdb=" O TYR c 49 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU c 51 " --> pdb=" O LEU c 34 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'f' and resid 1 through 5 removed outlier: 6.094A pdb=" N HIS f 33 " --> pdb=" O CYS f 27 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N CYS f 27 " --> pdb=" O HIS f 33 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.159A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY g 17 " --> pdb=" O HIS g 39 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'g' and resid 89 through 92 removed outlier: 3.574A pdb=" N LEU g 68 " --> pdb=" O ALA g 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA g 185 " --> pdb=" O PHE g 198 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'h' and resid 53 through 59 removed outlier: 3.513A pdb=" N ARG h 54 " --> pdb=" O HIS h 69 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'h' and resid 164 through 169 removed outlier: 5.379A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'i' and resid 140 through 145 removed outlier: 3.714A pdb=" N ASP i 141 " --> pdb=" O PHE i 182 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU i 179 " --> pdb=" O ASP i 174 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N TRP i 170 " --> pdb=" O LYS i 183 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'j' and resid 11 through 16 removed outlier: 6.519A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'j' and resid 84 through 88 removed outlier: 5.727A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'j' and resid 33 through 41 removed outlier: 7.206A pdb=" N ARG j 45 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'k' and resid 37 through 43 removed outlier: 5.062A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL k 7 " --> pdb=" O MET k 88 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG k 86 " --> pdb=" O MET k 9 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'k' and resid 44 through 47 removed outlier: 7.295A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'l' and resid 73 through 78 removed outlier: 5.597A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'm' and resid 23 through 29 removed outlier: 7.415A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'm' and resid 103 through 106 removed outlier: 6.934A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'n' and resid 5 through 11 removed outlier: 3.756A pdb=" N GLY n 10 " --> pdb=" O ALA n 17 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA n 16 " --> pdb=" O LYS n 68 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS n 22 " --> pdb=" O ASP n 62 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'o' and resid 39 through 42 removed outlier: 5.361A pdb=" N LEU o 71 " --> pdb=" O LEU o 42 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'o' and resid 44 through 52 Processing sheet with id= 63, first strand: chain 'p' and resid 29 through 36 removed outlier: 4.137A pdb=" N ASN p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL p 84 " --> pdb=" O THR p 108 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'p' and resid 83 through 88 removed outlier: 5.547A pdb=" N GLY p 88 " --> pdb=" O VAL p 113 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'q' and resid 29 through 33 removed outlier: 3.585A pdb=" N LYS q 30 " --> pdb=" O ILE q 82 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'q' and resid 37 through 41 removed outlier: 4.867A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'u' and resid 4 through 10 removed outlier: 4.044A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL u 19 " --> pdb=" O GLY u 37 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'v' and resid 7 through 11 removed outlier: 6.793A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER v 72 " --> pdb=" O CYS v 64 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'v' and resid 20 through 30 Processing sheet with id= 70, first strand: chain 'x' and resid 30 through 33 removed outlier: 3.912A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLN x 56 " --> pdb=" O ASN x 53 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '7' and resid 161 through 166 removed outlier: 6.225A pdb=" N THR 7 180 " --> pdb=" O ILE 7 166 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS 7 177 " --> pdb=" O ALA 7 134 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE 7 183 " --> pdb=" O CYS 7 128 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N CYS 7 128 " --> pdb=" O ILE 7 183 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY 7 185 " --> pdb=" O ALA 7 126 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ALA 7 126 " --> pdb=" O GLY 7 185 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASP 7 127 " --> pdb=" O GLU 7 225 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR 7 223 " --> pdb=" O TYR 7 129 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN 7 133 " --> pdb=" O SER 7 219 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG 7 324 " --> pdb=" O VAL 7 198 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG 7 200 " --> pdb=" O ARG 7 324 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LYS 7 204 " --> pdb=" O LEU 7 328 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain '7' and resid 241 through 245 Processing sheet with id= 73, first strand: chain '7' and resid 167 through 170 removed outlier: 3.500A pdb=" N SER 7 178 " --> pdb=" O SER 7 169 " (cutoff:3.500A) 1915 hydrogen bonds defined for protein. 5652 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2882 hydrogen bonds 3232 hydrogen bond angles 0 basepair planarities 1282 basepair parallelities 2458 stacking parallelities Total time for adding SS restraints: 240.26 Time building geometry restraints manager: 83.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 12151 1.29 - 1.42: 69057 1.42 - 1.55: 68412 1.55 - 1.68: 9296 1.68 - 1.81: 276 Bond restraints: 159192 Sorted by residual: bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.155 1.436 -0.281 2.00e-02 2.50e+03 1.97e+02 bond pdb=" C5 5MU 5 54 " pdb=" C6 5MU 5 54 " ideal model delta sigma weight residual 1.155 1.431 -0.276 2.00e-02 2.50e+03 1.91e+02 bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.155 1.429 -0.274 2.00e-02 2.50e+03 1.88e+02 bond pdb=" C4 5MU 11939 " pdb=" C5 5MU 11939 " ideal model delta sigma weight residual 1.802 1.601 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C4 5MU 5 54 " pdb=" C5 5MU 5 54 " ideal model delta sigma weight residual 1.802 1.603 0.199 2.00e-02 2.50e+03 9.86e+01 ... (remaining 159187 not shown) Histogram of bond angle deviations from ideal: 97.03 - 105.69: 24359 105.69 - 114.34: 105179 114.34 - 123.00: 81683 123.00 - 131.65: 25567 131.65 - 140.31: 1121 Bond angle restraints: 237909 Sorted by residual: angle pdb=" C1' G7M 12069 " pdb=" N9 G7M 12069 " pdb=" C8 G7M 12069 " ideal model delta sigma weight residual 94.96 136.22 -41.26 3.00e+00 1.11e-01 1.89e+02 angle pdb=" C1' G7M 2 527 " pdb=" N9 G7M 2 527 " pdb=" C8 G7M 2 527 " ideal model delta sigma weight residual 94.96 128.48 -33.52 3.00e+00 1.11e-01 1.25e+02 angle pdb=" C1' G7M 12069 " pdb=" N9 G7M 12069 " pdb=" C4 G7M 12069 " ideal model delta sigma weight residual 142.80 114.91 27.89 3.00e+00 1.11e-01 8.65e+01 angle pdb=" C1' 2MG 21207 " pdb=" N9 2MG 21207 " pdb=" C8 2MG 21207 " ideal model delta sigma weight residual 110.07 135.77 -25.70 3.00e+00 1.11e-01 7.34e+01 angle pdb=" C1' 2MG 21207 " pdb=" N9 2MG 21207 " pdb=" C4 2MG 21207 " ideal model delta sigma weight residual 138.70 115.81 22.89 3.00e+00 1.11e-01 5.82e+01 ... (remaining 237904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 88252 35.81 - 71.61: 12077 71.61 - 107.42: 1412 107.42 - 143.23: 23 143.23 - 179.03: 35 Dihedral angle restraints: 101799 sinusoidal: 84706 harmonic: 17093 Sorted by residual: dihedral pdb=" C5' C 12146 " pdb=" C4' C 12146 " pdb=" C3' C 12146 " pdb=" O3' C 12146 " ideal model delta sinusoidal sigma weight residual 147.00 77.78 69.22 1 8.00e+00 1.56e-02 9.68e+01 dihedral pdb=" C4' C 12146 " pdb=" C3' C 12146 " pdb=" C2' C 12146 " pdb=" C1' C 12146 " ideal model delta sinusoidal sigma weight residual -35.00 32.63 -67.63 1 8.00e+00 1.56e-02 9.29e+01 dihedral pdb=" O4' U 4 19 " pdb=" C1' U 4 19 " pdb=" N1 U 4 19 " pdb=" C2 U 4 19 " ideal model delta sinusoidal sigma weight residual 200.00 36.91 163.09 1 1.50e+01 4.44e-03 8.35e+01 ... (remaining 101796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 29172 0.121 - 0.241: 1062 0.241 - 0.362: 21 0.362 - 0.483: 3 0.483 - 0.603: 2 Chirality restraints: 30260 Sorted by residual: chirality pdb=" C3' G 1 784 " pdb=" C4' G 1 784 " pdb=" O3' G 1 784 " pdb=" C2' G 1 784 " both_signs ideal model delta sigma weight residual False -2.74 -2.14 -0.60 2.00e-01 2.50e+01 9.10e+00 chirality pdb=" C3' U 1 894 " pdb=" C4' U 1 894 " pdb=" O3' U 1 894 " pdb=" C2' U 1 894 " both_signs ideal model delta sigma weight residual False -2.74 -2.25 -0.50 2.00e-01 2.50e+01 6.15e+00 chirality pdb=" CA SER 7 315 " pdb=" N SER 7 315 " pdb=" C SER 7 315 " pdb=" CB SER 7 315 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.73e+00 ... (remaining 30257 not shown) Planarity restraints: 12919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21207 " 0.056 2.00e-02 2.50e+03 6.26e-01 8.83e+03 pdb=" C4' 2MG 21207 " 0.471 2.00e-02 2.50e+03 pdb=" O4' 2MG 21207 " 0.752 2.00e-02 2.50e+03 pdb=" C3' 2MG 21207 " -0.591 2.00e-02 2.50e+03 pdb=" O3' 2MG 21207 " -0.648 2.00e-02 2.50e+03 pdb=" C2' 2MG 21207 " -0.198 2.00e-02 2.50e+03 pdb=" O2' 2MG 21207 " 0.957 2.00e-02 2.50e+03 pdb=" C1' 2MG 21207 " 0.191 2.00e-02 2.50e+03 pdb=" N9 2MG 21207 " -0.990 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21516 " -0.057 2.00e-02 2.50e+03 6.16e-01 8.53e+03 pdb=" C4' 2MG 21516 " -0.464 2.00e-02 2.50e+03 pdb=" O4' 2MG 21516 " -0.728 2.00e-02 2.50e+03 pdb=" C3' 2MG 21516 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG 21516 " 0.638 2.00e-02 2.50e+03 pdb=" C2' 2MG 21516 " 0.203 2.00e-02 2.50e+03 pdb=" O2' 2MG 21516 " -0.948 2.00e-02 2.50e+03 pdb=" C1' 2MG 21516 " -0.199 2.00e-02 2.50e+03 pdb=" N9 2MG 21516 " 0.961 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 21407 " -0.069 2.00e-02 2.50e+03 6.11e-01 8.41e+03 pdb=" C4' 5MC 21407 " -0.450 2.00e-02 2.50e+03 pdb=" O4' 5MC 21407 " -0.585 2.00e-02 2.50e+03 pdb=" C3' 5MC 21407 " 0.590 2.00e-02 2.50e+03 pdb=" O3' 5MC 21407 " 0.697 2.00e-02 2.50e+03 pdb=" C2' 5MC 21407 " 0.148 2.00e-02 2.50e+03 pdb=" O2' 5MC 21407 " -1.028 2.00e-02 2.50e+03 pdb=" C1' 5MC 21407 " -0.226 2.00e-02 2.50e+03 pdb=" N1 5MC 21407 " 0.922 2.00e-02 2.50e+03 ... (remaining 12916 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 56 2.24 - 2.91: 61312 2.91 - 3.57: 277575 3.57 - 4.24: 494630 4.24 - 4.90: 640072 Nonbonded interactions: 1473645 Sorted by model distance: nonbonded pdb=" O3' A 5 76 " pdb=" C PHE 6 79 " model vdw 1.577 3.270 nonbonded pdb=" O2' A 21146 " pdb=" C6 C 21147 " model vdw 1.975 3.340 nonbonded pdb=" O6 G 3 18 " pdb="MG MG 3 204 " model vdw 2.048 2.170 nonbonded pdb=" O LEU i 82 " pdb="MG MG i 301 " model vdw 2.057 2.170 nonbonded pdb=" O2' U 11923 " pdb=" O5' C 11924 " model vdw 2.062 2.440 ... (remaining 1473640 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.320 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: 0.140 Extract box with map and model: 9.520 Check model and map are aligned: 1.580 Set scattering table: 0.970 Process input model: 587.180 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.370 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:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 606.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 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 : 0.009 0.281 159192 Z= 0.540 Angle : 0.994 41.262 237909 Z= 0.518 Chirality : 0.053 0.603 30260 Planarity : 0.019 0.626 12919 Dihedral : 24.184 179.035 90771 Min Nonbonded Distance : 1.577 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.94 % Favored : 92.99 % Rotamer: Outliers : 0.37 % Allowed : 3.48 % Favored : 96.15 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.09), residues: 5890 helix: -2.83 (0.08), residues: 1874 sheet: -2.67 (0.14), residues: 1082 loop : -2.15 (0.10), residues: 2934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP Q 61 HIS 0.020 0.003 HIS F 111 PHE 0.032 0.003 PHE E 77 TYR 0.033 0.003 TYR 7 244 ARG 0.022 0.002 ARG x 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1654 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1636 time to evaluate : 6.239 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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 23 GLU cc_start: 0.9528 (mm-30) cc_final: 0.9187 (mm-30) REVERT: B 68 LYS cc_start: 0.9537 (mtpt) cc_final: 0.9157 (mmmm) REVERT: B 82 GLU cc_start: 0.9022 (mt-10) cc_final: 0.7989 (mp0) REVERT: B 96 TYR cc_start: 0.8930 (m-80) cc_final: 0.8238 (m-80) REVERT: B 132 MET cc_start: 0.9541 (mtm) cc_final: 0.8815 (mtm) REVERT: B 146 MET cc_start: 0.8675 (mtt) cc_final: 0.8139 (mtt) REVERT: B 161 TYR cc_start: 0.9207 (p90) cc_final: 0.8920 (p90) REVERT: B 167 ARG cc_start: 0.8697 (ttp-110) cc_final: 0.8381 (ttm170) REVERT: B 183 LYS cc_start: 0.9785 (mttm) cc_final: 0.9560 (mmmm) REVERT: B 185 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8777 (tm-30) REVERT: B 201 MET cc_start: 0.9020 (ptt) cc_final: 0.8499 (ptt) REVERT: B 243 HIS cc_start: 0.9164 (m90) cc_final: 0.8890 (m170) REVERT: B 260 ASN cc_start: 0.8406 (t160) cc_final: 0.7888 (t0) REVERT: B 264 ASP cc_start: 0.9239 (m-30) cc_final: 0.8878 (m-30) REVERT: B 271 ARG cc_start: 0.9068 (ptt-90) cc_final: 0.8249 (pmt170) REVERT: C 2 ILE cc_start: 0.8529 (pt) cc_final: 0.7190 (mm) REVERT: C 18 ASP cc_start: 0.9636 (m-30) cc_final: 0.8721 (p0) REVERT: C 22 ILE cc_start: 0.9078 (mt) cc_final: 0.8877 (mp) REVERT: C 89 GLU cc_start: 0.9686 (pt0) cc_final: 0.9364 (mp0) REVERT: C 123 LYS cc_start: 0.9886 (tttp) cc_final: 0.9524 (mtmm) REVERT: C 138 LEU cc_start: 0.9463 (mt) cc_final: 0.9193 (mm) REVERT: C 139 SER cc_start: 0.9157 (m) cc_final: 0.8844 (t) REVERT: C 149 ASN cc_start: 0.9039 (t0) cc_final: 0.8669 (t0) REVERT: C 151 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9143 (p) REVERT: C 165 MET cc_start: 0.8392 (ttt) cc_final: 0.8133 (ttt) REVERT: D 30 GLN cc_start: 0.9565 (tt0) cc_final: 0.8838 (tm-30) REVERT: D 73 ILE cc_start: 0.9767 (tt) cc_final: 0.9564 (pt) REVERT: D 77 ILE cc_start: 0.9339 (pt) cc_final: 0.8819 (mt) REVERT: D 90 GLN cc_start: 0.8946 (pt0) cc_final: 0.8731 (pm20) REVERT: D 100 MET cc_start: 0.9400 (mtp) cc_final: 0.9091 (mtp) REVERT: D 124 PHE cc_start: 0.9157 (t80) cc_final: 0.8947 (t80) REVERT: D 144 GLU cc_start: 0.9513 (tt0) cc_final: 0.9251 (mp0) REVERT: D 149 ILE cc_start: 0.9613 (pt) cc_final: 0.8888 (tp) REVERT: E 26 MET cc_start: 0.9519 (mmm) cc_final: 0.9017 (mmt) REVERT: E 96 MET cc_start: 0.9305 (ttp) cc_final: 0.8777 (ttp) REVERT: E 101 GLU cc_start: 0.9094 (tt0) cc_final: 0.8796 (mt-10) REVERT: E 120 LYS cc_start: 0.9710 (mttt) cc_final: 0.9467 (tptp) REVERT: E 175 PHE cc_start: 0.9029 (t80) cc_final: 0.8635 (t80) REVERT: F 26 ILE cc_start: 0.9503 (mt) cc_final: 0.9247 (mm) REVERT: F 99 LYS cc_start: 0.9510 (mmmt) cc_final: 0.9275 (mmmt) REVERT: F 103 ILE cc_start: 0.9532 (mt) cc_final: 0.9006 (tp) REVERT: F 149 ARG cc_start: 0.9685 (ttt-90) cc_final: 0.9269 (ptm160) REVERT: G 1 MET cc_start: 0.9302 (tpt) cc_final: 0.9078 (tpp) REVERT: G 2 GLN cc_start: 0.9416 (mm-40) cc_final: 0.9110 (mm-40) REVERT: G 18 GLN cc_start: 0.9404 (tt0) cc_final: 0.9115 (tt0) REVERT: G 40 THR cc_start: 0.9260 (m) cc_final: 0.9014 (p) REVERT: G 101 ASP cc_start: 0.9744 (t70) cc_final: 0.9234 (m-30) REVERT: G 112 LYS cc_start: 0.7849 (ptpt) cc_final: 0.7571 (ttpt) REVERT: G 131 SER cc_start: 0.9879 (m) cc_final: 0.9487 (t) REVERT: G 132 PHE cc_start: 0.9314 (m-10) cc_final: 0.8665 (m-80) REVERT: G 139 PHE cc_start: 0.9436 (m-10) cc_final: 0.8808 (m-80) REVERT: G 141 LYS cc_start: 0.9248 (mppt) cc_final: 0.9036 (mmtm) REVERT: J 14 ASP cc_start: 0.9397 (m-30) cc_final: 0.8666 (m-30) REVERT: J 36 LEU cc_start: 0.9588 (mt) cc_final: 0.9105 (mm) REVERT: J 54 ILE cc_start: 0.9918 (mt) cc_final: 0.9627 (tp) REVERT: J 80 HIS cc_start: 0.8038 (m90) cc_final: 0.7694 (m90) REVERT: J 86 GLN cc_start: 0.9608 (tt0) cc_final: 0.9113 (pm20) REVERT: J 92 MET cc_start: 0.9689 (mmm) cc_final: 0.9214 (tpp) REVERT: J 102 GLU cc_start: 0.8821 (mt-10) cc_final: 0.7999 (mt-10) REVERT: J 118 MET cc_start: 0.9204 (mtt) cc_final: 0.8436 (mtt) REVERT: J 129 GLU cc_start: 0.9000 (pt0) cc_final: 0.8777 (mp0) REVERT: J 136 GLN cc_start: 0.9284 (mt0) cc_final: 0.8873 (mm-40) REVERT: K 1 MET cc_start: 0.9344 (ttt) cc_final: 0.8802 (ttt) REVERT: K 5 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8451 (tm-30) REVERT: K 7 MET cc_start: 0.8950 (mmt) cc_final: 0.8482 (mmt) REVERT: K 8 LEU cc_start: 0.9722 (mp) cc_final: 0.9351 (mm) REVERT: K 9 ASN cc_start: 0.9724 (m-40) cc_final: 0.9330 (m-40) REVERT: K 18 ARG cc_start: 0.9481 (tpp80) cc_final: 0.9125 (mmm-85) REVERT: K 44 LYS cc_start: 0.9532 (mmtt) cc_final: 0.9160 (mmmt) REVERT: K 79 PHE cc_start: 0.8878 (m-80) cc_final: 0.8466 (m-10) REVERT: K 88 ASN cc_start: 0.9390 (t0) cc_final: 0.8336 (t0) REVERT: K 90 ASN cc_start: 0.9734 (m-40) cc_final: 0.9368 (p0) REVERT: K 107 LEU cc_start: 0.9448 (tp) cc_final: 0.9234 (mm) REVERT: L 23 ILE cc_start: 0.9126 (mt) cc_final: 0.8723 (mt) REVERT: L 51 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8603 (mt-10) REVERT: L 57 LEU cc_start: 0.9442 (tp) cc_final: 0.9134 (tp) REVERT: L 58 TYR cc_start: 0.9008 (p90) cc_final: 0.8715 (p90) REVERT: L 59 ARG cc_start: 0.9448 (mtm180) cc_final: 0.9203 (mtm-85) REVERT: M 3 GLN cc_start: 0.9438 (tt0) cc_final: 0.9159 (tm-30) REVERT: M 25 ASP cc_start: 0.9476 (m-30) cc_final: 0.9244 (p0) REVERT: M 73 ILE cc_start: 0.9524 (mm) cc_final: 0.9182 (mp) REVERT: M 88 ASN cc_start: 0.9536 (m-40) cc_final: 0.9055 (m110) REVERT: M 91 TYR cc_start: 0.9177 (p90) cc_final: 0.8447 (p90) REVERT: M 105 MET cc_start: 0.9394 (ttm) cc_final: 0.8971 (tmm) REVERT: M 112 LEU cc_start: 0.9802 (tp) cc_final: 0.9281 (tt) REVERT: M 129 THR cc_start: 0.9388 (t) cc_final: 0.9166 (p) REVERT: M 136 MET cc_start: 0.8331 (ttm) cc_final: 0.7686 (mtp) REVERT: N 18 GLN cc_start: 0.9230 (tt0) cc_final: 0.8946 (pp30) REVERT: N 20 MET cc_start: 0.9280 (ttp) cc_final: 0.8389 (mmt) REVERT: N 21 PHE cc_start: 0.9269 (m-10) cc_final: 0.9017 (m-80) REVERT: N 24 MET cc_start: 0.9317 (ttm) cc_final: 0.8502 (mmm) REVERT: N 35 LYS cc_start: 0.9507 (tttt) cc_final: 0.9284 (ptpp) REVERT: N 43 GLU cc_start: 0.9141 (tp30) cc_final: 0.8398 (tp30) REVERT: N 87 PHE cc_start: 0.8652 (m-80) cc_final: 0.7691 (m-80) REVERT: N 98 LEU cc_start: 0.9457 (mt) cc_final: 0.9187 (mp) REVERT: N 114 GLU cc_start: 0.8596 (pt0) cc_final: 0.8037 (pt0) REVERT: N 115 LEU cc_start: 0.9356 (mt) cc_final: 0.9075 (mt) REVERT: O 4 LYS cc_start: 0.9456 (tptp) cc_final: 0.9232 (mttp) REVERT: O 69 ASP cc_start: 0.9759 (m-30) cc_final: 0.9395 (t0) REVERT: P 8 LEU cc_start: 0.9729 (mp) cc_final: 0.9450 (mt) REVERT: P 16 ASP cc_start: 0.9430 (p0) cc_final: 0.8826 (p0) REVERT: P 98 TYR cc_start: 0.8849 (m-10) cc_final: 0.8502 (m-10) REVERT: P 101 ARG cc_start: 0.9591 (mtt180) cc_final: 0.9288 (ttm110) REVERT: Q 59 GLN cc_start: 0.9446 (tt0) cc_final: 0.9117 (mm-40) REVERT: Q 78 LYS cc_start: 0.9689 (mtpp) cc_final: 0.9209 (mmmt) REVERT: R 43 ASN cc_start: 0.9579 (t0) cc_final: 0.9186 (m-40) REVERT: R 46 GLU cc_start: 0.9157 (tt0) cc_final: 0.8793 (mp0) REVERT: R 76 LYS cc_start: 0.9167 (mttm) cc_final: 0.8880 (mttt) REVERT: R 83 TYR cc_start: 0.8358 (t80) cc_final: 0.8125 (t80) REVERT: R 86 GLN cc_start: 0.8975 (mm110) cc_final: 0.7567 (pp30) REVERT: R 95 ASP cc_start: 0.9384 (m-30) cc_final: 0.9176 (m-30) REVERT: S 8 ARG cc_start: 0.9515 (mtp-110) cc_final: 0.9286 (ptt90) REVERT: S 11 ARG cc_start: 0.8750 (tpt90) cc_final: 0.8497 (tpt90) REVERT: S 78 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8717 (mt-10) REVERT: S 82 MET cc_start: 0.8936 (ptp) cc_final: 0.8729 (ptp) REVERT: S 92 ARG cc_start: 0.8351 (tmm-80) cc_final: 0.7962 (tmt170) REVERT: S 97 LEU cc_start: 0.9525 (mm) cc_final: 0.8676 (tp) REVERT: S 99 ARG cc_start: 0.9140 (mmt90) cc_final: 0.8806 (mpp-170) REVERT: S 103 ILE cc_start: 0.9460 (mt) cc_final: 0.9241 (mt) REVERT: T 42 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8464 (pp20) REVERT: T 50 LEU cc_start: 0.9390 (mp) cc_final: 0.8937 (mp) REVERT: T 86 THR cc_start: 0.9533 (m) cc_final: 0.8826 (m) REVERT: U 41 LEU cc_start: 0.9729 (mt) cc_final: 0.9328 (mm) REVERT: V 55 GLU cc_start: 0.9767 (tt0) cc_final: 0.9346 (tp30) REVERT: W 19 LYS cc_start: 0.7838 (mmtt) cc_final: 0.6844 (mmtt) REVERT: W 39 ARG cc_start: 0.9325 (mtp-110) cc_final: 0.8899 (ttm170) REVERT: W 66 LYS cc_start: 0.9603 (mttt) cc_final: 0.9365 (tmtt) REVERT: X 10 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7300 (mmmm) REVERT: X 38 PHE cc_start: 0.9028 (m-80) cc_final: 0.8130 (m-80) REVERT: X 47 VAL cc_start: 0.9446 (t) cc_final: 0.8757 (m) REVERT: X 49 LEU cc_start: 0.9206 (mt) cc_final: 0.8080 (mt) REVERT: Y 23 ARG cc_start: 0.9644 (mtt90) cc_final: 0.9443 (mtt-85) REVERT: Y 30 MET cc_start: 0.9080 (mmt) cc_final: 0.8828 (mmp) REVERT: Z 21 LYS cc_start: 0.9363 (mttt) cc_final: 0.8841 (mttm) REVERT: Z 32 ILE cc_start: 0.9578 (pt) cc_final: 0.9305 (mp) REVERT: Z 49 ASN cc_start: 0.9826 (t0) cc_final: 0.9555 (p0) REVERT: Z 54 MET cc_start: 0.9108 (ptm) cc_final: 0.8321 (ppp) REVERT: b 9 THR cc_start: 0.9310 (m) cc_final: 0.9032 (p) REVERT: b 55 ILE cc_start: 0.9570 (tt) cc_final: 0.9261 (tp) REVERT: c 5 ILE cc_start: 0.9433 (tt) cc_final: 0.9119 (tt) REVERT: d 6 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8339 (mm110) REVERT: d 11 LYS cc_start: 0.9541 (ttmt) cc_final: 0.9263 (mtpt) REVERT: d 25 LYS cc_start: 0.9260 (tmmt) cc_final: 0.8977 (tmmt) REVERT: e 7 VAL cc_start: 0.8962 (t) cc_final: 0.8616 (m) REVERT: e 14 PHE cc_start: 0.9748 (m-80) cc_final: 0.9278 (m-80) REVERT: e 15 LYS cc_start: 0.9422 (mmtm) cc_final: 0.8850 (mmtm) REVERT: f 22 VAL cc_start: 0.9141 (t) cc_final: 0.8787 (p) REVERT: g 32 PHE cc_start: 0.9282 (t80) cc_final: 0.8958 (t80) REVERT: g 50 PHE cc_start: 0.9558 (t80) cc_final: 0.9068 (t80) REVERT: g 100 MET cc_start: 0.9703 (ttm) cc_final: 0.9366 (mtp) REVERT: g 120 GLN cc_start: 0.9226 (tt0) cc_final: 0.8846 (tp-100) REVERT: g 143 LYS cc_start: 0.9307 (tttm) cc_final: 0.9019 (ttpp) REVERT: g 161 LEU cc_start: 0.9642 (tp) cc_final: 0.9133 (pp) REVERT: h 19 ASN cc_start: 0.9418 (m-40) cc_final: 0.8578 (p0) REVERT: h 29 PHE cc_start: 0.9523 (t80) cc_final: 0.9129 (t80) REVERT: h 42 TYR cc_start: 0.9463 (t80) cc_final: 0.9169 (t80) REVERT: h 51 SER cc_start: 0.9552 (m) cc_final: 0.9193 (p) REVERT: h 102 ASN cc_start: 0.8992 (m-40) cc_final: 0.8599 (t0) REVERT: h 114 LYS cc_start: 0.9567 (tptp) cc_final: 0.9067 (tppt) REVERT: h 115 LEU cc_start: 0.9608 (mt) cc_final: 0.9222 (mt) REVERT: h 118 ASP cc_start: 0.9560 (m-30) cc_final: 0.9051 (m-30) REVERT: h 134 MET cc_start: 0.9235 (mtp) cc_final: 0.7875 (ptp) REVERT: h 150 LYS cc_start: 0.9478 (ttpt) cc_final: 0.8887 (ttmm) REVERT: h 167 TRP cc_start: 0.9311 (p-90) cc_final: 0.8928 (p-90) REVERT: h 168 TYR cc_start: 0.7494 (m-80) cc_final: 0.6648 (m-80) REVERT: h 193 TYR cc_start: 0.9341 (m-80) cc_final: 0.8744 (m-80) REVERT: h 201 TRP cc_start: 0.9246 (m-90) cc_final: 0.8786 (m-90) REVERT: i 51 TYR cc_start: 0.9272 (t80) cc_final: 0.8912 (t80) REVERT: i 72 PHE cc_start: 0.9541 (t80) cc_final: 0.8879 (t80) REVERT: i 76 TYR cc_start: 0.9496 (t80) cc_final: 0.9101 (t80) REVERT: i 123 ILE cc_start: 0.9300 (mm) cc_final: 0.8655 (mp) REVERT: i 124 MET cc_start: 0.9097 (mtt) cc_final: 0.8718 (mmm) REVERT: j 29 ARG cc_start: 0.8825 (mpp80) cc_final: 0.8438 (mmt180) REVERT: j 52 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7238 (ttmt) REVERT: j 64 MET cc_start: 0.9314 (mmt) cc_final: 0.8707 (mmt) REVERT: j 66 LYS cc_start: 0.9717 (mttt) cc_final: 0.9247 (mtmm) REVERT: j 71 MET cc_start: 0.8087 (mmm) cc_final: 0.7618 (tpt) REVERT: j 78 ASN cc_start: 0.9682 (t0) cc_final: 0.9481 (p0) REVERT: j 81 LEU cc_start: 0.9757 (mp) cc_final: 0.9087 (mp) REVERT: j 126 LYS cc_start: 0.9412 (tptt) cc_final: 0.9114 (tptt) REVERT: j 134 ILE cc_start: 0.9492 (mt) cc_final: 0.9176 (tt) REVERT: j 138 ARG cc_start: 0.8728 (mtt-85) cc_final: 0.7932 (mtp85) REVERT: j 147 MET cc_start: 0.6974 (ttp) cc_final: 0.5960 (tmm) REVERT: k 9 MET cc_start: 0.9588 (mtp) cc_final: 0.9223 (mmp) REVERT: k 21 MET cc_start: 0.9328 (mtm) cc_final: 0.7820 (mtm) REVERT: k 24 ARG cc_start: 0.9620 (mtm180) cc_final: 0.9301 (ptt90) REVERT: k 80 PHE cc_start: 0.9645 (m-80) cc_final: 0.9388 (m-80) REVERT: k 87 SER cc_start: 0.8738 (p) cc_final: 0.8340 (m) REVERT: k 89 VAL cc_start: 0.9795 (t) cc_final: 0.9529 (t) REVERT: k 91 ARG cc_start: 0.9023 (ttt90) cc_final: 0.8185 (ttt90) REVERT: l 26 PHE cc_start: 0.9866 (t80) cc_final: 0.9651 (t80) REVERT: l 33 ASP cc_start: 0.9224 (m-30) cc_final: 0.8993 (m-30) REVERT: l 56 LYS cc_start: 0.9609 (mttt) cc_final: 0.9274 (ptpp) REVERT: l 101 MET cc_start: 0.9736 (mtm) cc_final: 0.9460 (mtt) REVERT: l 104 ILE cc_start: 0.9562 (mt) cc_final: 0.9260 (mm) REVERT: l 133 THR cc_start: 0.9755 (m) cc_final: 0.9380 (m) REVERT: l 137 LYS cc_start: 0.9801 (tppt) cc_final: 0.9562 (mmmm) REVERT: l 140 ASP cc_start: 0.9358 (m-30) cc_final: 0.9084 (m-30) REVERT: m 47 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8577 (mm-30) REVERT: m 63 LEU cc_start: 0.8781 (mt) cc_final: 0.8501 (mt) REVERT: m 114 ARG cc_start: 0.9217 (ttp80) cc_final: 0.8958 (ptm160) REVERT: n 25 ASN cc_start: 0.9516 (m-40) cc_final: 0.9272 (m-40) REVERT: n 39 PHE cc_start: 0.9493 (m-80) cc_final: 0.9253 (m-10) REVERT: n 55 VAL cc_start: 0.9399 (m) cc_final: 0.9131 (p) REVERT: n 64 TYR cc_start: 0.8609 (t80) cc_final: 0.8289 (t80) REVERT: n 66 THR cc_start: 0.9111 (p) cc_final: 0.8688 (t) REVERT: n 89 GLU cc_start: 0.9555 (tp30) cc_final: 0.9198 (tp30) REVERT: n 97 GLU cc_start: 0.9382 (mt-10) cc_final: 0.9037 (mp0) REVERT: n 115 LYS cc_start: 0.9518 (mttt) cc_final: 0.9296 (mmtt) REVERT: n 129 LYS cc_start: 0.6946 (mttt) cc_final: 0.6094 (mmtm) REVERT: o 9 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8159 (ttm-80) REVERT: o 49 PHE cc_start: 0.9544 (m-80) cc_final: 0.8986 (m-80) REVERT: o 66 GLU cc_start: 0.9457 (pt0) cc_final: 0.9036 (tm-30) REVERT: o 85 ASP cc_start: 0.9826 (p0) cc_final: 0.9484 (p0) REVERT: o 97 ASP cc_start: 0.9183 (t70) cc_final: 0.8983 (t0) REVERT: o 99 GLN cc_start: 0.9334 (tt0) cc_final: 0.9089 (tt0) REVERT: p 18 ASP cc_start: 0.9382 (p0) cc_final: 0.9105 (p0) REVERT: p 29 ASN cc_start: 0.6925 (t0) cc_final: 0.5959 (m-40) REVERT: p 56 ARG cc_start: 0.9469 (mpp80) cc_final: 0.9070 (mtm110) REVERT: p 64 GLN cc_start: 0.9601 (pt0) cc_final: 0.9316 (pp30) REVERT: p 82 LEU cc_start: 0.9536 (tp) cc_final: 0.9323 (tp) REVERT: p 83 GLU cc_start: 0.9436 (pt0) cc_final: 0.9019 (pm20) REVERT: p 84 VAL cc_start: 0.9649 (t) cc_final: 0.9114 (p) REVERT: p 85 MET cc_start: 0.9586 (mtt) cc_final: 0.9232 (mmp) REVERT: p 125 LYS cc_start: 0.8805 (pttt) cc_final: 0.8603 (pttt) REVERT: p 128 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7480 (mtm180) REVERT: q 30 LYS cc_start: 0.8947 (mmmt) cc_final: 0.8504 (tppp) REVERT: q 44 LYS cc_start: 0.7284 (ttpp) cc_final: 0.6965 (tttm) REVERT: q 66 TYR cc_start: 0.8141 (t80) cc_final: 0.7608 (t80) REVERT: q 79 VAL cc_start: 0.9464 (t) cc_final: 0.9197 (p) REVERT: q 116 LYS cc_start: 0.9175 (mttt) cc_final: 0.8947 (mmmt) REVERT: q 123 LYS cc_start: 0.9361 (mttt) cc_final: 0.9123 (tptp) REVERT: r 42 ASP cc_start: 0.8675 (p0) cc_final: 0.8117 (t70) REVERT: r 64 VAL cc_start: 0.9178 (t) cc_final: 0.8815 (t) REVERT: r 72 GLU cc_start: 0.9697 (mt-10) cc_final: 0.9402 (mt-10) REVERT: r 82 ASP cc_start: 0.9609 (m-30) cc_final: 0.9407 (p0) REVERT: r 86 TYR cc_start: 0.8863 (t80) cc_final: 0.8640 (t80) REVERT: s 40 ASP cc_start: 0.9746 (m-30) cc_final: 0.9530 (m-30) REVERT: s 47 LYS cc_start: 0.9738 (tptt) cc_final: 0.9504 (tppt) REVERT: s 65 ARG cc_start: 0.9114 (ttm170) cc_final: 0.8875 (mtp180) REVERT: s 74 LEU cc_start: 0.9553 (mt) cc_final: 0.9310 (mt) REVERT: s 77 PHE cc_start: 0.9459 (m-80) cc_final: 0.9105 (m-10) REVERT: s 82 ILE cc_start: 0.9278 (mt) cc_final: 0.8918 (mt) REVERT: s 83 LYS cc_start: 0.9352 (mmtt) cc_final: 0.9087 (mmtt) REVERT: s 89 MET cc_start: 0.8970 (mmp) cc_final: 0.8643 (mmm) REVERT: s 92 GLU cc_start: 0.8997 (mp0) cc_final: 0.8742 (mp0) REVERT: s 96 LEU cc_start: 0.8698 (tp) cc_final: 0.8477 (tp) REVERT: t 20 ASN cc_start: 0.9657 (t160) cc_final: 0.9324 (m-40) REVERT: t 37 ASN cc_start: 0.9694 (m-40) cc_final: 0.9482 (m-40) REVERT: t 58 ARG cc_start: 0.9370 (ttt180) cc_final: 0.8602 (ttt180) REVERT: t 62 GLN cc_start: 0.9627 (tt0) cc_final: 0.9120 (mt0) REVERT: t 65 LYS cc_start: 0.9376 (mttt) cc_final: 0.9057 (mmtt) REVERT: u 1 MET cc_start: 0.8822 (pmt) cc_final: 0.7283 (tpt) REVERT: v 6 ARG cc_start: 0.8414 (mtp-110) cc_final: 0.6860 (mtp85) REVERT: w 50 LYS cc_start: 0.9514 (tttt) cc_final: 0.9028 (ttpp) REVERT: w 52 GLN cc_start: 0.9388 (tp40) cc_final: 0.9185 (tp40) REVERT: w 54 GLN cc_start: 0.9056 (mt0) cc_final: 0.8810 (mt0) REVERT: w 65 LEU cc_start: 0.9691 (mt) cc_final: 0.9379 (tp) REVERT: w 67 LEU cc_start: 0.9454 (mt) cc_final: 0.8815 (mt) REVERT: w 70 TYR cc_start: 0.8639 (m-80) cc_final: 0.8395 (m-10) REVERT: x 66 MET cc_start: 0.7328 (mtt) cc_final: 0.7073 (mtp) REVERT: y 18 ARG cc_start: 0.9746 (ttp80) cc_final: 0.9154 (ttp-110) REVERT: y 32 ILE cc_start: 0.9778 (mt) cc_final: 0.9230 (pt) REVERT: y 36 TYR cc_start: 0.9565 (m-80) cc_final: 0.9132 (m-80) REVERT: y 78 ASN cc_start: 0.9735 (m-40) cc_final: 0.9155 (p0) REVERT: z 19 PHE cc_start: 0.9371 (t80) cc_final: 0.9051 (t80) REVERT: z 24 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8529 (pt0) REVERT: z 40 LYS cc_start: 0.9289 (mtpt) cc_final: 0.9026 (tttp) REVERT: z 60 LEU cc_start: 0.9318 (mm) cc_final: 0.9075 (mp) REVERT: 7 144 TRP cc_start: 0.9291 (t-100) cc_final: 0.8987 (t-100) REVERT: 7 182 LYS cc_start: 0.9566 (tttt) cc_final: 0.9350 (ttmm) REVERT: 7 186 ASP cc_start: 0.9730 (m-30) cc_final: 0.9475 (p0) REVERT: 7 187 TYR cc_start: 0.9697 (m-80) cc_final: 0.9443 (m-80) REVERT: 7 199 HIS cc_start: 0.8978 (m90) cc_final: 0.8246 (m-70) REVERT: 7 314 LYS cc_start: 0.5309 (OUTLIER) cc_final: 0.4683 (mmmt) outliers start: 18 outliers final: 6 residues processed: 1650 average time/residue: 1.4094 time to fit residues: 3868.5778 Evaluate side-chains 1044 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1034 time to evaluate : 6.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 876 optimal weight: 6.9990 chunk 786 optimal weight: 4.9990 chunk 436 optimal weight: 20.0000 chunk 268 optimal weight: 20.0000 chunk 530 optimal weight: 8.9990 chunk 420 optimal weight: 20.0000 chunk 813 optimal weight: 0.9990 chunk 314 optimal weight: 20.0000 chunk 494 optimal weight: 10.0000 chunk 605 optimal weight: 10.0000 chunk 942 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN B 86 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 GLN C 167 ASN F 20 ASN ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN F 116 GLN ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 HIS O 38 GLN O 61 GLN O 100 HIS ** P 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 ASN R 6 GLN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 50 ASN ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 5 GLN c 45 GLN e 28 ASN f 13 ASN ** g 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 177 ASN g 178 ASN h 32 ASN i 36 GLN i 59 GLN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 46 GLN ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 148 ASN ** m 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 126 GLN q 5 ASN r 14 HIS ** t 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 35 GLN t 37 ASN t 40 GLN t 80 GLN x 52 HIS y 48 GLN y 52 ASN 7 133 GLN 7 199 HIS 7 281 HIS 7 355 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 159192 Z= 0.205 Angle : 0.684 14.660 237909 Z= 0.361 Chirality : 0.035 0.256 30260 Planarity : 0.007 0.134 12919 Dihedral : 25.111 179.879 78958 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 27.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 0.08 % Allowed : 2.34 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.10), residues: 5890 helix: -1.17 (0.10), residues: 2056 sheet: -2.23 (0.14), residues: 1095 loop : -1.86 (0.11), residues: 2739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 31 HIS 0.009 0.001 HIS B 53 PHE 0.028 0.002 PHE E 138 TYR 0.022 0.002 TYR 7 296 ARG 0.015 0.001 ARG p 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1356 time to evaluate : 6.343 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash REVERT: B 21 ASN cc_start: 0.8783 (t0) cc_final: 0.7493 (t0) REVERT: B 68 LYS cc_start: 0.9412 (mtpt) cc_final: 0.9081 (mmmm) REVERT: B 79 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8846 (mm-30) REVERT: B 82 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8187 (mp0) REVERT: B 96 TYR cc_start: 0.8782 (m-80) cc_final: 0.7937 (m-80) REVERT: B 132 MET cc_start: 0.9465 (mtm) cc_final: 0.8873 (mtm) REVERT: B 146 MET cc_start: 0.8331 (mtt) cc_final: 0.8113 (mtp) REVERT: B 161 TYR cc_start: 0.9365 (p90) cc_final: 0.8943 (p90) REVERT: B 167 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8398 (ttm170) REVERT: B 183 LYS cc_start: 0.9783 (mttm) cc_final: 0.9430 (mmmt) REVERT: B 185 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8843 (tm-30) REVERT: B 201 MET cc_start: 0.9006 (ptt) cc_final: 0.8565 (ptt) REVERT: B 243 HIS cc_start: 0.9046 (m90) cc_final: 0.8729 (m-70) REVERT: B 260 ASN cc_start: 0.8354 (t0) cc_final: 0.7716 (t0) REVERT: B 264 ASP cc_start: 0.9441 (m-30) cc_final: 0.9142 (m-30) REVERT: B 266 PHE cc_start: 0.9058 (m-80) cc_final: 0.8824 (m-80) REVERT: B 271 ARG cc_start: 0.9094 (ptt-90) cc_final: 0.8431 (ptt90) REVERT: C 2 ILE cc_start: 0.7851 (pt) cc_final: 0.6851 (mm) REVERT: C 139 SER cc_start: 0.8899 (m) cc_final: 0.8596 (t) REVERT: C 149 ASN cc_start: 0.8759 (t0) cc_final: 0.8458 (t0) REVERT: C 165 MET cc_start: 0.8165 (ttt) cc_final: 0.7913 (ttt) REVERT: C 201 LEU cc_start: 0.9570 (mm) cc_final: 0.9305 (mm) REVERT: D 1 MET cc_start: 0.9391 (tpt) cc_final: 0.9065 (tpp) REVERT: D 3 LEU cc_start: 0.9730 (mt) cc_final: 0.9458 (mt) REVERT: D 30 GLN cc_start: 0.9542 (tt0) cc_final: 0.9249 (mm-40) REVERT: D 51 GLU cc_start: 0.9588 (mm-30) cc_final: 0.9148 (mm-30) REVERT: D 73 ILE cc_start: 0.9781 (tt) cc_final: 0.9545 (pt) REVERT: D 77 ILE cc_start: 0.9441 (pt) cc_final: 0.8832 (mt) REVERT: D 100 MET cc_start: 0.9394 (mtp) cc_final: 0.9091 (mtp) REVERT: D 119 ILE cc_start: 0.9507 (mm) cc_final: 0.9301 (mp) REVERT: D 124 PHE cc_start: 0.9180 (t80) cc_final: 0.8717 (t80) REVERT: E 26 MET cc_start: 0.9450 (mmm) cc_final: 0.8995 (mmt) REVERT: E 96 MET cc_start: 0.9048 (ttp) cc_final: 0.8520 (ttp) REVERT: E 120 LYS cc_start: 0.9738 (mttt) cc_final: 0.9465 (tptp) REVERT: E 138 PHE cc_start: 0.8304 (t80) cc_final: 0.7870 (t80) REVERT: E 175 PHE cc_start: 0.9137 (t80) cc_final: 0.8853 (t80) REVERT: F 69 ARG cc_start: 0.9192 (tmm-80) cc_final: 0.8690 (tmm-80) REVERT: F 103 ILE cc_start: 0.9656 (mt) cc_final: 0.9114 (tp) REVERT: F 149 ARG cc_start: 0.9635 (ttt-90) cc_final: 0.8924 (ptm160) REVERT: F 164 TYR cc_start: 0.9341 (m-10) cc_final: 0.8808 (m-10) REVERT: G 2 GLN cc_start: 0.9388 (mm-40) cc_final: 0.9033 (mm110) REVERT: G 18 GLN cc_start: 0.9426 (tt0) cc_final: 0.9140 (tt0) REVERT: G 40 THR cc_start: 0.9162 (m) cc_final: 0.8912 (p) REVERT: G 41 LYS cc_start: 0.9749 (ptpp) cc_final: 0.9507 (tptp) REVERT: G 43 ASN cc_start: 0.9758 (m-40) cc_final: 0.9486 (m-40) REVERT: G 101 ASP cc_start: 0.9662 (t70) cc_final: 0.9379 (m-30) REVERT: G 131 SER cc_start: 0.9735 (m) cc_final: 0.9268 (p) REVERT: G 132 PHE cc_start: 0.9213 (m-10) cc_final: 0.8473 (m-80) REVERT: J 1 MET cc_start: 0.9074 (ppp) cc_final: 0.8823 (ppp) REVERT: J 14 ASP cc_start: 0.8951 (m-30) cc_final: 0.8634 (m-30) REVERT: J 75 TYR cc_start: 0.9687 (m-10) cc_final: 0.9350 (m-10) REVERT: J 80 HIS cc_start: 0.8094 (m90) cc_final: 0.7650 (m90) REVERT: J 86 GLN cc_start: 0.9639 (tt0) cc_final: 0.9108 (pm20) REVERT: J 92 MET cc_start: 0.9558 (mmm) cc_final: 0.9113 (mmm) REVERT: J 102 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8414 (mp0) REVERT: J 109 LEU cc_start: 0.9656 (mm) cc_final: 0.9420 (tp) REVERT: J 118 MET cc_start: 0.8919 (mtt) cc_final: 0.8524 (mtt) REVERT: K 1 MET cc_start: 0.9241 (ttt) cc_final: 0.8759 (ttt) REVERT: K 5 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8587 (tm-30) REVERT: K 8 LEU cc_start: 0.9646 (mp) cc_final: 0.9397 (mm) REVERT: K 9 ASN cc_start: 0.9751 (m-40) cc_final: 0.9359 (m-40) REVERT: K 25 LEU cc_start: 0.9371 (mm) cc_final: 0.9127 (mm) REVERT: K 79 PHE cc_start: 0.8812 (m-80) cc_final: 0.7843 (m-10) REVERT: L 51 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8356 (mt-10) REVERT: L 59 ARG cc_start: 0.9288 (mtm180) cc_final: 0.9077 (mtm-85) REVERT: M 73 ILE cc_start: 0.9659 (mm) cc_final: 0.9198 (mp) REVERT: M 91 TYR cc_start: 0.9045 (p90) cc_final: 0.8562 (p90) REVERT: M 112 LEU cc_start: 0.9733 (tp) cc_final: 0.9461 (tp) REVERT: N 20 MET cc_start: 0.9094 (ttp) cc_final: 0.8419 (ttp) REVERT: N 21 PHE cc_start: 0.9050 (m-10) cc_final: 0.8612 (m-80) REVERT: N 24 MET cc_start: 0.9197 (ttm) cc_final: 0.8365 (mmm) REVERT: N 43 GLU cc_start: 0.9337 (tp30) cc_final: 0.8441 (tp30) REVERT: N 87 PHE cc_start: 0.8749 (m-80) cc_final: 0.7795 (m-80) REVERT: N 97 ILE cc_start: 0.9117 (pt) cc_final: 0.8897 (pt) REVERT: N 98 LEU cc_start: 0.9350 (mt) cc_final: 0.8754 (mp) REVERT: O 69 ASP cc_start: 0.9751 (m-30) cc_final: 0.9387 (t0) REVERT: O 89 ASP cc_start: 0.8374 (t70) cc_final: 0.7884 (t70) REVERT: P 71 GLU cc_start: 0.8045 (mt-10) cc_final: 0.5949 (pm20) REVERT: Q 31 VAL cc_start: 0.8945 (t) cc_final: 0.8612 (t) REVERT: Q 40 ILE cc_start: 0.9894 (mm) cc_final: 0.9653 (mm) REVERT: Q 44 GLN cc_start: 0.9710 (mt0) cc_final: 0.9468 (mp10) REVERT: Q 59 GLN cc_start: 0.9519 (tt0) cc_final: 0.9107 (mm-40) REVERT: Q 78 LYS cc_start: 0.9632 (mtpp) cc_final: 0.9269 (mmmt) REVERT: R 83 TYR cc_start: 0.8749 (t80) cc_final: 0.8257 (t80) REVERT: R 85 LYS cc_start: 0.7541 (tptm) cc_final: 0.6723 (tptm) REVERT: R 86 GLN cc_start: 0.8693 (mm110) cc_final: 0.8254 (pp30) REVERT: R 95 ASP cc_start: 0.9404 (m-30) cc_final: 0.8924 (p0) REVERT: R 98 ILE cc_start: 0.9690 (mm) cc_final: 0.9413 (mp) REVERT: S 6 LYS cc_start: 0.8981 (tttm) cc_final: 0.7566 (tptp) REVERT: S 78 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8673 (mt-10) REVERT: S 97 LEU cc_start: 0.9670 (mm) cc_final: 0.9162 (mm) REVERT: S 99 ARG cc_start: 0.9173 (mmt90) cc_final: 0.8787 (mpp-170) REVERT: S 103 ILE cc_start: 0.9515 (mt) cc_final: 0.9251 (mt) REVERT: T 1 MET cc_start: 0.6524 (mmm) cc_final: 0.5131 (mmm) REVERT: T 86 THR cc_start: 0.9503 (m) cc_final: 0.9031 (m) REVERT: V 50 MET cc_start: 0.9460 (mtm) cc_final: 0.9045 (ptp) REVERT: W 21 LEU cc_start: 0.8933 (mm) cc_final: 0.8331 (mm) REVERT: W 36 ILE cc_start: 0.9261 (mm) cc_final: 0.8979 (mm) REVERT: W 39 ARG cc_start: 0.9221 (mtp-110) cc_final: 0.8789 (ptp-110) REVERT: W 57 HIS cc_start: 0.9314 (m-70) cc_final: 0.9034 (m90) REVERT: X 17 ASN cc_start: 0.9370 (m-40) cc_final: 0.8937 (m-40) REVERT: X 38 PHE cc_start: 0.8907 (m-80) cc_final: 0.8024 (m-80) REVERT: X 41 GLU cc_start: 0.9229 (tp30) cc_final: 0.8989 (tp30) REVERT: X 47 VAL cc_start: 0.9452 (t) cc_final: 0.8912 (m) REVERT: X 49 LEU cc_start: 0.8674 (mt) cc_final: 0.8134 (mt) REVERT: X 56 MET cc_start: 0.9279 (mtp) cc_final: 0.9048 (mmm) REVERT: X 71 LEU cc_start: 0.9766 (mt) cc_final: 0.9544 (mt) REVERT: Y 24 GLU cc_start: 0.9727 (mt-10) cc_final: 0.9423 (pt0) REVERT: Z 6 LYS cc_start: 0.9739 (mppt) cc_final: 0.9445 (mmtm) REVERT: Z 21 LYS cc_start: 0.9383 (mttt) cc_final: 0.8890 (mttm) REVERT: Z 32 ILE cc_start: 0.9457 (pt) cc_final: 0.9211 (mp) REVERT: Z 49 ASN cc_start: 0.9826 (t0) cc_final: 0.9595 (p0) REVERT: Z 54 MET cc_start: 0.9272 (ptm) cc_final: 0.8626 (ppp) REVERT: Z 56 LYS cc_start: 0.9760 (tttm) cc_final: 0.9467 (tptp) REVERT: b 7 LYS cc_start: 0.9139 (tptm) cc_final: 0.8638 (tptp) REVERT: b 9 THR cc_start: 0.9165 (m) cc_final: 0.8877 (p) REVERT: b 46 ASP cc_start: 0.9223 (t0) cc_final: 0.8909 (t0) REVERT: d 6 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8041 (mm110) REVERT: d 14 ARG cc_start: 0.9137 (mtt180) cc_final: 0.8619 (mtp180) REVERT: d 25 LYS cc_start: 0.9160 (tmmt) cc_final: 0.8901 (ttpt) REVERT: d 29 GLN cc_start: 0.9116 (mp10) cc_final: 0.8908 (mp10) REVERT: e 14 PHE cc_start: 0.9754 (m-80) cc_final: 0.9286 (m-80) REVERT: e 15 LYS cc_start: 0.9289 (mmtm) cc_final: 0.8755 (mmtm) REVERT: f 22 VAL cc_start: 0.9187 (t) cc_final: 0.8961 (p) REVERT: g 27 MET cc_start: 0.8710 (mmm) cc_final: 0.8312 (mmm) REVERT: g 32 PHE cc_start: 0.9259 (t80) cc_final: 0.8924 (t80) REVERT: g 50 PHE cc_start: 0.9700 (t80) cc_final: 0.9194 (t80) REVERT: g 100 MET cc_start: 0.9593 (ttm) cc_final: 0.9136 (mtp) REVERT: g 120 GLN cc_start: 0.9262 (tt0) cc_final: 0.8901 (tp-100) REVERT: g 136 MET cc_start: 0.9671 (mtm) cc_final: 0.9449 (mtm) REVERT: g 143 LYS cc_start: 0.9222 (tttm) cc_final: 0.8935 (ttpp) REVERT: h 8 ASN cc_start: 0.8801 (m110) cc_final: 0.8554 (m110) REVERT: h 19 ASN cc_start: 0.9299 (m-40) cc_final: 0.8458 (p0) REVERT: h 29 PHE cc_start: 0.9457 (t80) cc_final: 0.9219 (t80) REVERT: h 51 SER cc_start: 0.9166 (m) cc_final: 0.8835 (p) REVERT: h 114 LYS cc_start: 0.9564 (tptp) cc_final: 0.9278 (tppt) REVERT: h 115 LEU cc_start: 0.9459 (mt) cc_final: 0.9017 (mp) REVERT: h 123 GLN cc_start: 0.9732 (mt0) cc_final: 0.9375 (mt0) REVERT: h 139 GLN cc_start: 0.9625 (mt0) cc_final: 0.9310 (mt0) REVERT: h 157 LEU cc_start: 0.9193 (mt) cc_final: 0.8855 (mt) REVERT: h 185 ASN cc_start: 0.9278 (t0) cc_final: 0.8979 (t0) REVERT: h 193 TYR cc_start: 0.9293 (m-80) cc_final: 0.8668 (m-80) REVERT: h 201 TRP cc_start: 0.8956 (m-90) cc_final: 0.8588 (m-90) REVERT: i 54 GLN cc_start: 0.9462 (mt0) cc_final: 0.9099 (mt0) REVERT: i 59 GLN cc_start: 0.9490 (mm110) cc_final: 0.9130 (mm-40) REVERT: i 70 ARG cc_start: 0.9161 (tpp80) cc_final: 0.8600 (mtm180) REVERT: i 72 PHE cc_start: 0.9645 (t80) cc_final: 0.8767 (t80) REVERT: i 123 ILE cc_start: 0.9153 (mm) cc_final: 0.8529 (mp) REVERT: i 124 MET cc_start: 0.9071 (mtt) cc_final: 0.8710 (mmm) REVERT: j 14 LYS cc_start: 0.9302 (mmpt) cc_final: 0.8830 (mtmm) REVERT: j 29 ARG cc_start: 0.8851 (mpp80) cc_final: 0.8387 (mmt180) REVERT: j 45 ARG cc_start: 0.8866 (mmt180) cc_final: 0.8581 (mmt-90) REVERT: j 64 MET cc_start: 0.9431 (mmt) cc_final: 0.9168 (mmt) REVERT: j 71 MET cc_start: 0.7752 (mmm) cc_final: 0.7449 (mmm) REVERT: j 81 LEU cc_start: 0.9723 (mp) cc_final: 0.9094 (mt) REVERT: j 116 GLU cc_start: 0.9700 (tt0) cc_final: 0.9410 (tt0) REVERT: j 126 LYS cc_start: 0.9305 (tptt) cc_final: 0.9097 (tptt) REVERT: j 147 MET cc_start: 0.6878 (ttp) cc_final: 0.6432 (tmm) REVERT: k 9 MET cc_start: 0.9565 (mtp) cc_final: 0.9324 (mmp) REVERT: k 18 VAL cc_start: 0.8914 (m) cc_final: 0.8714 (m) REVERT: k 21 MET cc_start: 0.9021 (mtm) cc_final: 0.8569 (ptp) REVERT: k 44 ARG cc_start: 0.8683 (tmm160) cc_final: 0.8381 (ttp80) REVERT: k 80 PHE cc_start: 0.9575 (m-80) cc_final: 0.9073 (m-80) REVERT: l 26 PHE cc_start: 0.9752 (t80) cc_final: 0.9488 (t80) REVERT: l 56 LYS cc_start: 0.9586 (mttt) cc_final: 0.9304 (ptpp) REVERT: l 101 MET cc_start: 0.9600 (mtm) cc_final: 0.9164 (mmm) REVERT: l 103 TRP cc_start: 0.9488 (m-10) cc_final: 0.9151 (m-10) REVERT: n 50 GLN cc_start: 0.9706 (mt0) cc_final: 0.9446 (mm-40) REVERT: n 64 TYR cc_start: 0.8518 (t80) cc_final: 0.8004 (t80) REVERT: n 66 THR cc_start: 0.8952 (p) cc_final: 0.7596 (t) REVERT: n 88 MET cc_start: 0.8253 (mmp) cc_final: 0.7830 (mmp) REVERT: n 97 GLU cc_start: 0.9350 (mt-10) cc_final: 0.8990 (mp0) REVERT: n 112 GLU cc_start: 0.7770 (tp30) cc_final: 0.7463 (tp30) REVERT: n 115 LYS cc_start: 0.9460 (mttt) cc_final: 0.9227 (mmtp) REVERT: o 11 LYS cc_start: 0.9428 (mtpt) cc_final: 0.9054 (mmtm) REVERT: o 47 GLU cc_start: 0.9137 (tt0) cc_final: 0.8923 (tt0) REVERT: o 49 PHE cc_start: 0.9102 (m-80) cc_final: 0.8471 (m-80) REVERT: o 52 LEU cc_start: 0.8300 (tp) cc_final: 0.7849 (tp) REVERT: o 66 GLU cc_start: 0.9335 (pt0) cc_final: 0.9051 (tm-30) REVERT: o 99 GLN cc_start: 0.9412 (tt0) cc_final: 0.8875 (tt0) REVERT: p 31 ILE cc_start: 0.9750 (mm) cc_final: 0.9545 (mp) REVERT: p 56 ARG cc_start: 0.9447 (mpp80) cc_final: 0.9036 (mtm110) REVERT: p 68 GLU cc_start: 0.9539 (mp0) cc_final: 0.9284 (mp0) REVERT: p 74 VAL cc_start: 0.9555 (m) cc_final: 0.9317 (m) REVERT: p 79 ILE cc_start: 0.9503 (mp) cc_final: 0.9267 (mp) REVERT: p 82 LEU cc_start: 0.9602 (tp) cc_final: 0.9158 (tp) REVERT: p 84 VAL cc_start: 0.9512 (t) cc_final: 0.9004 (p) REVERT: p 85 MET cc_start: 0.9485 (mtt) cc_final: 0.9155 (mmp) REVERT: p 105 PHE cc_start: 0.9512 (m-10) cc_final: 0.9259 (m-80) REVERT: q 20 ASN cc_start: 0.9608 (p0) cc_final: 0.9385 (p0) REVERT: q 66 TYR cc_start: 0.7800 (t80) cc_final: 0.7571 (t80) REVERT: q 123 LYS cc_start: 0.9334 (mttt) cc_final: 0.9126 (tptp) REVERT: r 27 LYS cc_start: 0.9162 (tppt) cc_final: 0.8866 (tppt) REVERT: r 31 LYS cc_start: 0.9612 (mtmm) cc_final: 0.9251 (ptpp) REVERT: r 41 GLU cc_start: 0.9329 (mt-10) cc_final: 0.8436 (mt-10) REVERT: r 42 ASP cc_start: 0.8930 (p0) cc_final: 0.8440 (t70) REVERT: r 64 VAL cc_start: 0.9182 (t) cc_final: 0.8818 (t) REVERT: r 69 LEU cc_start: 0.9798 (tp) cc_final: 0.9593 (tp) REVERT: r 72 GLU cc_start: 0.9676 (mt-10) cc_final: 0.9383 (pt0) REVERT: s 18 ASP cc_start: 0.8735 (m-30) cc_final: 0.8398 (m-30) REVERT: s 92 GLU cc_start: 0.9133 (mp0) cc_final: 0.8786 (mp0) REVERT: t 26 GLU cc_start: 0.9347 (mp0) cc_final: 0.8874 (pt0) REVERT: t 62 GLN cc_start: 0.9640 (tt0) cc_final: 0.9152 (mt0) REVERT: t 65 LYS cc_start: 0.9346 (mttt) cc_final: 0.9070 (mmtt) REVERT: t 68 ASP cc_start: 0.9716 (m-30) cc_final: 0.9241 (m-30) REVERT: t 73 LYS cc_start: 0.9089 (tptm) cc_final: 0.8750 (mmmm) REVERT: t 74 ASP cc_start: 0.9453 (t0) cc_final: 0.9170 (t0) REVERT: u 1 MET cc_start: 0.8689 (pmm) cc_final: 0.7596 (tpt) REVERT: v 6 ARG cc_start: 0.8191 (mtp-110) cc_final: 0.6531 (mtp85) REVERT: v 34 TYR cc_start: 0.9191 (m-80) cc_final: 0.8923 (m-10) REVERT: v 65 ARG cc_start: 0.8526 (ttp80) cc_final: 0.8156 (ttp-170) REVERT: v 74 THR cc_start: 0.9734 (m) cc_final: 0.9486 (p) REVERT: w 32 TYR cc_start: 0.9070 (m-80) cc_final: 0.8795 (m-80) REVERT: w 52 GLN cc_start: 0.9231 (tp40) cc_final: 0.8964 (tp40) REVERT: w 57 ARG cc_start: 0.9395 (ttm110) cc_final: 0.8898 (mtt180) REVERT: w 65 LEU cc_start: 0.9788 (mt) cc_final: 0.9390 (tp) REVERT: w 67 LEU cc_start: 0.9433 (mt) cc_final: 0.8935 (mt) REVERT: w 70 TYR cc_start: 0.8627 (m-80) cc_final: 0.8163 (m-10) REVERT: x 65 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8708 (tp30) REVERT: y 15 GLU cc_start: 0.9736 (tt0) cc_final: 0.9332 (tp30) REVERT: y 18 ARG cc_start: 0.9775 (ttp80) cc_final: 0.9155 (ttp-110) REVERT: y 32 ILE cc_start: 0.9749 (mt) cc_final: 0.9204 (pt) REVERT: y 78 ASN cc_start: 0.9626 (m-40) cc_final: 0.9285 (p0) REVERT: z 19 PHE cc_start: 0.9406 (t80) cc_final: 0.9044 (t80) REVERT: z 24 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8606 (pt0) REVERT: 7 144 TRP cc_start: 0.9424 (t-100) cc_final: 0.9155 (t-100) REVERT: 7 199 HIS cc_start: 0.9241 (m-70) cc_final: 0.8927 (m-70) REVERT: 7 310 MET cc_start: 0.5362 (tpp) cc_final: 0.4805 (mmm) outliers start: 4 outliers final: 1 residues processed: 1358 average time/residue: 1.3790 time to fit residues: 3149.5030 Evaluate side-chains 1009 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1008 time to evaluate : 6.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 523 optimal weight: 8.9990 chunk 292 optimal weight: 30.0000 chunk 784 optimal weight: 0.4980 chunk 641 optimal weight: 6.9990 chunk 260 optimal weight: 30.0000 chunk 944 optimal weight: 10.0000 chunk 1020 optimal weight: 3.9990 chunk 841 optimal weight: 5.9990 chunk 936 optimal weight: 9.9990 chunk 321 optimal weight: 30.0000 chunk 757 optimal weight: 30.0000 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 ASN F 30 ASN G 119 ASN J 136 GLN M 60 GLN N 81 ASN O 38 GLN ** P 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 ASN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 13 ASN ** g 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 32 ASN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 6 GLN s 4 GLN s 43 ASN t 37 ASN ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 78 ASN ** 7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 133 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 159192 Z= 0.196 Angle : 0.628 14.077 237909 Z= 0.338 Chirality : 0.034 0.235 30260 Planarity : 0.006 0.129 12919 Dihedral : 24.824 179.528 78958 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 27.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.14 % Favored : 94.82 % Rotamer: Outliers : 0.08 % Allowed : 3.66 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.10), residues: 5890 helix: -0.37 (0.11), residues: 2069 sheet: -2.03 (0.14), residues: 1090 loop : -1.60 (0.11), residues: 2731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 7 155 HIS 0.016 0.001 HIS t 46 PHE 0.031 0.002 PHE G 46 TYR 0.034 0.002 TYR 7 123 ARG 0.021 0.001 ARG v 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1250 time to evaluate : 6.308 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 CYS cc_start: 0.8438 (m) cc_final: 0.7921 (t) REVERT: B 21 ASN cc_start: 0.8431 (t0) cc_final: 0.7913 (t0) REVERT: B 68 LYS cc_start: 0.9424 (mtpt) cc_final: 0.9123 (mmmm) REVERT: B 79 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8806 (mm-30) REVERT: B 91 ILE cc_start: 0.9524 (pt) cc_final: 0.9213 (pt) REVERT: B 96 TYR cc_start: 0.8639 (m-80) cc_final: 0.7875 (m-80) REVERT: B 115 GLN cc_start: 0.9296 (tp-100) cc_final: 0.9005 (tp-100) REVERT: B 132 MET cc_start: 0.9421 (mtm) cc_final: 0.8795 (mtm) REVERT: B 146 MET cc_start: 0.8414 (mtt) cc_final: 0.8203 (mtp) REVERT: B 161 TYR cc_start: 0.9342 (p90) cc_final: 0.9124 (p90) REVERT: B 163 GLN cc_start: 0.9187 (tp40) cc_final: 0.8975 (tp40) REVERT: B 183 LYS cc_start: 0.9658 (mttm) cc_final: 0.9455 (mmmt) REVERT: B 185 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8829 (tm-30) REVERT: B 201 MET cc_start: 0.9013 (ptt) cc_final: 0.8541 (ptt) REVERT: B 260 ASN cc_start: 0.8060 (t0) cc_final: 0.7548 (t0) REVERT: B 264 ASP cc_start: 0.9378 (m-30) cc_final: 0.9053 (m-30) REVERT: B 266 PHE cc_start: 0.9156 (m-80) cc_final: 0.8869 (m-80) REVERT: B 271 ARG cc_start: 0.9066 (ptt-90) cc_final: 0.8190 (pmt170) REVERT: C 2 ILE cc_start: 0.7685 (pt) cc_final: 0.7112 (mm) REVERT: C 139 SER cc_start: 0.8907 (m) cc_final: 0.8579 (t) REVERT: C 149 ASN cc_start: 0.8634 (t0) cc_final: 0.8379 (t0) REVERT: C 165 MET cc_start: 0.8243 (ttt) cc_final: 0.7840 (ttt) REVERT: D 1 MET cc_start: 0.9381 (tpt) cc_final: 0.9034 (tpp) REVERT: D 30 GLN cc_start: 0.9571 (tt0) cc_final: 0.9290 (mm-40) REVERT: D 51 GLU cc_start: 0.9627 (mm-30) cc_final: 0.9204 (mm-30) REVERT: D 73 ILE cc_start: 0.9751 (tt) cc_final: 0.9498 (pt) REVERT: D 100 MET cc_start: 0.9410 (mtp) cc_final: 0.9064 (mtp) REVERT: D 141 MET cc_start: 0.9385 (mpp) cc_final: 0.9025 (mpp) REVERT: E 26 MET cc_start: 0.9528 (mmm) cc_final: 0.9020 (mmt) REVERT: E 96 MET cc_start: 0.8962 (ttp) cc_final: 0.8342 (ttp) REVERT: E 120 LYS cc_start: 0.9741 (mttt) cc_final: 0.9466 (tptp) REVERT: E 138 PHE cc_start: 0.8399 (t80) cc_final: 0.7914 (t80) REVERT: E 175 PHE cc_start: 0.9081 (t80) cc_final: 0.8763 (t80) REVERT: F 103 ILE cc_start: 0.9664 (mt) cc_final: 0.9121 (tp) REVERT: F 149 ARG cc_start: 0.9610 (ttt-90) cc_final: 0.8909 (ptm160) REVERT: F 164 TYR cc_start: 0.9348 (m-10) cc_final: 0.8865 (m-10) REVERT: F 166 ASP cc_start: 0.9632 (p0) cc_final: 0.9187 (p0) REVERT: G 2 GLN cc_start: 0.9486 (mm-40) cc_final: 0.9061 (mm110) REVERT: G 18 GLN cc_start: 0.9481 (tt0) cc_final: 0.9185 (tt0) REVERT: G 41 LYS cc_start: 0.9763 (ptpp) cc_final: 0.9383 (tptp) REVERT: G 46 PHE cc_start: 0.9565 (t80) cc_final: 0.9285 (t80) REVERT: G 83 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8440 (mmmm) REVERT: G 132 PHE cc_start: 0.9226 (m-10) cc_final: 0.8549 (m-80) REVERT: J 1 MET cc_start: 0.9060 (ppp) cc_final: 0.8860 (ppp) REVERT: J 14 ASP cc_start: 0.9189 (m-30) cc_final: 0.8624 (m-30) REVERT: J 16 TYR cc_start: 0.9208 (m-10) cc_final: 0.8954 (m-10) REVERT: J 67 ASN cc_start: 0.9647 (m-40) cc_final: 0.9425 (p0) REVERT: J 71 ASP cc_start: 0.9340 (p0) cc_final: 0.8696 (p0) REVERT: J 74 TYR cc_start: 0.8750 (m-10) cc_final: 0.8527 (m-80) REVERT: J 75 TYR cc_start: 0.9682 (m-80) cc_final: 0.9214 (m-10) REVERT: J 92 MET cc_start: 0.9517 (mmm) cc_final: 0.9173 (tpp) REVERT: J 102 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8249 (mt-10) REVERT: J 109 LEU cc_start: 0.9650 (mm) cc_final: 0.9422 (mm) REVERT: K 1 MET cc_start: 0.9102 (ttt) cc_final: 0.8852 (ttt) REVERT: K 5 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8400 (tm-30) REVERT: K 7 MET cc_start: 0.9051 (mmm) cc_final: 0.8559 (mmp) REVERT: K 9 ASN cc_start: 0.9644 (m-40) cc_final: 0.9211 (m-40) REVERT: K 20 MET cc_start: 0.8392 (ttm) cc_final: 0.8034 (ttt) REVERT: K 58 LEU cc_start: 0.9168 (pt) cc_final: 0.8924 (pt) REVERT: K 107 LEU cc_start: 0.9167 (mm) cc_final: 0.8955 (mp) REVERT: K 110 GLU cc_start: 0.9186 (pm20) cc_final: 0.8844 (pm20) REVERT: L 51 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8360 (mt-10) REVERT: L 73 ILE cc_start: 0.9723 (pt) cc_final: 0.9506 (pt) REVERT: M 65 ILE cc_start: 0.9212 (mp) cc_final: 0.8926 (mm) REVERT: M 73 ILE cc_start: 0.9690 (mm) cc_final: 0.9247 (mp) REVERT: M 91 TYR cc_start: 0.9135 (p90) cc_final: 0.8598 (p90) REVERT: M 112 LEU cc_start: 0.9712 (tp) cc_final: 0.9436 (tp) REVERT: N 20 MET cc_start: 0.9053 (ttp) cc_final: 0.8301 (mtp) REVERT: N 24 MET cc_start: 0.8936 (ttm) cc_final: 0.8197 (mmm) REVERT: N 32 GLU cc_start: 0.9314 (mt-10) cc_final: 0.9056 (mp0) REVERT: N 43 GLU cc_start: 0.9437 (tp30) cc_final: 0.8509 (tp30) REVERT: N 87 PHE cc_start: 0.8542 (m-80) cc_final: 0.7519 (m-80) REVERT: N 110 MET cc_start: 0.9165 (mmp) cc_final: 0.8915 (mmm) REVERT: N 117 ASP cc_start: 0.8630 (m-30) cc_final: 0.8386 (m-30) REVERT: O 69 ASP cc_start: 0.9725 (m-30) cc_final: 0.9387 (t0) REVERT: P 5 ILE cc_start: 0.9711 (mm) cc_final: 0.9391 (mm) REVERT: P 16 ASP cc_start: 0.9328 (p0) cc_final: 0.9064 (p0) REVERT: P 70 VAL cc_start: 0.9021 (t) cc_final: 0.8440 (t) REVERT: Q 59 GLN cc_start: 0.9544 (tt0) cc_final: 0.9188 (mm-40) REVERT: R 76 LYS cc_start: 0.9154 (mttt) cc_final: 0.8783 (mmmm) REVERT: R 83 TYR cc_start: 0.8788 (t80) cc_final: 0.8414 (t80) REVERT: R 85 LYS cc_start: 0.7738 (tptm) cc_final: 0.7460 (tptt) REVERT: R 86 GLN cc_start: 0.8723 (mm110) cc_final: 0.8427 (pp30) REVERT: R 95 ASP cc_start: 0.9362 (m-30) cc_final: 0.8939 (p0) REVERT: R 98 ILE cc_start: 0.9763 (mm) cc_final: 0.9260 (tt) REVERT: S 1 MET cc_start: 0.8949 (ptt) cc_final: 0.8468 (tmm) REVERT: S 8 ARG cc_start: 0.8737 (mmm160) cc_final: 0.8519 (mmm160) REVERT: S 65 ASP cc_start: 0.7744 (p0) cc_final: 0.7480 (p0) REVERT: S 78 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8606 (mt-10) REVERT: S 97 LEU cc_start: 0.9655 (mm) cc_final: 0.9089 (mm) REVERT: T 8 LEU cc_start: 0.9801 (mm) cc_final: 0.9575 (tt) REVERT: T 11 LEU cc_start: 0.9218 (mm) cc_final: 0.8659 (tp) REVERT: T 86 THR cc_start: 0.9394 (m) cc_final: 0.8643 (m) REVERT: V 48 MET cc_start: 0.9206 (mmm) cc_final: 0.8460 (mmm) REVERT: V 50 MET cc_start: 0.9505 (mtm) cc_final: 0.9166 (ptp) REVERT: W 17 GLU cc_start: 0.8638 (pt0) cc_final: 0.8261 (pp20) REVERT: W 21 LEU cc_start: 0.8833 (mm) cc_final: 0.8392 (mm) REVERT: W 36 ILE cc_start: 0.9223 (mm) cc_final: 0.8934 (mm) REVERT: X 38 PHE cc_start: 0.9137 (m-80) cc_final: 0.8191 (m-80) REVERT: X 47 VAL cc_start: 0.9571 (t) cc_final: 0.8989 (m) REVERT: X 49 LEU cc_start: 0.9134 (mt) cc_final: 0.8331 (mt) REVERT: X 56 MET cc_start: 0.9347 (mtp) cc_final: 0.8992 (mmm) REVERT: X 58 VAL cc_start: 0.9861 (t) cc_final: 0.9632 (t) REVERT: Y 24 GLU cc_start: 0.9723 (mt-10) cc_final: 0.9372 (pt0) REVERT: Y 30 MET cc_start: 0.8912 (mmp) cc_final: 0.8584 (mmm) REVERT: Y 54 LYS cc_start: 0.9642 (mmtp) cc_final: 0.9366 (mtpp) REVERT: Z 6 LYS cc_start: 0.9726 (mppt) cc_final: 0.9267 (mmtm) REVERT: Z 19 LYS cc_start: 0.9406 (mmmt) cc_final: 0.9055 (mmtt) REVERT: Z 21 LYS cc_start: 0.9367 (mttt) cc_final: 0.8842 (mttm) REVERT: Z 32 ILE cc_start: 0.9482 (pt) cc_final: 0.9241 (mp) REVERT: Z 49 ASN cc_start: 0.9854 (t0) cc_final: 0.9534 (p0) REVERT: Z 54 MET cc_start: 0.9289 (ptm) cc_final: 0.8294 (ttp) REVERT: b 7 LYS cc_start: 0.9033 (tptm) cc_final: 0.8747 (tptp) REVERT: b 9 THR cc_start: 0.9237 (m) cc_final: 0.9006 (p) REVERT: b 15 MET cc_start: 0.9133 (mtp) cc_final: 0.8722 (mtp) REVERT: b 46 ASP cc_start: 0.9237 (t0) cc_final: 0.8925 (t0) REVERT: c 54 ILE cc_start: 0.8484 (tp) cc_final: 0.8177 (tp) REVERT: d 1 MET cc_start: 0.6559 (mtt) cc_final: 0.6272 (mtt) REVERT: d 6 GLN cc_start: 0.8632 (mm-40) cc_final: 0.7965 (mp10) REVERT: e 14 PHE cc_start: 0.9747 (m-80) cc_final: 0.9138 (m-80) REVERT: f 13 ASN cc_start: 0.9544 (m110) cc_final: 0.9081 (t0) REVERT: f 22 VAL cc_start: 0.9128 (t) cc_final: 0.8912 (p) REVERT: g 27 MET cc_start: 0.8900 (mmm) cc_final: 0.8523 (mmm) REVERT: g 32 PHE cc_start: 0.9261 (t80) cc_final: 0.8926 (t80) REVERT: g 96 TRP cc_start: 0.8251 (t-100) cc_final: 0.7562 (t-100) REVERT: g 120 GLN cc_start: 0.9477 (tt0) cc_final: 0.9073 (tp-100) REVERT: g 132 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8490 (mmtt) REVERT: g 136 MET cc_start: 0.9691 (mtm) cc_final: 0.9443 (mtm) REVERT: g 157 LEU cc_start: 0.9443 (pp) cc_final: 0.9225 (pp) REVERT: g 198 PHE cc_start: 0.9065 (m-80) cc_final: 0.8635 (m-80) REVERT: h 8 ASN cc_start: 0.8769 (m110) cc_final: 0.8494 (m110) REVERT: h 19 ASN cc_start: 0.9404 (m-40) cc_final: 0.8655 (p0) REVERT: h 51 SER cc_start: 0.9444 (m) cc_final: 0.9050 (p) REVERT: h 115 LEU cc_start: 0.9471 (mt) cc_final: 0.8946 (mp) REVERT: h 123 GLN cc_start: 0.9711 (mt0) cc_final: 0.9350 (mt0) REVERT: h 154 SER cc_start: 0.8824 (m) cc_final: 0.8607 (p) REVERT: h 168 TYR cc_start: 0.8235 (m-80) cc_final: 0.7969 (m-80) REVERT: h 178 LEU cc_start: 0.9578 (tp) cc_final: 0.9318 (tp) REVERT: h 185 ASN cc_start: 0.9136 (t0) cc_final: 0.8846 (t0) REVERT: h 193 TYR cc_start: 0.9215 (m-80) cc_final: 0.8528 (m-80) REVERT: h 201 TRP cc_start: 0.8963 (m-90) cc_final: 0.8713 (m-90) REVERT: i 51 TYR cc_start: 0.9504 (t80) cc_final: 0.9278 (t80) REVERT: i 59 GLN cc_start: 0.9471 (mm110) cc_final: 0.9160 (mm110) REVERT: i 70 ARG cc_start: 0.8880 (tpp80) cc_final: 0.8594 (mtm180) REVERT: i 72 PHE cc_start: 0.9718 (t80) cc_final: 0.8780 (t80) REVERT: i 123 ILE cc_start: 0.9167 (mm) cc_final: 0.8534 (mp) REVERT: i 124 MET cc_start: 0.8949 (mtt) cc_final: 0.8543 (mmm) REVERT: j 14 LYS cc_start: 0.9302 (mmpt) cc_final: 0.8874 (mtmm) REVERT: j 29 ARG cc_start: 0.8905 (mpp80) cc_final: 0.8265 (mmt180) REVERT: j 34 THR cc_start: 0.8401 (t) cc_final: 0.8126 (p) REVERT: j 45 ARG cc_start: 0.9507 (tpp-160) cc_final: 0.9091 (tpp-160) REVERT: j 48 PHE cc_start: 0.9484 (p90) cc_final: 0.9193 (p90) REVERT: j 64 MET cc_start: 0.9601 (mmt) cc_final: 0.9265 (mmt) REVERT: j 81 LEU cc_start: 0.9729 (mp) cc_final: 0.8933 (mt) REVERT: j 93 ARG cc_start: 0.9071 (ttp-110) cc_final: 0.8694 (mtm110) REVERT: j 116 GLU cc_start: 0.9658 (tt0) cc_final: 0.9390 (tt0) REVERT: j 126 LYS cc_start: 0.9357 (tptt) cc_final: 0.9155 (tptt) REVERT: j 134 ILE cc_start: 0.9219 (tp) cc_final: 0.9014 (tt) REVERT: j 138 ARG cc_start: 0.8562 (mtt-85) cc_final: 0.8085 (mtp85) REVERT: j 142 ASP cc_start: 0.9610 (m-30) cc_final: 0.9388 (m-30) REVERT: j 147 MET cc_start: 0.7435 (ttp) cc_final: 0.7025 (tmm) REVERT: j 163 GLU cc_start: 0.9679 (pt0) cc_final: 0.9436 (pt0) REVERT: k 1 MET cc_start: 0.8519 (mpp) cc_final: 0.8110 (mpp) REVERT: k 6 ILE cc_start: 0.9882 (mm) cc_final: 0.9634 (mm) REVERT: k 9 MET cc_start: 0.9529 (mtp) cc_final: 0.9084 (mmp) REVERT: k 21 MET cc_start: 0.9127 (mtm) cc_final: 0.8544 (mtm) REVERT: k 33 GLU cc_start: 0.9358 (pm20) cc_final: 0.8601 (pp20) REVERT: k 35 LYS cc_start: 0.9724 (ptpp) cc_final: 0.9456 (ptpt) REVERT: k 52 ASN cc_start: 0.9499 (m110) cc_final: 0.9163 (m-40) REVERT: k 62 MET cc_start: 0.9484 (ppp) cc_final: 0.9275 (tmm) REVERT: k 80 PHE cc_start: 0.9570 (m-80) cc_final: 0.9012 (m-80) REVERT: k 89 VAL cc_start: 0.9251 (t) cc_final: 0.8912 (t) REVERT: k 90 MET cc_start: 0.8507 (mpp) cc_final: 0.8274 (mmm) REVERT: l 26 PHE cc_start: 0.9784 (t80) cc_final: 0.9491 (t80) REVERT: l 101 MET cc_start: 0.9601 (mtm) cc_final: 0.9347 (mtt) REVERT: n 39 PHE cc_start: 0.9523 (m-10) cc_final: 0.9306 (m-10) REVERT: n 54 LEU cc_start: 0.9145 (tt) cc_final: 0.8909 (mt) REVERT: n 97 GLU cc_start: 0.9546 (mt-10) cc_final: 0.9157 (mp0) REVERT: n 112 GLU cc_start: 0.7709 (tp30) cc_final: 0.7478 (tp30) REVERT: n 118 LEU cc_start: 0.9672 (mt) cc_final: 0.8690 (tp) REVERT: n 120 LYS cc_start: 0.8750 (mtpt) cc_final: 0.8514 (mtpt) REVERT: n 129 LYS cc_start: 0.6745 (mtmt) cc_final: 0.5994 (mppt) REVERT: o 49 PHE cc_start: 0.9237 (m-80) cc_final: 0.8570 (m-80) REVERT: o 51 VAL cc_start: 0.9460 (m) cc_final: 0.8737 (m) REVERT: o 52 LEU cc_start: 0.8660 (tp) cc_final: 0.8367 (tp) REVERT: o 66 GLU cc_start: 0.9400 (pt0) cc_final: 0.9123 (tm-30) REVERT: o 99 GLN cc_start: 0.9406 (tt0) cc_final: 0.9159 (tt0) REVERT: p 22 HIS cc_start: 0.8687 (m-70) cc_final: 0.8406 (m170) REVERT: p 56 ARG cc_start: 0.9440 (mpp80) cc_final: 0.9008 (mtm110) REVERT: p 79 ILE cc_start: 0.9361 (mp) cc_final: 0.9045 (mp) REVERT: p 83 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8372 (mm-30) REVERT: p 98 ARG cc_start: 0.9486 (ttm110) cc_final: 0.8868 (mtm110) REVERT: q 6 GLN cc_start: 0.8670 (mt0) cc_final: 0.7907 (mp10) REVERT: q 20 ASN cc_start: 0.9599 (p0) cc_final: 0.9365 (p0) REVERT: q 38 TYR cc_start: 0.6725 (p90) cc_final: 0.6484 (p90) REVERT: q 62 GLU cc_start: 0.8093 (tp30) cc_final: 0.7124 (tp30) REVERT: q 76 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8558 (mm-30) REVERT: q 123 LYS cc_start: 0.9328 (mttt) cc_final: 0.9112 (tptp) REVERT: r 27 LYS cc_start: 0.9178 (tppt) cc_final: 0.8855 (tppt) REVERT: r 41 GLU cc_start: 0.9426 (mt-10) cc_final: 0.8815 (mp0) REVERT: r 42 ASP cc_start: 0.8947 (p0) cc_final: 0.8468 (t70) REVERT: r 103 LYS cc_start: 0.9026 (tttt) cc_final: 0.8744 (tttp) REVERT: s 18 ASP cc_start: 0.8736 (m-30) cc_final: 0.8416 (m-30) REVERT: s 65 ARG cc_start: 0.9091 (ttm170) cc_final: 0.8865 (mtp180) REVERT: s 92 GLU cc_start: 0.8839 (mp0) cc_final: 0.8535 (mp0) REVERT: t 26 GLU cc_start: 0.9388 (mp0) cc_final: 0.8772 (tt0) REVERT: t 62 GLN cc_start: 0.9639 (tt0) cc_final: 0.9187 (mt0) REVERT: t 65 LYS cc_start: 0.9383 (mttt) cc_final: 0.9057 (mmtt) REVERT: t 68 ASP cc_start: 0.9589 (m-30) cc_final: 0.9165 (m-30) REVERT: t 71 LYS cc_start: 0.9107 (tppt) cc_final: 0.8765 (tppt) REVERT: t 74 ASP cc_start: 0.9489 (t0) cc_final: 0.9225 (t0) REVERT: u 1 MET cc_start: 0.8657 (pmm) cc_final: 0.7535 (tpt) REVERT: v 6 ARG cc_start: 0.8166 (mtp-110) cc_final: 0.6726 (mtp85) REVERT: w 31 ASN cc_start: 0.9463 (m110) cc_final: 0.9243 (m110) REVERT: w 54 GLN cc_start: 0.9273 (mt0) cc_final: 0.8907 (mt0) REVERT: w 65 LEU cc_start: 0.9762 (mt) cc_final: 0.9336 (tp) REVERT: w 67 LEU cc_start: 0.9457 (mt) cc_final: 0.8940 (mt) REVERT: w 70 TYR cc_start: 0.8657 (m-80) cc_final: 0.8234 (m-10) REVERT: x 39 THR cc_start: 0.9163 (m) cc_final: 0.8893 (p) REVERT: x 41 PHE cc_start: 0.9581 (t80) cc_final: 0.9339 (t80) REVERT: x 65 GLU cc_start: 0.9292 (mm-30) cc_final: 0.9050 (pm20) REVERT: y 15 GLU cc_start: 0.9747 (tt0) cc_final: 0.9383 (tp30) REVERT: y 18 ARG cc_start: 0.9751 (ttp80) cc_final: 0.9113 (ttp-110) REVERT: y 21 ASN cc_start: 0.9337 (m-40) cc_final: 0.9006 (m-40) REVERT: y 32 ILE cc_start: 0.9780 (mt) cc_final: 0.9365 (pt) REVERT: y 78 ASN cc_start: 0.9641 (m110) cc_final: 0.9376 (p0) REVERT: z 19 PHE cc_start: 0.9427 (t80) cc_final: 0.9125 (t80) REVERT: z 24 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8595 (pt0) REVERT: 7 144 TRP cc_start: 0.9414 (t-100) cc_final: 0.8958 (t-100) REVERT: 7 147 MET cc_start: 0.9613 (mtm) cc_final: 0.9289 (tpt) REVERT: 7 199 HIS cc_start: 0.9404 (m-70) cc_final: 0.8636 (m-70) REVERT: 7 310 MET cc_start: 0.5598 (tpp) cc_final: 0.5284 (mmm) REVERT: 7 327 VAL cc_start: 0.9120 (t) cc_final: 0.8776 (t) REVERT: 7 330 ASP cc_start: 0.8031 (m-30) cc_final: 0.7720 (m-30) outliers start: 4 outliers final: 1 residues processed: 1253 average time/residue: 1.4732 time to fit residues: 3172.3538 Evaluate side-chains 971 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 970 time to evaluate : 6.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 932 optimal weight: 30.0000 chunk 709 optimal weight: 30.0000 chunk 490 optimal weight: 20.0000 chunk 104 optimal weight: 30.0000 chunk 450 optimal weight: 30.0000 chunk 634 optimal weight: 8.9990 chunk 947 optimal weight: 20.0000 chunk 1003 optimal weight: 20.0000 chunk 495 optimal weight: 50.0000 chunk 898 optimal weight: 4.9990 chunk 270 optimal weight: 30.0000 overall best weight: 14.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 ASN ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 73 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 57 HIS ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 32 ASN ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 4 GLN ** t 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 21 ASN ** 7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.142 159192 Z= 0.399 Angle : 0.781 13.568 237909 Z= 0.407 Chirality : 0.040 0.261 30260 Planarity : 0.007 0.132 12919 Dihedral : 24.995 179.812 78958 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 44.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.96 % Favored : 93.02 % Rotamer: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.10), residues: 5890 helix: -0.29 (0.11), residues: 2046 sheet: -2.13 (0.14), residues: 1097 loop : -1.48 (0.12), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP 7 155 HIS 0.026 0.002 HIS t 46 PHE 0.032 0.003 PHE L 107 TYR 0.025 0.002 TYR S 38 ARG 0.016 0.001 ARG n 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1105 time to evaluate : 6.322 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ASN cc_start: 0.8407 (t0) cc_final: 0.7978 (t0) REVERT: B 68 LYS cc_start: 0.9433 (mtpt) cc_final: 0.9147 (mmmm) REVERT: B 79 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8736 (mm-30) REVERT: B 96 TYR cc_start: 0.8654 (m-80) cc_final: 0.7923 (m-80) REVERT: B 115 GLN cc_start: 0.9238 (tp-100) cc_final: 0.8919 (tp-100) REVERT: B 132 MET cc_start: 0.9354 (mtm) cc_final: 0.8705 (mtm) REVERT: B 146 MET cc_start: 0.8439 (mtt) cc_final: 0.8200 (mtp) REVERT: B 161 TYR cc_start: 0.9347 (p90) cc_final: 0.8780 (p90) REVERT: B 183 LYS cc_start: 0.9631 (mttm) cc_final: 0.9379 (mmmt) REVERT: B 185 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8833 (tm-30) REVERT: B 201 MET cc_start: 0.9020 (ptt) cc_final: 0.8545 (ptt) REVERT: B 243 HIS cc_start: 0.9137 (m90) cc_final: 0.8769 (m-70) REVERT: B 264 ASP cc_start: 0.9298 (m-30) cc_final: 0.8974 (m-30) REVERT: B 266 PHE cc_start: 0.9308 (m-80) cc_final: 0.8990 (m-80) REVERT: C 2 ILE cc_start: 0.8034 (pt) cc_final: 0.7578 (mm) REVERT: C 123 LYS cc_start: 0.9296 (mtmm) cc_final: 0.9000 (ptpp) REVERT: C 149 ASN cc_start: 0.8276 (t0) cc_final: 0.8000 (t0) REVERT: C 165 MET cc_start: 0.8317 (ttt) cc_final: 0.8035 (ttt) REVERT: D 1 MET cc_start: 0.9515 (tpt) cc_final: 0.9235 (tpp) REVERT: D 51 GLU cc_start: 0.9571 (mm-30) cc_final: 0.9201 (mm-30) REVERT: D 100 MET cc_start: 0.9381 (mtp) cc_final: 0.9031 (mtp) REVERT: D 188 MET cc_start: 0.9610 (mmm) cc_final: 0.9024 (mmm) REVERT: E 26 MET cc_start: 0.9451 (mmm) cc_final: 0.8959 (mmt) REVERT: E 96 MET cc_start: 0.8961 (ttp) cc_final: 0.8376 (ttp) REVERT: E 130 MET cc_start: 0.9665 (pmm) cc_final: 0.9455 (pmm) REVERT: E 138 PHE cc_start: 0.8696 (t80) cc_final: 0.8461 (t80) REVERT: E 175 PHE cc_start: 0.9157 (t80) cc_final: 0.8832 (t80) REVERT: F 69 ARG cc_start: 0.9444 (tmm160) cc_final: 0.9210 (tmm-80) REVERT: F 149 ARG cc_start: 0.9574 (ttt-90) cc_final: 0.8900 (ptm160) REVERT: F 164 TYR cc_start: 0.9248 (m-10) cc_final: 0.8768 (m-10) REVERT: G 1 MET cc_start: 0.9363 (tpp) cc_final: 0.8990 (tmm) REVERT: G 46 PHE cc_start: 0.9663 (t80) cc_final: 0.9413 (t80) REVERT: G 91 PHE cc_start: 0.8322 (m-10) cc_final: 0.7991 (m-10) REVERT: G 101 ASP cc_start: 0.9181 (m-30) cc_final: 0.8786 (m-30) REVERT: G 132 PHE cc_start: 0.9272 (m-10) cc_final: 0.8506 (m-80) REVERT: J 14 ASP cc_start: 0.9209 (m-30) cc_final: 0.8899 (m-30) REVERT: J 67 ASN cc_start: 0.9718 (m-40) cc_final: 0.9512 (p0) REVERT: J 75 TYR cc_start: 0.9508 (m-80) cc_final: 0.9203 (m-10) REVERT: J 92 MET cc_start: 0.9634 (mmm) cc_final: 0.9353 (tpp) REVERT: J 109 LEU cc_start: 0.9662 (mm) cc_final: 0.9453 (tp) REVERT: K 1 MET cc_start: 0.9122 (ttt) cc_final: 0.8723 (ttt) REVERT: K 5 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8303 (tm-30) REVERT: K 7 MET cc_start: 0.9124 (mmm) cc_final: 0.8259 (mmm) REVERT: K 9 ASN cc_start: 0.9638 (m-40) cc_final: 0.9148 (m-40) REVERT: K 20 MET cc_start: 0.8413 (ttm) cc_final: 0.7720 (ttp) REVERT: K 25 LEU cc_start: 0.9494 (mm) cc_final: 0.9222 (mm) REVERT: K 84 CYS cc_start: 0.9670 (p) cc_final: 0.9406 (p) REVERT: K 107 LEU cc_start: 0.9223 (mm) cc_final: 0.8988 (mm) REVERT: K 110 GLU cc_start: 0.9325 (pm20) cc_final: 0.9043 (pm20) REVERT: L 23 ILE cc_start: 0.8973 (mt) cc_final: 0.8579 (mt) REVERT: L 51 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8462 (mt-10) REVERT: L 57 LEU cc_start: 0.9542 (tp) cc_final: 0.9316 (tp) REVERT: L 67 THR cc_start: 0.9076 (m) cc_final: 0.8850 (p) REVERT: M 73 ILE cc_start: 0.9357 (mm) cc_final: 0.9085 (mp) REVERT: M 82 MET cc_start: 0.8892 (tpp) cc_final: 0.7366 (mmp) REVERT: M 91 TYR cc_start: 0.9195 (p90) cc_final: 0.8859 (p90) REVERT: M 112 LEU cc_start: 0.9687 (tp) cc_final: 0.9356 (tp) REVERT: M 128 THR cc_start: 0.7874 (p) cc_final: 0.7651 (p) REVERT: N 1 MET cc_start: 0.8264 (tpp) cc_final: 0.7845 (tpp) REVERT: N 20 MET cc_start: 0.8994 (ttp) cc_final: 0.8273 (mtp) REVERT: N 24 MET cc_start: 0.8935 (ttm) cc_final: 0.8524 (ttm) REVERT: N 32 GLU cc_start: 0.9315 (mt-10) cc_final: 0.9099 (mp0) REVERT: N 43 GLU cc_start: 0.9472 (tp30) cc_final: 0.8683 (tp30) REVERT: N 87 PHE cc_start: 0.8681 (m-80) cc_final: 0.7578 (m-80) REVERT: N 110 MET cc_start: 0.9118 (mmp) cc_final: 0.8864 (mmm) REVERT: N 117 ASP cc_start: 0.8611 (m-30) cc_final: 0.8381 (m-30) REVERT: O 69 ASP cc_start: 0.9702 (m-30) cc_final: 0.9416 (t0) REVERT: P 66 ASN cc_start: 0.9539 (m110) cc_final: 0.9274 (m110) REVERT: P 97 LEU cc_start: 0.8892 (mp) cc_final: 0.8180 (mp) REVERT: P 101 ARG cc_start: 0.9282 (mmm160) cc_final: 0.8966 (mmt90) REVERT: Q 59 GLN cc_start: 0.9529 (tt0) cc_final: 0.9071 (mm-40) REVERT: R 76 LYS cc_start: 0.9175 (mttt) cc_final: 0.8636 (mmmt) REVERT: R 83 TYR cc_start: 0.8965 (t80) cc_final: 0.8314 (t80) REVERT: R 86 GLN cc_start: 0.8857 (mm110) cc_final: 0.8317 (pp30) REVERT: R 95 ASP cc_start: 0.9352 (m-30) cc_final: 0.8916 (p0) REVERT: R 98 ILE cc_start: 0.9706 (mm) cc_final: 0.9109 (tt) REVERT: S 65 ASP cc_start: 0.8007 (p0) cc_final: 0.7761 (p0) REVERT: S 78 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8641 (mt-10) REVERT: S 84 ARG cc_start: 0.9028 (mmt-90) cc_final: 0.8516 (mmt90) REVERT: S 97 LEU cc_start: 0.9550 (mm) cc_final: 0.8619 (tp) REVERT: T 11 LEU cc_start: 0.9279 (mm) cc_final: 0.8724 (tp) REVERT: T 86 THR cc_start: 0.9366 (m) cc_final: 0.8698 (m) REVERT: V 48 MET cc_start: 0.9084 (mmm) cc_final: 0.8302 (mmm) REVERT: V 50 MET cc_start: 0.9416 (mtm) cc_final: 0.9085 (ptp) REVERT: V 55 GLU cc_start: 0.9757 (tt0) cc_final: 0.9349 (tp30) REVERT: W 17 GLU cc_start: 0.8608 (pt0) cc_final: 0.8237 (pp20) REVERT: X 38 PHE cc_start: 0.9041 (m-80) cc_final: 0.8230 (m-80) REVERT: X 47 VAL cc_start: 0.9604 (t) cc_final: 0.9095 (m) REVERT: X 49 LEU cc_start: 0.9059 (mt) cc_final: 0.8547 (mt) REVERT: X 56 MET cc_start: 0.9361 (mtp) cc_final: 0.8845 (ttm) REVERT: X 60 ASP cc_start: 0.8991 (m-30) cc_final: 0.8775 (m-30) REVERT: Y 23 ARG cc_start: 0.9605 (mtt90) cc_final: 0.9360 (mtt-85) REVERT: Y 24 GLU cc_start: 0.9725 (mt-10) cc_final: 0.9476 (pt0) REVERT: Y 30 MET cc_start: 0.8959 (mmp) cc_final: 0.8550 (mmm) REVERT: Z 19 LYS cc_start: 0.9403 (mmmt) cc_final: 0.9163 (mmtt) REVERT: Z 21 LYS cc_start: 0.9344 (mttt) cc_final: 0.8836 (mttm) REVERT: Z 32 ILE cc_start: 0.9531 (pt) cc_final: 0.9271 (mp) REVERT: Z 47 MET cc_start: 0.9462 (mtt) cc_final: 0.9255 (mtt) REVERT: Z 49 ASN cc_start: 0.9854 (t0) cc_final: 0.9536 (p0) REVERT: b 7 LYS cc_start: 0.9081 (tptm) cc_final: 0.8664 (tptp) REVERT: b 46 ASP cc_start: 0.9334 (t0) cc_final: 0.9013 (t0) REVERT: d 25 LYS cc_start: 0.9237 (ttpt) cc_final: 0.9035 (pptt) REVERT: d 29 GLN cc_start: 0.9023 (mp10) cc_final: 0.8776 (mp10) REVERT: e 14 PHE cc_start: 0.9746 (m-80) cc_final: 0.9198 (m-80) REVERT: f 22 VAL cc_start: 0.9136 (t) cc_final: 0.8914 (p) REVERT: g 27 MET cc_start: 0.8897 (mmm) cc_final: 0.8442 (mmm) REVERT: g 32 PHE cc_start: 0.9145 (t80) cc_final: 0.8877 (t80) REVERT: g 96 TRP cc_start: 0.8189 (t-100) cc_final: 0.7537 (t-100) REVERT: g 120 GLN cc_start: 0.9528 (tt0) cc_final: 0.9237 (tp-100) REVERT: h 8 ASN cc_start: 0.8851 (m110) cc_final: 0.8548 (m110) REVERT: h 19 ASN cc_start: 0.9409 (m-40) cc_final: 0.8534 (p0) REVERT: h 51 SER cc_start: 0.9536 (m) cc_final: 0.9158 (p) REVERT: h 110 GLU cc_start: 0.9377 (pm20) cc_final: 0.8784 (tm-30) REVERT: h 123 GLN cc_start: 0.9646 (mt0) cc_final: 0.9187 (mt0) REVERT: h 130 PHE cc_start: 0.9303 (p90) cc_final: 0.8997 (p90) REVERT: h 134 MET cc_start: 0.9176 (mtp) cc_final: 0.8453 (ttt) REVERT: h 168 TYR cc_start: 0.8066 (m-80) cc_final: 0.7013 (m-80) REVERT: h 193 TYR cc_start: 0.9250 (m-80) cc_final: 0.8941 (m-80) REVERT: h 201 TRP cc_start: 0.8987 (m-90) cc_final: 0.8712 (m-90) REVERT: i 51 TYR cc_start: 0.9507 (t80) cc_final: 0.9264 (t80) REVERT: i 59 GLN cc_start: 0.9540 (mm110) cc_final: 0.9149 (mm110) REVERT: i 72 PHE cc_start: 0.9601 (t80) cc_final: 0.9256 (t80) REVERT: i 123 ILE cc_start: 0.9145 (mm) cc_final: 0.8157 (mp) REVERT: i 124 MET cc_start: 0.8963 (mtt) cc_final: 0.8557 (mmm) REVERT: i 128 ARG cc_start: 0.9728 (mtp180) cc_final: 0.9490 (mmm160) REVERT: j 14 LYS cc_start: 0.9412 (mmpt) cc_final: 0.8955 (mtmm) REVERT: j 29 ARG cc_start: 0.8921 (mpp80) cc_final: 0.8241 (mmt180) REVERT: j 34 THR cc_start: 0.8610 (t) cc_final: 0.8409 (m) REVERT: j 43 ASN cc_start: 0.9662 (m-40) cc_final: 0.9448 (m-40) REVERT: j 45 ARG cc_start: 0.9360 (tpp-160) cc_final: 0.9015 (tpp-160) REVERT: j 48 PHE cc_start: 0.9410 (p90) cc_final: 0.9120 (p90) REVERT: j 93 ARG cc_start: 0.8887 (ttp-110) cc_final: 0.8671 (ttp-110) REVERT: j 116 GLU cc_start: 0.9716 (tt0) cc_final: 0.9450 (tt0) REVERT: j 142 ASP cc_start: 0.9539 (m-30) cc_final: 0.9299 (m-30) REVERT: j 152 MET cc_start: 0.9695 (tpt) cc_final: 0.9459 (tpt) REVERT: k 21 MET cc_start: 0.9225 (mtm) cc_final: 0.8695 (mtm) REVERT: k 80 PHE cc_start: 0.9641 (m-80) cc_final: 0.9410 (m-80) REVERT: k 89 VAL cc_start: 0.9294 (t) cc_final: 0.8954 (t) REVERT: k 90 MET cc_start: 0.8500 (mpp) cc_final: 0.7927 (mmm) REVERT: k 91 ARG cc_start: 0.9211 (ttt90) cc_final: 0.8447 (ttt90) REVERT: l 33 ASP cc_start: 0.9463 (m-30) cc_final: 0.9255 (m-30) REVERT: l 130 ASN cc_start: 0.9441 (p0) cc_final: 0.9017 (p0) REVERT: l 131 LYS cc_start: 0.9633 (tmtt) cc_final: 0.9359 (mmtt) REVERT: m 9 ASP cc_start: 0.9437 (t0) cc_final: 0.9076 (t0) REVERT: m 47 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8659 (tm-30) REVERT: n 39 PHE cc_start: 0.9468 (m-10) cc_final: 0.9225 (m-10) REVERT: n 55 VAL cc_start: 0.9359 (p) cc_final: 0.8939 (p) REVERT: n 97 GLU cc_start: 0.9562 (mt-10) cc_final: 0.9221 (mp0) REVERT: o 11 LYS cc_start: 0.9395 (mmtp) cc_final: 0.9166 (mmtm) REVERT: o 52 LEU cc_start: 0.8717 (tp) cc_final: 0.8487 (tp) REVERT: o 99 GLN cc_start: 0.9364 (tt0) cc_final: 0.8841 (mt0) REVERT: p 24 HIS cc_start: 0.9105 (t-90) cc_final: 0.8693 (t-90) REVERT: p 31 ILE cc_start: 0.9804 (mm) cc_final: 0.9527 (mm) REVERT: p 56 ARG cc_start: 0.9334 (mpp80) cc_final: 0.8863 (mtm110) REVERT: p 79 ILE cc_start: 0.9398 (mp) cc_final: 0.9160 (mp) REVERT: p 84 VAL cc_start: 0.9693 (t) cc_final: 0.9404 (m) REVERT: p 105 PHE cc_start: 0.9667 (m-10) cc_final: 0.9319 (m-80) REVERT: p 119 ASN cc_start: 0.8723 (m-40) cc_final: 0.8522 (m110) REVERT: p 128 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.7328 (mtm180) REVERT: q 20 ASN cc_start: 0.9594 (p0) cc_final: 0.9348 (p0) REVERT: q 35 THR cc_start: 0.7905 (m) cc_final: 0.7569 (m) REVERT: q 38 TYR cc_start: 0.6382 (p90) cc_final: 0.6113 (p90) REVERT: q 57 LEU cc_start: 0.9448 (mp) cc_final: 0.9227 (mp) REVERT: r 27 LYS cc_start: 0.9295 (tppt) cc_final: 0.8852 (tppt) REVERT: r 42 ASP cc_start: 0.8969 (p0) cc_final: 0.8384 (t70) REVERT: r 103 LYS cc_start: 0.9126 (tttt) cc_final: 0.8895 (tttp) REVERT: s 18 ASP cc_start: 0.8833 (m-30) cc_final: 0.8519 (m-30) REVERT: s 65 ARG cc_start: 0.9173 (ttm170) cc_final: 0.8957 (mtp180) REVERT: s 77 PHE cc_start: 0.9374 (m-10) cc_final: 0.9156 (m-80) REVERT: s 92 GLU cc_start: 0.8379 (mp0) cc_final: 0.8037 (mp0) REVERT: t 37 ASN cc_start: 0.9762 (m110) cc_final: 0.9519 (m110) REVERT: t 62 GLN cc_start: 0.9647 (tt0) cc_final: 0.9353 (pt0) REVERT: t 65 LYS cc_start: 0.9412 (mttt) cc_final: 0.9097 (mmtt) REVERT: t 71 LYS cc_start: 0.9276 (tppt) cc_final: 0.8917 (tppt) REVERT: t 73 LYS cc_start: 0.9192 (mmtm) cc_final: 0.8879 (ptmt) REVERT: u 1 MET cc_start: 0.8705 (pmm) cc_final: 0.7771 (tpt) REVERT: v 53 CYS cc_start: 0.8883 (m) cc_final: 0.8657 (m) REVERT: v 65 ARG cc_start: 0.9011 (ttp80) cc_final: 0.8490 (ttp80) REVERT: w 31 ASN cc_start: 0.9338 (m110) cc_final: 0.9075 (m110) REVERT: w 54 GLN cc_start: 0.9127 (mt0) cc_final: 0.8917 (mt0) REVERT: w 61 ARG cc_start: 0.9280 (mpp-170) cc_final: 0.8266 (mtt90) REVERT: w 70 TYR cc_start: 0.8743 (m-80) cc_final: 0.8447 (m-10) REVERT: x 18 LYS cc_start: 0.9754 (mttt) cc_final: 0.9471 (mttm) REVERT: x 39 THR cc_start: 0.9119 (m) cc_final: 0.8915 (p) REVERT: y 15 GLU cc_start: 0.9769 (tt0) cc_final: 0.9505 (tp30) REVERT: y 18 ARG cc_start: 0.9697 (ttp80) cc_final: 0.9095 (ptm-80) REVERT: y 21 ASN cc_start: 0.9350 (m110) cc_final: 0.9129 (m-40) REVERT: y 32 ILE cc_start: 0.9837 (mt) cc_final: 0.9256 (pt) REVERT: y 80 THR cc_start: 0.9507 (m) cc_final: 0.9246 (p) REVERT: z 24 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8649 (pt0) REVERT: z 49 LYS cc_start: 0.9616 (ptpp) cc_final: 0.9337 (pttm) REVERT: 7 144 TRP cc_start: 0.9351 (t-100) cc_final: 0.9037 (t-100) REVERT: 7 147 MET cc_start: 0.9630 (mtm) cc_final: 0.9424 (tmm) REVERT: 7 199 HIS cc_start: 0.9424 (m-70) cc_final: 0.8599 (m-70) REVERT: 7 310 MET cc_start: 0.5620 (tpp) cc_final: 0.5318 (mmm) REVERT: 7 327 VAL cc_start: 0.9157 (t) cc_final: 0.8853 (t) outliers start: 2 outliers final: 0 residues processed: 1106 average time/residue: 1.3460 time to fit residues: 2536.7655 Evaluate side-chains 863 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 863 time to evaluate : 6.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 835 optimal weight: 40.0000 chunk 569 optimal weight: 6.9990 chunk 14 optimal weight: 30.0000 chunk 747 optimal weight: 10.0000 chunk 413 optimal weight: 30.0000 chunk 856 optimal weight: 20.0000 chunk 693 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 512 optimal weight: 10.0000 chunk 900 optimal weight: 10.0000 chunk 253 optimal weight: 20.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 ASN O 38 GLN ** P 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 32 ASN ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 36 GLN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 136 GLN ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 38 ASN ** m 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 6 GLN ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 355 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 159192 Z= 0.228 Angle : 0.644 13.451 237909 Z= 0.344 Chirality : 0.034 0.264 30260 Planarity : 0.006 0.127 12919 Dihedral : 24.902 179.989 78958 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 32.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.02 % Allowed : 2.54 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.11), residues: 5890 helix: 0.10 (0.11), residues: 2056 sheet: -1.85 (0.15), residues: 1049 loop : -1.36 (0.12), residues: 2785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP 7 155 HIS 0.014 0.001 HIS t 46 PHE 0.021 0.002 PHE L 107 TYR 0.021 0.002 TYR S 38 ARG 0.016 0.001 ARG d 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1120 time to evaluate : 6.267 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: 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: 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: 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: 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: 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: 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: 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: 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: 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 21 ASN cc_start: 0.8633 (t0) cc_final: 0.8155 (t0) REVERT: B 79 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8725 (mm-30) REVERT: B 96 TYR cc_start: 0.8636 (m-80) cc_final: 0.7823 (m-80) REVERT: B 115 GLN cc_start: 0.9179 (tp-100) cc_final: 0.8835 (tp-100) REVERT: B 132 MET cc_start: 0.9316 (mtm) cc_final: 0.8696 (mtt) REVERT: B 153 GLN cc_start: 0.9128 (mt0) cc_final: 0.8450 (mt0) REVERT: B 163 GLN cc_start: 0.9083 (tp40) cc_final: 0.8710 (tp40) REVERT: B 183 LYS cc_start: 0.9597 (mttm) cc_final: 0.9328 (mmmm) REVERT: B 185 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8836 (tm-30) REVERT: B 201 MET cc_start: 0.8952 (ptt) cc_final: 0.8480 (ptt) REVERT: B 225 MET cc_start: 0.8121 (ptp) cc_final: 0.7824 (ptp) REVERT: B 243 HIS cc_start: 0.9119 (m90) cc_final: 0.8693 (m-70) REVERT: B 264 ASP cc_start: 0.9298 (m-30) cc_final: 0.8969 (m-30) REVERT: B 266 PHE cc_start: 0.9350 (m-80) cc_final: 0.9031 (m-80) REVERT: C 2 ILE cc_start: 0.7998 (pt) cc_final: 0.7459 (mm) REVERT: C 123 LYS cc_start: 0.9242 (mtmm) cc_final: 0.8896 (ptpp) REVERT: C 149 ASN cc_start: 0.8527 (t0) cc_final: 0.8279 (t0) REVERT: C 165 MET cc_start: 0.8268 (ttt) cc_final: 0.7966 (ttt) REVERT: D 1 MET cc_start: 0.9476 (tpt) cc_final: 0.9163 (tpp) REVERT: D 100 MET cc_start: 0.9288 (mtp) cc_final: 0.9013 (mtp) REVERT: D 141 MET cc_start: 0.9407 (mpp) cc_final: 0.9081 (mpp) REVERT: D 188 MET cc_start: 0.9554 (mmm) cc_final: 0.8991 (mmm) REVERT: E 26 MET cc_start: 0.9523 (mmm) cc_final: 0.8976 (mmt) REVERT: E 38 MET cc_start: 0.5847 (mtp) cc_final: 0.5599 (mtp) REVERT: E 96 MET cc_start: 0.8939 (ttp) cc_final: 0.8325 (ttp) REVERT: E 120 LYS cc_start: 0.9627 (tptp) cc_final: 0.9403 (tptt) REVERT: E 138 PHE cc_start: 0.8723 (t80) cc_final: 0.8490 (t80) REVERT: E 175 PHE cc_start: 0.9136 (t80) cc_final: 0.8763 (t80) REVERT: F 103 ILE cc_start: 0.9715 (mt) cc_final: 0.9113 (tp) REVERT: F 149 ARG cc_start: 0.9579 (ttt-90) cc_final: 0.8888 (ptm160) REVERT: F 164 TYR cc_start: 0.9240 (m-10) cc_final: 0.8731 (m-10) REVERT: G 46 PHE cc_start: 0.9619 (t80) cc_final: 0.9358 (t80) REVERT: G 101 ASP cc_start: 0.9269 (m-30) cc_final: 0.8965 (m-30) REVERT: G 132 PHE cc_start: 0.9290 (m-10) cc_final: 0.8409 (m-80) REVERT: J 14 ASP cc_start: 0.9342 (m-30) cc_final: 0.9078 (m-30) REVERT: J 67 ASN cc_start: 0.9685 (m-40) cc_final: 0.9476 (p0) REVERT: J 92 MET cc_start: 0.9611 (mmm) cc_final: 0.9342 (tpp) REVERT: J 136 GLN cc_start: 0.9153 (mt0) cc_final: 0.8802 (mm110) REVERT: K 4 GLU cc_start: 0.8820 (mp0) cc_final: 0.8549 (mp0) REVERT: K 5 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8485 (tm-30) REVERT: K 7 MET cc_start: 0.9159 (mmm) cc_final: 0.8157 (mmm) REVERT: K 20 MET cc_start: 0.8443 (ttm) cc_final: 0.7974 (ttm) REVERT: K 25 LEU cc_start: 0.9303 (mm) cc_final: 0.9092 (mm) REVERT: K 58 LEU cc_start: 0.9217 (pt) cc_final: 0.8991 (pt) REVERT: K 80 ASP cc_start: 0.8222 (m-30) cc_final: 0.7723 (m-30) REVERT: K 110 GLU cc_start: 0.9378 (pm20) cc_final: 0.9070 (pm20) REVERT: L 51 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8266 (mt-10) REVERT: L 67 THR cc_start: 0.9044 (m) cc_final: 0.8814 (p) REVERT: M 65 ILE cc_start: 0.9194 (mp) cc_final: 0.8888 (mm) REVERT: M 73 ILE cc_start: 0.9399 (mm) cc_final: 0.9172 (mp) REVERT: M 82 MET cc_start: 0.8846 (tpp) cc_final: 0.7253 (mmp) REVERT: M 91 TYR cc_start: 0.9136 (p90) cc_final: 0.8907 (p90) REVERT: M 112 LEU cc_start: 0.9679 (tp) cc_final: 0.9395 (tp) REVERT: M 128 THR cc_start: 0.7811 (p) cc_final: 0.7567 (p) REVERT: N 1 MET cc_start: 0.8181 (tpp) cc_final: 0.7606 (tpp) REVERT: N 20 MET cc_start: 0.8965 (ttp) cc_final: 0.8097 (ttp) REVERT: N 24 MET cc_start: 0.8878 (ttm) cc_final: 0.8132 (mmm) REVERT: N 43 GLU cc_start: 0.9475 (tp30) cc_final: 0.8621 (tp30) REVERT: N 87 PHE cc_start: 0.8506 (m-80) cc_final: 0.7484 (m-80) REVERT: N 110 MET cc_start: 0.9079 (mmp) cc_final: 0.8865 (mmm) REVERT: N 114 GLU cc_start: 0.9268 (pm20) cc_final: 0.8841 (pm20) REVERT: O 69 ASP cc_start: 0.9707 (m-30) cc_final: 0.9407 (t0) REVERT: O 89 ASP cc_start: 0.8263 (t70) cc_final: 0.7838 (t70) REVERT: Q 59 GLN cc_start: 0.9552 (tt0) cc_final: 0.8987 (mm-40) REVERT: R 76 LYS cc_start: 0.9150 (mttt) cc_final: 0.8850 (mmtp) REVERT: R 83 TYR cc_start: 0.9012 (t80) cc_final: 0.8671 (t80) REVERT: R 85 LYS cc_start: 0.8826 (tmtt) cc_final: 0.8408 (tptt) REVERT: R 86 GLN cc_start: 0.8979 (mm110) cc_final: 0.8378 (pp30) REVERT: R 95 ASP cc_start: 0.9354 (m-30) cc_final: 0.9003 (p0) REVERT: R 98 ILE cc_start: 0.9787 (mm) cc_final: 0.9149 (tt) REVERT: S 65 ASP cc_start: 0.8149 (p0) cc_final: 0.7857 (p0) REVERT: S 78 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8499 (mt-10) REVERT: S 97 LEU cc_start: 0.9616 (mm) cc_final: 0.8878 (tp) REVERT: T 11 LEU cc_start: 0.8934 (mm) cc_final: 0.8452 (tp) REVERT: T 86 THR cc_start: 0.9413 (m) cc_final: 0.8839 (m) REVERT: V 48 MET cc_start: 0.9207 (mmm) cc_final: 0.8772 (mmm) REVERT: V 50 MET cc_start: 0.9396 (mtm) cc_final: 0.9058 (ptp) REVERT: W 17 GLU cc_start: 0.8534 (pt0) cc_final: 0.8134 (pp20) REVERT: W 36 ILE cc_start: 0.9157 (mm) cc_final: 0.8889 (mm) REVERT: X 38 PHE cc_start: 0.9106 (m-80) cc_final: 0.8701 (m-80) REVERT: X 46 PHE cc_start: 0.9522 (m-80) cc_final: 0.8937 (m-80) REVERT: X 47 VAL cc_start: 0.9653 (t) cc_final: 0.9146 (m) REVERT: Y 17 GLU cc_start: 0.9409 (tm-30) cc_final: 0.9163 (tm-30) REVERT: Y 24 GLU cc_start: 0.9698 (mt-10) cc_final: 0.9357 (pt0) REVERT: Y 30 MET cc_start: 0.8931 (mmp) cc_final: 0.8473 (mmm) REVERT: Z 19 LYS cc_start: 0.9375 (mmmt) cc_final: 0.9100 (mmtt) REVERT: Z 21 LYS cc_start: 0.9295 (mttt) cc_final: 0.8800 (mttm) REVERT: Z 32 ILE cc_start: 0.9520 (pt) cc_final: 0.9273 (mp) REVERT: Z 49 ASN cc_start: 0.9851 (t0) cc_final: 0.9521 (p0) REVERT: Z 54 MET cc_start: 0.9269 (ptm) cc_final: 0.8014 (ttt) REVERT: b 7 LYS cc_start: 0.9168 (tptm) cc_final: 0.8866 (tptp) REVERT: b 12 LYS cc_start: 0.9125 (mmpt) cc_final: 0.8625 (mmmt) REVERT: b 46 ASP cc_start: 0.9311 (t0) cc_final: 0.9010 (t0) REVERT: c 33 LYS cc_start: 0.9275 (mmmt) cc_final: 0.8711 (mmtt) REVERT: e 14 PHE cc_start: 0.9769 (m-80) cc_final: 0.9459 (m-80) REVERT: f 13 ASN cc_start: 0.9584 (m-40) cc_final: 0.9032 (t0) REVERT: f 22 VAL cc_start: 0.9084 (t) cc_final: 0.8868 (p) REVERT: g 27 MET cc_start: 0.8985 (mmm) cc_final: 0.8580 (mmm) REVERT: g 32 PHE cc_start: 0.9203 (t80) cc_final: 0.8891 (t80) REVERT: g 96 TRP cc_start: 0.8130 (t-100) cc_final: 0.7480 (t-100) REVERT: g 120 GLN cc_start: 0.9546 (tt0) cc_final: 0.9128 (tp-100) REVERT: g 136 MET cc_start: 0.9706 (mmp) cc_final: 0.9504 (mmp) REVERT: h 8 ASN cc_start: 0.8995 (m110) cc_final: 0.8699 (m110) REVERT: h 19 ASN cc_start: 0.9253 (m-40) cc_final: 0.8199 (p0) REVERT: h 37 PHE cc_start: 0.9594 (t80) cc_final: 0.9221 (t80) REVERT: h 51 SER cc_start: 0.9550 (m) cc_final: 0.9181 (p) REVERT: h 110 GLU cc_start: 0.9389 (pm20) cc_final: 0.8836 (tm-30) REVERT: h 123 GLN cc_start: 0.9641 (mt0) cc_final: 0.9161 (mt0) REVERT: h 130 PHE cc_start: 0.9244 (p90) cc_final: 0.8877 (p90) REVERT: h 168 TYR cc_start: 0.8090 (m-80) cc_final: 0.7688 (m-80) REVERT: h 185 ASN cc_start: 0.9125 (t0) cc_final: 0.8917 (t0) REVERT: h 193 TYR cc_start: 0.9151 (m-80) cc_final: 0.8790 (m-80) REVERT: h 201 TRP cc_start: 0.9128 (m-90) cc_final: 0.8862 (m-90) REVERT: i 51 TYR cc_start: 0.9465 (t80) cc_final: 0.9133 (t80) REVERT: i 59 GLN cc_start: 0.9466 (mm110) cc_final: 0.9123 (mm110) REVERT: i 72 PHE cc_start: 0.9658 (t80) cc_final: 0.9307 (t80) REVERT: i 123 ILE cc_start: 0.9251 (mm) cc_final: 0.8367 (mp) REVERT: i 124 MET cc_start: 0.8932 (mtt) cc_final: 0.8527 (mmm) REVERT: j 14 LYS cc_start: 0.9360 (mmpt) cc_final: 0.8890 (mtmm) REVERT: j 29 ARG cc_start: 0.8887 (mpp80) cc_final: 0.8270 (mmt180) REVERT: j 34 THR cc_start: 0.8518 (t) cc_final: 0.8232 (m) REVERT: j 45 ARG cc_start: 0.9424 (tpp-160) cc_final: 0.9070 (tpp-160) REVERT: j 48 PHE cc_start: 0.9429 (p90) cc_final: 0.9151 (p90) REVERT: j 142 ASP cc_start: 0.9524 (m-30) cc_final: 0.9099 (m-30) REVERT: j 152 MET cc_start: 0.9653 (tpt) cc_final: 0.9427 (tpt) REVERT: k 6 ILE cc_start: 0.9828 (mm) cc_final: 0.8760 (mm) REVERT: k 7 VAL cc_start: 0.9723 (p) cc_final: 0.8903 (p) REVERT: k 21 MET cc_start: 0.9188 (mtm) cc_final: 0.8621 (mtm) REVERT: k 80 PHE cc_start: 0.9624 (m-80) cc_final: 0.9090 (m-10) REVERT: k 91 ARG cc_start: 0.9248 (ttt90) cc_final: 0.8613 (ttt90) REVERT: l 26 PHE cc_start: 0.9805 (t80) cc_final: 0.9597 (t80) REVERT: l 33 ASP cc_start: 0.9450 (m-30) cc_final: 0.9247 (m-30) REVERT: m 14 ILE cc_start: 0.9731 (mt) cc_final: 0.9418 (mm) REVERT: m 38 ASN cc_start: 0.9640 (m-40) cc_final: 0.9403 (m-40) REVERT: m 47 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8853 (tm-30) REVERT: n 39 PHE cc_start: 0.9476 (m-10) cc_final: 0.9155 (m-10) REVERT: n 66 THR cc_start: 0.9136 (p) cc_final: 0.7820 (t) REVERT: n 97 GLU cc_start: 0.9633 (mt-10) cc_final: 0.9190 (mp0) REVERT: n 112 GLU cc_start: 0.8370 (tp30) cc_final: 0.7911 (mp0) REVERT: n 129 LYS cc_start: 0.6957 (mtmt) cc_final: 0.6134 (mppt) REVERT: o 52 LEU cc_start: 0.8688 (tp) cc_final: 0.8417 (tp) REVERT: o 99 GLN cc_start: 0.9349 (tt0) cc_final: 0.8822 (mt0) REVERT: p 56 ARG cc_start: 0.9325 (mpp80) cc_final: 0.8839 (mtm110) REVERT: p 79 ILE cc_start: 0.9419 (mp) cc_final: 0.9086 (mp) REVERT: p 84 VAL cc_start: 0.9656 (t) cc_final: 0.9394 (m) REVERT: p 87 LYS cc_start: 0.9422 (pptt) cc_final: 0.8957 (pptt) REVERT: p 105 PHE cc_start: 0.9591 (m-10) cc_final: 0.9208 (m-80) REVERT: q 20 ASN cc_start: 0.9583 (p0) cc_final: 0.9301 (p0) REVERT: q 40 THR cc_start: 0.8959 (t) cc_final: 0.8557 (p) REVERT: q 123 LYS cc_start: 0.8999 (tmtt) cc_final: 0.8566 (tptp) REVERT: r 27 LYS cc_start: 0.9313 (tppt) cc_final: 0.8862 (tppt) REVERT: r 42 ASP cc_start: 0.8962 (p0) cc_final: 0.8194 (t70) REVERT: r 103 LYS cc_start: 0.9052 (tttt) cc_final: 0.8756 (tttp) REVERT: s 18 ASP cc_start: 0.8784 (m-30) cc_final: 0.8485 (m-30) REVERT: s 65 ARG cc_start: 0.9190 (ttm170) cc_final: 0.8529 (ttp80) REVERT: s 92 GLU cc_start: 0.8292 (mp0) cc_final: 0.7991 (mp0) REVERT: t 26 GLU cc_start: 0.9558 (mp0) cc_final: 0.9014 (tt0) REVERT: t 37 ASN cc_start: 0.9784 (m110) cc_final: 0.9520 (m110) REVERT: t 62 GLN cc_start: 0.9643 (tt0) cc_final: 0.9346 (pt0) REVERT: t 65 LYS cc_start: 0.9375 (mttt) cc_final: 0.9081 (mmtt) REVERT: t 68 ASP cc_start: 0.9507 (m-30) cc_final: 0.9272 (m-30) REVERT: t 71 LYS cc_start: 0.9351 (tppt) cc_final: 0.8881 (tppt) REVERT: t 73 LYS cc_start: 0.9142 (mmtm) cc_final: 0.8847 (ptmt) REVERT: u 1 MET cc_start: 0.8811 (pmm) cc_final: 0.7795 (tpt) REVERT: v 18 GLU cc_start: 0.9674 (pt0) cc_final: 0.9320 (pm20) REVERT: v 30 LYS cc_start: 0.9593 (tmmt) cc_final: 0.9360 (tmtt) REVERT: v 53 CYS cc_start: 0.8773 (m) cc_final: 0.8484 (m) REVERT: v 60 GLU cc_start: 0.9065 (tt0) cc_final: 0.8820 (tt0) REVERT: w 31 ASN cc_start: 0.9332 (m110) cc_final: 0.9118 (m110) REVERT: w 50 LYS cc_start: 0.9575 (ptmm) cc_final: 0.9344 (ptmm) REVERT: w 61 ARG cc_start: 0.9007 (mtm-85) cc_final: 0.8733 (mtt90) REVERT: w 65 LEU cc_start: 0.9850 (mm) cc_final: 0.9488 (tp) REVERT: w 67 LEU cc_start: 0.9426 (mt) cc_final: 0.8804 (mt) REVERT: w 70 TYR cc_start: 0.8732 (m-80) cc_final: 0.8461 (m-10) REVERT: x 39 THR cc_start: 0.9215 (m) cc_final: 0.9012 (p) REVERT: x 41 PHE cc_start: 0.9499 (t80) cc_final: 0.9287 (t80) REVERT: y 15 GLU cc_start: 0.9767 (tt0) cc_final: 0.9496 (tp30) REVERT: y 18 ARG cc_start: 0.9674 (ttp80) cc_final: 0.8886 (ttp-110) REVERT: y 21 ASN cc_start: 0.9430 (m110) cc_final: 0.9208 (m-40) REVERT: y 28 MET cc_start: 0.9779 (tmm) cc_final: 0.9572 (tmm) REVERT: y 32 ILE cc_start: 0.9844 (mt) cc_final: 0.9263 (pt) REVERT: y 36 TYR cc_start: 0.9565 (m-10) cc_final: 0.9348 (m-80) REVERT: y 80 THR cc_start: 0.9585 (m) cc_final: 0.9357 (p) REVERT: z 19 PHE cc_start: 0.9234 (t80) cc_final: 0.8885 (t80) REVERT: z 24 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8597 (pt0) REVERT: 7 73 MET cc_start: 0.3047 (mmp) cc_final: 0.2653 (mtt) REVERT: 7 144 TRP cc_start: 0.9400 (t-100) cc_final: 0.8976 (t-100) REVERT: 7 147 MET cc_start: 0.9619 (mtm) cc_final: 0.9233 (tmm) REVERT: 7 186 ASP cc_start: 0.9359 (t0) cc_final: 0.9129 (t70) REVERT: 7 199 HIS cc_start: 0.9480 (m-70) cc_final: 0.8967 (m-70) REVERT: 7 266 ILE cc_start: 0.8121 (mm) cc_final: 0.7550 (mm) REVERT: 7 310 MET cc_start: 0.5176 (tpp) cc_final: 0.4747 (mmm) REVERT: 7 327 VAL cc_start: 0.9106 (t) cc_final: 0.8785 (t) REVERT: 7 330 ASP cc_start: 0.7923 (m-30) cc_final: 0.7712 (m-30) REVERT: 7 354 ASP cc_start: 0.9777 (p0) cc_final: 0.9563 (p0) outliers start: 1 outliers final: 1 residues processed: 1121 average time/residue: 1.3253 time to fit residues: 2539.6645 Evaluate side-chains 898 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 897 time to evaluate : 6.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 337 optimal weight: 40.0000 chunk 903 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 chunk 589 optimal weight: 9.9990 chunk 247 optimal weight: 30.0000 chunk 1004 optimal weight: 1.9990 chunk 833 optimal weight: 7.9990 chunk 464 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 332 optimal weight: 40.0000 chunk 527 optimal weight: 5.9990 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 ASN O 38 GLN O 61 GLN ** P 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 5 ASN ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 32 ASN ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 119 ASN s 62 ASN ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 50 ASN y 48 GLN y 52 ASN y 70 ASN ** 7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 159192 Z= 0.266 Angle : 0.663 13.341 237909 Z= 0.353 Chirality : 0.035 0.301 30260 Planarity : 0.006 0.128 12919 Dihedral : 24.855 179.914 78958 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 36.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.42 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.11), residues: 5890 helix: 0.11 (0.11), residues: 2056 sheet: -1.85 (0.15), residues: 1085 loop : -1.33 (0.12), residues: 2749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP 7 155 HIS 0.016 0.001 HIS t 46 PHE 0.020 0.002 PHE K 112 TYR 0.025 0.002 TYR q 38 ARG 0.014 0.001 ARG h 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1083 time to evaluate : 6.280 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: 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: 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: 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: 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: 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: 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: 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: 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 21 ASN cc_start: 0.8485 (t0) cc_final: 0.7998 (t0) REVERT: B 79 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8737 (mm-30) REVERT: B 96 TYR cc_start: 0.8507 (m-80) cc_final: 0.7787 (m-80) REVERT: B 115 GLN cc_start: 0.9204 (tp-100) cc_final: 0.8879 (tp-100) REVERT: B 132 MET cc_start: 0.9288 (mtm) cc_final: 0.8646 (mtm) REVERT: B 146 MET cc_start: 0.8278 (mtp) cc_final: 0.7697 (mpp) REVERT: B 163 GLN cc_start: 0.8968 (tp40) cc_final: 0.8615 (tp40) REVERT: B 183 LYS cc_start: 0.9593 (mttm) cc_final: 0.9339 (mmmt) REVERT: B 185 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8821 (tm-30) REVERT: B 201 MET cc_start: 0.8976 (ptt) cc_final: 0.8486 (ptt) REVERT: B 225 MET cc_start: 0.8241 (ptp) cc_final: 0.7925 (ptp) REVERT: B 243 HIS cc_start: 0.9159 (m90) cc_final: 0.8768 (m-70) REVERT: B 264 ASP cc_start: 0.9303 (m-30) cc_final: 0.8950 (m-30) REVERT: B 266 PHE cc_start: 0.9390 (m-80) cc_final: 0.9054 (m-80) REVERT: C 2 ILE cc_start: 0.8270 (pt) cc_final: 0.7667 (mm) REVERT: C 149 ASN cc_start: 0.8539 (t0) cc_final: 0.8302 (t0) REVERT: C 165 MET cc_start: 0.8294 (ttt) cc_final: 0.8018 (ttt) REVERT: D 1 MET cc_start: 0.9513 (tpt) cc_final: 0.9196 (tpp) REVERT: D 100 MET cc_start: 0.9286 (mtp) cc_final: 0.9005 (mtp) REVERT: D 141 MET cc_start: 0.9430 (mpp) cc_final: 0.9076 (mpp) REVERT: D 188 MET cc_start: 0.9548 (mmm) cc_final: 0.9022 (mmm) REVERT: E 26 MET cc_start: 0.9509 (mmm) cc_final: 0.8950 (mmm) REVERT: E 96 MET cc_start: 0.8905 (ttp) cc_final: 0.8329 (ttp) REVERT: E 120 LYS cc_start: 0.9635 (tptp) cc_final: 0.9419 (tptt) REVERT: E 175 PHE cc_start: 0.9136 (t80) cc_final: 0.8788 (t80) REVERT: F 69 ARG cc_start: 0.9303 (tmm-80) cc_final: 0.9060 (tmm-80) REVERT: F 149 ARG cc_start: 0.9595 (ttt-90) cc_final: 0.8887 (ptm160) REVERT: F 164 TYR cc_start: 0.9262 (m-10) cc_final: 0.8759 (m-10) REVERT: G 1 MET cc_start: 0.9329 (tpp) cc_final: 0.8896 (tmm) REVERT: G 83 LYS cc_start: 0.8689 (ptmm) cc_final: 0.8421 (ptmt) REVERT: G 91 PHE cc_start: 0.8587 (m-80) cc_final: 0.7927 (m-80) REVERT: G 101 ASP cc_start: 0.9292 (m-30) cc_final: 0.9087 (m-30) REVERT: G 132 PHE cc_start: 0.9271 (m-10) cc_final: 0.8433 (m-80) REVERT: J 14 ASP cc_start: 0.9595 (m-30) cc_final: 0.9330 (t70) REVERT: J 67 ASN cc_start: 0.9704 (m-40) cc_final: 0.9453 (p0) REVERT: J 92 MET cc_start: 0.9646 (mmm) cc_final: 0.9446 (tpp) REVERT: J 102 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8174 (mt-10) REVERT: J 136 GLN cc_start: 0.9118 (mt0) cc_final: 0.8874 (mm110) REVERT: K 1 MET cc_start: 0.8382 (ttp) cc_final: 0.8011 (ppp) REVERT: K 4 GLU cc_start: 0.8660 (mp0) cc_final: 0.8369 (mp0) REVERT: K 5 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8552 (tm-30) REVERT: K 7 MET cc_start: 0.9125 (mmm) cc_final: 0.8354 (mmp) REVERT: K 20 MET cc_start: 0.8505 (ttm) cc_final: 0.7946 (ttp) REVERT: K 25 LEU cc_start: 0.9320 (mm) cc_final: 0.9103 (mm) REVERT: K 58 LEU cc_start: 0.9244 (pt) cc_final: 0.9012 (pt) REVERT: K 107 LEU cc_start: 0.9280 (mm) cc_final: 0.9016 (mp) REVERT: L 51 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8392 (mt-10) REVERT: L 67 THR cc_start: 0.8957 (m) cc_final: 0.8558 (p) REVERT: M 82 MET cc_start: 0.8877 (tpp) cc_final: 0.7467 (mmm) REVERT: M 91 TYR cc_start: 0.9166 (p90) cc_final: 0.8493 (p90) REVERT: M 105 MET cc_start: 0.8859 (mmp) cc_final: 0.8509 (mmm) REVERT: M 112 LEU cc_start: 0.9678 (tp) cc_final: 0.9341 (tp) REVERT: M 128 THR cc_start: 0.7812 (p) cc_final: 0.7601 (p) REVERT: N 1 MET cc_start: 0.8258 (tpp) cc_final: 0.7850 (tpp) REVERT: N 20 MET cc_start: 0.8875 (ttp) cc_final: 0.7946 (mtp) REVERT: N 24 MET cc_start: 0.8848 (ttm) cc_final: 0.8113 (mmm) REVERT: N 32 GLU cc_start: 0.9331 (mt-10) cc_final: 0.8643 (tt0) REVERT: N 43 GLU cc_start: 0.9500 (tp30) cc_final: 0.8683 (tp30) REVERT: N 87 PHE cc_start: 0.8654 (m-80) cc_final: 0.7466 (m-80) REVERT: N 110 MET cc_start: 0.9079 (mmp) cc_final: 0.8843 (mmm) REVERT: N 114 GLU cc_start: 0.9234 (pm20) cc_final: 0.8888 (pm20) REVERT: O 20 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8838 (mm-30) REVERT: O 69 ASP cc_start: 0.9700 (m-30) cc_final: 0.9409 (t0) REVERT: P 99 TYR cc_start: 0.9078 (p90) cc_final: 0.8628 (p90) REVERT: Q 25 TYR cc_start: 0.8651 (t80) cc_final: 0.8450 (t80) REVERT: Q 59 GLN cc_start: 0.9544 (tt0) cc_final: 0.9048 (mm-40) REVERT: Q 109 LEU cc_start: 0.9509 (mt) cc_final: 0.9268 (mt) REVERT: R 83 TYR cc_start: 0.9071 (t80) cc_final: 0.8687 (t80) REVERT: R 85 LYS cc_start: 0.8794 (tmtt) cc_final: 0.8236 (tppt) REVERT: R 86 GLN cc_start: 0.8939 (mm110) cc_final: 0.8341 (pp30) REVERT: R 95 ASP cc_start: 0.9358 (m-30) cc_final: 0.9005 (p0) REVERT: R 98 ILE cc_start: 0.9794 (mm) cc_final: 0.9255 (tt) REVERT: S 65 ASP cc_start: 0.8182 (p0) cc_final: 0.7850 (p0) REVERT: S 78 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8514 (mt-10) REVERT: S 84 ARG cc_start: 0.9072 (mmt-90) cc_final: 0.8750 (mmt90) REVERT: S 97 LEU cc_start: 0.9628 (mm) cc_final: 0.9353 (tp) REVERT: T 11 LEU cc_start: 0.8924 (mm) cc_final: 0.8378 (tp) REVERT: T 86 THR cc_start: 0.9450 (m) cc_final: 0.9153 (m) REVERT: V 48 MET cc_start: 0.9209 (mmm) cc_final: 0.8356 (mmm) REVERT: V 50 MET cc_start: 0.9470 (mtm) cc_final: 0.9144 (ptp) REVERT: V 55 GLU cc_start: 0.9759 (tt0) cc_final: 0.9346 (tp30) REVERT: W 17 GLU cc_start: 0.8579 (pt0) cc_final: 0.8128 (pp20) REVERT: W 36 ILE cc_start: 0.9140 (mm) cc_final: 0.8879 (mm) REVERT: X 38 PHE cc_start: 0.9075 (m-80) cc_final: 0.8576 (m-80) REVERT: X 46 PHE cc_start: 0.9484 (m-80) cc_final: 0.8956 (m-80) REVERT: X 47 VAL cc_start: 0.9498 (t) cc_final: 0.9157 (m) REVERT: X 49 LEU cc_start: 0.9095 (mm) cc_final: 0.8653 (mm) REVERT: X 56 MET cc_start: 0.9318 (mtp) cc_final: 0.8292 (ttm) REVERT: X 60 ASP cc_start: 0.8950 (m-30) cc_final: 0.8688 (m-30) REVERT: X 70 GLU cc_start: 0.9351 (mp0) cc_final: 0.9136 (mp0) REVERT: Y 23 ARG cc_start: 0.9651 (mtt90) cc_final: 0.9446 (mtt-85) REVERT: Y 30 MET cc_start: 0.8960 (mmp) cc_final: 0.8417 (mmm) REVERT: Z 21 LYS cc_start: 0.9298 (mttt) cc_final: 0.8770 (mttm) REVERT: Z 32 ILE cc_start: 0.9525 (pt) cc_final: 0.9277 (mp) REVERT: Z 47 MET cc_start: 0.9438 (mtt) cc_final: 0.9201 (mtt) REVERT: Z 49 ASN cc_start: 0.9845 (t0) cc_final: 0.9521 (p0) REVERT: Z 54 MET cc_start: 0.9223 (ptm) cc_final: 0.8218 (ttt) REVERT: b 7 LYS cc_start: 0.9069 (tptm) cc_final: 0.8727 (tptp) REVERT: b 12 LYS cc_start: 0.9063 (mmpt) cc_final: 0.8576 (mmmt) REVERT: b 46 ASP cc_start: 0.9320 (t0) cc_final: 0.9016 (t0) REVERT: c 33 LYS cc_start: 0.9237 (mmmt) cc_final: 0.8648 (mmtt) REVERT: d 29 GLN cc_start: 0.9179 (mp10) cc_final: 0.8865 (mp10) REVERT: e 14 PHE cc_start: 0.9746 (m-80) cc_final: 0.9426 (m-80) REVERT: e 58 VAL cc_start: 0.9721 (t) cc_final: 0.9184 (t) REVERT: f 13 ASN cc_start: 0.9560 (m-40) cc_final: 0.9044 (t0) REVERT: f 22 VAL cc_start: 0.9093 (t) cc_final: 0.8874 (p) REVERT: g 27 MET cc_start: 0.8655 (mmm) cc_final: 0.8170 (mmm) REVERT: g 96 TRP cc_start: 0.8115 (t-100) cc_final: 0.7503 (t-100) REVERT: g 132 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8417 (mmtt) REVERT: h 8 ASN cc_start: 0.8912 (m110) cc_final: 0.8515 (m110) REVERT: h 19 ASN cc_start: 0.9295 (m-40) cc_final: 0.8245 (p0) REVERT: h 34 ASP cc_start: 0.9335 (t70) cc_final: 0.9050 (t70) REVERT: h 37 PHE cc_start: 0.9626 (t80) cc_final: 0.9215 (t80) REVERT: h 51 SER cc_start: 0.9560 (m) cc_final: 0.9200 (p) REVERT: h 110 GLU cc_start: 0.9256 (pm20) cc_final: 0.8610 (tm-30) REVERT: h 123 GLN cc_start: 0.9646 (mt0) cc_final: 0.9170 (mt0) REVERT: h 130 PHE cc_start: 0.9297 (p90) cc_final: 0.8974 (p90) REVERT: h 168 TYR cc_start: 0.8045 (m-80) cc_final: 0.7733 (m-80) REVERT: i 30 THR cc_start: 0.8899 (p) cc_final: 0.8678 (p) REVERT: i 51 TYR cc_start: 0.9435 (t80) cc_final: 0.9191 (t80) REVERT: i 59 GLN cc_start: 0.9490 (mm110) cc_final: 0.9019 (mm110) REVERT: i 72 PHE cc_start: 0.9631 (t80) cc_final: 0.9232 (t80) REVERT: i 123 ILE cc_start: 0.9208 (mm) cc_final: 0.8347 (mp) REVERT: i 124 MET cc_start: 0.8921 (mtt) cc_final: 0.8594 (mmt) REVERT: j 14 LYS cc_start: 0.9365 (mmpt) cc_final: 0.8948 (mtmm) REVERT: j 29 ARG cc_start: 0.8880 (mpp80) cc_final: 0.8250 (mmt180) REVERT: j 45 ARG cc_start: 0.9442 (tpp-160) cc_final: 0.9085 (tpp-160) REVERT: j 48 PHE cc_start: 0.9437 (p90) cc_final: 0.9148 (p90) REVERT: j 54 ARG cc_start: 0.8626 (mmt90) cc_final: 0.7973 (mpt-90) REVERT: j 64 MET cc_start: 0.9463 (mmt) cc_final: 0.9263 (mmt) REVERT: j 96 MET cc_start: 0.9537 (tpt) cc_final: 0.9293 (tpt) REVERT: j 116 GLU cc_start: 0.9713 (tt0) cc_final: 0.9440 (tt0) REVERT: j 142 ASP cc_start: 0.9415 (m-30) cc_final: 0.9060 (m-30) REVERT: j 162 GLU cc_start: 0.9572 (mm-30) cc_final: 0.9308 (mp0) REVERT: k 21 MET cc_start: 0.9224 (mtm) cc_final: 0.8671 (mtm) REVERT: k 35 LYS cc_start: 0.9733 (ptpp) cc_final: 0.9490 (ptpt) REVERT: k 80 PHE cc_start: 0.9637 (m-80) cc_final: 0.9100 (m-10) REVERT: k 91 ARG cc_start: 0.9155 (ttt90) cc_final: 0.8614 (ttt90) REVERT: l 26 PHE cc_start: 0.9807 (t80) cc_final: 0.9441 (t80) REVERT: l 33 ASP cc_start: 0.9434 (m-30) cc_final: 0.9222 (m-30) REVERT: l 101 MET cc_start: 0.9592 (mtt) cc_final: 0.9049 (mmm) REVERT: m 47 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8896 (tm-30) REVERT: n 39 PHE cc_start: 0.9464 (m-10) cc_final: 0.9158 (m-10) REVERT: n 92 GLU cc_start: 0.8924 (tp30) cc_final: 0.8715 (tp30) REVERT: n 97 GLU cc_start: 0.9622 (mt-10) cc_final: 0.9224 (mp0) REVERT: n 112 GLU cc_start: 0.8405 (tp30) cc_final: 0.8121 (tp30) REVERT: n 120 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8657 (ttmt) REVERT: n 129 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6378 (mppt) REVERT: o 52 LEU cc_start: 0.8733 (tp) cc_final: 0.8522 (tp) REVERT: o 77 VAL cc_start: 0.8949 (t) cc_final: 0.8732 (t) REVERT: o 99 GLN cc_start: 0.9451 (tt0) cc_final: 0.8996 (mt0) REVERT: p 56 ARG cc_start: 0.9354 (mpp80) cc_final: 0.8832 (mtm110) REVERT: p 79 ILE cc_start: 0.9423 (mp) cc_final: 0.9110 (mp) REVERT: p 85 MET cc_start: 0.9106 (ppp) cc_final: 0.8856 (ppp) REVERT: p 87 LYS cc_start: 0.9458 (pptt) cc_final: 0.8904 (pptt) REVERT: p 105 PHE cc_start: 0.9640 (m-10) cc_final: 0.9246 (m-80) REVERT: q 20 ASN cc_start: 0.9541 (p0) cc_final: 0.9232 (p0) REVERT: q 38 TYR cc_start: 0.5876 (p90) cc_final: 0.5625 (p90) REVERT: q 40 THR cc_start: 0.9020 (t) cc_final: 0.8670 (p) REVERT: q 123 LYS cc_start: 0.9022 (tmtt) cc_final: 0.8575 (tptp) REVERT: r 13 LYS cc_start: 0.8806 (ptmm) cc_final: 0.8262 (tptt) REVERT: r 27 LYS cc_start: 0.9327 (tppt) cc_final: 0.8862 (tppt) REVERT: r 41 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8637 (mt-10) REVERT: r 42 ASP cc_start: 0.9148 (p0) cc_final: 0.8417 (t70) REVERT: r 63 PHE cc_start: 0.9634 (m-80) cc_final: 0.9427 (m-80) REVERT: r 103 LYS cc_start: 0.9066 (tttt) cc_final: 0.8765 (tttp) REVERT: s 18 ASP cc_start: 0.8820 (m-30) cc_final: 0.8513 (m-30) REVERT: s 65 ARG cc_start: 0.9135 (ttm170) cc_final: 0.8426 (ttp80) REVERT: s 92 GLU cc_start: 0.8516 (mp0) cc_final: 0.8214 (mp0) REVERT: t 26 GLU cc_start: 0.9547 (mp0) cc_final: 0.9014 (tt0) REVERT: t 37 ASN cc_start: 0.9780 (m110) cc_final: 0.9514 (m110) REVERT: t 62 GLN cc_start: 0.9660 (tt0) cc_final: 0.9336 (pt0) REVERT: t 65 LYS cc_start: 0.9352 (mttt) cc_final: 0.9068 (mmtt) REVERT: t 71 LYS cc_start: 0.9362 (tppt) cc_final: 0.8885 (tppt) REVERT: t 73 LYS cc_start: 0.9136 (mmtm) cc_final: 0.8874 (ptmt) REVERT: u 1 MET cc_start: 0.8845 (pmm) cc_final: 0.7532 (mmm) REVERT: v 53 CYS cc_start: 0.8427 (m) cc_final: 0.8056 (m) REVERT: v 65 ARG cc_start: 0.8909 (ttp80) cc_final: 0.8434 (ttp-110) REVERT: w 30 LYS cc_start: 0.9526 (mtmm) cc_final: 0.9289 (mttt) REVERT: w 31 ASN cc_start: 0.9264 (m110) cc_final: 0.9041 (m110) REVERT: w 50 LYS cc_start: 0.9556 (ptmm) cc_final: 0.9340 (ptmm) REVERT: w 61 ARG cc_start: 0.8694 (mtm-85) cc_final: 0.8381 (mtt90) REVERT: w 65 LEU cc_start: 0.9874 (mm) cc_final: 0.9544 (tp) REVERT: w 67 LEU cc_start: 0.9453 (mt) cc_final: 0.8842 (mt) REVERT: w 70 TYR cc_start: 0.8758 (m-80) cc_final: 0.8495 (m-10) REVERT: y 15 GLU cc_start: 0.9726 (tt0) cc_final: 0.9504 (tp30) REVERT: y 18 ARG cc_start: 0.9661 (ttp80) cc_final: 0.9012 (ptm-80) REVERT: y 32 ILE cc_start: 0.9865 (mt) cc_final: 0.9240 (pt) REVERT: y 36 TYR cc_start: 0.9549 (m-10) cc_final: 0.9312 (m-80) REVERT: y 80 THR cc_start: 0.9625 (m) cc_final: 0.9400 (p) REVERT: z 19 PHE cc_start: 0.9251 (t80) cc_final: 0.8921 (t80) REVERT: z 24 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8826 (pt0) REVERT: 7 73 MET cc_start: 0.3254 (mmp) cc_final: 0.2683 (mtt) REVERT: 7 147 MET cc_start: 0.9760 (mtm) cc_final: 0.9424 (mtt) REVERT: 7 199 HIS cc_start: 0.9409 (m-70) cc_final: 0.8782 (m-70) REVERT: 7 327 VAL cc_start: 0.9189 (t) cc_final: 0.8734 (t) REVERT: 7 330 ASP cc_start: 0.7676 (m-30) cc_final: 0.7454 (m-30) outliers start: 0 outliers final: 0 residues processed: 1083 average time/residue: 1.4402 time to fit residues: 2689.3642 Evaluate side-chains 868 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 868 time to evaluate : 6.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 968 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 572 optimal weight: 20.0000 chunk 733 optimal weight: 10.0000 chunk 568 optimal weight: 40.0000 chunk 845 optimal weight: 10.0000 chunk 560 optimal weight: 0.7980 chunk 1000 optimal weight: 4.9990 chunk 626 optimal weight: 8.9990 chunk 609 optimal weight: 20.0000 chunk 461 optimal weight: 5.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN F 30 ASN ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 ASN N 81 ASN O 38 GLN ** P 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 6 ASN ** e 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 32 ASN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 136 GLN ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 24 HIS ** t 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 50 ASN y 70 ASN ** 7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 159192 Z= 0.188 Angle : 0.611 13.556 237909 Z= 0.329 Chirality : 0.033 0.288 30260 Planarity : 0.006 0.126 12919 Dihedral : 24.727 179.721 78958 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 29.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.02 % Allowed : 1.89 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.11), residues: 5890 helix: 0.34 (0.11), residues: 2065 sheet: -1.74 (0.15), residues: 1099 loop : -1.21 (0.12), residues: 2726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 60 HIS 0.010 0.001 HIS t 46 PHE 0.034 0.001 PHE G 46 TYR 0.018 0.002 TYR q 38 ARG 0.022 0.001 ARG g 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1097 time to evaluate : 6.204 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash REVERT: B 21 ASN cc_start: 0.8511 (t0) cc_final: 0.8156 (t0) REVERT: B 79 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8871 (mm-30) REVERT: B 96 TYR cc_start: 0.8695 (m-80) cc_final: 0.7993 (m-80) REVERT: B 115 GLN cc_start: 0.9174 (tp-100) cc_final: 0.8827 (tp-100) REVERT: B 132 MET cc_start: 0.9272 (mtm) cc_final: 0.8627 (mtm) REVERT: B 146 MET cc_start: 0.8194 (mtp) cc_final: 0.7672 (mpp) REVERT: B 161 TYR cc_start: 0.9123 (p90) cc_final: 0.8764 (p90) REVERT: B 181 MET cc_start: 0.9559 (mmp) cc_final: 0.9290 (mmp) REVERT: B 185 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8837 (tm-30) REVERT: B 201 MET cc_start: 0.8984 (ptt) cc_final: 0.8542 (ptt) REVERT: B 243 HIS cc_start: 0.9150 (m90) cc_final: 0.8760 (m-70) REVERT: B 264 ASP cc_start: 0.9323 (m-30) cc_final: 0.8975 (m-30) REVERT: B 266 PHE cc_start: 0.9412 (m-80) cc_final: 0.9079 (m-80) REVERT: C 2 ILE cc_start: 0.8243 (pt) cc_final: 0.7639 (mm) REVERT: C 149 ASN cc_start: 0.8623 (t0) cc_final: 0.8388 (t0) REVERT: C 165 MET cc_start: 0.8245 (ttt) cc_final: 0.7901 (ttt) REVERT: D 1 MET cc_start: 0.9466 (tpt) cc_final: 0.9158 (tpp) REVERT: D 100 MET cc_start: 0.9297 (mtp) cc_final: 0.8984 (mtp) REVERT: D 183 PHE cc_start: 0.9016 (m-10) cc_final: 0.8627 (m-10) REVERT: D 199 MET cc_start: 0.9662 (mmp) cc_final: 0.9415 (mmm) REVERT: E 26 MET cc_start: 0.9497 (mmm) cc_final: 0.8947 (mmm) REVERT: E 96 MET cc_start: 0.8883 (ttp) cc_final: 0.8381 (ttp) REVERT: E 120 LYS cc_start: 0.9669 (tptp) cc_final: 0.9409 (tptt) REVERT: E 175 PHE cc_start: 0.9134 (t80) cc_final: 0.8768 (t80) REVERT: F 149 ARG cc_start: 0.9595 (ttt-90) cc_final: 0.8908 (ptm160) REVERT: F 164 TYR cc_start: 0.9231 (m-10) cc_final: 0.8712 (m-10) REVERT: G 1 MET cc_start: 0.9326 (tpp) cc_final: 0.8868 (tmm) REVERT: G 46 PHE cc_start: 0.9642 (t80) cc_final: 0.9406 (t80) REVERT: G 83 LYS cc_start: 0.8568 (ptmm) cc_final: 0.8260 (ptmt) REVERT: G 91 PHE cc_start: 0.8589 (m-80) cc_final: 0.7887 (m-80) REVERT: G 101 ASP cc_start: 0.9311 (m-30) cc_final: 0.9025 (m-30) REVERT: G 132 PHE cc_start: 0.9281 (m-10) cc_final: 0.8553 (m-80) REVERT: J 14 ASP cc_start: 0.9490 (m-30) cc_final: 0.9274 (t70) REVERT: J 67 ASN cc_start: 0.9686 (m-40) cc_final: 0.9329 (p0) REVERT: J 71 ASP cc_start: 0.9487 (p0) cc_final: 0.8745 (p0) REVERT: J 102 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8030 (mt-10) REVERT: J 118 MET cc_start: 0.8567 (tpp) cc_final: 0.8225 (tpp) REVERT: J 136 GLN cc_start: 0.9065 (mt0) cc_final: 0.8848 (mm110) REVERT: K 1 MET cc_start: 0.8663 (ttp) cc_final: 0.7913 (ppp) REVERT: K 4 GLU cc_start: 0.8763 (mp0) cc_final: 0.8532 (mp0) REVERT: K 5 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8518 (tm-30) REVERT: K 7 MET cc_start: 0.9114 (mmm) cc_final: 0.8186 (mmp) REVERT: K 20 MET cc_start: 0.8467 (ttm) cc_final: 0.7906 (ttp) REVERT: K 25 LEU cc_start: 0.9213 (mm) cc_final: 0.9002 (mm) REVERT: K 58 LEU cc_start: 0.9322 (pt) cc_final: 0.9081 (pt) REVERT: K 107 LEU cc_start: 0.9223 (mm) cc_final: 0.8994 (mp) REVERT: L 23 ILE cc_start: 0.8967 (mt) cc_final: 0.8416 (mt) REVERT: L 51 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8318 (mt-10) REVERT: L 67 THR cc_start: 0.8924 (m) cc_final: 0.8444 (p) REVERT: M 82 MET cc_start: 0.8634 (tpp) cc_final: 0.7106 (mmm) REVERT: M 112 LEU cc_start: 0.9677 (tp) cc_final: 0.9318 (tp) REVERT: N 1 MET cc_start: 0.8151 (tpp) cc_final: 0.7693 (tpp) REVERT: N 20 MET cc_start: 0.8942 (ttp) cc_final: 0.8399 (mtp) REVERT: N 24 MET cc_start: 0.8764 (ttm) cc_final: 0.8419 (ttm) REVERT: N 32 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8600 (tt0) REVERT: N 43 GLU cc_start: 0.9460 (tp30) cc_final: 0.8624 (tp30) REVERT: N 87 PHE cc_start: 0.8600 (m-80) cc_final: 0.7463 (m-80) REVERT: N 110 MET cc_start: 0.9069 (mmp) cc_final: 0.8830 (mmm) REVERT: N 114 GLU cc_start: 0.9310 (pm20) cc_final: 0.9046 (pm20) REVERT: O 69 ASP cc_start: 0.9715 (m-30) cc_final: 0.9401 (t0) REVERT: O 88 LYS cc_start: 0.9354 (tmtt) cc_final: 0.9025 (tptp) REVERT: P 9 GLU cc_start: 0.9269 (pm20) cc_final: 0.9037 (pm20) REVERT: P 24 ASP cc_start: 0.5242 (m-30) cc_final: 0.4762 (m-30) REVERT: Q 59 GLN cc_start: 0.9564 (tt0) cc_final: 0.9012 (mm-40) REVERT: R 48 LYS cc_start: 0.9484 (tmtt) cc_final: 0.9268 (tmtt) REVERT: R 76 LYS cc_start: 0.9312 (mttt) cc_final: 0.8758 (mmtp) REVERT: R 85 LYS cc_start: 0.8775 (tmtt) cc_final: 0.8202 (tptm) REVERT: R 86 GLN cc_start: 0.8959 (mm110) cc_final: 0.8532 (pp30) REVERT: R 95 ASP cc_start: 0.9346 (m-30) cc_final: 0.9003 (p0) REVERT: R 98 ILE cc_start: 0.9784 (mm) cc_final: 0.9242 (tt) REVERT: S 1 MET cc_start: 0.9025 (ptt) cc_final: 0.8789 (tmm) REVERT: S 78 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8492 (mt-10) REVERT: S 84 ARG cc_start: 0.9122 (mmt-90) cc_final: 0.8667 (mmt90) REVERT: S 92 ARG cc_start: 0.8759 (ptt180) cc_final: 0.8523 (ptt-90) REVERT: S 97 LEU cc_start: 0.9561 (mm) cc_final: 0.9251 (tp) REVERT: T 11 LEU cc_start: 0.8890 (mm) cc_final: 0.8336 (tp) REVERT: T 86 THR cc_start: 0.9442 (m) cc_final: 0.8764 (m) REVERT: V 48 MET cc_start: 0.9225 (mmm) cc_final: 0.8729 (mmm) REVERT: V 50 MET cc_start: 0.9455 (mtm) cc_final: 0.9130 (ptp) REVERT: W 17 GLU cc_start: 0.8588 (pt0) cc_final: 0.8143 (pp20) REVERT: W 36 ILE cc_start: 0.9147 (mm) cc_final: 0.8929 (mm) REVERT: X 10 LYS cc_start: 0.9235 (mmpt) cc_final: 0.8749 (mmtp) REVERT: X 14 THR cc_start: 0.8951 (t) cc_final: 0.8561 (m) REVERT: X 38 PHE cc_start: 0.9092 (m-80) cc_final: 0.8217 (m-80) REVERT: X 47 VAL cc_start: 0.9487 (t) cc_final: 0.9070 (m) REVERT: X 49 LEU cc_start: 0.9090 (mm) cc_final: 0.8712 (mm) REVERT: X 56 MET cc_start: 0.9336 (mtp) cc_final: 0.8165 (ttm) REVERT: X 60 ASP cc_start: 0.8968 (m-30) cc_final: 0.8707 (m-30) REVERT: Y 30 MET cc_start: 0.8847 (mmp) cc_final: 0.8282 (mmm) REVERT: Z 19 LYS cc_start: 0.9355 (mmmt) cc_final: 0.9052 (mmtt) REVERT: Z 21 LYS cc_start: 0.9335 (mttt) cc_final: 0.8807 (mttm) REVERT: Z 32 ILE cc_start: 0.9498 (pt) cc_final: 0.9279 (mp) REVERT: Z 47 MET cc_start: 0.9370 (mtt) cc_final: 0.9163 (mtt) REVERT: Z 49 ASN cc_start: 0.9837 (t0) cc_final: 0.9451 (p0) REVERT: Z 54 MET cc_start: 0.9194 (ptm) cc_final: 0.8159 (ttt) REVERT: b 7 LYS cc_start: 0.9094 (tptm) cc_final: 0.8778 (tptp) REVERT: b 9 THR cc_start: 0.8848 (m) cc_final: 0.8466 (p) REVERT: b 46 ASP cc_start: 0.9323 (t0) cc_final: 0.8998 (t0) REVERT: c 33 LYS cc_start: 0.9346 (mmmt) cc_final: 0.8776 (mmtt) REVERT: d 14 ARG cc_start: 0.9217 (mtp85) cc_final: 0.8899 (mmm-85) REVERT: d 25 LYS cc_start: 0.9146 (tmmt) cc_final: 0.8705 (tmmt) REVERT: d 29 GLN cc_start: 0.9198 (mp10) cc_final: 0.8822 (mp10) REVERT: e 14 PHE cc_start: 0.9760 (m-80) cc_final: 0.9493 (m-80) REVERT: f 13 ASN cc_start: 0.9569 (m-40) cc_final: 0.9058 (t0) REVERT: f 22 VAL cc_start: 0.9088 (t) cc_final: 0.8877 (p) REVERT: g 9 MET cc_start: 0.9168 (mtm) cc_final: 0.8918 (mpp) REVERT: g 27 MET cc_start: 0.8647 (mmm) cc_final: 0.8200 (mmm) REVERT: g 96 TRP cc_start: 0.8070 (t-100) cc_final: 0.7582 (t-100) REVERT: g 100 MET cc_start: 0.9586 (ttm) cc_final: 0.9136 (mtp) REVERT: g 120 GLN cc_start: 0.9228 (tt0) cc_final: 0.8895 (tp40) REVERT: g 132 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8410 (mmtt) REVERT: g 136 MET cc_start: 0.9808 (mmp) cc_final: 0.9603 (mmp) REVERT: h 8 ASN cc_start: 0.9084 (m110) cc_final: 0.8836 (m110) REVERT: h 19 ASN cc_start: 0.9236 (m-40) cc_final: 0.8198 (p0) REVERT: h 37 PHE cc_start: 0.9621 (t80) cc_final: 0.9254 (t80) REVERT: h 51 SER cc_start: 0.9581 (m) cc_final: 0.9222 (p) REVERT: h 110 GLU cc_start: 0.9260 (pm20) cc_final: 0.8613 (tm-30) REVERT: h 123 GLN cc_start: 0.9659 (mt0) cc_final: 0.9191 (mt0) REVERT: h 168 TYR cc_start: 0.7998 (m-80) cc_final: 0.7640 (m-80) REVERT: h 201 TRP cc_start: 0.9299 (m-90) cc_final: 0.9075 (m-90) REVERT: i 51 TYR cc_start: 0.9423 (t80) cc_final: 0.9191 (t80) REVERT: i 59 GLN cc_start: 0.9339 (mm110) cc_final: 0.8765 (mm110) REVERT: i 72 PHE cc_start: 0.9692 (t80) cc_final: 0.8772 (t80) REVERT: i 123 ILE cc_start: 0.9241 (mm) cc_final: 0.8503 (mp) REVERT: i 124 MET cc_start: 0.8900 (mtt) cc_final: 0.8571 (mmt) REVERT: j 14 LYS cc_start: 0.9357 (mmpt) cc_final: 0.8948 (mtmm) REVERT: j 29 ARG cc_start: 0.8887 (mpp80) cc_final: 0.8251 (mmt180) REVERT: j 45 ARG cc_start: 0.9505 (tpp-160) cc_final: 0.9213 (tpp-160) REVERT: j 48 PHE cc_start: 0.9385 (p90) cc_final: 0.9126 (p90) REVERT: j 54 ARG cc_start: 0.8593 (mmt90) cc_final: 0.7963 (mpt-90) REVERT: j 96 MET cc_start: 0.9527 (tpt) cc_final: 0.9271 (tpt) REVERT: j 116 GLU cc_start: 0.9694 (tt0) cc_final: 0.9426 (tt0) REVERT: j 162 GLU cc_start: 0.9639 (mm-30) cc_final: 0.9259 (pm20) REVERT: k 7 VAL cc_start: 0.9782 (p) cc_final: 0.9348 (t) REVERT: k 21 MET cc_start: 0.9164 (mtm) cc_final: 0.8581 (mtm) REVERT: k 35 LYS cc_start: 0.9668 (ptpp) cc_final: 0.9389 (ptpt) REVERT: k 61 LEU cc_start: 0.9047 (tt) cc_final: 0.8055 (tt) REVERT: k 80 PHE cc_start: 0.9629 (m-80) cc_final: 0.9062 (m-10) REVERT: k 88 MET cc_start: 0.8730 (tpt) cc_final: 0.8372 (tpt) REVERT: k 89 VAL cc_start: 0.9510 (t) cc_final: 0.9026 (p) REVERT: k 91 ARG cc_start: 0.9234 (ttt90) cc_final: 0.8802 (ttt90) REVERT: m 10 MET cc_start: 0.9641 (tmm) cc_final: 0.9343 (tmm) REVERT: m 27 MET cc_start: 0.8855 (ptp) cc_final: 0.8522 (ptp) REVERT: m 47 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8907 (tm-30) REVERT: n 27 LYS cc_start: 0.9503 (mtmm) cc_final: 0.9175 (mttp) REVERT: n 39 PHE cc_start: 0.9550 (m-10) cc_final: 0.9313 (m-10) REVERT: n 60 LYS cc_start: 0.9522 (mmtp) cc_final: 0.9257 (mmmm) REVERT: n 66 THR cc_start: 0.9098 (p) cc_final: 0.8615 (t) REVERT: n 97 GLU cc_start: 0.9603 (mt-10) cc_final: 0.9170 (mp0) REVERT: n 112 GLU cc_start: 0.8454 (tp30) cc_final: 0.8131 (tp30) REVERT: o 47 GLU cc_start: 0.8720 (tt0) cc_final: 0.8246 (tm-30) REVERT: o 49 PHE cc_start: 0.9415 (m-80) cc_final: 0.8290 (m-80) REVERT: o 52 LEU cc_start: 0.8747 (tp) cc_final: 0.8516 (tp) REVERT: o 99 GLN cc_start: 0.9514 (tt0) cc_final: 0.8897 (mt0) REVERT: p 31 ILE cc_start: 0.9774 (mm) cc_final: 0.9571 (mm) REVERT: p 38 GLN cc_start: 0.9325 (mp10) cc_final: 0.9122 (mp10) REVERT: p 56 ARG cc_start: 0.9362 (mpp80) cc_final: 0.8825 (mtm110) REVERT: p 87 LYS cc_start: 0.9390 (pptt) cc_final: 0.8692 (pptt) REVERT: p 105 PHE cc_start: 0.9652 (m-10) cc_final: 0.9274 (m-80) REVERT: q 20 ASN cc_start: 0.9546 (p0) cc_final: 0.9267 (p0) REVERT: q 35 THR cc_start: 0.7879 (m) cc_final: 0.7655 (m) REVERT: q 38 TYR cc_start: 0.6197 (p90) cc_final: 0.5965 (p90) REVERT: q 40 THR cc_start: 0.8980 (t) cc_final: 0.8636 (p) REVERT: q 123 LYS cc_start: 0.9036 (tmtt) cc_final: 0.8572 (tptp) REVERT: r 13 LYS cc_start: 0.8905 (ptmm) cc_final: 0.8538 (tptt) REVERT: r 27 LYS cc_start: 0.9365 (tppt) cc_final: 0.8879 (tppt) REVERT: r 42 ASP cc_start: 0.9108 (p0) cc_final: 0.8573 (t70) REVERT: r 103 LYS cc_start: 0.9021 (tttt) cc_final: 0.8818 (tttt) REVERT: s 18 ASP cc_start: 0.8889 (m-30) cc_final: 0.8606 (m-30) REVERT: s 65 ARG cc_start: 0.8820 (ttm170) cc_final: 0.7615 (ttp80) REVERT: s 92 GLU cc_start: 0.8420 (mp0) cc_final: 0.8158 (mp0) REVERT: t 26 GLU cc_start: 0.9553 (mp0) cc_final: 0.9108 (pt0) REVERT: t 37 ASN cc_start: 0.9772 (m110) cc_final: 0.9495 (m110) REVERT: t 62 GLN cc_start: 0.9632 (tt0) cc_final: 0.9346 (pt0) REVERT: t 65 LYS cc_start: 0.9326 (mttt) cc_final: 0.9041 (mmtt) REVERT: t 68 ASP cc_start: 0.9510 (m-30) cc_final: 0.9267 (m-30) REVERT: t 71 LYS cc_start: 0.9373 (tppt) cc_final: 0.8873 (tppt) REVERT: t 73 LYS cc_start: 0.9128 (mmtm) cc_final: 0.8885 (ptmt) REVERT: u 1 MET cc_start: 0.8836 (pmm) cc_final: 0.7505 (mmm) REVERT: v 18 GLU cc_start: 0.9692 (pt0) cc_final: 0.9358 (pm20) REVERT: v 65 ARG cc_start: 0.8932 (ttp80) cc_final: 0.8552 (ttp-110) REVERT: v 80 GLU cc_start: 0.9177 (pm20) cc_final: 0.8915 (tm-30) REVERT: w 31 ASN cc_start: 0.9286 (m110) cc_final: 0.9062 (m110) REVERT: w 35 GLU cc_start: 0.7556 (pp20) cc_final: 0.7271 (tm-30) REVERT: w 50 LYS cc_start: 0.9559 (ptmm) cc_final: 0.9315 (ptmm) REVERT: w 61 ARG cc_start: 0.8658 (mtm-85) cc_final: 0.8259 (mtt90) REVERT: w 65 LEU cc_start: 0.9865 (mm) cc_final: 0.9547 (tp) REVERT: w 67 LEU cc_start: 0.9412 (mt) cc_final: 0.8770 (mt) REVERT: w 70 TYR cc_start: 0.8791 (m-80) cc_final: 0.8459 (m-10) REVERT: x 28 LYS cc_start: 0.9327 (mmmt) cc_final: 0.9017 (tppt) REVERT: x 66 MET cc_start: 0.8274 (mtp) cc_final: 0.8057 (mtp) REVERT: y 15 GLU cc_start: 0.9769 (tt0) cc_final: 0.9512 (tp30) REVERT: y 18 ARG cc_start: 0.9646 (ttp80) cc_final: 0.8817 (ttp-110) REVERT: y 21 ASN cc_start: 0.9666 (m110) cc_final: 0.9364 (m110) REVERT: y 28 MET cc_start: 0.9781 (tmm) cc_final: 0.9571 (tmm) REVERT: y 32 ILE cc_start: 0.9861 (mt) cc_final: 0.9223 (pt) REVERT: y 36 TYR cc_start: 0.9529 (m-10) cc_final: 0.9244 (m-80) REVERT: y 80 THR cc_start: 0.9585 (m) cc_final: 0.9362 (p) REVERT: z 19 PHE cc_start: 0.9288 (t80) cc_final: 0.8861 (t80) REVERT: z 24 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8801 (pt0) REVERT: z 49 LYS cc_start: 0.9669 (ptpp) cc_final: 0.9428 (ptpp) REVERT: 7 73 MET cc_start: 0.3039 (mmp) cc_final: 0.2489 (mtt) REVERT: 7 199 HIS cc_start: 0.9429 (m-70) cc_final: 0.8752 (m-70) REVERT: 7 327 VAL cc_start: 0.9102 (t) cc_final: 0.8600 (t) REVERT: 7 330 ASP cc_start: 0.7637 (m-30) cc_final: 0.7395 (m-30) outliers start: 1 outliers final: 1 residues processed: 1098 average time/residue: 1.4395 time to fit residues: 2728.5197 Evaluate side-chains 883 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 882 time to evaluate : 6.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 618 optimal weight: 6.9990 chunk 399 optimal weight: 40.0000 chunk 597 optimal weight: 30.0000 chunk 301 optimal weight: 30.0000 chunk 196 optimal weight: 30.0000 chunk 193 optimal weight: 9.9990 chunk 636 optimal weight: 30.0000 chunk 681 optimal weight: 2.9990 chunk 494 optimal weight: 30.0000 chunk 93 optimal weight: 30.0000 chunk 786 optimal weight: 40.0000 overall best weight: 15.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 ASN N 81 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN W 50 ASN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 136 GLN j 73 ASN ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 94 HIS ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 24 HIS ** t 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.135 159192 Z= 0.410 Angle : 0.790 13.218 237909 Z= 0.411 Chirality : 0.040 0.308 30260 Planarity : 0.007 0.132 12919 Dihedral : 24.977 179.471 78958 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 48.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.11), residues: 5890 helix: -0.14 (0.11), residues: 2043 sheet: -1.91 (0.15), residues: 1072 loop : -1.33 (0.12), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP D 78 HIS 0.012 0.002 HIS F 111 PHE 0.037 0.003 PHE W 69 TYR 0.025 0.002 TYR r 86 ARG 0.010 0.001 ARG x 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1016 time to evaluate : 6.399 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: 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: 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: 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: 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: 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: 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: symmetry clash REVERT: B 21 ASN cc_start: 0.8617 (t0) cc_final: 0.8134 (t0) REVERT: B 68 LYS cc_start: 0.9412 (mtpt) cc_final: 0.9048 (mmmm) REVERT: B 79 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8775 (mm-30) REVERT: B 96 TYR cc_start: 0.8631 (m-80) cc_final: 0.8007 (m-80) REVERT: B 115 GLN cc_start: 0.9172 (tp-100) cc_final: 0.8886 (tp-100) REVERT: B 132 MET cc_start: 0.9270 (mtm) cc_final: 0.8615 (mtm) REVERT: B 146 MET cc_start: 0.8223 (mtp) cc_final: 0.7661 (mpp) REVERT: B 161 TYR cc_start: 0.9391 (p90) cc_final: 0.8974 (p90) REVERT: B 185 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8776 (tm-30) REVERT: B 201 MET cc_start: 0.9051 (ptt) cc_final: 0.8588 (ptt) REVERT: B 236 GLU cc_start: 0.8050 (tp30) cc_final: 0.7661 (tp30) REVERT: B 243 HIS cc_start: 0.9207 (m90) cc_final: 0.8809 (m-70) REVERT: B 264 ASP cc_start: 0.9334 (m-30) cc_final: 0.9029 (m-30) REVERT: B 266 PHE cc_start: 0.9515 (m-80) cc_final: 0.9220 (m-80) REVERT: C 2 ILE cc_start: 0.8425 (pt) cc_final: 0.7886 (mm) REVERT: C 149 ASN cc_start: 0.8237 (t0) cc_final: 0.7806 (t0) REVERT: C 165 MET cc_start: 0.8317 (ttt) cc_final: 0.7978 (ttt) REVERT: D 1 MET cc_start: 0.9511 (tpt) cc_final: 0.9215 (tpp) REVERT: D 90 GLN cc_start: 0.8882 (pm20) cc_final: 0.8397 (pm20) REVERT: D 100 MET cc_start: 0.9272 (mtp) cc_final: 0.8986 (mtp) REVERT: D 188 MET cc_start: 0.9594 (mmm) cc_final: 0.9087 (mmm) REVERT: D 199 MET cc_start: 0.9685 (mmp) cc_final: 0.9485 (mmm) REVERT: E 26 MET cc_start: 0.9469 (mmm) cc_final: 0.8921 (mmt) REVERT: E 143 TYR cc_start: 0.9202 (t80) cc_final: 0.8884 (t80) REVERT: E 175 PHE cc_start: 0.9173 (t80) cc_final: 0.8856 (t80) REVERT: F 69 ARG cc_start: 0.9378 (tmm160) cc_final: 0.9132 (tmm-80) REVERT: G 1 MET cc_start: 0.9370 (tpp) cc_final: 0.8899 (tmm) REVERT: G 46 PHE cc_start: 0.9660 (t80) cc_final: 0.9452 (t80) REVERT: G 83 LYS cc_start: 0.8362 (ptmm) cc_final: 0.8125 (ptmt) REVERT: G 91 PHE cc_start: 0.8697 (m-80) cc_final: 0.7865 (m-80) REVERT: G 101 ASP cc_start: 0.9200 (m-30) cc_final: 0.8869 (m-30) REVERT: G 132 PHE cc_start: 0.9329 (m-10) cc_final: 0.8469 (m-80) REVERT: J 67 ASN cc_start: 0.9699 (m-40) cc_final: 0.9457 (p0) REVERT: J 75 TYR cc_start: 0.9487 (m-80) cc_final: 0.9181 (m-10) REVERT: J 102 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8111 (mt-10) REVERT: K 1 MET cc_start: 0.9100 (ttp) cc_final: 0.8320 (ppp) REVERT: K 5 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8517 (tp-100) REVERT: K 7 MET cc_start: 0.9060 (mmm) cc_final: 0.8824 (mmm) REVERT: K 20 MET cc_start: 0.8481 (ttm) cc_final: 0.8034 (tmm) REVERT: K 25 LEU cc_start: 0.9464 (mm) cc_final: 0.9217 (mm) REVERT: L 23 ILE cc_start: 0.9010 (mt) cc_final: 0.8435 (mt) REVERT: L 51 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8346 (mt-10) REVERT: L 67 THR cc_start: 0.8979 (m) cc_final: 0.8566 (p) REVERT: M 53 MET cc_start: 0.9490 (mtm) cc_final: 0.9265 (mtm) REVERT: M 82 MET cc_start: 0.8840 (tpp) cc_final: 0.7484 (mmm) REVERT: M 91 TYR cc_start: 0.9013 (p90) cc_final: 0.8688 (p90) REVERT: M 105 MET cc_start: 0.8812 (mmp) cc_final: 0.8515 (mmm) REVERT: M 112 LEU cc_start: 0.9665 (tp) cc_final: 0.9332 (tt) REVERT: N 5 LYS cc_start: 0.9405 (mttt) cc_final: 0.9105 (mmmm) REVERT: N 20 MET cc_start: 0.8844 (ttp) cc_final: 0.8144 (mtp) REVERT: N 24 MET cc_start: 0.8838 (ttm) cc_final: 0.8486 (ttm) REVERT: N 32 GLU cc_start: 0.9359 (mt-10) cc_final: 0.9122 (mp0) REVERT: N 43 GLU cc_start: 0.9447 (tp30) cc_final: 0.8561 (tp30) REVERT: N 87 PHE cc_start: 0.8847 (m-80) cc_final: 0.7852 (m-80) REVERT: N 110 MET cc_start: 0.9123 (mmp) cc_final: 0.8849 (mmm) REVERT: N 114 GLU cc_start: 0.9264 (pm20) cc_final: 0.9004 (pm20) REVERT: N 117 ASP cc_start: 0.8605 (m-30) cc_final: 0.8404 (m-30) REVERT: O 69 ASP cc_start: 0.9698 (m-30) cc_final: 0.9404 (t0) REVERT: P 24 ASP cc_start: 0.5114 (m-30) cc_final: 0.4705 (m-30) REVERT: P 66 ASN cc_start: 0.9536 (m110) cc_final: 0.9298 (m110) REVERT: Q 25 TYR cc_start: 0.8861 (t80) cc_final: 0.8524 (t80) REVERT: Q 59 GLN cc_start: 0.9489 (tt0) cc_final: 0.8934 (mm-40) REVERT: Q 62 ILE cc_start: 0.9668 (mt) cc_final: 0.9449 (mt) REVERT: R 48 LYS cc_start: 0.9554 (tmtt) cc_final: 0.9214 (tptm) REVERT: R 74 ILE cc_start: 0.9384 (mt) cc_final: 0.8987 (mt) REVERT: R 76 LYS cc_start: 0.9363 (mttt) cc_final: 0.8472 (mmtm) REVERT: R 83 TYR cc_start: 0.8581 (t80) cc_final: 0.8304 (t80) REVERT: R 85 LYS cc_start: 0.8776 (tmtt) cc_final: 0.8216 (tptm) REVERT: R 86 GLN cc_start: 0.8934 (mm110) cc_final: 0.8468 (pp30) REVERT: R 95 ASP cc_start: 0.9327 (m-30) cc_final: 0.9049 (p0) REVERT: R 98 ILE cc_start: 0.9798 (mm) cc_final: 0.9314 (tt) REVERT: S 78 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8403 (mt-10) REVERT: S 84 ARG cc_start: 0.9129 (mmt-90) cc_final: 0.8871 (mmt90) REVERT: S 92 ARG cc_start: 0.8819 (ptt180) cc_final: 0.8559 (ptt-90) REVERT: S 97 LEU cc_start: 0.9537 (mm) cc_final: 0.9103 (tp) REVERT: T 11 LEU cc_start: 0.8939 (mm) cc_final: 0.8402 (tp) REVERT: T 86 THR cc_start: 0.9381 (m) cc_final: 0.8744 (m) REVERT: V 48 MET cc_start: 0.9238 (mmm) cc_final: 0.8391 (mmm) REVERT: V 50 MET cc_start: 0.9495 (mtm) cc_final: 0.9186 (ptp) REVERT: V 55 GLU cc_start: 0.9776 (tt0) cc_final: 0.9375 (tp30) REVERT: W 17 GLU cc_start: 0.8657 (pt0) cc_final: 0.8167 (pp20) REVERT: W 36 ILE cc_start: 0.9144 (mm) cc_final: 0.8897 (mm) REVERT: X 38 PHE cc_start: 0.9106 (m-80) cc_final: 0.8530 (m-80) REVERT: X 47 VAL cc_start: 0.9593 (t) cc_final: 0.9264 (m) REVERT: X 56 MET cc_start: 0.9287 (mtp) cc_final: 0.8557 (ttm) REVERT: X 60 ASP cc_start: 0.9116 (m-30) cc_final: 0.8894 (m-30) REVERT: Y 23 ARG cc_start: 0.9660 (mtt90) cc_final: 0.9392 (mtt-85) REVERT: Y 30 MET cc_start: 0.8914 (mmp) cc_final: 0.8198 (mmp) REVERT: Z 21 LYS cc_start: 0.9281 (mttt) cc_final: 0.8723 (mttm) REVERT: Z 32 ILE cc_start: 0.9542 (pt) cc_final: 0.9315 (mp) REVERT: Z 47 MET cc_start: 0.9461 (mtt) cc_final: 0.9095 (mtt) REVERT: b 7 LYS cc_start: 0.9090 (tptm) cc_final: 0.8736 (tptp) REVERT: b 12 LYS cc_start: 0.9199 (mmpt) cc_final: 0.8564 (mmmt) REVERT: b 46 ASP cc_start: 0.9365 (t0) cc_final: 0.9033 (t0) REVERT: c 8 LYS cc_start: 0.9086 (pttt) cc_final: 0.8879 (pttt) REVERT: c 33 LYS cc_start: 0.9379 (mmmt) cc_final: 0.8887 (mmtt) REVERT: d 29 GLN cc_start: 0.9094 (mp10) cc_final: 0.8767 (mp10) REVERT: e 14 PHE cc_start: 0.9734 (m-80) cc_final: 0.9511 (m-80) REVERT: f 22 VAL cc_start: 0.9132 (t) cc_final: 0.8916 (p) REVERT: g 96 TRP cc_start: 0.8072 (t-100) cc_final: 0.7471 (t-100) REVERT: g 120 GLN cc_start: 0.9298 (tt0) cc_final: 0.8904 (tp40) REVERT: g 132 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8457 (mmtt) REVERT: g 136 MET cc_start: 0.9832 (mmp) cc_final: 0.9523 (mtt) REVERT: h 8 ASN cc_start: 0.8927 (m110) cc_final: 0.8364 (m110) REVERT: h 19 ASN cc_start: 0.9222 (m-40) cc_final: 0.7807 (p0) REVERT: h 37 PHE cc_start: 0.9650 (t80) cc_final: 0.9384 (t80) REVERT: h 51 SER cc_start: 0.9561 (m) cc_final: 0.9205 (p) REVERT: h 110 GLU cc_start: 0.9203 (pm20) cc_final: 0.8676 (tm-30) REVERT: h 123 GLN cc_start: 0.9633 (mt0) cc_final: 0.9192 (mt0) REVERT: h 134 MET cc_start: 0.9333 (mtp) cc_final: 0.8771 (ttt) REVERT: h 168 TYR cc_start: 0.7815 (m-80) cc_final: 0.6274 (m-80) REVERT: i 59 GLN cc_start: 0.9528 (mm110) cc_final: 0.9028 (mm110) REVERT: i 72 PHE cc_start: 0.9559 (t80) cc_final: 0.8531 (t80) REVERT: i 128 ARG cc_start: 0.9732 (mtp180) cc_final: 0.9521 (mmm160) REVERT: i 206 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8553 (mmmt) REVERT: j 13 GLU cc_start: 0.8547 (mm-30) cc_final: 0.7927 (tp30) REVERT: j 14 LYS cc_start: 0.9368 (mmpt) cc_final: 0.8737 (mtmm) REVERT: j 29 ARG cc_start: 0.8872 (mpp80) cc_final: 0.8159 (mmt180) REVERT: j 45 ARG cc_start: 0.9319 (tpp-160) cc_final: 0.8976 (tpp-160) REVERT: j 48 PHE cc_start: 0.9365 (p90) cc_final: 0.9159 (p90) REVERT: j 64 MET cc_start: 0.9528 (mpp) cc_final: 0.9325 (mpp) REVERT: j 96 MET cc_start: 0.9617 (tpt) cc_final: 0.9290 (tpt) REVERT: j 116 GLU cc_start: 0.9689 (tt0) cc_final: 0.8728 (mt-10) REVERT: k 21 MET cc_start: 0.9244 (mtm) cc_final: 0.8776 (mtm) REVERT: k 80 PHE cc_start: 0.9642 (m-80) cc_final: 0.9100 (m-10) REVERT: k 88 MET cc_start: 0.8530 (tpt) cc_final: 0.7814 (tpt) REVERT: k 89 VAL cc_start: 0.9471 (t) cc_final: 0.9229 (t) REVERT: k 91 ARG cc_start: 0.9090 (ttt90) cc_final: 0.8471 (ttt90) REVERT: m 10 MET cc_start: 0.9686 (tmm) cc_final: 0.9345 (tmm) REVERT: m 27 MET cc_start: 0.9127 (ptp) cc_final: 0.8068 (ptp) REVERT: m 38 ASN cc_start: 0.9555 (m-40) cc_final: 0.9277 (m-40) REVERT: m 47 GLU cc_start: 0.9284 (tm-30) cc_final: 0.9015 (tm-30) REVERT: n 39 PHE cc_start: 0.9459 (m-10) cc_final: 0.9153 (m-10) REVERT: n 88 MET cc_start: 0.8933 (mmp) cc_final: 0.8607 (mmp) REVERT: n 92 GLU cc_start: 0.8848 (tp30) cc_final: 0.8602 (tp30) REVERT: n 97 GLU cc_start: 0.9615 (mt-10) cc_final: 0.9286 (mp0) REVERT: n 112 GLU cc_start: 0.8365 (tp30) cc_final: 0.7991 (tp30) REVERT: o 52 LEU cc_start: 0.8801 (tp) cc_final: 0.8579 (tp) REVERT: o 99 GLN cc_start: 0.9536 (tt0) cc_final: 0.9221 (mt0) REVERT: p 31 ILE cc_start: 0.9735 (mm) cc_final: 0.9511 (mm) REVERT: p 52 PHE cc_start: 0.8725 (m-10) cc_final: 0.8485 (m-10) REVERT: p 75 LYS cc_start: 0.9545 (ptpp) cc_final: 0.9344 (ptpp) REVERT: p 79 ILE cc_start: 0.9266 (mp) cc_final: 0.8891 (mp) REVERT: p 85 MET cc_start: 0.9000 (ppp) cc_final: 0.8679 (ppp) REVERT: p 87 LYS cc_start: 0.9567 (pptt) cc_final: 0.9102 (pptt) REVERT: p 105 PHE cc_start: 0.9652 (m-10) cc_final: 0.9273 (m-80) REVERT: q 20 ASN cc_start: 0.9537 (p0) cc_final: 0.9235 (p0) REVERT: q 38 TYR cc_start: 0.6618 (p90) cc_final: 0.6282 (p90) REVERT: q 40 THR cc_start: 0.9054 (t) cc_final: 0.8660 (p) REVERT: r 13 LYS cc_start: 0.8746 (ptmm) cc_final: 0.8252 (tptt) REVERT: r 27 LYS cc_start: 0.9383 (tppt) cc_final: 0.8959 (tppt) REVERT: r 31 LYS cc_start: 0.9638 (mtmm) cc_final: 0.9335 (ptpp) REVERT: r 42 ASP cc_start: 0.8993 (p0) cc_final: 0.8309 (t70) REVERT: r 103 LYS cc_start: 0.9088 (tttt) cc_final: 0.8831 (tttp) REVERT: s 18 ASP cc_start: 0.8877 (m-30) cc_final: 0.8573 (m-30) REVERT: s 92 GLU cc_start: 0.8401 (mp0) cc_final: 0.8065 (mp0) REVERT: t 37 ASN cc_start: 0.9706 (m110) cc_final: 0.9443 (m110) REVERT: t 62 GLN cc_start: 0.9685 (tt0) cc_final: 0.9240 (mt0) REVERT: t 65 LYS cc_start: 0.9388 (mttt) cc_final: 0.9092 (mmtt) REVERT: u 1 MET cc_start: 0.8958 (pmm) cc_final: 0.8036 (tpt) REVERT: v 60 GLU cc_start: 0.9130 (tt0) cc_final: 0.8490 (tt0) REVERT: v 77 ARG cc_start: 0.9165 (ttp80) cc_final: 0.8575 (ttp80) REVERT: w 30 LYS cc_start: 0.9512 (mtmm) cc_final: 0.9290 (mttt) REVERT: w 31 ASN cc_start: 0.9222 (m110) cc_final: 0.9011 (m110) REVERT: w 65 LEU cc_start: 0.9858 (mm) cc_final: 0.9435 (tp) REVERT: w 67 LEU cc_start: 0.9362 (mt) cc_final: 0.8695 (mt) REVERT: w 70 TYR cc_start: 0.8656 (m-80) cc_final: 0.8410 (m-80) REVERT: x 41 PHE cc_start: 0.9547 (t80) cc_final: 0.9331 (t80) REVERT: y 18 ARG cc_start: 0.9650 (ttp80) cc_final: 0.9253 (ttp80) REVERT: y 21 ASN cc_start: 0.9550 (m110) cc_final: 0.9105 (m110) REVERT: y 32 ILE cc_start: 0.9864 (mt) cc_final: 0.9179 (pt) REVERT: y 36 TYR cc_start: 0.9568 (m-10) cc_final: 0.9348 (m-80) REVERT: z 19 PHE cc_start: 0.9212 (t80) cc_final: 0.8831 (t80) REVERT: z 24 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8838 (pt0) REVERT: 7 73 MET cc_start: 0.3469 (mmp) cc_final: 0.2551 (mtt) REVERT: 7 152 TYR cc_start: 0.9225 (m-80) cc_final: 0.8851 (m-80) REVERT: 7 199 HIS cc_start: 0.9334 (m-70) cc_final: 0.8521 (m-70) REVERT: 7 327 VAL cc_start: 0.9159 (t) cc_final: 0.8703 (t) REVERT: 7 330 ASP cc_start: 0.7674 (m-30) cc_final: 0.7439 (m-30) outliers start: 0 outliers final: 0 residues processed: 1016 average time/residue: 1.3114 time to fit residues: 2286.9920 Evaluate side-chains 815 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 815 time to evaluate : 6.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 910 optimal weight: 9.9990 chunk 958 optimal weight: 10.0000 chunk 874 optimal weight: 9.9990 chunk 932 optimal weight: 30.0000 chunk 561 optimal weight: 8.9990 chunk 406 optimal weight: 30.0000 chunk 732 optimal weight: 6.9990 chunk 286 optimal weight: 20.0000 chunk 842 optimal weight: 0.0370 chunk 881 optimal weight: 30.0000 chunk 929 optimal weight: 9.9990 overall best weight: 7.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 GLN ** G 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 ASN O 38 GLN ** P 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 50 ASN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 32 ASN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 24 HIS ** t 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 355 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 159192 Z= 0.219 Angle : 0.645 13.629 237909 Z= 0.346 Chirality : 0.034 0.301 30260 Planarity : 0.006 0.127 12919 Dihedral : 24.853 179.145 78958 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 33.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.11), residues: 5890 helix: 0.12 (0.11), residues: 2056 sheet: -1.85 (0.15), residues: 1100 loop : -1.22 (0.12), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 7 155 HIS 0.010 0.001 HIS N 3 PHE 0.030 0.002 PHE h 23 TYR 0.021 0.002 TYR n 6 ARG 0.014 0.001 ARG w 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1055 time to evaluate : 6.297 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash REVERT: B 21 ASN cc_start: 0.8569 (t0) cc_final: 0.7814 (t0) REVERT: B 68 LYS cc_start: 0.9372 (mtpt) cc_final: 0.8980 (mmmm) REVERT: B 79 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8746 (mm-30) REVERT: B 96 TYR cc_start: 0.8651 (m-80) cc_final: 0.7955 (m-80) REVERT: B 115 GLN cc_start: 0.9112 (tp-100) cc_final: 0.8796 (tp-100) REVERT: B 125 LYS cc_start: 0.9461 (tptp) cc_final: 0.9218 (tptt) REVERT: B 132 MET cc_start: 0.9230 (mtm) cc_final: 0.8571 (mtm) REVERT: B 146 MET cc_start: 0.8242 (mtp) cc_final: 0.7667 (mpp) REVERT: B 161 TYR cc_start: 0.9299 (p90) cc_final: 0.8960 (p90) REVERT: B 181 MET cc_start: 0.9470 (mmp) cc_final: 0.9210 (mmp) REVERT: B 185 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8777 (tm-30) REVERT: B 201 MET cc_start: 0.8980 (ptt) cc_final: 0.8547 (ptt) REVERT: B 236 GLU cc_start: 0.7429 (tp30) cc_final: 0.7009 (tp30) REVERT: B 243 HIS cc_start: 0.9161 (m90) cc_final: 0.8777 (m-70) REVERT: B 264 ASP cc_start: 0.9360 (m-30) cc_final: 0.9047 (m-30) REVERT: B 266 PHE cc_start: 0.9510 (m-80) cc_final: 0.9146 (m-80) REVERT: C 2 ILE cc_start: 0.8296 (pt) cc_final: 0.7710 (mm) REVERT: C 149 ASN cc_start: 0.8542 (t0) cc_final: 0.8293 (t0) REVERT: C 165 MET cc_start: 0.8259 (ttt) cc_final: 0.7920 (ttt) REVERT: D 1 MET cc_start: 0.9469 (tpt) cc_final: 0.9191 (tpp) REVERT: D 90 GLN cc_start: 0.8938 (pm20) cc_final: 0.8506 (pm20) REVERT: D 100 MET cc_start: 0.9293 (mtp) cc_final: 0.8977 (mtp) REVERT: D 141 MET cc_start: 0.9475 (mpp) cc_final: 0.9203 (mpp) REVERT: D 188 MET cc_start: 0.9554 (mmm) cc_final: 0.9009 (mmm) REVERT: D 199 MET cc_start: 0.9656 (mmp) cc_final: 0.9436 (mmm) REVERT: E 26 MET cc_start: 0.9491 (mmm) cc_final: 0.8936 (mmt) REVERT: E 96 MET cc_start: 0.9230 (ttm) cc_final: 0.8934 (ttt) REVERT: E 120 LYS cc_start: 0.9582 (tptp) cc_final: 0.9298 (tptp) REVERT: E 143 TYR cc_start: 0.9361 (t80) cc_final: 0.9107 (t80) REVERT: E 175 PHE cc_start: 0.9122 (t80) cc_final: 0.8767 (t80) REVERT: F 153 ARG cc_start: 0.8558 (ptm-80) cc_final: 0.8320 (ptm-80) REVERT: G 1 MET cc_start: 0.9374 (tpp) cc_final: 0.8879 (tmm) REVERT: G 91 PHE cc_start: 0.8496 (m-80) cc_final: 0.8199 (m-80) REVERT: G 101 ASP cc_start: 0.9285 (m-30) cc_final: 0.8988 (m-30) REVERT: G 132 PHE cc_start: 0.9264 (m-10) cc_final: 0.8364 (m-80) REVERT: J 67 ASN cc_start: 0.9669 (m-40) cc_final: 0.9339 (p0) REVERT: J 71 ASP cc_start: 0.9560 (p0) cc_final: 0.8966 (p0) REVERT: J 102 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8100 (mt-10) REVERT: J 118 MET cc_start: 0.8701 (tpp) cc_final: 0.8469 (tpp) REVERT: K 1 MET cc_start: 0.8760 (ttp) cc_final: 0.8151 (ppp) REVERT: K 5 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8514 (tp-100) REVERT: K 7 MET cc_start: 0.9096 (mmm) cc_final: 0.8743 (mmm) REVERT: K 9 ASN cc_start: 0.9826 (m-40) cc_final: 0.9425 (m-40) REVERT: K 20 MET cc_start: 0.8585 (ttm) cc_final: 0.7951 (tmm) REVERT: K 25 LEU cc_start: 0.9277 (mm) cc_final: 0.9053 (mm) REVERT: K 37 ASP cc_start: 0.8937 (m-30) cc_final: 0.8722 (m-30) REVERT: K 58 LEU cc_start: 0.9243 (pt) cc_final: 0.9019 (pt) REVERT: L 23 ILE cc_start: 0.9042 (mt) cc_final: 0.8354 (mt) REVERT: L 51 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8284 (mt-10) REVERT: L 67 THR cc_start: 0.8903 (m) cc_final: 0.8482 (p) REVERT: M 82 MET cc_start: 0.8645 (tpp) cc_final: 0.7246 (mmm) REVERT: M 91 TYR cc_start: 0.9120 (p90) cc_final: 0.8787 (p90) REVERT: M 105 MET cc_start: 0.8927 (mmp) cc_final: 0.8647 (mmm) REVERT: M 112 LEU cc_start: 0.9664 (tp) cc_final: 0.9300 (tp) REVERT: M 128 THR cc_start: 0.7739 (p) cc_final: 0.7527 (p) REVERT: N 20 MET cc_start: 0.8920 (ttp) cc_final: 0.8469 (mtp) REVERT: N 24 MET cc_start: 0.8761 (ttm) cc_final: 0.8419 (ttm) REVERT: N 32 GLU cc_start: 0.9336 (mt-10) cc_final: 0.9063 (mp0) REVERT: N 43 GLU cc_start: 0.9509 (tp30) cc_final: 0.8741 (tp30) REVERT: N 87 PHE cc_start: 0.8644 (m-80) cc_final: 0.7510 (m-80) REVERT: N 110 MET cc_start: 0.9046 (mmp) cc_final: 0.8787 (mmm) REVERT: N 114 GLU cc_start: 0.9247 (pm20) cc_final: 0.9043 (pm20) REVERT: N 117 ASP cc_start: 0.8632 (m-30) cc_final: 0.8412 (m-30) REVERT: O 69 ASP cc_start: 0.9687 (m-30) cc_final: 0.9401 (t0) REVERT: O 88 LYS cc_start: 0.9448 (tmmt) cc_final: 0.9133 (tmtt) REVERT: O 89 ASP cc_start: 0.8589 (t70) cc_final: 0.8193 (t70) REVERT: P 16 ASP cc_start: 0.9488 (p0) cc_final: 0.9287 (p0) REVERT: Q 59 GLN cc_start: 0.9548 (tt0) cc_final: 0.9058 (mm-40) REVERT: R 1 MET cc_start: 0.9624 (tmm) cc_final: 0.9411 (tmm) REVERT: R 18 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8541 (tm-30) REVERT: R 48 LYS cc_start: 0.9483 (tmtt) cc_final: 0.9212 (tmtt) REVERT: R 76 LYS cc_start: 0.9423 (mttt) cc_final: 0.8671 (mmtp) REVERT: R 85 LYS cc_start: 0.8833 (tmtt) cc_final: 0.8267 (tptt) REVERT: R 86 GLN cc_start: 0.8912 (mm110) cc_final: 0.8544 (pp30) REVERT: R 95 ASP cc_start: 0.9336 (m-30) cc_final: 0.8999 (p0) REVERT: R 98 ILE cc_start: 0.9792 (mm) cc_final: 0.9228 (tt) REVERT: S 78 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8543 (mt-10) REVERT: S 84 ARG cc_start: 0.9179 (mmt-90) cc_final: 0.8860 (mmt90) REVERT: S 92 ARG cc_start: 0.8692 (ptt180) cc_final: 0.8486 (ptt-90) REVERT: S 97 LEU cc_start: 0.9469 (mm) cc_final: 0.9045 (tp) REVERT: T 11 LEU cc_start: 0.8916 (mm) cc_final: 0.8404 (tp) REVERT: T 74 ILE cc_start: 0.9424 (mp) cc_final: 0.9185 (tp) REVERT: T 86 THR cc_start: 0.9484 (m) cc_final: 0.8837 (m) REVERT: V 48 MET cc_start: 0.9259 (mmm) cc_final: 0.8323 (mmm) REVERT: V 50 MET cc_start: 0.9492 (mtm) cc_final: 0.9161 (ptp) REVERT: V 55 GLU cc_start: 0.9779 (tt0) cc_final: 0.9375 (tp30) REVERT: W 19 LYS cc_start: 0.7144 (mmtt) cc_final: 0.5946 (mmtt) REVERT: X 14 THR cc_start: 0.8966 (t) cc_final: 0.8578 (m) REVERT: X 38 PHE cc_start: 0.9060 (m-80) cc_final: 0.8422 (m-80) REVERT: X 47 VAL cc_start: 0.9576 (t) cc_final: 0.9202 (m) REVERT: X 56 MET cc_start: 0.9326 (mtp) cc_final: 0.8192 (ttm) REVERT: X 60 ASP cc_start: 0.8964 (m-30) cc_final: 0.8719 (m-30) REVERT: Y 17 GLU cc_start: 0.9381 (tm-30) cc_final: 0.9118 (tm-30) REVERT: Y 30 MET cc_start: 0.8828 (mmp) cc_final: 0.8207 (mmp) REVERT: Z 19 LYS cc_start: 0.9332 (mmmt) cc_final: 0.9067 (mmtt) REVERT: Z 21 LYS cc_start: 0.9299 (mttt) cc_final: 0.8908 (mttm) REVERT: Z 32 ILE cc_start: 0.9495 (pt) cc_final: 0.9292 (mt) REVERT: Z 47 MET cc_start: 0.9401 (mtt) cc_final: 0.9087 (mtt) REVERT: Z 54 MET cc_start: 0.9287 (ptm) cc_final: 0.8382 (ttt) REVERT: b 7 LYS cc_start: 0.9141 (tptm) cc_final: 0.8838 (tptp) REVERT: b 9 THR cc_start: 0.8992 (m) cc_final: 0.8744 (p) REVERT: b 46 ASP cc_start: 0.9339 (t0) cc_final: 0.9011 (t0) REVERT: c 8 LYS cc_start: 0.9039 (pttt) cc_final: 0.8729 (pttt) REVERT: c 33 LYS cc_start: 0.9350 (mmmt) cc_final: 0.9116 (mmmm) REVERT: e 14 PHE cc_start: 0.9775 (m-80) cc_final: 0.9557 (m-80) REVERT: f 22 VAL cc_start: 0.9091 (t) cc_final: 0.8877 (p) REVERT: g 96 TRP cc_start: 0.8096 (t-100) cc_final: 0.7622 (t-100) REVERT: g 100 MET cc_start: 0.9611 (ttm) cc_final: 0.9153 (mtp) REVERT: g 120 GLN cc_start: 0.9295 (tt0) cc_final: 0.8913 (tp40) REVERT: g 136 MET cc_start: 0.9818 (mmp) cc_final: 0.9608 (mmp) REVERT: h 8 ASN cc_start: 0.8821 (m110) cc_final: 0.8284 (m110) REVERT: h 19 ASN cc_start: 0.9111 (m-40) cc_final: 0.7729 (p0) REVERT: h 37 PHE cc_start: 0.9595 (t80) cc_final: 0.9355 (t80) REVERT: h 42 TYR cc_start: 0.9430 (t80) cc_final: 0.9224 (t80) REVERT: h 110 GLU cc_start: 0.9212 (pm20) cc_final: 0.8469 (tm-30) REVERT: h 123 GLN cc_start: 0.9634 (mt0) cc_final: 0.9157 (mt0) REVERT: h 134 MET cc_start: 0.9291 (mtp) cc_final: 0.8806 (ttt) REVERT: h 201 TRP cc_start: 0.9178 (m-90) cc_final: 0.8754 (m-90) REVERT: i 51 TYR cc_start: 0.9052 (t80) cc_final: 0.8734 (t80) REVERT: i 59 GLN cc_start: 0.9390 (mm110) cc_final: 0.8830 (mm110) REVERT: i 72 PHE cc_start: 0.9666 (t80) cc_final: 0.8769 (t80) REVERT: i 124 MET cc_start: 0.9054 (mtt) cc_final: 0.8720 (mmm) REVERT: j 13 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8449 (tp30) REVERT: j 14 LYS cc_start: 0.9346 (mmpt) cc_final: 0.8578 (mtmm) REVERT: j 29 ARG cc_start: 0.8822 (mpp80) cc_final: 0.8169 (mmt90) REVERT: j 45 ARG cc_start: 0.9390 (tpp-160) cc_final: 0.9109 (tpp-160) REVERT: j 48 PHE cc_start: 0.9347 (p90) cc_final: 0.9101 (p90) REVERT: j 54 ARG cc_start: 0.8598 (mmt90) cc_final: 0.7954 (mpt-90) REVERT: j 71 MET cc_start: 0.7981 (mmm) cc_final: 0.6716 (mmm) REVERT: j 96 MET cc_start: 0.9551 (tpt) cc_final: 0.9263 (tpt) REVERT: j 116 GLU cc_start: 0.9674 (tt0) cc_final: 0.8730 (mt-10) REVERT: j 162 GLU cc_start: 0.9576 (mm-30) cc_final: 0.9259 (pm20) REVERT: k 1 MET cc_start: 0.8889 (mpp) cc_final: 0.8587 (mpp) REVERT: k 21 MET cc_start: 0.9282 (mtm) cc_final: 0.8807 (mtm) REVERT: k 35 LYS cc_start: 0.9693 (ptpp) cc_final: 0.9378 (ptpt) REVERT: k 52 ASN cc_start: 0.9520 (m110) cc_final: 0.9290 (m-40) REVERT: k 80 PHE cc_start: 0.9611 (m-80) cc_final: 0.9081 (m-10) REVERT: k 88 MET cc_start: 0.8600 (tpt) cc_final: 0.8083 (tpt) REVERT: k 89 VAL cc_start: 0.9496 (t) cc_final: 0.9115 (t) REVERT: k 91 ARG cc_start: 0.8977 (ttt90) cc_final: 0.8352 (ttt90) REVERT: m 10 MET cc_start: 0.9711 (tmm) cc_final: 0.9446 (tmm) REVERT: m 38 ASN cc_start: 0.9505 (m-40) cc_final: 0.9212 (m-40) REVERT: m 47 GLU cc_start: 0.9321 (tm-30) cc_final: 0.9027 (tm-30) REVERT: m 96 MET cc_start: 0.8037 (tpt) cc_final: 0.7829 (tpt) REVERT: n 97 GLU cc_start: 0.9583 (mt-10) cc_final: 0.9249 (mp0) REVERT: n 112 GLU cc_start: 0.8475 (tp30) cc_final: 0.8192 (tp30) REVERT: o 52 LEU cc_start: 0.8780 (tp) cc_final: 0.8551 (tp) REVERT: o 99 GLN cc_start: 0.9568 (tt0) cc_final: 0.9180 (mt0) REVERT: p 38 GLN cc_start: 0.9389 (mp10) cc_final: 0.9178 (mp10) REVERT: p 79 ILE cc_start: 0.9313 (mp) cc_final: 0.8590 (mm) REVERT: p 83 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8539 (mm-30) REVERT: p 87 LYS cc_start: 0.9546 (pptt) cc_final: 0.8984 (pptt) REVERT: p 105 PHE cc_start: 0.9673 (m-10) cc_final: 0.9323 (m-80) REVERT: q 20 ASN cc_start: 0.9539 (p0) cc_final: 0.9277 (p0) REVERT: q 35 THR cc_start: 0.8103 (m) cc_final: 0.7849 (m) REVERT: q 38 TYR cc_start: 0.6657 (p90) cc_final: 0.6436 (p90) REVERT: q 40 THR cc_start: 0.8982 (t) cc_final: 0.8615 (p) REVERT: r 13 LYS cc_start: 0.8944 (ptmm) cc_final: 0.8617 (tptt) REVERT: r 27 LYS cc_start: 0.9359 (tppt) cc_final: 0.8874 (tppt) REVERT: r 42 ASP cc_start: 0.9121 (p0) cc_final: 0.8503 (t70) REVERT: r 103 LYS cc_start: 0.8991 (tttt) cc_final: 0.8791 (tttt) REVERT: s 18 ASP cc_start: 0.8902 (m-30) cc_final: 0.8619 (m-30) REVERT: s 65 ARG cc_start: 0.8760 (ttm170) cc_final: 0.8481 (ptp-110) REVERT: s 82 ILE cc_start: 0.9578 (mp) cc_final: 0.9055 (mp) REVERT: s 92 GLU cc_start: 0.8512 (mp0) cc_final: 0.8155 (mp0) REVERT: t 26 GLU cc_start: 0.9514 (mp0) cc_final: 0.9126 (pt0) REVERT: t 37 ASN cc_start: 0.9767 (m110) cc_final: 0.9547 (m110) REVERT: t 62 GLN cc_start: 0.9647 (tt0) cc_final: 0.9344 (pt0) REVERT: t 65 LYS cc_start: 0.9341 (mttt) cc_final: 0.9038 (mmtt) REVERT: t 68 ASP cc_start: 0.9464 (m-30) cc_final: 0.9206 (m-30) REVERT: t 73 LYS cc_start: 0.9177 (mmtm) cc_final: 0.8907 (ptmt) REVERT: u 1 MET cc_start: 0.8872 (pmm) cc_final: 0.7875 (tpt) REVERT: v 53 CYS cc_start: 0.8186 (m) cc_final: 0.7931 (t) REVERT: v 77 ARG cc_start: 0.9341 (ttp80) cc_final: 0.9050 (ttp80) REVERT: v 80 GLU cc_start: 0.9038 (pm20) cc_final: 0.8829 (tm-30) REVERT: w 20 GLU cc_start: 0.8867 (pm20) cc_final: 0.8444 (mp0) REVERT: w 28 THR cc_start: 0.9762 (m) cc_final: 0.9543 (t) REVERT: w 61 ARG cc_start: 0.8681 (mtm-85) cc_final: 0.8292 (mtt90) REVERT: w 65 LEU cc_start: 0.9891 (mm) cc_final: 0.9526 (tp) REVERT: w 67 LEU cc_start: 0.9326 (mt) cc_final: 0.8609 (mt) REVERT: w 70 TYR cc_start: 0.8768 (m-80) cc_final: 0.8495 (m-80) REVERT: y 18 ARG cc_start: 0.9515 (ttp80) cc_final: 0.9028 (ttp-110) REVERT: y 21 ASN cc_start: 0.9659 (m110) cc_final: 0.9347 (m110) REVERT: y 32 ILE cc_start: 0.9862 (mt) cc_final: 0.9191 (pt) REVERT: y 36 TYR cc_start: 0.9535 (m-10) cc_final: 0.9284 (m-80) REVERT: z 19 PHE cc_start: 0.9254 (t80) cc_final: 0.8817 (t80) REVERT: z 24 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8815 (pt0) REVERT: 7 73 MET cc_start: 0.3402 (mmp) cc_final: 0.2723 (mtt) REVERT: 7 147 MET cc_start: 0.9701 (mtm) cc_final: 0.9484 (mtt) REVERT: 7 199 HIS cc_start: 0.9371 (m-70) cc_final: 0.8706 (m-70) REVERT: 7 327 VAL cc_start: 0.9096 (t) cc_final: 0.8590 (t) REVERT: 7 330 ASP cc_start: 0.7604 (m-30) cc_final: 0.7379 (m-30) outliers start: 0 outliers final: 0 residues processed: 1055 average time/residue: 1.3368 time to fit residues: 2422.8706 Evaluate side-chains 864 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 864 time to evaluate : 6.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 612 optimal weight: 0.5980 chunk 985 optimal weight: 6.9990 chunk 601 optimal weight: 6.9990 chunk 467 optimal weight: 7.9990 chunk 685 optimal weight: 20.0000 chunk 1034 optimal weight: 30.0000 chunk 951 optimal weight: 30.0000 chunk 823 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 636 optimal weight: 20.0000 chunk 504 optimal weight: 9.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** P 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 HIS ** e 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 32 ASN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 136 GLN ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 24 HIS t 28 GLN ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 61 GLN y 70 ASN ** 7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 159192 Z= 0.193 Angle : 0.625 13.728 237909 Z= 0.335 Chirality : 0.033 0.313 30260 Planarity : 0.006 0.126 12919 Dihedral : 24.696 179.381 78958 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 31.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.11), residues: 5890 helix: 0.24 (0.11), residues: 2069 sheet: -1.71 (0.15), residues: 1102 loop : -1.14 (0.12), residues: 2719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP v 73 HIS 0.012 0.001 HIS M 13 PHE 0.031 0.002 PHE G 46 TYR 0.025 0.002 TYR r 86 ARG 0.015 0.001 ARG g 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11780 Ramachandran restraints generated. 5890 Oldfield, 0 Emsley, 5890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1076 time to evaluate : 6.377 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ASN cc_start: 0.8424 (t0) cc_final: 0.7804 (t0) REVERT: B 23 GLU cc_start: 0.9351 (pm20) cc_final: 0.9030 (pm20) REVERT: B 79 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8746 (mm-30) REVERT: B 96 TYR cc_start: 0.8652 (m-80) cc_final: 0.7939 (m-80) REVERT: B 115 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8804 (tp-100) REVERT: B 132 MET cc_start: 0.9167 (mtm) cc_final: 0.8492 (mtm) REVERT: B 146 MET cc_start: 0.8214 (mtp) cc_final: 0.7640 (mpp) REVERT: B 161 TYR cc_start: 0.9312 (p90) cc_final: 0.8959 (p90) REVERT: B 181 MET cc_start: 0.9511 (mmp) cc_final: 0.9268 (mmp) REVERT: B 185 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8768 (tm-30) REVERT: B 201 MET cc_start: 0.8943 (ptt) cc_final: 0.8496 (ptt) REVERT: B 236 GLU cc_start: 0.7455 (tp30) cc_final: 0.7035 (tp30) REVERT: B 243 HIS cc_start: 0.9171 (m90) cc_final: 0.8795 (m-70) REVERT: B 264 ASP cc_start: 0.9335 (m-30) cc_final: 0.8999 (m-30) REVERT: B 266 PHE cc_start: 0.9510 (m-80) cc_final: 0.9133 (m-80) REVERT: C 2 ILE cc_start: 0.8248 (pt) cc_final: 0.7674 (mm) REVERT: C 149 ASN cc_start: 0.8464 (t0) cc_final: 0.8224 (t0) REVERT: C 156 PHE cc_start: 0.9286 (m-10) cc_final: 0.8898 (m-80) REVERT: C 160 LYS cc_start: 0.9316 (mttt) cc_final: 0.8877 (mtmm) REVERT: D 1 MET cc_start: 0.9453 (tpt) cc_final: 0.9178 (tpp) REVERT: D 77 ILE cc_start: 0.9583 (pt) cc_final: 0.9328 (mp) REVERT: D 90 GLN cc_start: 0.8952 (pm20) cc_final: 0.8530 (pm20) REVERT: D 100 MET cc_start: 0.9298 (mtp) cc_final: 0.8886 (mtp) REVERT: D 141 MET cc_start: 0.9466 (mpp) cc_final: 0.9195 (mpp) REVERT: D 183 PHE cc_start: 0.9004 (m-10) cc_final: 0.8400 (m-80) REVERT: D 188 MET cc_start: 0.9522 (mmm) cc_final: 0.8855 (mmm) REVERT: D 199 MET cc_start: 0.9651 (mmp) cc_final: 0.9422 (mmm) REVERT: E 26 MET cc_start: 0.9583 (mmm) cc_final: 0.8984 (mmm) REVERT: E 96 MET cc_start: 0.9174 (ttm) cc_final: 0.8765 (ttt) REVERT: E 120 LYS cc_start: 0.9622 (tptp) cc_final: 0.9320 (tptp) REVERT: E 138 PHE cc_start: 0.8574 (t80) cc_final: 0.8350 (t80) REVERT: E 143 TYR cc_start: 0.9327 (t80) cc_final: 0.9105 (t80) REVERT: E 175 PHE cc_start: 0.9127 (t80) cc_final: 0.8763 (t80) REVERT: F 60 ASP cc_start: 0.9141 (p0) cc_final: 0.8499 (p0) REVERT: F 149 ARG cc_start: 0.9584 (ttt-90) cc_final: 0.9269 (ptm160) REVERT: G 1 MET cc_start: 0.9369 (tpp) cc_final: 0.8936 (tmm) REVERT: G 91 PHE cc_start: 0.8254 (m-80) cc_final: 0.7962 (m-80) REVERT: G 101 ASP cc_start: 0.9300 (m-30) cc_final: 0.9033 (m-30) REVERT: G 132 PHE cc_start: 0.9265 (m-10) cc_final: 0.8394 (m-80) REVERT: J 14 ASP cc_start: 0.8403 (t70) cc_final: 0.8086 (t70) REVERT: J 67 ASN cc_start: 0.9636 (m-40) cc_final: 0.9315 (p0) REVERT: J 71 ASP cc_start: 0.9552 (p0) cc_final: 0.8807 (p0) REVERT: J 102 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8031 (mt-10) REVERT: J 118 MET cc_start: 0.8575 (tpp) cc_final: 0.8356 (tpp) REVERT: K 1 MET cc_start: 0.8631 (ttp) cc_final: 0.8367 (ppp) REVERT: K 4 GLU cc_start: 0.8719 (mp0) cc_final: 0.8362 (mp0) REVERT: K 7 MET cc_start: 0.9132 (mmm) cc_final: 0.8302 (mmp) REVERT: K 9 ASN cc_start: 0.9826 (m-40) cc_final: 0.9538 (m-40) REVERT: K 20 MET cc_start: 0.8573 (ttm) cc_final: 0.6703 (ttm) REVERT: K 58 LEU cc_start: 0.9229 (pt) cc_final: 0.8977 (pt) REVERT: L 23 ILE cc_start: 0.9009 (mt) cc_final: 0.8323 (mt) REVERT: L 51 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8289 (mt-10) REVERT: L 67 THR cc_start: 0.8886 (m) cc_final: 0.8460 (p) REVERT: M 12 MET cc_start: 0.8500 (mmm) cc_final: 0.8202 (mmp) REVERT: M 82 MET cc_start: 0.8645 (tpp) cc_final: 0.7246 (mmm) REVERT: M 91 TYR cc_start: 0.8867 (p90) cc_final: 0.8650 (p90) REVERT: M 112 LEU cc_start: 0.9668 (tp) cc_final: 0.9262 (tp) REVERT: M 136 MET cc_start: 0.7943 (ptt) cc_final: 0.7068 (ptt) REVERT: N 5 LYS cc_start: 0.9396 (mttt) cc_final: 0.9033 (mmmm) REVERT: N 20 MET cc_start: 0.8856 (ttp) cc_final: 0.8416 (ttp) REVERT: N 21 PHE cc_start: 0.9160 (m-80) cc_final: 0.8891 (m-80) REVERT: N 24 MET cc_start: 0.8791 (ttm) cc_final: 0.8462 (ttm) REVERT: N 32 GLU cc_start: 0.9333 (mt-10) cc_final: 0.9051 (mp0) REVERT: N 43 GLU cc_start: 0.9511 (tp30) cc_final: 0.8728 (tp30) REVERT: N 47 VAL cc_start: 0.8570 (t) cc_final: 0.7792 (t) REVERT: N 87 PHE cc_start: 0.8655 (m-80) cc_final: 0.7426 (m-80) REVERT: N 117 ASP cc_start: 0.8638 (m-30) cc_final: 0.8434 (m-30) REVERT: O 69 ASP cc_start: 0.9685 (m-30) cc_final: 0.9399 (t0) REVERT: O 88 LYS cc_start: 0.9606 (tmmt) cc_final: 0.9252 (tmtt) REVERT: O 89 ASP cc_start: 0.8582 (t70) cc_final: 0.8176 (t70) REVERT: P 16 ASP cc_start: 0.9539 (p0) cc_final: 0.9327 (p0) REVERT: Q 25 TYR cc_start: 0.8523 (t80) cc_final: 0.8254 (t80) REVERT: Q 59 GLN cc_start: 0.9530 (tt0) cc_final: 0.9077 (mm-40) REVERT: R 18 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8574 (tm-30) REVERT: R 48 LYS cc_start: 0.9525 (tmtt) cc_final: 0.9256 (tmtt) REVERT: R 85 LYS cc_start: 0.8845 (tmtt) cc_final: 0.8064 (tptt) REVERT: R 86 GLN cc_start: 0.8951 (mm110) cc_final: 0.8490 (pp30) REVERT: R 95 ASP cc_start: 0.9332 (m-30) cc_final: 0.8988 (p0) REVERT: R 98 ILE cc_start: 0.9788 (mm) cc_final: 0.9179 (tt) REVERT: S 78 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8531 (mt-10) REVERT: S 84 ARG cc_start: 0.9196 (mmt-90) cc_final: 0.8801 (mmt90) REVERT: S 92 ARG cc_start: 0.8744 (ptt180) cc_final: 0.8510 (ptt-90) REVERT: S 97 LEU cc_start: 0.9437 (mm) cc_final: 0.9049 (tp) REVERT: T 11 LEU cc_start: 0.8888 (mm) cc_final: 0.8363 (tp) REVERT: T 77 ARG cc_start: 0.8586 (mmm160) cc_final: 0.8384 (mmm160) REVERT: T 87 LEU cc_start: 0.9743 (mp) cc_final: 0.9452 (mp) REVERT: V 48 MET cc_start: 0.9244 (mmm) cc_final: 0.8296 (mmm) REVERT: V 50 MET cc_start: 0.9503 (mtm) cc_final: 0.9181 (ptp) REVERT: V 59 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8435 (tt0) REVERT: W 36 ILE cc_start: 0.9017 (mm) cc_final: 0.8740 (mm) REVERT: W 56 ASP cc_start: 0.9190 (p0) cc_final: 0.8928 (m-30) REVERT: X 14 THR cc_start: 0.8970 (t) cc_final: 0.8580 (m) REVERT: X 38 PHE cc_start: 0.9092 (m-80) cc_final: 0.8436 (m-80) REVERT: X 47 VAL cc_start: 0.9584 (t) cc_final: 0.9222 (m) REVERT: X 56 MET cc_start: 0.9435 (mtp) cc_final: 0.8629 (ttm) REVERT: X 60 ASP cc_start: 0.9051 (m-30) cc_final: 0.8830 (m-30) REVERT: X 70 GLU cc_start: 0.9365 (mp0) cc_final: 0.9158 (mp0) REVERT: Y 17 GLU cc_start: 0.9390 (tm-30) cc_final: 0.9152 (tm-30) REVERT: Y 30 MET cc_start: 0.8801 (mmp) cc_final: 0.8157 (mmp) REVERT: Z 19 LYS cc_start: 0.9309 (mmmt) cc_final: 0.9034 (mmtt) REVERT: Z 21 LYS cc_start: 0.9344 (mttt) cc_final: 0.8852 (mttm) REVERT: Z 47 MET cc_start: 0.9367 (mtt) cc_final: 0.9070 (mtt) REVERT: Z 54 MET cc_start: 0.9290 (ptm) cc_final: 0.8394 (ttt) REVERT: b 5 GLN cc_start: 0.8873 (mt0) cc_final: 0.8328 (mt0) REVERT: b 7 LYS cc_start: 0.9089 (tptm) cc_final: 0.8789 (tptp) REVERT: b 46 ASP cc_start: 0.9347 (t0) cc_final: 0.9008 (t0) REVERT: c 8 LYS cc_start: 0.9107 (pttt) cc_final: 0.8752 (pttt) REVERT: c 35 GLU cc_start: 0.9632 (mt-10) cc_final: 0.9021 (mp0) REVERT: d 25 LYS cc_start: 0.9162 (tmmt) cc_final: 0.8788 (pptt) REVERT: d 29 GLN cc_start: 0.9153 (mp10) cc_final: 0.8928 (mp10) REVERT: e 14 PHE cc_start: 0.9781 (m-80) cc_final: 0.9533 (m-80) REVERT: f 13 ASN cc_start: 0.9498 (m-40) cc_final: 0.8800 (t0) REVERT: f 22 VAL cc_start: 0.9092 (t) cc_final: 0.8873 (p) REVERT: g 27 MET cc_start: 0.9039 (mmm) cc_final: 0.8708 (mmm) REVERT: g 96 TRP cc_start: 0.8064 (t-100) cc_final: 0.7387 (t-100) REVERT: g 100 MET cc_start: 0.9622 (ttm) cc_final: 0.9138 (mtp) REVERT: g 120 GLN cc_start: 0.9309 (tt0) cc_final: 0.8919 (tp40) REVERT: g 136 MET cc_start: 0.9816 (mmp) cc_final: 0.9574 (mtp) REVERT: g 142 GLU cc_start: 0.9423 (tt0) cc_final: 0.9192 (tp30) REVERT: h 8 ASN cc_start: 0.8662 (m110) cc_final: 0.8140 (m-40) REVERT: h 19 ASN cc_start: 0.9290 (m-40) cc_final: 0.8199 (p0) REVERT: h 37 PHE cc_start: 0.9592 (t80) cc_final: 0.9346 (t80) REVERT: h 42 TYR cc_start: 0.9430 (t80) cc_final: 0.9221 (t80) REVERT: h 51 SER cc_start: 0.9639 (m) cc_final: 0.9328 (p) REVERT: h 110 GLU cc_start: 0.9190 (pm20) cc_final: 0.8559 (tm-30) REVERT: h 123 GLN cc_start: 0.9632 (mt0) cc_final: 0.9127 (mt0) REVERT: h 134 MET cc_start: 0.9400 (mtp) cc_final: 0.8912 (ttt) REVERT: h 201 TRP cc_start: 0.9204 (m-90) cc_final: 0.8740 (m-90) REVERT: i 51 TYR cc_start: 0.9034 (t80) cc_final: 0.8682 (t80) REVERT: i 59 GLN cc_start: 0.9383 (mm110) cc_final: 0.8838 (mm110) REVERT: i 72 PHE cc_start: 0.9679 (t80) cc_final: 0.8802 (t80) REVERT: i 124 MET cc_start: 0.9017 (mtt) cc_final: 0.8664 (mmm) REVERT: j 13 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8500 (tp30) REVERT: j 14 LYS cc_start: 0.9316 (mmpt) cc_final: 0.8778 (mttm) REVERT: j 45 ARG cc_start: 0.9387 (tpp-160) cc_final: 0.9172 (tpp-160) REVERT: j 54 ARG cc_start: 0.8612 (mmt90) cc_final: 0.8033 (mpt-90) REVERT: j 64 MET cc_start: 0.9423 (mpp) cc_final: 0.9193 (mpp) REVERT: j 71 MET cc_start: 0.7729 (mmm) cc_final: 0.7143 (mmt) REVERT: j 96 MET cc_start: 0.9392 (tpt) cc_final: 0.9110 (tpt) REVERT: j 116 GLU cc_start: 0.9704 (tt0) cc_final: 0.8666 (mt-10) REVERT: k 1 MET cc_start: 0.8982 (mpp) cc_final: 0.8702 (mpp) REVERT: k 21 MET cc_start: 0.9048 (mtm) cc_final: 0.8518 (mtm) REVERT: k 35 LYS cc_start: 0.9691 (ptpp) cc_final: 0.9340 (ptpt) REVERT: k 80 PHE cc_start: 0.9612 (m-80) cc_final: 0.9073 (m-10) REVERT: k 90 MET cc_start: 0.8368 (mpp) cc_final: 0.8135 (mpp) REVERT: k 91 ARG cc_start: 0.9018 (ttt90) cc_final: 0.8385 (ttt90) REVERT: m 10 MET cc_start: 0.9670 (tmm) cc_final: 0.9336 (tmm) REVERT: m 14 ILE cc_start: 0.9501 (mm) cc_final: 0.9288 (mm) REVERT: m 27 MET cc_start: 0.8775 (ptp) cc_final: 0.8456 (ptp) REVERT: m 38 ASN cc_start: 0.9516 (m-40) cc_final: 0.9253 (m-40) REVERT: m 47 GLU cc_start: 0.9336 (tm-30) cc_final: 0.9028 (tm-30) REVERT: m 96 MET cc_start: 0.7991 (tpt) cc_final: 0.7717 (tpt) REVERT: n 27 LYS cc_start: 0.9515 (mtmm) cc_final: 0.9200 (mttp) REVERT: n 97 GLU cc_start: 0.9570 (mt-10) cc_final: 0.9255 (mp0) REVERT: n 112 GLU cc_start: 0.8533 (tp30) cc_final: 0.8212 (tp30) REVERT: o 10 LEU cc_start: 0.9617 (mm) cc_final: 0.9384 (mm) REVERT: o 52 LEU cc_start: 0.8803 (tp) cc_final: 0.8550 (tp) REVERT: o 99 GLN cc_start: 0.9619 (tt0) cc_final: 0.9240 (mt0) REVERT: p 38 GLN cc_start: 0.9372 (mp10) cc_final: 0.9143 (mp10) REVERT: p 56 ARG cc_start: 0.9341 (mpp80) cc_final: 0.8928 (mtm110) REVERT: p 79 ILE cc_start: 0.9292 (mp) cc_final: 0.8821 (mp) REVERT: p 85 MET cc_start: 0.8937 (ppp) cc_final: 0.8728 (ppp) REVERT: p 87 LYS cc_start: 0.9567 (pptt) cc_final: 0.9096 (pptt) REVERT: p 105 PHE cc_start: 0.9686 (m-10) cc_final: 0.9299 (m-80) REVERT: q 20 ASN cc_start: 0.9546 (p0) cc_final: 0.9292 (p0) REVERT: q 38 TYR cc_start: 0.6911 (p90) cc_final: 0.6687 (p90) REVERT: q 40 THR cc_start: 0.8960 (t) cc_final: 0.8602 (p) REVERT: r 13 LYS cc_start: 0.8935 (ptmm) cc_final: 0.8604 (tptt) REVERT: r 42 ASP cc_start: 0.9131 (p0) cc_final: 0.8542 (t70) REVERT: s 18 ASP cc_start: 0.8894 (m-30) cc_final: 0.8613 (m-30) REVERT: s 40 ASP cc_start: 0.9808 (t70) cc_final: 0.9549 (t70) REVERT: s 65 ARG cc_start: 0.8709 (ttm170) cc_final: 0.8479 (ptp-110) REVERT: s 82 ILE cc_start: 0.9597 (mp) cc_final: 0.9220 (mp) REVERT: s 92 GLU cc_start: 0.8646 (mp0) cc_final: 0.8348 (mp0) REVERT: t 26 GLU cc_start: 0.9510 (mp0) cc_final: 0.9129 (pt0) REVERT: t 37 ASN cc_start: 0.9761 (m110) cc_final: 0.9537 (m110) REVERT: t 62 GLN cc_start: 0.9631 (tt0) cc_final: 0.9345 (pt0) REVERT: t 65 LYS cc_start: 0.9346 (mttt) cc_final: 0.9076 (mmtt) REVERT: t 71 LYS cc_start: 0.9453 (tptp) cc_final: 0.9093 (tppt) REVERT: t 73 LYS cc_start: 0.9089 (mmtm) cc_final: 0.8846 (ptmt) REVERT: u 1 MET cc_start: 0.8843 (pmm) cc_final: 0.7890 (tpt) REVERT: v 30 LYS cc_start: 0.9623 (tmmt) cc_final: 0.9405 (tmtt) REVERT: w 31 ASN cc_start: 0.9349 (m110) cc_final: 0.9119 (m110) REVERT: w 61 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.8337 (mtt90) REVERT: w 65 LEU cc_start: 0.9882 (mm) cc_final: 0.9546 (tp) REVERT: w 67 LEU cc_start: 0.9329 (mt) cc_final: 0.8631 (mt) REVERT: w 70 TYR cc_start: 0.8814 (m-80) cc_final: 0.8545 (m-80) REVERT: x 28 LYS cc_start: 0.9031 (tptt) cc_final: 0.8725 (tppt) REVERT: y 21 ASN cc_start: 0.9685 (m110) cc_final: 0.9359 (m110) REVERT: y 32 ILE cc_start: 0.9866 (mt) cc_final: 0.9201 (pt) REVERT: y 36 TYR cc_start: 0.9537 (m-10) cc_final: 0.9314 (m-80) REVERT: y 82 GLN cc_start: 0.9642 (mp10) cc_final: 0.9355 (mp10) REVERT: z 19 PHE cc_start: 0.9272 (t80) cc_final: 0.8848 (t80) REVERT: z 24 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8797 (pt0) REVERT: 7 73 MET cc_start: 0.3456 (mmp) cc_final: 0.2649 (mtt) REVERT: 7 147 MET cc_start: 0.9694 (mtm) cc_final: 0.9474 (mtt) REVERT: 7 199 HIS cc_start: 0.9358 (m-70) cc_final: 0.8628 (m-70) REVERT: 7 327 VAL cc_start: 0.9102 (t) cc_final: 0.8597 (t) REVERT: 7 330 ASP cc_start: 0.7605 (m-30) cc_final: 0.7355 (m-30) REVERT: 7 358 GLU cc_start: 0.9666 (tp30) cc_final: 0.9455 (tp30) outliers start: 0 outliers final: 0 residues processed: 1076 average time/residue: 1.3401 time to fit residues: 2478.0687 Evaluate side-chains 867 residues out of total 4913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 867 time to evaluate : 6.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 654 optimal weight: 9.9990 chunk 877 optimal weight: 7.9990 chunk 252 optimal weight: 30.0000 chunk 759 optimal weight: 10.0000 chunk 121 optimal weight: 30.0000 chunk 228 optimal weight: 30.0000 chunk 824 optimal weight: 2.9990 chunk 345 optimal weight: 30.0000 chunk 846 optimal weight: 20.0000 chunk 104 optimal weight: 30.0000 chunk 151 optimal weight: 30.0000 overall best weight: 10.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 HIS ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 ASN O 38 GLN ** P 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 50 ASN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 32 ASN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 136 GLN ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 24 HIS ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 70 ASN ** 7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 97 ASN ** 7 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.028549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.023297 restraints weight = 1856701.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.024140 restraints weight = 789234.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.024637 restraints weight = 450687.574| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 159192 Z= 0.280 Angle : 0.674 13.560 237909 Z= 0.358 Chirality : 0.035 0.344 30260 Planarity : 0.006 0.128 12919 Dihedral : 24.757 179.282 78958 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 38.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.11), residues: 5890 helix: 0.11 (0.11), residues: 2058 sheet: -1.76 (0.15), residues: 1095 loop : -1.19 (0.12), residues: 2737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP v 73 HIS 0.008 0.001 HIS M 13 PHE 0.029 0.002 PHE G 46 TYR 0.022 0.002 TYR n 6 ARG 0.015 0.001 ARG o 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37462.07 seconds wall clock time: 661 minutes 25.85 seconds (39685.85 seconds total)