Starting phenix.real_space_refine on Tue Apr 16 13:03:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ore_20173/04_2024/6ore_20173_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ore_20173/04_2024/6ore_20173.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ore_20173/04_2024/6ore_20173_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ore_20173/04_2024/6ore_20173_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ore_20173/04_2024/6ore_20173_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ore_20173/04_2024/6ore_20173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ore_20173/04_2024/6ore_20173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ore_20173/04_2024/6ore_20173_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ore_20173/04_2024/6ore_20173_updated.pdb" } resolution = 2.9 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= 0.004 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 2 6.06 5 P 4642 5.49 5 Mg 436 5.21 5 S 150 5.16 5 C 72452 2.51 5 N 26904 2.21 5 O 40188 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 "D ARG 170": "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 "O PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P ARG 89": "NH1" <-> "NH2" 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 "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "V ARG 19": "NH1" <-> "NH2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "a ARG 56": "NH1" <-> "NH2" Residue "a ARG 63": "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 PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 144774 Number of models: 1 Model: "" Number of chains: 67 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': 165, 'rna3p': 16, 'rna3p_pur': 1378, 'rna3p_pyr': 1049} Link IDs: {'rna2p': 459, 'rna3p': 2443} 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': 117, 'rna2p_pyr': 89, 'rna3p': 10, 'rna3p_pur': 752, 'rna3p_pyr': 564} Link IDs: {'rna2p': 206, 'rna3p': 1327} 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: "4" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 7} Link IDs: {'rna3p': 8} 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: "A" 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: "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: "a" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} 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: "1" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 290 Unusual residues: {' MG': 290} Classifications: {'undetermined': 290} Link IDs: {None: 289} Chain: "2" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 126 Unusual residues: {' MG': 126} Classifications: {'undetermined': 126} Link IDs: {None: 125} 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: "5" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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} Chain: "r" 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 A0HN5 SG CYS a 16 121.850 176.952 195.612 1.00160.13 S ATOM A0HNH SG CYS a 18 121.624 176.510 200.037 1.00161.32 S ATOM A0HRF SG CYS a 37 123.831 174.086 198.235 1.00154.27 S ATOM A0HS0 SG CYS a 40 120.322 174.167 197.312 1.00156.06 S ATOM A0JD1 SG CYS f 11 125.353 69.834 164.386 1.00109.84 S ATOM A0JDQ SG CYS f 14 128.686 70.132 162.986 1.00108.28 S ATOM A0JGL SG CYS f 27 125.498 67.063 162.046 1.00108.49 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG 13145 " occ=0.50 Time building chain proxies: 55.32, per 1000 atoms: 0.38 Number of scatterers: 144774 At special positions: 0 Unit cell: (273.377, 244.926, 235.03, 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 2 29.99 S 150 16.00 P 4642 15.00 Mg 436 11.99 O 40188 8.00 N 26904 7.00 C 72452 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: 63.98 Conformation dependent library (CDL) restraints added in 6.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 101 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 16 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 37 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 18 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 40 " pdb=" ZN f 102 " pdb="ZN ZN f 102 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 11 " Number of angles added : 9 11212 Ramachandran restraints generated. 5606 Oldfield, 0 Emsley, 5606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10490 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: 170 helices and 73 sheets defined 38.6% alpha, 19.9% beta 1509 base pairs and 2630 stacking pairs defined. Time for finding SS restraints: 75.90 Creating SS restraints... Processing helix chain 'B' and resid 10 through 17 removed outlier: 7.598A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.793A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 5.836A 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 removed outlier: 3.602A pdb=" N ILE B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Proline residue: B 136 - end of helix No H-bonds generated for 'chain 'B' and resid 131 through 136' Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.085A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 268 removed outlier: 4.026A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 268' Processing helix chain 'B' and resid 197 through 202 removed outlier: 4.312A pdb=" N MET B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 6.110A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.677A pdb=" N ALA C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 removed outlier: 4.199A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.184A 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 15 through 20 Processing helix chain 'D' and resid 24 through 41 removed outlier: 3.771A pdb=" N ARG D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 removed outlier: 3.867A pdb=" N SER D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 154 through 163 removed outlier: 4.563A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.521A pdb=" N LEU D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 removed outlier: 3.604A pdb=" N LYS D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 removed outlier: 3.688A pdb=" N ASP E 10 " --> pdb=" O ASP E 6 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 47 removed outlier: 4.415A pdb=" N ASP E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 42 through 47' Processing helix chain 'E' and resid 48 through 62 removed outlier: 3.893A pdb=" N GLY E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 3.539A pdb=" N ILE E 104 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 5.333A 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 142 through 147 removed outlier: 3.515A pdb=" N VAL E 146 " --> pdb=" O ASP E 142 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASP E 147 " --> pdb=" O TYR E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 142 through 147' Processing helix chain 'E' and resid 162 through 174 removed outlier: 4.471A pdb=" N GLY E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG E 167 " --> pdb=" O ASP E 163 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.604A 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 8 removed outlier: 3.802A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Proline residue: F 8 - end of helix Processing helix chain 'F' and resid 60 through 81 removed outlier: 3.631A pdb=" N LEU F 72 " --> pdb=" O ALA F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.693A pdb=" N TYR F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 40 through 50 removed outlier: 3.609A pdb=" N GLU G 45 " --> pdb=" O LYS G 41 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA G 49 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG G 50 " --> pdb=" O PHE G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 74 removed outlier: 4.645A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA G 74 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 removed outlier: 3.551A pdb=" N GLY G 107 " --> pdb=" O VAL G 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.974A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.467A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.638A 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: 3.545A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 removed outlier: 3.529A pdb=" N ILE K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 42 removed outlier: 4.096A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' 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: 3.916A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.597A 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: 3.993A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.965A 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 removed outlier: 3.745A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.370A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.862A 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 Processing helix chain 'N' and resid 38 through 57 removed outlier: 3.682A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.794A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 3.528A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 4.618A 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: 3.526A pdb=" N ILE O 8 " --> pdb=" O LYS O 4 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG O 16 " --> pdb=" O THR O 12 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY O 22 " --> pdb=" O LEU O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 5.130A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 2 through 14 removed outlier: 3.630A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LYS P 14 " --> pdb=" O GLN P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 104 removed outlier: 3.916A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 99 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.591A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.892A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 4.101A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 3.652A pdb=" N ASN Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY Q 82 " --> pdb=" O LYS Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 102 removed outlier: 3.631A pdb=" N VAL Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.642A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 4.002A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.876A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS S 49 " --> pdb=" O VAL S 45 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 3.742A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 removed outlier: 3.548A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 50 Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.776A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.063A 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: 3.552A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.527A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 3.981A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 Processing helix chain 'X' and resid 64 through 75 Processing helix chain 'Y' and resid 2 through 10 removed outlier: 3.680A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N SER Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 35 removed outlier: 3.579A pdb=" N ARG Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 61 removed outlier: 4.713A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 Processing helix chain 'a' and resid 44 through 51 removed outlier: 5.807A pdb=" N GLN a 48 " --> pdb=" O PHE a 44 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG a 49 " --> pdb=" O THR a 45 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL a 51 " --> pdb=" O LYS a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 55 through 65 removed outlier: 3.827A pdb=" N ARG a 63 " --> pdb=" O ARG a 59 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE a 64 " --> pdb=" O PHE a 60 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASN a 65 " --> pdb=" O ASN a 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 19 removed outlier: 4.924A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 25 removed outlier: 4.414A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 38 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.704A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 37 removed outlier: 4.950A pdb=" N LYS e 36 " --> pdb=" O ILE e 32 " (cutoff:3.500A) removed outlier: 5.948A 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: 3.608A 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 51 through 63 removed outlier: 4.677A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL e 58 " --> pdb=" O ASP e 54 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE e 59 " --> pdb=" O LEU e 55 " (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 42 through 64 Proline residue: g 48 - end of helix removed outlier: 3.517A pdb=" N GLU g 56 " --> pdb=" O GLU g 52 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG g 63 " --> pdb=" O LYS g 59 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 73 through 88 removed outlier: 6.004A pdb=" N SER g 77 " --> pdb=" O LYS g 73 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS g 81 " --> pdb=" O SER g 77 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS g 87 " --> pdb=" O ALA g 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 122 removed outlier: 3.960A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER g 110 " --> pdb=" O THR g 106 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG g 113 " --> pdb=" O GLN g 109 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 Processing helix chain 'g' and resid 165 through 170 removed outlier: 4.377A pdb=" N HIS g 170 " --> pdb=" O ALA g 166 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 180 Processing helix chain 'g' and resid 206 through 227 removed outlier: 3.536A pdb=" N ALA g 216 " --> pdb=" O LEU g 212 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR g 220 " --> pdb=" O ALA g 216 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG g 222 " --> pdb=" O ALA g 218 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN g 227 " --> pdb=" O GLU g 223 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 12 removed outlier: 3.760A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 48 removed outlier: 3.691A pdb=" N ASN h 32 " --> pdb=" O GLU h 28 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL h 39 " --> pdb=" O SER h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 removed outlier: 4.182A pdb=" N VAL h 76 " --> pdb=" O ARG h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 82 through 96 removed outlier: 3.850A pdb=" N VAL h 90 " --> pdb=" O LYS h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 4.226A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 5.872A 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: 3.526A pdb=" N ARG h 126 " --> pdb=" O SER h 122 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 145 removed outlier: 3.673A pdb=" N ALA h 141 " --> pdb=" O ALA h 137 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.050A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 removed outlier: 3.704A pdb=" N LYS i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 66 Processing helix chain 'i' and resid 68 through 83 removed outlier: 5.413A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 3.586A 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: 3.888A pdb=" N LYS i 121 " --> pdb=" O LEU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 4.058A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU i 163 " --> pdb=" O LEU i 159 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN i 164 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG i 165 " --> pdb=" O LEU i 161 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 3.783A pdb=" N LEU i 191 " --> pdb=" O GLU i 187 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 187 through 192' Processing helix chain 'i' and resid 196 through 206 removed outlier: 4.023A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER i 205 " --> pdb=" O VAL i 201 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS i 206 " --> pdb=" O GLU i 202 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 3.521A pdb=" N GLN j 61 " --> pdb=" O PRO j 57 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG j 69 " --> pdb=" O GLU j 65 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 3.658A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL j 117 " --> pdb=" O ALA j 113 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY j 119 " --> pdb=" O LEU j 115 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 148 removed outlier: 3.836A pdb=" N ASN j 146 " --> pdb=" O ASP j 142 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET j 147 " --> pdb=" O GLY j 143 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASN j 148 " --> pdb=" O LEU j 144 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 Processing helix chain 'j' and resid 160 through 165 removed outlier: 3.769A pdb=" N ILE j 164 " --> pdb=" O SER j 160 " (cutoff:3.500A) Processing helix chain 'k' and resid 11 through 17 removed outlier: 3.702A pdb=" N SER k 15 " --> pdb=" O HIS k 11 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLU k 16 " --> pdb=" O PRO k 12 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLN k 17 " --> pdb=" O ASP k 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 11 through 17' Processing helix chain 'k' and resid 18 through 33 removed outlier: 3.674A pdb=" N ARG k 24 " --> pdb=" O GLY k 20 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 81 removed outlier: 3.796A pdb=" N ILE k 71 " --> pdb=" O PRO k 67 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR k 76 " --> pdb=" O ASP k 72 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 31 removed outlier: 3.625A pdb=" N ALA l 24 " --> pdb=" O SER l 20 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.572A pdb=" N ALA l 39 " --> pdb=" O LYS l 35 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER l 54 " --> pdb=" O LEU l 50 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 3.573A pdb=" N ALA l 65 " --> pdb=" O ALA l 61 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN l 68 " --> pdb=" O VAL l 64 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 112 removed outlier: 3.715A pdb=" N LYS l 110 " --> pdb=" O GLU l 106 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY l 112 " --> pdb=" O ALA l 108 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 Processing helix chain 'l' and resid 132 through 149 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 30 through 44 removed outlier: 3.827A pdb=" N ALA m 35 " --> pdb=" O LYS m 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 112 through 120 Processing helix chain 'n' and resid 34 through 40 removed outlier: 4.973A pdb=" N GLY n 40 " --> pdb=" O GLU n 36 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 56 removed outlier: 3.582A pdb=" N VAL n 48 " --> pdb=" O ALA n 44 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 51 - end of helix removed outlier: 4.652A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 92 removed outlier: 3.759A pdb=" N GLU n 89 " --> pdb=" O ARG n 85 " (cutoff:3.500A) Processing helix chain 'n' and resid 93 through 102 removed outlier: 4.834A pdb=" N GLU n 97 " --> pdb=" O SER n 93 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS n 100 " --> pdb=" O SER n 96 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 33 removed outlier: 3.560A pdb=" N GLU o 24 " --> pdb=" O GLN o 20 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU o 27 " --> pdb=" O ALA o 23 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR o 28 " --> pdb=" O GLU o 24 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA o 29 " --> pdb=" O ILE o 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 91 removed outlier: 3.837A pdb=" N VAL o 84 " --> pdb=" O THR o 80 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP o 85 " --> pdb=" O GLU o 81 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU o 87 " --> pdb=" O THR o 83 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 4.589A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 3.712A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.508A 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 76 removed outlier: 3.794A pdb=" N GLU p 68 " --> pdb=" O GLN p 64 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL p 74 " --> pdb=" O CYS p 70 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS p 75 " --> pdb=" O ALA p 71 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLU p 76 " --> pdb=" O ASP p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 94 through 104 removed outlier: 3.612A pdb=" N ARG p 98 " --> pdb=" O GLU p 94 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA p 99 " --> pdb=" O SER p 95 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 10 Processing helix chain 'q' and resid 113 through 118 removed outlier: 4.150A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY q 118 " --> pdb=" O ARG q 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 113 through 118' Processing helix chain 'r' and resid 14 through 22 removed outlier: 3.608A pdb=" N THR r 20 " --> pdb=" O VAL r 16 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 removed outlier: 3.526A pdb=" N LYS r 31 " --> pdb=" O LYS r 27 " (cutoff:3.500A) Processing helix chain 'r' and resid 49 through 64 removed outlier: 4.279A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 3.774A pdb=" N ARG r 70 " --> pdb=" O GLU r 66 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG r 71 " --> pdb=" O GLY r 67 " (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: 3.601A pdb=" N ALA s 17 " --> pdb=" O ARG s 13 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE s 21 " --> pdb=" O ALA s 17 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 33 Processing helix chain 's' and resid 37 through 52 removed outlier: 3.593A pdb=" N GLN s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU s 51 " --> pdb=" O LYS s 47 " (cutoff:3.500A) Proline residue: s 52 - end of helix Processing helix chain 's' and resid 80 through 91 removed outlier: 3.683A pdb=" N ARG s 85 " --> pdb=" O ARG s 81 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG s 90 " --> pdb=" O GLU s 86 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 16 removed outlier: 3.557A pdb=" N GLU t 14 " --> pdb=" O LYS t 10 " (cutoff:3.500A) Processing helix chain 't' and resid 24 through 43 removed outlier: 4.844A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 3.945A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG t 72 " --> pdb=" O ASP t 68 " (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 82 removed outlier: 3.589A pdb=" N ALA u 73 " --> pdb=" O ASP u 69 " (cutoff:3.500A) Processing helix chain 'w' and resid 11 through 17 removed outlier: 3.612A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 34 removed outlier: 3.959A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 removed outlier: 3.505A pdb=" N THR w 45 " --> pdb=" O PRO w 41 " (cutoff:3.500A) Processing helix chain 'w' and resid 48 through 66 removed outlier: 3.596A pdb=" N ARG w 61 " --> pdb=" O ARG w 57 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR w 64 " --> pdb=" O LYS w 60 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 removed outlier: 3.544A pdb=" N LYS x 18 " --> pdb=" O HIS x 14 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU x 24 " --> pdb=" O GLU x 20 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.462A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 3.905A 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 'y' and resid 4 through 41 Processing helix chain 'y' and resid 44 through 65 Proline residue: y 56 - end of helix removed outlier: 4.059A pdb=" N GLN y 61 " --> pdb=" O ILE y 57 " (cutoff:3.500A) Processing helix chain 'y' and resid 68 through 87 removed outlier: 3.562A pdb=" N LEU y 79 " --> pdb=" O HIS y 75 " (cutoff:3.500A) removed outlier: 5.065A 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: 4.968A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 69 removed outlier: 3.698A pdb=" N LYS z 58 " --> pdb=" O LYS z 54 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS z 59 " --> pdb=" O ARG z 55 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG z 67 " --> pdb=" O GLU z 63 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR z 68 " --> pdb=" O ASN z 64 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG z 69 " --> pdb=" O ALA z 65 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 80 through 83 removed outlier: 3.540A pdb=" N ARG B 80 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.461A 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: 4.264A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.096A 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 96 removed outlier: 5.553A pdb=" N ASN B 90 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 3 through 6 removed outlier: 4.090A pdb=" N GLU C 168 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 10 through 16 removed outlier: 3.612A pdb=" N GLY C 10 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 189 " --> pdb=" O THR C 25 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 36 through 40 removed outlier: 3.996A pdb=" N LEU C 40 " --> pdb=" O TYR C 45 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TYR C 45 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.837A 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: 5.675A 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: 6.477A 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: 4.021A pdb=" N MET D 1 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 4.398A 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: 5.544A pdb=" N ARG D 117 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 65 through 69 removed outlier: 5.215A pdb=" N ILE E 85 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY E 39 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY E 151 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 152 " --> pdb=" O VAL E 132 " (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 41 through 45 Processing sheet with id= 14, first strand: chain 'F' and resid 82 through 89 removed outlier: 5.859A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 94 through 98 Processing sheet with id= 16, first strand: chain 'G' and resid 17 through 20 removed outlier: 4.941A pdb=" N ASP G 17 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL G 3 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS G 35 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 76 through 83 removed outlier: 6.237A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE G 143 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL G 78 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA G 140 " --> pdb=" O PHE G 132 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.849A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'J' and resid 74 through 78 removed outlier: 3.536A pdb=" N HIS J 76 " --> pdb=" O LYS J 85 " (cutoff:3.500A) removed outlier: 7.100A 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: 4.898A pdb=" N ASP K 56 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.931A 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: 3.749A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.545A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'M' and resid 73 through 76 removed outlier: 6.846A pdb=" N ILE M 73 " --> pdb=" O GLU M 90 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.868A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.190A pdb=" N ARG N 103 " --> pdb=" O ASN N 107 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLY N 101 " --> pdb=" O PRO N 109 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA N 111 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS N 99 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE N 113 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE N 97 " --> pdb=" O ILE N 113 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU N 115 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 6.188A 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: 3.831A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.519A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'P' and resid 49 through 53 removed outlier: 3.684A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) removed outlier: 7.641A 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 15 removed outlier: 3.628A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN R 43 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 3.907A 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: 4.775A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.373A 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: 4.229A 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 removed outlier: 6.876A pdb=" N VAL S 106 " --> pdb=" O THR S 72 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 80 through 88 removed outlier: 3.791A pdb=" N THR S 100 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'T' and resid 12 through 15 removed outlier: 5.338A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'U' and resid 40 through 46 removed outlier: 4.828A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'U' and resid 83 through 86 Processing sheet with id= 39, first strand: chain 'V' and resid 69 through 72 removed outlier: 6.820A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'W' and resid 51 through 54 removed outlier: 4.265A 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: 4.751A 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 41 Processing sheet with id= 44, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.235A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN Z 9 " --> pdb=" O HIS Z 34 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS Z 6 " --> pdb=" O GLU Z 58 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'a' and resid 20 through 25 removed outlier: 4.398A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS a 16 " --> pdb=" O ASN a 20 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'b' and resid 29 through 32 removed outlier: 4.471A pdb=" N GLU b 36 " --> pdb=" O ASP b 31 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'c' and resid 6 through 13 removed outlier: 6.081A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'c' and resid 34 through 39 removed outlier: 6.380A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'e' and resid 22 through 25 removed outlier: 5.588A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'f' and resid 14 through 19 Processing sheet with id= 51, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.234A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY g 17 " --> pdb=" O HIS g 39 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'g' and resid 89 through 93 removed outlier: 3.917A pdb=" N ALA g 185 " --> pdb=" O PHE g 198 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'h' and resid 53 through 59 removed outlier: 3.740A pdb=" N ARG h 54 " --> pdb=" O HIS h 69 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'h' and resid 164 through 169 removed outlier: 5.730A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN h 185 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'i' and resid 141 through 145 removed outlier: 6.547A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'j' and resid 11 through 16 removed outlier: 6.959A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'j' and resid 83 through 88 removed outlier: 7.194A pdb=" N HIS j 83 " --> pdb=" O PRO j 98 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG j 93 " --> pdb=" O TYR j 128 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'j' and resid 33 through 41 removed outlier: 6.886A pdb=" N ARG j 45 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'k' and resid 38 through 43 removed outlier: 4.237A pdb=" N ARG k 38 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'k' and resid 44 through 47 removed outlier: 7.427A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'l' and resid 73 through 79 removed outlier: 5.876A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'm' and resid 23 through 29 removed outlier: 7.013A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'm' and resid 74 through 77 removed outlier: 6.614A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'n' and resid 5 through 11 Processing sheet with id= 65, first strand: chain 'o' and resid 35 through 38 removed outlier: 8.018A pdb=" N GLN o 35 " --> pdb=" O VAL o 77 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP o 75 " --> pdb=" O ARG o 37 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'o' and resid 42 through 52 removed outlier: 4.933A pdb=" N LEU o 71 " --> pdb=" O PRO o 43 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'p' and resid 29 through 36 removed outlier: 3.959A pdb=" N ASN p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 29 through 33 removed outlier: 5.125A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'q' and resid 36 through 41 removed outlier: 5.062A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE q 61 " --> pdb=" O LEU q 57 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'u' and resid 4 through 10 removed outlier: 3.998A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL u 19 " --> pdb=" O GLY u 37 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N GLY u 49 " --> pdb=" O ASN u 40 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'v' and resid 7 through 11 removed outlier: 7.239A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N SER v 72 " --> pdb=" O CYS v 64 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'v' and resid 19 through 30 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain 'x' and resid 30 through 33 removed outlier: 4.807A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) 1839 hydrogen bonds defined for protein. 5427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3772 hydrogen bonds 5896 hydrogen bond angles 0 basepair planarities 1509 basepair parallelities 2630 stacking parallelities Total time for adding SS restraints: 283.17 Time building geometry restraints manager: 69.17 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: 11679 1.29 - 1.42: 67917 1.42 - 1.55: 67709 1.55 - 1.68: 9321 1.68 - 1.81: 266 Bond restraints: 156892 Sorted by residual: bond pdb=" C5 5MU 5 54 " pdb=" C6 5MU 5 54 " ideal model delta sigma weight residual 1.155 1.434 -0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.155 1.430 -0.275 2.00e-02 2.50e+03 1.89e+02 bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " 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 1 747 " pdb=" C5 5MU 1 747 " ideal model delta sigma weight residual 1.802 1.591 0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C4 5MU 11939 " pdb=" C5 5MU 11939 " ideal model delta sigma weight residual 1.802 1.596 0.206 2.00e-02 2.50e+03 1.06e+02 ... (remaining 156887 not shown) Histogram of bond angle deviations from ideal: 96.37 - 104.99: 21399 104.99 - 113.61: 102198 113.61 - 122.23: 78687 122.23 - 130.85: 31030 130.85 - 139.47: 1489 Bond angle restraints: 234803 Sorted by residual: angle pdb=" C1' 2MG 21516 " pdb=" N9 2MG 21516 " pdb=" C8 2MG 21516 " ideal model delta sigma weight residual 110.07 134.84 -24.77 3.00e+00 1.11e-01 6.82e+01 angle pdb=" C LYS L 36 " pdb=" N GLY L 37 " pdb=" CA GLY L 37 " ideal model delta sigma weight residual 122.43 115.14 7.29 8.90e-01 1.26e+00 6.70e+01 angle pdb=" C1' 2MG 21207 " pdb=" N9 2MG 21207 " pdb=" C8 2MG 21207 " ideal model delta sigma weight residual 110.07 132.84 -22.77 3.00e+00 1.11e-01 5.76e+01 angle pdb=" C1' 2MG 12445 " pdb=" N9 2MG 12445 " pdb=" C8 2MG 12445 " ideal model delta sigma weight residual 110.07 132.28 -22.21 3.00e+00 1.11e-01 5.48e+01 angle pdb=" C1' G7M 12069 " pdb=" N9 G7M 12069 " pdb=" C8 G7M 12069 " ideal model delta sigma weight residual 112.61 134.30 -21.69 3.00e+00 1.11e-01 5.23e+01 ... (remaining 234798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 88547 35.94 - 71.87: 10520 71.87 - 107.81: 1267 107.81 - 143.75: 9 143.75 - 179.69: 42 Dihedral angle restraints: 100385 sinusoidal: 84125 harmonic: 16260 Sorted by residual: dihedral pdb=" O4' U 1 102 " pdb=" C1' U 1 102 " pdb=" N1 U 1 102 " pdb=" C2 U 1 102 " ideal model delta sinusoidal sigma weight residual 200.00 43.51 156.49 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" O4' U 1 138 " pdb=" C1' U 1 138 " pdb=" N1 U 1 138 " pdb=" C2 U 1 138 " ideal model delta sinusoidal sigma weight residual 200.00 44.06 155.94 1 1.50e+01 4.44e-03 8.16e+01 dihedral pdb=" O4' U 2 467 " pdb=" C1' U 2 467 " pdb=" N1 U 2 467 " pdb=" C2 U 2 467 " ideal model delta sinusoidal sigma weight residual 200.00 44.10 155.90 1 1.50e+01 4.44e-03 8.16e+01 ... (remaining 100382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 29499 0.132 - 0.265: 413 0.265 - 0.397: 4 0.397 - 0.530: 3 0.530 - 0.662: 1 Chirality restraints: 29920 Sorted by residual: chirality pdb=" CA LYS C 154 " pdb=" N LYS C 154 " pdb=" C LYS C 154 " pdb=" CB LYS C 154 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" C3' A 1 404 " pdb=" C4' A 1 404 " pdb=" O3' A 1 404 " pdb=" C2' A 1 404 " both_signs ideal model delta sigma weight residual False -2.74 -2.23 -0.52 2.00e-01 2.50e+01 6.66e+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 6.24e+00 ... (remaining 29917 not shown) Planarity restraints: 12502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21516 " 0.073 2.00e-02 2.50e+03 6.27e-01 8.85e+03 pdb=" C4' 2MG 21516 " 0.448 2.00e-02 2.50e+03 pdb=" O4' 2MG 21516 " 0.684 2.00e-02 2.50e+03 pdb=" C3' 2MG 21516 " -0.602 2.00e-02 2.50e+03 pdb=" O3' 2MG 21516 " -0.678 2.00e-02 2.50e+03 pdb=" C2' 2MG 21516 " -0.167 2.00e-02 2.50e+03 pdb=" O2' 2MG 21516 " 1.012 2.00e-02 2.50e+03 pdb=" C1' 2MG 21516 " 0.204 2.00e-02 2.50e+03 pdb=" N9 2MG 21516 " -0.976 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 12445 " 0.023 2.00e-02 2.50e+03 6.03e-01 8.19e+03 pdb=" C4' 2MG 12445 " 0.464 2.00e-02 2.50e+03 pdb=" O4' 2MG 12445 " 0.807 2.00e-02 2.50e+03 pdb=" C3' 2MG 12445 " -0.586 2.00e-02 2.50e+03 pdb=" O3' 2MG 12445 " -0.559 2.00e-02 2.50e+03 pdb=" C2' 2MG 12445 " -0.248 2.00e-02 2.50e+03 pdb=" O2' 2MG 12445 " 0.866 2.00e-02 2.50e+03 pdb=" C1' 2MG 12445 " 0.185 2.00e-02 2.50e+03 pdb=" N9 2MG 12445 " -0.953 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21207 " -0.037 2.00e-02 2.50e+03 5.98e-01 8.04e+03 pdb=" C4' 2MG 21207 " -0.451 2.00e-02 2.50e+03 pdb=" O4' 2MG 21207 " -0.712 2.00e-02 2.50e+03 pdb=" C3' 2MG 21207 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 2MG 21207 " 0.597 2.00e-02 2.50e+03 pdb=" C2' 2MG 21207 " 0.211 2.00e-02 2.50e+03 pdb=" O2' 2MG 21207 " -0.921 2.00e-02 2.50e+03 pdb=" C1' 2MG 21207 " -0.210 2.00e-02 2.50e+03 pdb=" N9 2MG 21207 " 0.928 2.00e-02 2.50e+03 ... (remaining 12499 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 246 2.14 - 2.83: 42723 2.83 - 3.52: 206202 3.52 - 4.21: 481205 4.21 - 4.90: 632365 Nonbonded interactions: 1362741 Sorted by model distance: nonbonded pdb=" O3' A 5 76 " pdb=" C PHE A 77 " model vdw 1.454 3.270 nonbonded pdb=" O PHE E 173 " pdb=" OD1 ASP E 174 " model vdw 1.806 3.040 nonbonded pdb=" N4 C 12313 " pdb=" N6 A 12314 " model vdw 1.934 3.200 nonbonded pdb=" O6 G 12190 " pdb=" N6 A 12191 " model vdw 1.962 2.520 nonbonded pdb=" OP2 U 1 963 " pdb="MG MG 13024 " model vdw 2.012 2.170 ... (remaining 1362736 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.590 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: 0.080 Extract box with map and model: 16.940 Check model and map are aligned: 1.590 Set scattering table: 0.960 Process input model: 603.250 Find NCS groups from input model: 3.210 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: 0.020 Load rotamer database and sin/cos tables:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 642.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 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 : 0.008 0.279 156892 Z= 0.477 Angle : 0.758 24.766 234803 Z= 0.392 Chirality : 0.044 0.662 29920 Planarity : 0.020 0.627 12502 Dihedral : 22.734 179.686 89895 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.35 % Favored : 96.54 % Rotamer: Outliers : 0.34 % Allowed : 3.25 % Favored : 96.40 % Cbeta Deviations : 0.04 % 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: -3.76 (0.09), residues: 5606 helix: -3.68 (0.06), residues: 1833 sheet: -1.81 (0.14), residues: 1081 loop : -1.75 (0.10), residues: 2692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP D 78 HIS 0.033 0.002 HIS M 13 PHE 0.052 0.003 PHE N 80 TYR 0.031 0.003 TYR B 103 ARG 0.027 0.001 ARG N 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11212 Ramachandran restraints generated. 5606 Oldfield, 0 Emsley, 5606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11212 Ramachandran restraints generated. 5606 Oldfield, 0 Emsley, 5606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2266 residues out of total 4670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 2250 time to evaluate : 6.279 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: A 77 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8198 (p90) REVERT: B 66 ASP cc_start: 0.9046 (t0) cc_final: 0.8734 (t0) REVERT: B 114 ASP cc_start: 0.8542 (m-30) cc_final: 0.8306 (m-30) REVERT: B 117 GLN cc_start: 0.8879 (tt0) cc_final: 0.8561 (tt0) REVERT: B 161 TYR cc_start: 0.9260 (p90) cc_final: 0.9059 (p90) REVERT: C 2 ILE cc_start: 0.9226 (pt) cc_final: 0.9005 (pp) REVERT: C 39 ASP cc_start: 0.9014 (p0) cc_final: 0.8654 (p0) REVERT: C 137 SER cc_start: 0.9605 (m) cc_final: 0.9248 (m) REVERT: C 181 ASP cc_start: 0.8607 (t0) cc_final: 0.7856 (t0) REVERT: D 9 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8468 (mp10) REVERT: D 136 GLN cc_start: 0.9241 (tp-100) cc_final: 0.9018 (tp-100) REVERT: D 149 ILE cc_start: 0.9448 (pt) cc_final: 0.9245 (pp) REVERT: D 153 LEU cc_start: 0.8627 (tp) cc_final: 0.8357 (tm) REVERT: D 156 ASN cc_start: 0.9348 (m-40) cc_final: 0.8827 (m-40) REVERT: E 27 GLN cc_start: 0.9101 (tt0) cc_final: 0.8844 (tt0) REVERT: E 35 THR cc_start: 0.9456 (m) cc_final: 0.8956 (p) REVERT: E 38 MET cc_start: 0.8949 (mtt) cc_final: 0.8619 (mtm) REVERT: E 69 LYS cc_start: 0.8801 (mttp) cc_final: 0.8563 (mmtm) REVERT: E 81 GLN cc_start: 0.8759 (tt0) cc_final: 0.8533 (tm-30) REVERT: E 83 TYR cc_start: 0.8740 (m-10) cc_final: 0.8322 (m-80) REVERT: E 98 GLU cc_start: 0.8975 (mt-10) cc_final: 0.7890 (mt-10) REVERT: E 118 SER cc_start: 0.8995 (t) cc_final: 0.8357 (t) REVERT: E 142 ASP cc_start: 0.8492 (t70) cc_final: 0.6957 (t0) REVERT: E 155 THR cc_start: 0.9578 (m) cc_final: 0.9365 (m) REVERT: E 165 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8535 (mt-10) REVERT: F 19 ILE cc_start: 0.9558 (mm) cc_final: 0.9220 (mp) REVERT: F 26 ILE cc_start: 0.9411 (mt) cc_final: 0.9076 (tt) REVERT: F 60 ASP cc_start: 0.8525 (p0) cc_final: 0.8276 (p0) REVERT: F 88 GLN cc_start: 0.9003 (pt0) cc_final: 0.8782 (pt0) REVERT: F 101 ASN cc_start: 0.8814 (p0) cc_final: 0.8231 (p0) REVERT: F 116 GLN cc_start: 0.9201 (tp40) cc_final: 0.8763 (tp-100) REVERT: F 128 GLN cc_start: 0.8473 (mt0) cc_final: 0.8247 (mt0) REVERT: F 139 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8608 (tm-30) REVERT: G 28 ASN cc_start: 0.8825 (m-40) cc_final: 0.8602 (m110) REVERT: G 45 GLU cc_start: 0.9290 (mt-10) cc_final: 0.9001 (pp20) REVERT: G 55 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8380 (mm-30) REVERT: G 114 GLU cc_start: 0.8855 (mm-30) cc_final: 0.7908 (tp30) REVERT: G 129 GLU cc_start: 0.8474 (pt0) cc_final: 0.8118 (tp30) REVERT: J 31 GLU cc_start: 0.8562 (tp30) cc_final: 0.7949 (tp30) REVERT: J 37 ARG cc_start: 0.9403 (tpt-90) cc_final: 0.8870 (ttm170) REVERT: J 90 GLU cc_start: 0.8646 (pt0) cc_final: 0.8406 (pt0) REVERT: J 91 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8278 (mt-10) REVERT: J 98 GLU cc_start: 0.8540 (mp0) cc_final: 0.8210 (mp0) REVERT: J 102 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8676 (mt-10) REVERT: J 106 LYS cc_start: 0.9251 (tttm) cc_final: 0.8947 (ttmm) REVERT: K 12 ASP cc_start: 0.8860 (p0) cc_final: 0.8520 (p0) REVERT: K 14 SER cc_start: 0.9338 (p) cc_final: 0.8657 (p) REVERT: K 88 ASN cc_start: 0.8507 (t0) cc_final: 0.7959 (t0) REVERT: K 106 GLU cc_start: 0.8197 (mp0) cc_final: 0.7796 (mp0) REVERT: K 109 SER cc_start: 0.8702 (t) cc_final: 0.8098 (p) REVERT: M 2 LEU cc_start: 0.9358 (mt) cc_final: 0.9010 (mp) REVERT: M 30 SER cc_start: 0.9383 (t) cc_final: 0.9133 (p) REVERT: M 47 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7768 (tm-30) REVERT: M 88 ASN cc_start: 0.8966 (m-40) cc_final: 0.8618 (m110) REVERT: M 90 GLU cc_start: 0.8285 (tp30) cc_final: 0.8022 (tp30) REVERT: M 95 LEU cc_start: 0.9669 (mt) cc_final: 0.9402 (mm) REVERT: M 110 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8184 (tm-30) REVERT: M 112 LEU cc_start: 0.9593 (tp) cc_final: 0.9296 (tm) REVERT: M 115 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8061 (tp30) REVERT: M 119 LEU cc_start: 0.9718 (mt) cc_final: 0.9446 (mp) REVERT: N 40 LYS cc_start: 0.9405 (mttt) cc_final: 0.9195 (mttt) REVERT: N 57 THR cc_start: 0.9235 (m) cc_final: 0.8869 (p) REVERT: N 72 ASP cc_start: 0.8552 (t0) cc_final: 0.8312 (t0) REVERT: N 78 LYS cc_start: 0.9318 (tttt) cc_final: 0.9108 (tttm) REVERT: N 110 MET cc_start: 0.8940 (mmm) cc_final: 0.8296 (mmm) REVERT: O 55 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8062 (mt-10) REVERT: O 68 LYS cc_start: 0.9384 (mttt) cc_final: 0.9170 (mttm) REVERT: P 6 LYS cc_start: 0.9195 (mtpt) cc_final: 0.8984 (mtpm) REVERT: P 7 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8167 (tm-30) REVERT: P 9 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8313 (mt-10) REVERT: P 11 GLU cc_start: 0.8545 (pt0) cc_final: 0.8199 (pt0) REVERT: P 27 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8308 (tp30) REVERT: P 82 ASP cc_start: 0.8795 (t70) cc_final: 0.8579 (t0) REVERT: Q 49 ASP cc_start: 0.8131 (m-30) cc_final: 0.7701 (m-30) REVERT: Q 59 GLN cc_start: 0.9200 (tt0) cc_final: 0.8935 (tt0) REVERT: R 18 GLN cc_start: 0.8732 (mt0) cc_final: 0.8380 (mt0) REVERT: R 43 ASN cc_start: 0.8964 (t0) cc_final: 0.8436 (t0) REVERT: R 97 LYS cc_start: 0.9367 (tttt) cc_final: 0.8958 (tttt) REVERT: R 101 ILE cc_start: 0.9374 (mt) cc_final: 0.8866 (mt) REVERT: S 52 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8229 (mt-10) REVERT: S 84 ARG cc_start: 0.9198 (mmt-90) cc_final: 0.8934 (mpt180) REVERT: S 96 ILE cc_start: 0.9291 (pt) cc_final: 0.9028 (pp) REVERT: T 6 ARG cc_start: 0.8624 (tpt-90) cc_final: 0.8232 (tpt170) REVERT: T 27 SER cc_start: 0.9276 (m) cc_final: 0.8991 (p) REVERT: T 37 ASP cc_start: 0.8727 (p0) cc_final: 0.8468 (p0) REVERT: T 50 LEU cc_start: 0.9430 (mp) cc_final: 0.9191 (mp) REVERT: T 91 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8439 (mm-40) REVERT: U 9 ASP cc_start: 0.8321 (m-30) cc_final: 0.8086 (m-30) REVERT: U 41 LEU cc_start: 0.9283 (mt) cc_final: 0.8949 (mm) REVERT: V 7 GLU cc_start: 0.8308 (mp0) cc_final: 0.7541 (mp0) REVERT: V 41 GLU cc_start: 0.8401 (pp20) cc_final: 0.7286 (pp20) REVERT: V 43 ASP cc_start: 0.8808 (t70) cc_final: 0.8532 (t0) REVERT: V 46 LYS cc_start: 0.9449 (mmtt) cc_final: 0.9222 (mmmm) REVERT: V 48 MET cc_start: 0.9030 (tpt) cc_final: 0.8823 (tpt) REVERT: V 73 LYS cc_start: 0.9304 (mtpp) cc_final: 0.9017 (mmmm) REVERT: V 77 VAL cc_start: 0.9524 (p) cc_final: 0.9301 (m) REVERT: W 29 GLU cc_start: 0.8379 (tt0) cc_final: 0.7990 (tt0) REVERT: W 56 ASP cc_start: 0.9273 (p0) cc_final: 0.9019 (p0) REVERT: W 68 LYS cc_start: 0.9321 (tptp) cc_final: 0.8484 (tppp) REVERT: W 83 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8168 (mt-10) REVERT: X 62 LYS cc_start: 0.9364 (mttt) cc_final: 0.9105 (mttp) REVERT: X 66 THR cc_start: 0.9687 (m) cc_final: 0.9409 (p) REVERT: Y 16 THR cc_start: 0.9557 (m) cc_final: 0.9240 (p) REVERT: Y 17 GLU cc_start: 0.8986 (tp30) cc_final: 0.8749 (tp30) REVERT: Y 20 ASN cc_start: 0.8987 (m-40) cc_final: 0.8521 (m110) REVERT: Y 30 MET cc_start: 0.8790 (mmt) cc_final: 0.8547 (mpp) REVERT: Y 31 GLN cc_start: 0.9152 (tt0) cc_final: 0.8880 (tt0) REVERT: Y 40 SER cc_start: 0.9604 (m) cc_final: 0.9111 (p) REVERT: Y 45 GLN cc_start: 0.8515 (mt0) cc_final: 0.7905 (mt0) REVERT: Y 49 ASP cc_start: 0.8767 (m-30) cc_final: 0.8331 (m-30) REVERT: Z 6 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8312 (mmtm) REVERT: b 9 THR cc_start: 0.9074 (m) cc_final: 0.8861 (p) REVERT: c 5 ILE cc_start: 0.9117 (tt) cc_final: 0.8637 (mm) REVERT: c 7 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7244 (mt-10) REVERT: c 27 LYS cc_start: 0.9260 (mttt) cc_final: 0.8772 (mttp) REVERT: c 40 ASP cc_start: 0.9355 (t0) cc_final: 0.9059 (t0) REVERT: c 43 VAL cc_start: 0.9542 (t) cc_final: 0.8591 (p) REVERT: c 44 ARG cc_start: 0.9055 (mtp180) cc_final: 0.8765 (mmm-85) REVERT: c 45 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8308 (mp10) REVERT: d 3 ARG cc_start: 0.9076 (mmt180) cc_final: 0.8658 (mmt180) REVERT: d 25 LYS cc_start: 0.9060 (tmmt) cc_final: 0.8854 (ttpt) REVERT: d 29 GLN cc_start: 0.8511 (mt0) cc_final: 0.8151 (mt0) REVERT: f 6 SER cc_start: 0.9328 (t) cc_final: 0.8708 (p) REVERT: f 8 LYS cc_start: 0.8815 (mttt) cc_final: 0.8432 (mttm) REVERT: g 40 ILE cc_start: 0.8910 (mm) cc_final: 0.8676 (mm) REVERT: g 49 MET cc_start: 0.8714 (mtp) cc_final: 0.8169 (mmp) REVERT: g 106 THR cc_start: 0.9235 (m) cc_final: 0.8859 (p) REVERT: g 116 ASP cc_start: 0.9116 (m-30) cc_final: 0.8909 (m-30) REVERT: g 132 LYS cc_start: 0.8991 (ptpt) cc_final: 0.8646 (tptt) REVERT: g 137 ARG cc_start: 0.8733 (mmt180) cc_final: 0.8136 (ttt180) REVERT: g 140 GLU cc_start: 0.8709 (tt0) cc_final: 0.8216 (tt0) REVERT: g 142 GLU cc_start: 0.9122 (tt0) cc_final: 0.8740 (tp30) REVERT: g 151 ILE cc_start: 0.9448 (pt) cc_final: 0.9104 (pp) REVERT: g 154 MET cc_start: 0.9012 (ttp) cc_final: 0.8763 (ttt) REVERT: g 157 LEU cc_start: 0.9188 (mt) cc_final: 0.8874 (pt) REVERT: g 159 ASP cc_start: 0.9111 (m-30) cc_final: 0.8887 (m-30) REVERT: g 167 ASP cc_start: 0.8396 (p0) cc_final: 0.8055 (p0) REVERT: g 169 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8654 (mp0) REVERT: g 173 ILE cc_start: 0.9557 (mm) cc_final: 0.9354 (mm) REVERT: g 174 LYS cc_start: 0.9225 (mtpm) cc_final: 0.8895 (mptt) REVERT: g 184 PHE cc_start: 0.8597 (m-10) cc_final: 0.8393 (m-80) REVERT: g 208 ARG cc_start: 0.8155 (mtt90) cc_final: 0.7828 (mtt90) REVERT: g 223 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8166 (tm-30) REVERT: h 25 ASN cc_start: 0.8879 (m-40) cc_final: 0.8496 (m-40) REVERT: h 32 ASN cc_start: 0.8688 (m-40) cc_final: 0.8040 (m-40) REVERT: h 35 SER cc_start: 0.8821 (t) cc_final: 0.8614 (p) REVERT: h 36 ASP cc_start: 0.8656 (m-30) cc_final: 0.8056 (m-30) REVERT: h 44 THR cc_start: 0.9565 (m) cc_final: 0.9251 (p) REVERT: h 102 ASN cc_start: 0.8779 (m-40) cc_final: 0.8308 (m-40) REVERT: h 121 THR cc_start: 0.9181 (m) cc_final: 0.8961 (p) REVERT: h 139 GLN cc_start: 0.9001 (mt0) cc_final: 0.8784 (mt0) REVERT: h 181 ASP cc_start: 0.8502 (t0) cc_final: 0.8170 (t0) REVERT: i 4 TYR cc_start: 0.9118 (t80) cc_final: 0.8885 (t80) REVERT: i 20 PHE cc_start: 0.9325 (m-80) cc_final: 0.9091 (m-10) REVERT: i 77 LYS cc_start: 0.9431 (mttm) cc_final: 0.9089 (mtpt) REVERT: i 141 ASP cc_start: 0.8027 (m-30) cc_final: 0.7720 (m-30) REVERT: i 182 PHE cc_start: 0.9364 (t80) cc_final: 0.8665 (t80) REVERT: j 14 LYS cc_start: 0.9184 (mtpp) cc_final: 0.8899 (mtpp) REVERT: j 19 ASN cc_start: 0.8726 (t0) cc_final: 0.8246 (t0) REVERT: j 20 ARG cc_start: 0.8884 (ttp-170) cc_final: 0.8387 (ttp80) REVERT: j 60 ILE cc_start: 0.9217 (pp) cc_final: 0.8995 (mt) REVERT: j 116 GLU cc_start: 0.8403 (tt0) cc_final: 0.8174 (tt0) REVERT: j 131 THR cc_start: 0.9142 (p) cc_final: 0.8897 (p) REVERT: j 152 MET cc_start: 0.8784 (mtp) cc_final: 0.8470 (mtp) REVERT: j 159 LYS cc_start: 0.8841 (mttt) cc_final: 0.8199 (mttt) REVERT: k 6 ILE cc_start: 0.9458 (mt) cc_final: 0.9100 (mp) REVERT: k 25 TYR cc_start: 0.9616 (m-10) cc_final: 0.9351 (m-10) REVERT: k 46 GLN cc_start: 0.8837 (tp40) cc_final: 0.8401 (tp40) REVERT: k 61 LEU cc_start: 0.9356 (tp) cc_final: 0.8761 (tm) REVERT: k 62 MET cc_start: 0.8625 (ttp) cc_final: 0.8246 (ttm) REVERT: k 74 LEU cc_start: 0.9642 (tp) cc_final: 0.9336 (tp) REVERT: k 76 THR cc_start: 0.9455 (p) cc_final: 0.9004 (p) REVERT: k 77 THR cc_start: 0.9503 (m) cc_final: 0.9236 (m) REVERT: k 92 THR cc_start: 0.8911 (m) cc_final: 0.8467 (p) REVERT: k 94 HIS cc_start: 0.8288 (m90) cc_final: 0.8087 (m170) REVERT: l 31 MET cc_start: 0.8733 (ttp) cc_final: 0.8344 (ttp) REVERT: l 35 LYS cc_start: 0.9029 (mttt) cc_final: 0.8682 (mtpp) REVERT: l 44 TYR cc_start: 0.9187 (m-10) cc_final: 0.8795 (m-80) REVERT: l 49 THR cc_start: 0.9289 (p) cc_final: 0.9086 (p) REVERT: l 54 SER cc_start: 0.9060 (m) cc_final: 0.8746 (p) REVERT: l 68 ASN cc_start: 0.9249 (m-40) cc_final: 0.9006 (m-40) REVERT: l 74 GLU cc_start: 0.8579 (pt0) cc_final: 0.8346 (pm20) REVERT: l 85 TYR cc_start: 0.7857 (m-10) cc_final: 0.7454 (m-80) REVERT: l 101 MET cc_start: 0.9106 (mtm) cc_final: 0.8821 (mtm) REVERT: l 122 ASN cc_start: 0.8982 (m-40) cc_final: 0.8751 (m110) REVERT: l 137 LYS cc_start: 0.9326 (tptt) cc_final: 0.8943 (tppp) REVERT: m 5 ASP cc_start: 0.8697 (t0) cc_final: 0.8352 (t0) REVERT: m 29 SER cc_start: 0.9496 (t) cc_final: 0.8760 (m) REVERT: m 58 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8439 (mp0) REVERT: m 60 GLU cc_start: 0.8738 (tt0) cc_final: 0.8491 (tm-30) REVERT: m 61 LEU cc_start: 0.9060 (mt) cc_final: 0.8589 (mt) REVERT: m 76 GLN cc_start: 0.8497 (mt0) cc_final: 0.8180 (mm110) REVERT: m 85 ILE cc_start: 0.9533 (mm) cc_final: 0.9301 (mp) REVERT: m 105 SER cc_start: 0.9481 (t) cc_final: 0.9255 (t) REVERT: n 4 ASN cc_start: 0.8102 (t0) cc_final: 0.7662 (t160) REVERT: n 19 VAL cc_start: 0.9576 (t) cc_final: 0.9359 (m) REVERT: n 29 VAL cc_start: 0.9180 (t) cc_final: 0.8856 (t) REVERT: n 54 LEU cc_start: 0.9465 (tp) cc_final: 0.9090 (tp) REVERT: n 88 MET cc_start: 0.8690 (mtm) cc_final: 0.8120 (mtm) REVERT: n 91 ASP cc_start: 0.9131 (t0) cc_final: 0.8664 (t70) REVERT: n 100 LYS cc_start: 0.9453 (ttmm) cc_final: 0.9247 (pttt) REVERT: o 6 ILE cc_start: 0.8996 (mt) cc_final: 0.8652 (tp) REVERT: o 11 LYS cc_start: 0.9173 (mtpt) cc_final: 0.8772 (mttp) REVERT: o 17 LEU cc_start: 0.9271 (tt) cc_final: 0.8939 (tm) REVERT: o 37 ARG cc_start: 0.7995 (tpm170) cc_final: 0.7596 (tpm-80) REVERT: o 49 PHE cc_start: 0.8669 (m-80) cc_final: 0.8451 (m-80) REVERT: o 53 ILE cc_start: 0.9603 (pt) cc_final: 0.9202 (pp) REVERT: o 63 ASP cc_start: 0.7660 (m-30) cc_final: 0.7358 (m-30) REVERT: o 65 TYR cc_start: 0.8993 (m-80) cc_final: 0.8723 (m-80) REVERT: p 30 THR cc_start: 0.9514 (m) cc_final: 0.8998 (p) REVERT: p 32 VAL cc_start: 0.9577 (t) cc_final: 0.9345 (p) REVERT: p 46 THR cc_start: 0.9343 (p) cc_final: 0.8943 (t) REVERT: p 64 GLN cc_start: 0.8750 (pt0) cc_final: 0.8358 (pp30) REVERT: p 65 VAL cc_start: 0.9551 (m) cc_final: 0.9203 (p) REVERT: p 68 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8524 (mt-10) REVERT: p 83 GLU cc_start: 0.8549 (pt0) cc_final: 0.8128 (pp20) REVERT: p 87 LYS cc_start: 0.9120 (ttmt) cc_final: 0.8845 (ttmm) REVERT: p 127 ARG cc_start: 0.9279 (mtp-110) cc_final: 0.8994 (mtp-110) REVERT: q 47 SER cc_start: 0.9296 (t) cc_final: 0.8947 (t) REVERT: q 59 ASN cc_start: 0.8962 (p0) cc_final: 0.8693 (p0) REVERT: q 62 GLU cc_start: 0.7553 (tp30) cc_final: 0.7024 (tp30) REVERT: q 70 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8111 (mt-10) REVERT: q 74 LEU cc_start: 0.8758 (mm) cc_final: 0.8284 (mt) REVERT: q 75 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8407 (mm-40) REVERT: r 27 LYS cc_start: 0.9338 (tttt) cc_final: 0.9126 (tppp) REVERT: r 31 LYS cc_start: 0.9519 (mttt) cc_final: 0.9311 (mtpp) REVERT: r 41 GLU cc_start: 0.8560 (mt-10) cc_final: 0.7893 (mt-10) REVERT: r 49 SER cc_start: 0.9408 (t) cc_final: 0.8974 (p) REVERT: r 52 GLN cc_start: 0.9524 (mt0) cc_final: 0.9275 (mt0) REVERT: r 76 SER cc_start: 0.9658 (m) cc_final: 0.9203 (p) REVERT: r 89 LEU cc_start: 0.9491 (mt) cc_final: 0.9277 (mm) REVERT: r 97 VAL cc_start: 0.9458 (t) cc_final: 0.9221 (m) REVERT: r 104 THR cc_start: 0.9075 (m) cc_final: 0.8537 (p) REVERT: s 10 GLU cc_start: 0.8964 (tp30) cc_final: 0.8473 (tp30) REVERT: s 14 VAL cc_start: 0.9699 (t) cc_final: 0.9099 (p) REVERT: s 33 ASP cc_start: 0.8644 (t0) cc_final: 0.8271 (t70) REVERT: s 40 ASP cc_start: 0.9109 (m-30) cc_final: 0.8437 (m-30) REVERT: s 43 ASN cc_start: 0.9406 (m-40) cc_final: 0.9120 (m110) REVERT: t 15 PHE cc_start: 0.8190 (m-10) cc_final: 0.7930 (m-80) REVERT: t 37 ASN cc_start: 0.9514 (m-40) cc_final: 0.9191 (m-40) REVERT: t 68 ASP cc_start: 0.8629 (m-30) cc_final: 0.8419 (m-30) REVERT: t 79 THR cc_start: 0.9355 (m) cc_final: 0.9148 (p) REVERT: u 53 ASP cc_start: 0.8960 (t0) cc_final: 0.8192 (t0) REVERT: u 56 ARG cc_start: 0.8879 (mmm160) cc_final: 0.8541 (mmm-85) REVERT: v 14 SER cc_start: 0.9257 (t) cc_final: 0.8986 (p) REVERT: v 15 ASP cc_start: 0.8585 (p0) cc_final: 0.8347 (p0) REVERT: v 17 MET cc_start: 0.8798 (ptt) cc_final: 0.8546 (ptp) REVERT: v 69 LYS cc_start: 0.9351 (tttt) cc_final: 0.8959 (ttpp) REVERT: v 77 ARG cc_start: 0.8756 (ptm-80) cc_final: 0.8111 (ptm-80) REVERT: w 22 ASP cc_start: 0.8678 (t0) cc_final: 0.8342 (t0) REVERT: x 12 ASP cc_start: 0.8616 (m-30) cc_final: 0.8063 (m-30) REVERT: x 16 LEU cc_start: 0.9511 (tp) cc_final: 0.9113 (tt) REVERT: x 35 SER cc_start: 0.8590 (m) cc_final: 0.8326 (m) REVERT: x 49 ILE cc_start: 0.8724 (pt) cc_final: 0.8454 (pp) REVERT: x 56 GLN cc_start: 0.9238 (pt0) cc_final: 0.9030 (pp30) REVERT: y 14 SER cc_start: 0.9322 (m) cc_final: 0.8957 (p) REVERT: y 48 GLN cc_start: 0.9216 (tp40) cc_final: 0.8891 (tp40) REVERT: y 57 ILE cc_start: 0.9584 (tt) cc_final: 0.9191 (pp) REVERT: y 67 ILE cc_start: 0.9471 (pt) cc_final: 0.9188 (pp) REVERT: y 70 ASN cc_start: 0.9433 (m110) cc_final: 0.9173 (m-40) REVERT: y 80 THR cc_start: 0.9507 (m) cc_final: 0.9144 (p) REVERT: y 82 GLN cc_start: 0.9271 (mm-40) cc_final: 0.8947 (mm110) REVERT: z 12 PHE cc_start: 0.8378 (t80) cc_final: 0.8141 (t80) REVERT: z 36 GLU cc_start: 0.8696 (tt0) cc_final: 0.8155 (tp30) REVERT: z 37 PHE cc_start: 0.8542 (m-80) cc_final: 0.7590 (m-80) outliers start: 16 outliers final: 9 residues processed: 2259 average time/residue: 2.1150 time to fit residues: 6844.8440 Evaluate side-chains 1779 residues out of total 4670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1769 time to evaluate : 6.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain U residue 37 GLU Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain j residue 65 GLU Chi-restraints excluded: chain n residue 83 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 852 optimal weight: 0.9990 chunk 764 optimal weight: 6.9990 chunk 424 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 515 optimal weight: 5.9990 chunk 408 optimal weight: 10.0000 chunk 790 optimal weight: 5.9990 chunk 306 optimal weight: 10.0000 chunk 480 optimal weight: 5.9990 chunk 588 optimal weight: 3.9990 chunk 916 optimal weight: 0.0270 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 HIS B 70 ASN B 86 ASN B 260 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 136 ASN C 150 GLN D 163 ASN ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 GLN F 104 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN J 131 ASN J 136 GLN K 82 ASN L 93 ASN N 18 GLN N 31 HIS O 38 GLN O 100 HIS P 12 GLN P 15 GLN Q 72 ASN R 6 GLN S 61 ASN U 66 GLN X 6 GLN X 23 ASN Y 15 ASN Y 27 ASN a 20 ASN b 4 GLN b 42 HIS c 26 ASN f 13 ASN g 18 HIS g 39 HIS ** g 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 177 ASN g 178 ASN ** h 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 140 ASN h 185 ASN i 36 GLN i 40 GLN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 132 ASN k 52 ASN k 58 HIS k 63 ASN l 130 ASN m 38 ASN n 5 GLN n 31 ASN ** n 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 126 GLN p 22 HIS p 119 ASN t 20 ASN t 62 GLN t 80 GLN u 29 ASN u 59 HIS w 19 GLN x 52 HIS y 3 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 156892 Z= 0.199 Angle : 0.654 14.593 234803 Z= 0.349 Chirality : 0.035 0.391 29920 Planarity : 0.007 0.132 12502 Dihedral : 23.729 179.059 78667 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.07 % Favored : 96.91 % Rotamer: Outliers : 4.56 % Allowed : 19.70 % Favored : 75.74 % 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: -1.77 (0.10), residues: 5606 helix: -0.81 (0.11), residues: 1877 sheet: -1.36 (0.15), residues: 1096 loop : -1.25 (0.11), residues: 2633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 78 HIS 0.013 0.001 HIS M 13 PHE 0.027 0.002 PHE g 184 TYR 0.018 0.001 TYR i 76 ARG 0.023 0.001 ARG g 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11212 Ramachandran restraints generated. 5606 Oldfield, 0 Emsley, 5606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11212 Ramachandran restraints generated. 5606 Oldfield, 0 Emsley, 5606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2102 residues out of total 4670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1889 time to evaluate : 6.171 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: B 66 ASP cc_start: 0.9033 (t0) cc_final: 0.8673 (t0) REVERT: B 117 GLN cc_start: 0.8766 (tt0) cc_final: 0.8426 (tt0) REVERT: C 33 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8387 (ptt-90) REVERT: C 39 ASP cc_start: 0.9049 (p0) cc_final: 0.8607 (p0) REVERT: C 137 SER cc_start: 0.9413 (m) cc_final: 0.9132 (m) REVERT: C 165 MET cc_start: 0.9019 (ttt) cc_final: 0.8793 (ttm) REVERT: C 173 GLN cc_start: 0.8372 (mt0) cc_final: 0.7998 (mt0) REVERT: D 67 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8292 (mtp-110) REVERT: D 136 GLN cc_start: 0.9186 (tp-100) cc_final: 0.8933 (tp40) REVERT: D 156 ASN cc_start: 0.9233 (m-40) cc_final: 0.8665 (m-40) REVERT: D 188 MET cc_start: 0.8628 (mtp) cc_final: 0.8220 (mtp) REVERT: E 35 THR cc_start: 0.9324 (m) cc_final: 0.8822 (p) REVERT: E 72 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8884 (ptpp) REVERT: E 81 GLN cc_start: 0.8789 (tt0) cc_final: 0.8539 (tm-30) REVERT: E 83 TYR cc_start: 0.8728 (m-10) cc_final: 0.8446 (m-10) REVERT: E 98 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7647 (mt-10) REVERT: E 101 GLU cc_start: 0.8714 (tt0) cc_final: 0.8456 (mt-10) REVERT: E 127 ASN cc_start: 0.7294 (m-40) cc_final: 0.7059 (m-40) REVERT: E 155 THR cc_start: 0.9599 (m) cc_final: 0.9394 (m) REVERT: F 26 ILE cc_start: 0.9350 (mt) cc_final: 0.9010 (mp) REVERT: F 60 ASP cc_start: 0.8493 (p0) cc_final: 0.8102 (p0) REVERT: F 101 ASN cc_start: 0.8750 (p0) cc_final: 0.8149 (p0) REVERT: F 116 GLN cc_start: 0.9138 (tp40) cc_final: 0.8649 (tp-100) REVERT: F 130 GLU cc_start: 0.8069 (mp0) cc_final: 0.7806 (mp0) REVERT: F 139 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8570 (tm-30) REVERT: G 28 ASN cc_start: 0.8580 (m-40) cc_final: 0.8374 (m110) REVERT: G 35 LYS cc_start: 0.9039 (mttp) cc_final: 0.8571 (mttp) REVERT: G 45 GLU cc_start: 0.9386 (mt-10) cc_final: 0.9153 (pp20) REVERT: G 55 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8323 (mm-30) REVERT: G 114 GLU cc_start: 0.8820 (mm-30) cc_final: 0.7863 (tp30) REVERT: G 129 GLU cc_start: 0.8509 (pt0) cc_final: 0.8152 (tp30) REVERT: J 31 GLU cc_start: 0.8305 (tp30) cc_final: 0.8071 (tp30) REVERT: J 37 ARG cc_start: 0.9160 (tpt-90) cc_final: 0.8450 (ttm170) REVERT: J 90 GLU cc_start: 0.8594 (pt0) cc_final: 0.8391 (pt0) REVERT: J 106 LYS cc_start: 0.9278 (tttm) cc_final: 0.9018 (ttmm) REVERT: J 128 ASN cc_start: 0.8939 (t0) cc_final: 0.8670 (t0) REVERT: K 8 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9330 (mt) REVERT: K 12 ASP cc_start: 0.8761 (p0) cc_final: 0.8526 (p0) REVERT: K 14 SER cc_start: 0.9439 (p) cc_final: 0.9147 (p) REVERT: K 45 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7230 (tm-30) REVERT: K 88 ASN cc_start: 0.8364 (t0) cc_final: 0.7758 (t0) REVERT: K 106 GLU cc_start: 0.7948 (mp0) cc_final: 0.7691 (mp0) REVERT: M 47 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7531 (tm-30) REVERT: M 60 GLN cc_start: 0.8480 (mm-40) cc_final: 0.7534 (mm-40) REVERT: M 75 GLU cc_start: 0.7051 (pp20) cc_final: 0.6136 (pp20) REVERT: M 95 LEU cc_start: 0.9619 (mt) cc_final: 0.9388 (mm) REVERT: M 104 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7845 (mt-10) REVERT: M 119 LEU cc_start: 0.9658 (mt) cc_final: 0.9421 (mp) REVERT: M 136 MET cc_start: 0.7612 (ttm) cc_final: 0.7352 (ttm) REVERT: N 57 THR cc_start: 0.9115 (m) cc_final: 0.8908 (t) REVERT: N 72 ASP cc_start: 0.8553 (t0) cc_final: 0.8241 (t0) REVERT: N 110 MET cc_start: 0.8891 (mmm) cc_final: 0.7937 (mmm) REVERT: O 4 LYS cc_start: 0.9279 (tppp) cc_final: 0.8957 (tppp) REVERT: O 17 LYS cc_start: 0.9457 (tppp) cc_final: 0.9240 (tppt) REVERT: O 46 GLU cc_start: 0.8423 (pp20) cc_final: 0.8180 (pp20) REVERT: O 61 GLN cc_start: 0.8761 (mm110) cc_final: 0.8453 (mm110) REVERT: O 104 GLN cc_start: 0.9188 (tt0) cc_final: 0.8479 (tt0) REVERT: O 108 ASP cc_start: 0.8544 (p0) cc_final: 0.8314 (p0) REVERT: P 6 LYS cc_start: 0.9220 (mtpt) cc_final: 0.8958 (mtpm) REVERT: P 7 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8254 (tm-30) REVERT: P 11 GLU cc_start: 0.8569 (pt0) cc_final: 0.8188 (pt0) REVERT: P 27 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8470 (tp30) REVERT: P 82 ASP cc_start: 0.8830 (t70) cc_final: 0.8604 (t0) REVERT: P 111 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8880 (ptmm) REVERT: Q 49 ASP cc_start: 0.8098 (m-30) cc_final: 0.7641 (m-30) REVERT: Q 59 GLN cc_start: 0.9104 (tt0) cc_final: 0.8796 (tt0) REVERT: Q 97 ASP cc_start: 0.8805 (t70) cc_final: 0.8292 (t0) REVERT: R 18 GLN cc_start: 0.8551 (mt0) cc_final: 0.8215 (mt0) REVERT: R 46 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7112 (tm-30) REVERT: R 60 LYS cc_start: 0.9161 (mtpp) cc_final: 0.8892 (mtpp) REVERT: S 52 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8272 (mt-10) REVERT: S 84 ARG cc_start: 0.9302 (mmt-90) cc_final: 0.8882 (mpt180) REVERT: S 96 ILE cc_start: 0.9251 (pt) cc_final: 0.8946 (pp) REVERT: T 6 ARG cc_start: 0.8623 (tpt-90) cc_final: 0.7954 (tpt170) REVERT: T 27 SER cc_start: 0.9275 (m) cc_final: 0.8930 (p) REVERT: T 37 ASP cc_start: 0.8704 (p0) cc_final: 0.8466 (p0) REVERT: T 91 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8676 (mm-40) REVERT: U 9 ASP cc_start: 0.8281 (m-30) cc_final: 0.8001 (m-30) REVERT: U 46 GLN cc_start: 0.9309 (mm-40) cc_final: 0.9083 (tp-100) REVERT: V 7 GLU cc_start: 0.8192 (mp0) cc_final: 0.7411 (mp0) REVERT: V 12 GLN cc_start: 0.8079 (pp30) cc_final: 0.7821 (pp30) REVERT: V 41 GLU cc_start: 0.8012 (pp20) cc_final: 0.7241 (pp20) REVERT: V 43 ASP cc_start: 0.8627 (t70) cc_final: 0.8405 (t0) REVERT: V 48 MET cc_start: 0.9177 (tpt) cc_final: 0.8968 (tpt) REVERT: V 49 ASN cc_start: 0.9142 (m-40) cc_final: 0.8878 (m-40) REVERT: V 70 ILE cc_start: 0.9489 (mt) cc_final: 0.9265 (mp) REVERT: V 73 LYS cc_start: 0.9303 (mtpp) cc_final: 0.9045 (mmmm) REVERT: W 29 GLU cc_start: 0.8324 (tt0) cc_final: 0.7932 (mt-10) REVERT: W 41 ARG cc_start: 0.9024 (mmp-170) cc_final: 0.8739 (mmp-170) REVERT: W 68 LYS cc_start: 0.9181 (tptp) cc_final: 0.8728 (tppp) REVERT: W 70 GLU cc_start: 0.7434 (pm20) cc_final: 0.7151 (pm20) REVERT: X 41 GLU cc_start: 0.8666 (tp30) cc_final: 0.7913 (tp30) REVERT: X 62 LYS cc_start: 0.9416 (mttt) cc_final: 0.9130 (mttp) REVERT: Y 11 VAL cc_start: 0.9640 (t) cc_final: 0.9259 (p) REVERT: Y 15 ASN cc_start: 0.9307 (m-40) cc_final: 0.8993 (m110) REVERT: Y 20 ASN cc_start: 0.8952 (m-40) cc_final: 0.8591 (m110) REVERT: Y 29 ARG cc_start: 0.9238 (ttp-110) cc_final: 0.8818 (ttp-170) REVERT: Y 30 MET cc_start: 0.8879 (mmt) cc_final: 0.8671 (mpp) REVERT: Y 31 GLN cc_start: 0.8905 (tt0) cc_final: 0.8677 (tt0) REVERT: Y 45 GLN cc_start: 0.8529 (mt0) cc_final: 0.8091 (mt0) REVERT: Y 49 ASP cc_start: 0.8806 (m-30) cc_final: 0.8494 (m-30) REVERT: Y 58 ASN cc_start: 0.9098 (m110) cc_final: 0.8456 (t0) REVERT: a 25 ARG cc_start: 0.7855 (mtp85) cc_final: 0.7632 (mtp85) REVERT: a 34 LEU cc_start: 0.9323 (tp) cc_final: 0.9104 (tp) REVERT: a 39 LYS cc_start: 0.9367 (tttt) cc_final: 0.9077 (pttt) REVERT: b 9 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8754 (p) REVERT: b 52 ARG cc_start: 0.8801 (ptm160) cc_final: 0.8563 (ptm160) REVERT: c 7 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7334 (mt-10) REVERT: c 28 ARG cc_start: 0.7237 (mpp-170) cc_final: 0.6561 (mpp-170) REVERT: c 33 LYS cc_start: 0.9015 (mtpp) cc_final: 0.8709 (mmmm) REVERT: c 40 ASP cc_start: 0.9377 (t0) cc_final: 0.9085 (t0) REVERT: c 44 ARG cc_start: 0.9138 (mtp180) cc_final: 0.8770 (mmm-85) REVERT: c 45 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8253 (mp10) REVERT: c 51 GLU cc_start: 0.7771 (tt0) cc_final: 0.6446 (tt0) REVERT: d 25 LYS cc_start: 0.9066 (tmmt) cc_final: 0.8778 (ttpt) REVERT: d 29 GLN cc_start: 0.8415 (mt0) cc_final: 0.8147 (mt0) REVERT: f 6 SER cc_start: 0.9368 (t) cc_final: 0.8770 (p) REVERT: f 9 LYS cc_start: 0.9335 (mtmm) cc_final: 0.8995 (mtpp) REVERT: g 44 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7802 (pp20) REVERT: g 56 GLU cc_start: 0.9034 (tp30) cc_final: 0.8575 (tp30) REVERT: g 58 ASN cc_start: 0.8596 (t0) cc_final: 0.8364 (m-40) REVERT: g 109 GLN cc_start: 0.8955 (mp10) cc_final: 0.8589 (mp10) REVERT: g 113 ARG cc_start: 0.9152 (mmm160) cc_final: 0.8784 (mmm160) REVERT: g 133 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7500 (tm-30) REVERT: g 138 THR cc_start: 0.9319 (m) cc_final: 0.9107 (p) REVERT: g 142 GLU cc_start: 0.8985 (tt0) cc_final: 0.8763 (tp30) REVERT: g 143 LYS cc_start: 0.9149 (mmtm) cc_final: 0.8927 (mmtt) REVERT: g 145 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8060 (pp20) REVERT: g 151 ILE cc_start: 0.9395 (pt) cc_final: 0.9069 (pp) REVERT: g 157 LEU cc_start: 0.9154 (mt) cc_final: 0.8856 (pt) REVERT: g 159 ASP cc_start: 0.9023 (m-30) cc_final: 0.8777 (m-30) REVERT: g 169 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8390 (mp0) REVERT: g 174 LYS cc_start: 0.9210 (mtpm) cc_final: 0.8958 (mmtt) REVERT: g 208 ARG cc_start: 0.8206 (mtt90) cc_final: 0.7642 (ttp-170) REVERT: g 223 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8028 (tm-30) REVERT: h 32 ASN cc_start: 0.8758 (m-40) cc_final: 0.8068 (m110) REVERT: h 36 ASP cc_start: 0.8892 (m-30) cc_final: 0.8384 (m-30) REVERT: h 41 GLN cc_start: 0.9286 (tt0) cc_final: 0.8658 (pp30) REVERT: h 44 THR cc_start: 0.9518 (m) cc_final: 0.9225 (p) REVERT: h 100 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7266 (tm-30) REVERT: h 102 ASN cc_start: 0.8514 (m-40) cc_final: 0.8301 (m-40) REVERT: h 181 ASP cc_start: 0.8571 (t0) cc_final: 0.8207 (t0) REVERT: i 4 TYR cc_start: 0.8953 (t80) cc_final: 0.8721 (t80) REVERT: i 141 ASP cc_start: 0.8245 (m-30) cc_final: 0.7758 (m-30) REVERT: i 181 THR cc_start: 0.9037 (m) cc_final: 0.8788 (m) REVERT: i 182 PHE cc_start: 0.9095 (t80) cc_final: 0.8443 (t80) REVERT: j 14 LYS cc_start: 0.9130 (mtpp) cc_final: 0.8887 (mtpp) REVERT: j 19 ASN cc_start: 0.8667 (t0) cc_final: 0.8217 (t0) REVERT: j 20 ARG cc_start: 0.9008 (ttp-170) cc_final: 0.8635 (ttp80) REVERT: j 147 MET cc_start: 0.8315 (ttt) cc_final: 0.8031 (ttt) REVERT: k 14 GLN cc_start: 0.9337 (mm110) cc_final: 0.8407 (mp10) REVERT: k 17 GLN cc_start: 0.9085 (pt0) cc_final: 0.8807 (pm20) REVERT: k 68 GLN cc_start: 0.8501 (pt0) cc_final: 0.7776 (pt0) REVERT: k 74 LEU cc_start: 0.9436 (tp) cc_final: 0.9164 (tp) REVERT: k 77 THR cc_start: 0.9339 (m) cc_final: 0.8936 (p) REVERT: k 91 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8362 (tpt-90) REVERT: k 92 THR cc_start: 0.9289 (m) cc_final: 0.8652 (p) REVERT: l 44 TYR cc_start: 0.9167 (m-10) cc_final: 0.8931 (m-80) REVERT: l 54 SER cc_start: 0.9176 (m) cc_final: 0.8806 (p) REVERT: l 68 ASN cc_start: 0.9372 (m-40) cc_final: 0.9169 (m-40) REVERT: l 74 GLU cc_start: 0.8418 (pt0) cc_final: 0.8175 (pm20) REVERT: l 101 MET cc_start: 0.9241 (mtm) cc_final: 0.8879 (mtm) REVERT: m 5 ASP cc_start: 0.8423 (t0) cc_final: 0.7758 (t0) REVERT: m 9 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8656 (t0) REVERT: m 13 ARG cc_start: 0.9253 (mtp85) cc_final: 0.8706 (mtp85) REVERT: m 42 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8073 (tm-30) REVERT: m 50 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7114 (tmmm) REVERT: m 52 GLU cc_start: 0.7551 (pm20) cc_final: 0.7175 (pm20) REVERT: m 58 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8143 (mp0) REVERT: m 60 GLU cc_start: 0.8718 (tt0) cc_final: 0.8498 (tm-30) REVERT: m 61 LEU cc_start: 0.9249 (mt) cc_final: 0.8721 (mt) REVERT: m 80 ARG cc_start: 0.8692 (ptt90) cc_final: 0.8173 (ptt90) REVERT: n 15 SER cc_start: 0.9093 (m) cc_final: 0.8836 (m) REVERT: n 19 VAL cc_start: 0.9481 (t) cc_final: 0.9184 (m) REVERT: n 25 ASN cc_start: 0.8806 (p0) cc_final: 0.8152 (p0) REVERT: n 27 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8659 (ptpp) REVERT: n 57 MET cc_start: 0.8088 (mmm) cc_final: 0.7296 (mmm) REVERT: n 59 GLU cc_start: 0.8806 (pm20) cc_final: 0.8371 (pm20) REVERT: n 91 ASP cc_start: 0.8832 (t0) cc_final: 0.8499 (t0) REVERT: n 94 LEU cc_start: 0.9469 (mt) cc_final: 0.9174 (mt) REVERT: n 115 LYS cc_start: 0.8593 (mttp) cc_final: 0.8316 (mttp) REVERT: n 126 GLN cc_start: 0.8348 (tt0) cc_final: 0.8056 (tt0) REVERT: n 130 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.5386 (mtm180) REVERT: o 24 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8752 (tm-30) REVERT: o 53 ILE cc_start: 0.9426 (pt) cc_final: 0.8856 (pp) REVERT: o 63 ASP cc_start: 0.7623 (m-30) cc_final: 0.7222 (m-30) REVERT: o 77 VAL cc_start: 0.9209 (t) cc_final: 0.9003 (t) REVERT: o 89 ARG cc_start: 0.8728 (ttp-110) cc_final: 0.8309 (ptt90) REVERT: o 97 ASP cc_start: 0.8513 (m-30) cc_final: 0.8195 (m-30) REVERT: p 30 THR cc_start: 0.9507 (m) cc_final: 0.8872 (p) REVERT: p 31 ILE cc_start: 0.9770 (mt) cc_final: 0.9498 (mm) REVERT: p 46 THR cc_start: 0.9145 (p) cc_final: 0.8916 (t) REVERT: p 64 GLN cc_start: 0.8762 (pt0) cc_final: 0.8348 (pp30) REVERT: p 65 VAL cc_start: 0.9458 (m) cc_final: 0.9195 (p) REVERT: p 68 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8407 (mt-10) REVERT: p 80 LYS cc_start: 0.8911 (mppt) cc_final: 0.8654 (mppt) REVERT: p 110 ILE cc_start: 0.9496 (mt) cc_final: 0.9267 (mp) REVERT: q 70 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8091 (mt-10) REVERT: q 74 LEU cc_start: 0.8664 (mm) cc_final: 0.8291 (mt) REVERT: q 75 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8259 (mm-40) REVERT: r 11 ASP cc_start: 0.8514 (m-30) cc_final: 0.8274 (t0) REVERT: r 27 LYS cc_start: 0.9251 (tttt) cc_final: 0.8960 (tppp) REVERT: r 31 LYS cc_start: 0.9427 (mttt) cc_final: 0.9220 (mtpp) REVERT: r 49 SER cc_start: 0.9330 (t) cc_final: 0.8760 (p) REVERT: r 72 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8772 (pt0) REVERT: r 97 VAL cc_start: 0.9444 (t) cc_final: 0.9188 (m) REVERT: r 104 THR cc_start: 0.9203 (m) cc_final: 0.8719 (p) REVERT: r 105 ASN cc_start: 0.8520 (m-40) cc_final: 0.8129 (m-40) REVERT: s 4 GLN cc_start: 0.9251 (mm110) cc_final: 0.8879 (mm-40) REVERT: s 14 VAL cc_start: 0.9504 (t) cc_final: 0.9243 (p) REVERT: s 26 GLU cc_start: 0.9157 (tt0) cc_final: 0.8897 (tm-30) REVERT: s 30 ILE cc_start: 0.9539 (mp) cc_final: 0.9258 (mp) REVERT: s 33 ASP cc_start: 0.8806 (t0) cc_final: 0.8410 (t0) REVERT: s 40 ASP cc_start: 0.8832 (m-30) cc_final: 0.8341 (m-30) REVERT: s 43 ASN cc_start: 0.9459 (m-40) cc_final: 0.9215 (m110) REVERT: s 90 ARG cc_start: 0.9085 (mtm-85) cc_final: 0.8884 (mtp180) REVERT: t 37 ASN cc_start: 0.9482 (m-40) cc_final: 0.9168 (m-40) REVERT: t 68 ASP cc_start: 0.8900 (m-30) cc_final: 0.8597 (m-30) REVERT: t 71 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.8855 (tppp) REVERT: t 80 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8051 (tm-30) REVERT: t 84 ARG cc_start: 0.8521 (ttp-170) cc_final: 0.8196 (ttp-170) REVERT: u 5 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.8874 (ptp90) REVERT: u 9 HIS cc_start: 0.8439 (m90) cc_final: 0.8214 (m90) REVERT: u 53 ASP cc_start: 0.8641 (t0) cc_final: 0.7735 (t70) REVERT: v 14 SER cc_start: 0.9170 (t) cc_final: 0.8937 (p) REVERT: v 15 ASP cc_start: 0.8698 (p0) cc_final: 0.8422 (p0) REVERT: v 48 ASP cc_start: 0.8496 (p0) cc_final: 0.8197 (p0) REVERT: v 69 LYS cc_start: 0.9319 (tttt) cc_final: 0.9014 (ttpp) REVERT: v 77 ARG cc_start: 0.8651 (ptm-80) cc_final: 0.8256 (ppp80) REVERT: w 25 ASP cc_start: 0.8501 (t0) cc_final: 0.8056 (t0) REVERT: w 31 ASN cc_start: 0.8859 (m-40) cc_final: 0.8401 (m110) REVERT: w 61 ARG cc_start: 0.8375 (mtt180) cc_final: 0.8149 (mtt90) REVERT: w 72 ASP cc_start: 0.9280 (p0) cc_final: 0.9008 (p0) REVERT: x 12 ASP cc_start: 0.8571 (m-30) cc_final: 0.8040 (m-30) REVERT: x 21 LYS cc_start: 0.9296 (ttmm) cc_final: 0.8993 (tmmt) REVERT: x 27 ASP cc_start: 0.7787 (t0) cc_final: 0.7440 (t0) REVERT: x 35 SER cc_start: 0.8606 (m) cc_final: 0.8234 (m) REVERT: x 37 ARG cc_start: 0.8745 (ptm-80) cc_final: 0.8436 (ptm-80) REVERT: x 70 LYS cc_start: 0.8985 (mttm) cc_final: 0.8321 (mmmt) REVERT: x 73 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8501 (mp0) REVERT: y 14 SER cc_start: 0.9306 (m) cc_final: 0.8992 (p) REVERT: y 28 MET cc_start: 0.9208 (ttp) cc_final: 0.8902 (ttp) REVERT: y 55 GLN cc_start: 0.9155 (tt0) cc_final: 0.8747 (tt0) REVERT: y 67 ILE cc_start: 0.9405 (pt) cc_final: 0.9205 (pp) REVERT: y 70 ASN cc_start: 0.9316 (m110) cc_final: 0.9091 (m-40) REVERT: y 78 ASN cc_start: 0.9081 (m-40) cc_final: 0.8361 (m110) REVERT: z 4 ILE cc_start: 0.8665 (mp) cc_final: 0.8284 (mp) REVERT: z 5 LYS cc_start: 0.8942 (tmmt) cc_final: 0.8727 (tmmt) REVERT: z 20 LYS cc_start: 0.9089 (mtpm) cc_final: 0.8827 (mppt) outliers start: 213 outliers final: 80 residues processed: 1962 average time/residue: 1.9959 time to fit residues: 5710.4093 Evaluate side-chains 1836 residues out of total 4670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1742 time to evaluate : 6.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain E residue 7 TYR Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 111 LYS Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 34 ASP Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 191 THR Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 91 ARG Chi-restraints excluded: chain k residue 100 SER Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 5 ARG Chi-restraints excluded: chain l residue 42 ILE Chi-restraints excluded: chain l residue 57 SER Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain m residue 9 ASP Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 50 LYS Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 62 ASP Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain n residue 130 ARG Chi-restraints excluded: chain o residue 28 THR Chi-restraints excluded: chain o residue 96 VAL Chi-restraints excluded: chain p residue 50 SER Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 15 LYS Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 21 SER Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 46 SER Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 71 LYS Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain t residue 80 GLN Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain x residue 33 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain y residue 66 LEU Chi-restraints excluded: chain z residue 28 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 509 optimal weight: 6.9990 chunk 284 optimal weight: 10.0000 chunk 762 optimal weight: 9.9990 chunk 623 optimal weight: 4.9990 chunk 252 optimal weight: 10.0000 chunk 917 optimal weight: 5.9990 chunk 991 optimal weight: 0.0370 chunk 817 optimal weight: 8.9990 chunk 910 optimal weight: 0.8980 chunk 312 optimal weight: 10.0000 chunk 736 optimal weight: 10.0000 overall best weight: 3.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN B 143 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN C 130 GLN E 23 ASN ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 HIS F 104 ASN J 86 GLN J 131 ASN L 93 ASN N 18 GLN P 12 GLN Q 71 GLN R 43 ASN R 86 GLN S 31 GLN U 53 ASN W 40 GLN X 6 GLN X 17 ASN X 23 ASN b 4 GLN g 51 ASN ** g 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 178 ASN ** h 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 140 ASN h 185 ASN i 36 GLN i 40 GLN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 131 ASN i 152 GLN i 198 HIS k 46 GLN k 52 ASN k 94 HIS l 28 ASN l 122 ASN l 130 ASN n 4 ASN n 5 GLN ** o 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 5 ASN t 20 ASN t 62 GLN x 14 HIS y 3 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 156892 Z= 0.259 Angle : 0.620 13.657 234803 Z= 0.335 Chirality : 0.035 0.383 29920 Planarity : 0.006 0.131 12502 Dihedral : 23.584 179.048 78646 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.29 % Allowed : 22.74 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.11), residues: 5606 helix: 0.33 (0.12), residues: 1903 sheet: -1.06 (0.15), residues: 1091 loop : -0.96 (0.11), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP s 42 HIS 0.009 0.001 HIS M 13 PHE 0.019 0.002 PHE F 52 TYR 0.021 0.002 TYR R 2 ARG 0.010 0.001 ARG K 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11212 Ramachandran restraints generated. 5606 Oldfield, 0 Emsley, 5606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11212 Ramachandran restraints generated. 5606 Oldfield, 0 Emsley, 5606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2006 residues out of total 4670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1759 time to evaluate : 6.300 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: B 66 ASP cc_start: 0.9010 (t0) cc_final: 0.8639 (t0) REVERT: B 117 GLN cc_start: 0.8687 (tt0) cc_final: 0.8206 (tt0) REVERT: B 163 GLN cc_start: 0.8531 (mm110) cc_final: 0.8041 (mm-40) REVERT: C 1 MET cc_start: 0.7556 (tmm) cc_final: 0.7339 (tmm) REVERT: C 39 ASP cc_start: 0.9062 (p0) cc_final: 0.8597 (p0) REVERT: C 173 GLN cc_start: 0.8455 (mt0) cc_final: 0.8106 (mt0) REVERT: D 67 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8614 (mtp180) REVERT: D 136 GLN cc_start: 0.9158 (tp-100) cc_final: 0.8911 (tp-100) REVERT: D 156 ASN cc_start: 0.9236 (m-40) cc_final: 0.8718 (m-40) REVERT: E 33 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8677 (ptpp) REVERT: E 35 THR cc_start: 0.9398 (m) cc_final: 0.8798 (p) REVERT: E 72 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8987 (ptpp) REVERT: E 81 GLN cc_start: 0.8887 (tt0) cc_final: 0.8607 (tm-30) REVERT: E 83 TYR cc_start: 0.8722 (m-10) cc_final: 0.8514 (m-10) REVERT: E 101 GLU cc_start: 0.8746 (tt0) cc_final: 0.8528 (mt-10) REVERT: E 122 PHE cc_start: 0.8282 (m-80) cc_final: 0.8019 (m-10) REVERT: E 127 ASN cc_start: 0.7297 (m-40) cc_final: 0.7046 (m-40) REVERT: E 130 MET cc_start: 0.8739 (ppp) cc_final: 0.8446 (ppp) REVERT: F 60 ASP cc_start: 0.8495 (p0) cc_final: 0.8090 (p0) REVERT: F 101 ASN cc_start: 0.8840 (p0) cc_final: 0.8320 (p0) REVERT: F 116 GLN cc_start: 0.9104 (tp40) cc_final: 0.8618 (tp-100) REVERT: F 121 ILE cc_start: 0.9549 (mp) cc_final: 0.8996 (pp) REVERT: F 130 GLU cc_start: 0.8051 (mp0) cc_final: 0.7828 (mp0) REVERT: F 139 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8546 (tm-30) REVERT: G 28 ASN cc_start: 0.8595 (m-40) cc_final: 0.8370 (m110) REVERT: G 35 LYS cc_start: 0.8959 (mttp) cc_final: 0.8620 (mttp) REVERT: G 45 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9116 (pp20) REVERT: G 70 GLU cc_start: 0.6973 (tm-30) cc_final: 0.6089 (pt0) REVERT: G 114 GLU cc_start: 0.8762 (mm-30) cc_final: 0.7753 (tp30) REVERT: G 129 GLU cc_start: 0.8492 (pt0) cc_final: 0.8099 (mm-30) REVERT: J 31 GLU cc_start: 0.8439 (tp30) cc_final: 0.7990 (tp30) REVERT: J 90 GLU cc_start: 0.8623 (pt0) cc_final: 0.8394 (pt0) REVERT: J 106 LYS cc_start: 0.9311 (tttm) cc_final: 0.9078 (ttmm) REVERT: K 8 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9248 (mt) REVERT: K 12 ASP cc_start: 0.8821 (p0) cc_final: 0.8603 (p0) REVERT: K 14 SER cc_start: 0.9469 (p) cc_final: 0.9216 (p) REVERT: K 45 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7519 (tm-30) REVERT: K 88 ASN cc_start: 0.8328 (t0) cc_final: 0.7760 (t0) REVERT: K 106 GLU cc_start: 0.8162 (mp0) cc_final: 0.7865 (mp0) REVERT: M 47 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7577 (tm-30) REVERT: M 90 GLU cc_start: 0.8035 (tp30) cc_final: 0.7749 (tp30) REVERT: M 95 LEU cc_start: 0.9625 (mt) cc_final: 0.9409 (mm) REVERT: M 104 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7707 (mt-10) REVERT: M 110 GLU cc_start: 0.8239 (tm-30) cc_final: 0.8019 (tm-30) REVERT: M 115 GLU cc_start: 0.8466 (tp30) cc_final: 0.7811 (tp30) REVERT: M 119 LEU cc_start: 0.9714 (mt) cc_final: 0.9406 (mp) REVERT: M 136 MET cc_start: 0.7697 (ttm) cc_final: 0.7447 (ttm) REVERT: N 35 LYS cc_start: 0.9366 (ttpt) cc_final: 0.9126 (mtpt) REVERT: N 57 THR cc_start: 0.9072 (m) cc_final: 0.8600 (p) REVERT: N 72 ASP cc_start: 0.8647 (t0) cc_final: 0.8334 (t0) REVERT: N 110 MET cc_start: 0.8875 (mmm) cc_final: 0.7937 (mmm) REVERT: O 24 THR cc_start: 0.9520 (m) cc_final: 0.9121 (p) REVERT: O 55 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7806 (mt-10) REVERT: O 60 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7195 (pp20) REVERT: O 104 GLN cc_start: 0.9118 (tt0) cc_final: 0.8506 (tt0) REVERT: O 108 ASP cc_start: 0.8620 (p0) cc_final: 0.8370 (p0) REVERT: P 7 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8180 (tm-30) REVERT: P 11 GLU cc_start: 0.8573 (pt0) cc_final: 0.8236 (pt0) REVERT: P 27 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8402 (tp30) REVERT: P 82 ASP cc_start: 0.8854 (t70) cc_final: 0.8646 (t0) REVERT: P 111 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8908 (ptmm) REVERT: Q 11 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.8061 (ttp-170) REVERT: Q 49 ASP cc_start: 0.8156 (m-30) cc_final: 0.7754 (m-30) REVERT: Q 59 GLN cc_start: 0.9098 (tt0) cc_final: 0.8840 (tt0) REVERT: Q 97 ASP cc_start: 0.8800 (t70) cc_final: 0.8280 (t0) REVERT: R 18 GLN cc_start: 0.8529 (mt0) cc_final: 0.8138 (mt0) REVERT: R 46 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7351 (tm-30) REVERT: R 60 LYS cc_start: 0.9224 (mtpp) cc_final: 0.8934 (mtpp) REVERT: S 52 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8265 (mt-10) REVERT: S 96 ILE cc_start: 0.9303 (pt) cc_final: 0.8981 (pp) REVERT: T 6 ARG cc_start: 0.8507 (tpt-90) cc_final: 0.7777 (tpt170) REVERT: T 27 SER cc_start: 0.9298 (m) cc_final: 0.8937 (p) REVERT: T 52 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: T 91 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8765 (mm-40) REVERT: U 9 ASP cc_start: 0.8356 (m-30) cc_final: 0.8075 (m-30) REVERT: U 37 GLU cc_start: 0.8035 (pp20) cc_final: 0.7773 (pp20) REVERT: U 46 GLN cc_start: 0.9281 (mm-40) cc_final: 0.9035 (tp-100) REVERT: V 7 GLU cc_start: 0.8217 (mp0) cc_final: 0.7303 (mp0) REVERT: V 12 GLN cc_start: 0.8112 (pp30) cc_final: 0.7816 (pp30) REVERT: V 41 GLU cc_start: 0.8069 (pp20) cc_final: 0.7292 (pp20) REVERT: V 49 ASN cc_start: 0.9146 (m-40) cc_final: 0.8915 (m110) REVERT: V 90 ASP cc_start: 0.8830 (m-30) cc_final: 0.8561 (m-30) REVERT: W 29 GLU cc_start: 0.8359 (tt0) cc_final: 0.7886 (mt-10) REVERT: W 56 ASP cc_start: 0.9372 (p0) cc_final: 0.9134 (p0) REVERT: W 68 LYS cc_start: 0.9113 (tptp) cc_final: 0.8768 (tppp) REVERT: W 70 GLU cc_start: 0.7642 (pm20) cc_final: 0.7349 (pm20) REVERT: X 41 GLU cc_start: 0.8510 (tp30) cc_final: 0.8184 (tp30) REVERT: X 44 LYS cc_start: 0.9010 (mmtm) cc_final: 0.8400 (mmtt) REVERT: X 62 LYS cc_start: 0.9413 (mttt) cc_final: 0.9123 (mttp) REVERT: Y 11 VAL cc_start: 0.9516 (t) cc_final: 0.9098 (p) REVERT: Y 15 ASN cc_start: 0.9230 (m-40) cc_final: 0.8906 (m110) REVERT: Y 20 ASN cc_start: 0.8987 (m-40) cc_final: 0.8746 (m-40) REVERT: Y 31 GLN cc_start: 0.8933 (tt0) cc_final: 0.8698 (tt0) REVERT: Y 45 GLN cc_start: 0.8509 (mt0) cc_final: 0.7982 (mt0) REVERT: Y 49 ASP cc_start: 0.8812 (m-30) cc_final: 0.8477 (m-30) REVERT: Y 58 ASN cc_start: 0.8862 (m110) cc_final: 0.8288 (t0) REVERT: a 34 LEU cc_start: 0.9293 (tp) cc_final: 0.8995 (tp) REVERT: a 59 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8461 (ppp-140) REVERT: c 7 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7337 (mt-10) REVERT: c 28 ARG cc_start: 0.7322 (mpp-170) cc_final: 0.6794 (mpp-170) REVERT: c 33 LYS cc_start: 0.9053 (mtpp) cc_final: 0.8704 (mmmm) REVERT: c 44 ARG cc_start: 0.9097 (mtp180) cc_final: 0.8777 (mmm-85) REVERT: c 45 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8243 (mp10) REVERT: c 51 GLU cc_start: 0.7818 (tt0) cc_final: 0.6501 (tt0) REVERT: d 25 LYS cc_start: 0.9092 (tmmt) cc_final: 0.8803 (ttpt) REVERT: d 29 GLN cc_start: 0.8418 (mt0) cc_final: 0.8107 (mt0) REVERT: e 52 LYS cc_start: 0.8833 (tmtt) cc_final: 0.8402 (tttp) REVERT: f 9 LYS cc_start: 0.9384 (mtmm) cc_final: 0.9108 (mtpp) REVERT: f 18 LYS cc_start: 0.9512 (OUTLIER) cc_final: 0.9137 (ttpm) REVERT: g 49 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.7682 (mmp) REVERT: g 56 GLU cc_start: 0.8926 (tp30) cc_final: 0.8492 (tp30) REVERT: g 136 MET cc_start: 0.8648 (ppp) cc_final: 0.8286 (ppp) REVERT: g 142 GLU cc_start: 0.9056 (tt0) cc_final: 0.8729 (tp30) REVERT: g 145 GLU cc_start: 0.8666 (pp20) cc_final: 0.8125 (pp20) REVERT: g 151 ILE cc_start: 0.9375 (pt) cc_final: 0.9078 (pp) REVERT: g 157 LEU cc_start: 0.9218 (mt) cc_final: 0.8876 (pt) REVERT: g 159 ASP cc_start: 0.9002 (m-30) cc_final: 0.8700 (m-30) REVERT: g 167 ASP cc_start: 0.8332 (p0) cc_final: 0.7981 (p0) REVERT: g 168 HIS cc_start: 0.8408 (t70) cc_final: 0.7986 (t-90) REVERT: g 169 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8636 (mm-30) REVERT: g 174 LYS cc_start: 0.9156 (mtpm) cc_final: 0.8884 (mmtt) REVERT: g 194 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7701 (m-30) REVERT: g 223 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8293 (tm-30) REVERT: h 32 ASN cc_start: 0.8533 (m-40) cc_final: 0.8071 (m110) REVERT: h 36 ASP cc_start: 0.8644 (m-30) cc_final: 0.8432 (m-30) REVERT: h 41 GLN cc_start: 0.9303 (tt0) cc_final: 0.8707 (pp30) REVERT: h 44 THR cc_start: 0.9496 (m) cc_final: 0.9168 (p) REVERT: h 58 GLU cc_start: 0.8323 (tt0) cc_final: 0.8070 (tt0) REVERT: h 100 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7361 (tm-30) REVERT: h 181 ASP cc_start: 0.8577 (t0) cc_final: 0.8209 (t0) REVERT: i 4 TYR cc_start: 0.8995 (t80) cc_final: 0.8781 (t80) REVERT: i 141 ASP cc_start: 0.8295 (m-30) cc_final: 0.7799 (m-30) REVERT: i 182 PHE cc_start: 0.9005 (t80) cc_final: 0.8383 (t80) REVERT: j 14 LYS cc_start: 0.8962 (mtpp) cc_final: 0.8459 (mtpp) REVERT: j 20 ARG cc_start: 0.8948 (ttp-170) cc_final: 0.8703 (ttp80) REVERT: j 116 GLU cc_start: 0.8436 (tt0) cc_final: 0.8079 (tt0) REVERT: j 131 THR cc_start: 0.9241 (p) cc_final: 0.9004 (p) REVERT: j 147 MET cc_start: 0.8541 (ttt) cc_final: 0.8157 (ttt) REVERT: k 14 GLN cc_start: 0.9356 (mm110) cc_final: 0.8916 (mp10) REVERT: k 40 GLU cc_start: 0.8114 (mp0) cc_final: 0.7868 (mp0) REVERT: k 74 LEU cc_start: 0.9440 (tp) cc_final: 0.9182 (tp) REVERT: k 77 THR cc_start: 0.9282 (m) cc_final: 0.8995 (p) REVERT: k 87 SER cc_start: 0.8718 (p) cc_final: 0.8492 (p) REVERT: k 93 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8345 (pmtt) REVERT: k 94 HIS cc_start: 0.8260 (m90) cc_final: 0.7736 (m90) REVERT: k 96 VAL cc_start: 0.9314 (m) cc_final: 0.9080 (p) REVERT: l 44 TYR cc_start: 0.9159 (m-10) cc_final: 0.8887 (m-80) REVERT: l 54 SER cc_start: 0.9252 (m) cc_final: 0.8959 (p) REVERT: l 68 ASN cc_start: 0.9396 (m-40) cc_final: 0.9154 (m-40) REVERT: l 74 GLU cc_start: 0.8430 (pt0) cc_final: 0.8215 (pm20) REVERT: l 101 MET cc_start: 0.9184 (mtm) cc_final: 0.8902 (mtm) REVERT: l 136 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8684 (mmtt) REVERT: m 5 ASP cc_start: 0.8482 (t0) cc_final: 0.7818 (t0) REVERT: m 7 ILE cc_start: 0.9608 (mt) cc_final: 0.9231 (mt) REVERT: m 9 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8685 (t0) REVERT: m 13 ARG cc_start: 0.9277 (mtp85) cc_final: 0.8881 (mtp85) REVERT: m 42 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8090 (tm-30) REVERT: m 50 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7050 (tmmm) REVERT: m 52 GLU cc_start: 0.7663 (pm20) cc_final: 0.7398 (pm20) REVERT: m 60 GLU cc_start: 0.8754 (tt0) cc_final: 0.8482 (tm-30) REVERT: m 61 LEU cc_start: 0.9257 (mt) cc_final: 0.8747 (mt) REVERT: n 15 SER cc_start: 0.9118 (m) cc_final: 0.8854 (m) REVERT: n 19 VAL cc_start: 0.9433 (t) cc_final: 0.8990 (m) REVERT: n 25 ASN cc_start: 0.8741 (p0) cc_final: 0.8330 (p0) REVERT: n 61 LEU cc_start: 0.9383 (pt) cc_final: 0.9103 (pp) REVERT: n 63 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9041 (pp) REVERT: n 88 MET cc_start: 0.8912 (mtm) cc_final: 0.8378 (mmm) REVERT: n 89 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8095 (pp20) REVERT: n 91 ASP cc_start: 0.8797 (t0) cc_final: 0.8431 (t70) REVERT: n 94 LEU cc_start: 0.9457 (mt) cc_final: 0.9099 (mt) REVERT: n 130 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.5393 (mtm180) REVERT: o 8 ILE cc_start: 0.9122 (mm) cc_final: 0.8282 (pp) REVERT: o 15 HIS cc_start: 0.8580 (p-80) cc_final: 0.8370 (p-80) REVERT: o 47 GLU cc_start: 0.8505 (tt0) cc_final: 0.8170 (tp30) REVERT: o 53 ILE cc_start: 0.9470 (pt) cc_final: 0.9254 (pp) REVERT: o 57 VAL cc_start: 0.8728 (p) cc_final: 0.8455 (t) REVERT: o 58 ASN cc_start: 0.7739 (m110) cc_final: 0.7315 (m110) REVERT: p 30 THR cc_start: 0.9478 (m) cc_final: 0.8973 (p) REVERT: p 56 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7492 (mtm-85) REVERT: p 68 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8568 (mt-10) REVERT: p 85 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8486 (mmm) REVERT: p 110 ILE cc_start: 0.9388 (mt) cc_final: 0.9076 (mp) REVERT: q 70 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8181 (mt-10) REVERT: q 74 LEU cc_start: 0.8694 (mm) cc_final: 0.8430 (mm) REVERT: q 75 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8188 (mm-40) REVERT: r 7 ILE cc_start: 0.9374 (tp) cc_final: 0.9124 (pp) REVERT: r 11 ASP cc_start: 0.8525 (m-30) cc_final: 0.8271 (t0) REVERT: r 27 LYS cc_start: 0.9260 (tttt) cc_final: 0.9052 (tppp) REVERT: r 69 LEU cc_start: 0.9387 (tp) cc_final: 0.8983 (tp) REVERT: r 72 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8751 (pt0) REVERT: r 97 VAL cc_start: 0.9468 (t) cc_final: 0.9235 (m) REVERT: r 104 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.8778 (p) REVERT: r 105 ASN cc_start: 0.8541 (m-40) cc_final: 0.8012 (m110) REVERT: s 3 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8837 (mttp) REVERT: s 4 GLN cc_start: 0.9190 (mm110) cc_final: 0.8561 (mm-40) REVERT: s 10 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8567 (mm-30) REVERT: s 30 ILE cc_start: 0.9475 (mp) cc_final: 0.9169 (mp) REVERT: s 33 ASP cc_start: 0.8748 (t0) cc_final: 0.8425 (t0) REVERT: s 40 ASP cc_start: 0.8838 (m-30) cc_final: 0.8318 (m-30) REVERT: s 43 ASN cc_start: 0.9459 (m-40) cc_final: 0.9237 (m110) REVERT: t 37 ASN cc_start: 0.9512 (m-40) cc_final: 0.9258 (m-40) REVERT: t 68 ASP cc_start: 0.8808 (m-30) cc_final: 0.8490 (m-30) REVERT: t 71 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.8900 (tppp) REVERT: t 80 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8386 (tp40) REVERT: t 84 ARG cc_start: 0.8676 (ttp-170) cc_final: 0.8473 (ttp-170) REVERT: u 35 ARG cc_start: 0.8069 (ttt-90) cc_final: 0.7818 (ttt-90) REVERT: u 53 ASP cc_start: 0.8947 (t0) cc_final: 0.8085 (t70) REVERT: v 6 ARG cc_start: 0.8573 (ttp-110) cc_final: 0.8055 (ttm170) REVERT: v 14 SER cc_start: 0.9154 (t) cc_final: 0.8953 (p) REVERT: v 15 ASP cc_start: 0.8617 (p0) cc_final: 0.8334 (p0) REVERT: v 65 ARG cc_start: 0.8655 (ptt-90) cc_final: 0.8254 (ptt-90) REVERT: v 69 LYS cc_start: 0.9323 (tttt) cc_final: 0.9015 (ttpp) REVERT: v 77 ARG cc_start: 0.8713 (ptm-80) cc_final: 0.8166 (ptm-80) REVERT: w 25 ASP cc_start: 0.8578 (t0) cc_final: 0.8209 (t0) REVERT: w 61 ARG cc_start: 0.8247 (mtt180) cc_final: 0.8034 (mtt90) REVERT: w 72 ASP cc_start: 0.9279 (p0) cc_final: 0.8993 (p0) REVERT: x 12 ASP cc_start: 0.8600 (m-30) cc_final: 0.8061 (m-30) REVERT: x 21 LYS cc_start: 0.9316 (ttmm) cc_final: 0.8596 (tmmt) REVERT: x 27 ASP cc_start: 0.8015 (t0) cc_final: 0.7800 (t0) REVERT: x 35 SER cc_start: 0.8587 (m) cc_final: 0.8165 (m) REVERT: y 14 SER cc_start: 0.9281 (m) cc_final: 0.9030 (p) REVERT: y 28 MET cc_start: 0.9210 (ttp) cc_final: 0.8963 (ttp) REVERT: y 55 GLN cc_start: 0.9141 (tt0) cc_final: 0.8827 (tt0) REVERT: y 67 ILE cc_start: 0.9444 (pt) cc_final: 0.9218 (pp) REVERT: y 70 ASN cc_start: 0.9268 (m110) cc_final: 0.9057 (m-40) REVERT: y 80 THR cc_start: 0.9525 (m) cc_final: 0.9123 (p) REVERT: z 5 LYS cc_start: 0.8944 (tmmt) cc_final: 0.8735 (tmmm) outliers start: 247 outliers final: 119 residues processed: 1846 average time/residue: 1.8983 time to fit residues: 5163.0538 Evaluate side-chains 1831 residues out of total 4670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1689 time to evaluate : 5.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 111 LYS Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 52 GLU Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 41 ARG Chi-restraints excluded: chain W residue 72 LYS Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 24 ILE Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 59 ARG Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain f residue 18 LYS Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain g residue 49 MET Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 194 ASP Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 34 ASP Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 191 THR Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 140 THR Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 93 LYS Chi-restraints excluded: chain k residue 100 SER Chi-restraints excluded: chain k residue 102 MET Chi-restraints excluded: chain l residue 45 SER Chi-restraints excluded: chain l residue 57 SER Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 136 LYS Chi-restraints excluded: chain m residue 9 ASP Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 50 LYS Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 62 ASP Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain n residue 130 ARG Chi-restraints excluded: chain o residue 28 THR Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain o residue 96 VAL Chi-restraints excluded: chain p residue 50 SER Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain p residue 85 MET Chi-restraints excluded: chain q residue 15 LYS Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 46 SER Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 76 SER Chi-restraints excluded: chain r residue 102 THR Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 3 LYS Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain s residue 74 LEU Chi-restraints excluded: chain t residue 71 LYS Chi-restraints excluded: chain t residue 80 GLN Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain w residue 36 SER Chi-restraints excluded: chain x residue 33 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 77 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain z residue 28 VAL Chi-restraints excluded: chain z residue 68 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 906 optimal weight: 30.0000 chunk 690 optimal weight: 9.9990 chunk 476 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 438 optimal weight: 10.0000 chunk 616 optimal weight: 0.8980 chunk 921 optimal weight: 3.9990 chunk 975 optimal weight: 9.9990 chunk 481 optimal weight: 3.9990 chunk 873 optimal weight: 5.9990 chunk 262 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: