Starting phenix.real_space_refine on Fri Mar 1 09:20:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lzc_4123/03_2024/5lzc_4123_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lzc_4123/03_2024/5lzc_4123.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lzc_4123/03_2024/5lzc_4123_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lzc_4123/03_2024/5lzc_4123_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lzc_4123/03_2024/5lzc_4123_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lzc_4123/03_2024/5lzc_4123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lzc_4123/03_2024/5lzc_4123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lzc_4123/03_2024/5lzc_4123_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lzc_4123/03_2024/5lzc_4123_updated.pdb" } resolution = 4.8 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= 0.020 sd= 0.191 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Se 1 7.20 5 Zn 2 6.06 5 P 4788 5.49 5 Mg 1 5.21 5 S 169 5.16 5 C 77291 2.51 5 N 28458 2.21 5 O 42271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b ARG 107": "NH1" <-> "NH2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c ARG 125": "NH1" <-> "NH2" Residue "c ARG 135": "NH1" <-> "NH2" Residue "f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "o PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "z ARG 27": "NH1" <-> "NH2" Residue "z ARG 181": "NH1" <-> "NH2" Residue "z TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 361": "NH1" <-> "NH2" Residue "z ARG 387": "NH1" <-> "NH2" Residue "z ARG 444": "NH1" <-> "NH2" Residue "z ARG 466": "NH1" <-> "NH2" Residue "z ARG 510": "NH1" <-> "NH2" Residue "z ARG 543": "NH1" <-> "NH2" Residue "z TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 47": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "H PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "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 TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "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 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "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 71": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "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 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "V PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 39": "NH1" <-> "NH2" Residue "0 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "6 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 152981 Number of models: 1 Model: "" Number of chains: 64 Chain: "a" Number of atoms: 33029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33029 Classifications: {'RNA': 1539} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 118, 'rna2p_pyr': 90, 'rna3p': 10, 'rna3p_pur': 750, 'rna3p_pyr': 570} Link IDs: {'rna2p': 209, 'rna3p': 1329} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "b" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "c" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "f" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "g" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 794 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 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: "q" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 505 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "s" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "u" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 496 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "v" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1642 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p': 3, 'rna3p_pur': 32, 'rna3p_pyr': 28} Link IDs: {'rna2p': 12, 'rna3p': 64} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "x" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1025 Classifications: {'RNA': 48} Modifications used: {'p5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 16, 'rna3p_pyr': 16} Link IDs: {'rna2p': 15, 'rna3p': 32} Chain: "y" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 2031 Classifications: {'RNA': 95} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p': 3, 'rna3p_pur': 38, 'rna3p_pyr': 38} Link IDs: {'rna2p': 15, 'rna3p': 79} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "z" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4853 Classifications: {'peptide': 614} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 586} Chain: "A" Number of atoms: 62335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62335 Classifications: {'RNA': 2903} Modifications used: {'p5*END': 1, 'rna2p': 7, 'rna2p_pur': 275, 'rna2p_pyr': 151, 'rna3p': 17, 'rna3p_pur': 1391, 'rna3p_pyr': 1062} Link IDs: {'rna2p': 433, 'rna3p': 2469} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "B" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2570 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 56, 'rna3p_pyr': 51} Link IDs: {'rna2p': 13, 'rna3p': 106} Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" 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: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "H" 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: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} 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: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} 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: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} 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: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} 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: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "0" 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: "1" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" 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: "3" 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: "4" 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: "6" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "w" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "v" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} 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: "y" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'SEC:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A148N SG CYS 4 14 182.569 113.810 138.023 1.00228.57 S ATOM A14HL SG CYS 6 16 119.233 122.784 231.479 1.00279.60 S ATOM A14HX SG CYS 6 18 118.722 118.475 230.296 1.00224.02 S ATOM A14LV SG CYS 6 37 122.508 122.085 230.413 1.00268.17 S ATOM A14MG SG CYS 6 40 121.859 118.878 229.223 1.00298.38 S Time building chain proxies: 56.90, per 1000 atoms: 0.37 Number of scatterers: 152981 At special positions: 0 Unit cell: (240.12, 278.4, 250.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Se 1 33.99 Zn 2 29.99 S 169 16.00 P 4788 15.00 Mg 1 11.99 O 42271 8.00 N 28458 7.00 C 77291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 27 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 70.64 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" ND1 HIS 4 33 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 14 " pdb=" ZN 6 100 " pdb="ZN ZN 6 100 " - pdb=" SG CYS 6 37 " pdb="ZN ZN 6 100 " - pdb=" SG CYS 6 16 " pdb="ZN ZN 6 100 " - pdb=" SG CYS 6 40 " pdb="ZN ZN 6 100 " - pdb=" SG CYS 6 18 " Number of angles added : 6 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11824 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: 203 helices and 75 sheets defined 39.5% alpha, 17.5% beta 1609 base pairs and 2438 stacking pairs defined. Time for finding SS restraints: 75.61 Creating SS restraints... Processing helix chain 'b' and resid 8 through 13 removed outlier: 3.783A pdb=" N GLY b 12 " --> pdb=" O MET b 8 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL b 13 " --> pdb=" O LEU b 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 8 through 13' Processing helix chain 'b' and resid 26 through 31 removed outlier: 4.148A pdb=" N ILE b 30 " --> pdb=" O MET b 26 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N PHE b 31 " --> pdb=" O LYS b 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 26 through 31' Processing helix chain 'b' and resid 43 through 63 Proline residue: b 47 - end of helix removed outlier: 3.863A pdb=" N ARG b 62 " --> pdb=" O LYS b 58 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS b 63 " --> pdb=" O ILE b 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 87 removed outlier: 4.620A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA b 82 " --> pdb=" O ALA b 78 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N CYS b 86 " --> pdb=" O ALA b 82 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 4.743A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP b 122 " --> pdb=" O THR b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 147 Processing helix chain 'b' and resid 164 through 169 removed outlier: 4.116A pdb=" N GLU b 168 " --> pdb=" O ASP b 164 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS b 169 " --> pdb=" O ALA b 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 164 through 169' Processing helix chain 'b' and resid 170 through 179 removed outlier: 4.184A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY b 179 " --> pdb=" O ALA b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 191 through 196 removed outlier: 4.757A pdb=" N VAL b 195 " --> pdb=" O ASP b 191 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASP b 196 " --> pdb=" O PRO b 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 191 through 196' Processing helix chain 'b' and resid 205 through 224 Processing helix chain 'c' and resid 5 through 11 Processing helix chain 'c' and resid 27 through 47 Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.868A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.740A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.802A pdb=" N LEU c 143 " --> pdb=" O ASN c 139 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY c 144 " --> pdb=" O ALA c 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 15 removed outlier: 4.491A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 Processing helix chain 'd' and resid 67 through 82 removed outlier: 5.302A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 removed outlier: 3.816A pdb=" N ARG d 96 " --> pdb=" O LEU d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 105 removed outlier: 3.532A pdb=" N GLY d 105 " --> pdb=" O VAL d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 120 removed outlier: 3.805A pdb=" N LYS d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 145 through 150 removed outlier: 5.264A pdb=" N LYS d 150 " --> pdb=" O GLU d 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 165 removed outlier: 3.535A pdb=" N ALA d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN d 163 " --> pdb=" O GLU d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 191 removed outlier: 4.025A pdb=" N LEU d 190 " --> pdb=" O GLU d 186 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N SER d 191 " --> pdb=" O ARG d 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 186 through 191' Processing helix chain 'd' and resid 196 through 205 removed outlier: 3.855A pdb=" N VAL d 200 " --> pdb=" O GLU d 196 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS d 205 " --> pdb=" O GLU d 201 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.614A pdb=" N ALA e 58 " --> pdb=" O GLU e 54 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 6.115A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 removed outlier: 3.544A pdb=" N ASN e 145 " --> pdb=" O ASP e 141 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N MET e 146 " --> pdb=" O GLY e 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 148 through 156 Processing helix chain 'e' and resid 159 through 165 removed outlier: 3.764A pdb=" N ILE e 163 " --> pdb=" O SER e 159 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 16 removed outlier: 4.193A pdb=" N SER f 15 " --> pdb=" O HIS f 11 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N GLU f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 11 through 16' Processing helix chain 'f' and resid 17 through 33 removed outlier: 3.642A pdb=" N ILE f 22 " --> pdb=" O VAL f 18 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU f 23 " --> pdb=" O PRO f 19 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 82 removed outlier: 5.684A pdb=" N ASP f 82 " --> pdb=" O PHE f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 31 removed outlier: 4.045A pdb=" N ALA g 23 " --> pdb=" O SER g 19 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL g 31 " --> pdb=" O ASN g 27 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 54 removed outlier: 3.640A pdb=" N ALA g 38 " --> pdb=" O LYS g 34 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN g 51 " --> pdb=" O GLU g 47 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ARG g 52 " --> pdb=" O THR g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 69 removed outlier: 7.136A pdb=" N ALA g 60 " --> pdb=" O SER g 56 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE g 61 " --> pdb=" O GLU g 57 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL g 68 " --> pdb=" O ALA g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 111 removed outlier: 4.261A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 129 Processing helix chain 'g' and resid 131 through 148 Processing helix chain 'h' and resid 4 through 20 Processing helix chain 'h' and resid 29 through 43 removed outlier: 3.583A pdb=" N GLU h 42 " --> pdb=" O VAL h 38 " (cutoff:3.500A) Processing helix chain 'h' and resid 111 through 119 Processing helix chain 'i' and resid 33 through 38 removed outlier: 3.625A pdb=" N PHE i 38 " --> pdb=" O LEU i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 43 through 55 removed outlier: 4.938A pdb=" N VAL i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG i 48 " --> pdb=" O ARG i 44 " (cutoff:3.500A) Proline residue: i 50 - end of helix removed outlier: 4.163A pdb=" N VAL i 54 " --> pdb=" O PRO i 50 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP i 55 " --> pdb=" O LEU i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 86 Processing helix chain 'i' and resid 89 through 101 removed outlier: 4.117A pdb=" N SER i 95 " --> pdb=" O GLU i 91 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.763A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA j 21 " --> pdb=" O LEU j 17 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 5.132A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 4.313A pdb=" N SER k 49 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 45 through 50' Processing helix chain 'k' and resid 53 through 58 removed outlier: 4.138A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 53 through 58' Processing helix chain 'k' and resid 59 through 77 removed outlier: 6.270A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL k 73 " --> pdb=" O CYS k 69 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS k 74 " --> pdb=" O ALA k 70 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N GLU k 75 " --> pdb=" O ASP k 71 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TYR k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 103 removed outlier: 3.880A pdb=" N ARG k 97 " --> pdb=" O GLU k 93 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA k 98 " --> pdb=" O SER k 94 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU k 99 " --> pdb=" O THR k 95 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN k 100 " --> pdb=" O ILE k 96 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA k 101 " --> pdb=" O ARG k 97 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 10 Proline residue: l 10 - end of helix Processing helix chain 'l' and resid 112 through 117 removed outlier: 5.015A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 21 removed outlier: 4.203A pdb=" N SER m 20 " --> pdb=" O ILE m 16 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 Processing helix chain 'm' and resid 43 through 48 removed outlier: 3.663A pdb=" N LEU m 47 " --> pdb=" O LYS m 43 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N SER m 48 " --> pdb=" O ILE m 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 43 through 48' Processing helix chain 'm' and resid 49 through 63 removed outlier: 3.576A pdb=" N ASP m 57 " --> pdb=" O ASP m 53 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 Processing helix chain 'm' and resid 84 through 93 Processing helix chain 'm' and resid 105 through 110 removed outlier: 3.561A pdb=" N LYS m 109 " --> pdb=" O ALA m 105 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 20 Processing helix chain 'n' and resid 24 through 29 Processing helix chain 'n' and resid 37 through 50 removed outlier: 3.740A pdb=" N TRP n 41 " --> pdb=" O ASP n 37 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU n 50 " --> pdb=" O LYS n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 79 through 90 Processing helix chain 'o' and resid 3 through 15 Processing helix chain 'o' and resid 23 through 43 removed outlier: 4.421A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 Processing helix chain 'o' and resid 74 through 85 Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.612A pdb=" N ILE p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 82 Processing helix chain 'r' and resid 11 through 17 removed outlier: 6.139A pdb=" N GLU r 15 " --> pdb=" O ARG r 11 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 33 removed outlier: 3.713A pdb=" N LEU r 28 " --> pdb=" O ASP r 24 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N THR r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 removed outlier: 4.114A pdb=" N THR r 44 " --> pdb=" O PRO r 40 " (cutoff:3.500A) Processing helix chain 'r' and resid 47 through 65 Processing helix chain 's' and resid 11 through 25 Processing helix chain 's' and resid 69 through 75 removed outlier: 4.604A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA s 74 " --> pdb=" O LEU s 70 " (cutoff:3.500A) Proline residue: s 75 - end of helix No H-bonds generated for 'chain 's' and resid 69 through 75' Processing helix chain 't' and resid 6 through 41 removed outlier: 4.230A pdb=" N ALA t 10 " --> pdb=" O ALA t 6 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS t 15 " --> pdb=" O ILE t 11 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG t 17 " --> pdb=" O SER t 13 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS t 18 " --> pdb=" O GLU t 14 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS t 19 " --> pdb=" O LYS t 15 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG t 23 " --> pdb=" O HIS t 19 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG t 28 " --> pdb=" O ARG t 24 " (cutoff:3.500A) Processing helix chain 't' and resid 42 through 64 Proline residue: t 55 - end of helix removed outlier: 3.558A pdb=" N GLY t 64 " --> pdb=" O GLN t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 86 removed outlier: 4.091A pdb=" N ALA t 86 " --> pdb=" O ILE t 82 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 23 removed outlier: 4.074A pdb=" N LEU u 15 " --> pdb=" O PHE u 11 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG u 16 " --> pdb=" O ASP u 12 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG u 17 " --> pdb=" O VAL u 13 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N PHE u 18 " --> pdb=" O ALA u 14 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N LYS u 19 " --> pdb=" O LEU u 15 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ARG u 20 " --> pdb=" O ARG u 16 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER u 21 " --> pdb=" O ARG u 17 " (cutoff:3.500A) Processing helix chain 'u' and resid 24 through 34 removed outlier: 4.765A pdb=" N LEU u 28 " --> pdb=" O LYS u 24 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU u 30 " --> pdb=" O GLY u 26 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL u 31 " --> pdb=" O VAL u 27 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG u 32 " --> pdb=" O LEU u 28 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG u 33 " --> pdb=" O ALA u 29 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARG u 34 " --> pdb=" O GLU u 30 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 61 removed outlier: 4.716A pdb=" N THR u 41 " --> pdb=" O TYR u 37 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR u 42 " --> pdb=" O GLU u 38 " (cutoff:3.500A) Processing helix chain 'z' and resid 12 through 21 Processing helix chain 'z' and resid 28 through 35 Processing helix chain 'z' and resid 61 through 73 removed outlier: 4.418A pdb=" N SER z 66 " --> pdb=" O GLU z 62 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASN z 67 " --> pdb=" O LYS z 63 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY z 73 " --> pdb=" O LEU z 69 " (cutoff:3.500A) Processing helix chain 'z' and resid 89 through 103 Processing helix chain 'z' and resid 113 through 118 removed outlier: 3.773A pdb=" N VAL z 117 " --> pdb=" O LYS z 113 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASP z 118 " --> pdb=" O ALA z 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 113 through 118' Processing helix chain 'z' and resid 119 through 137 removed outlier: 4.016A pdb=" N ARG z 134 " --> pdb=" O LYS z 130 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU z 135 " --> pdb=" O GLU z 131 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR z 136 " --> pdb=" O VAL z 132 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY z 137 " --> pdb=" O LEU z 133 " (cutoff:3.500A) Processing helix chain 'z' and resid 153 through 164 removed outlier: 3.754A pdb=" N LEU z 162 " --> pdb=" O ARG z 158 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU z 164 " --> pdb=" O HIS z 160 " (cutoff:3.500A) Processing helix chain 'z' and resid 246 through 251 removed outlier: 3.512A pdb=" N ILE z 250 " --> pdb=" O GLU z 246 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN z 251 " --> pdb=" O LYS z 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 246 through 251' Processing helix chain 'z' and resid 348 through 360 removed outlier: 3.731A pdb=" N TYR z 352 " --> pdb=" O ARG z 348 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU z 353 " --> pdb=" O LYS z 349 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN z 354 " --> pdb=" O PRO z 350 " (cutoff:3.500A) Processing helix chain 'z' and resid 364 through 376 Processing helix chain 'z' and resid 379 through 388 Processing helix chain 'z' and resid 390 through 401 removed outlier: 4.259A pdb=" N GLU z 396 " --> pdb=" O GLU z 392 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU z 397 " --> pdb=" O GLY z 393 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU z 398 " --> pdb=" O MET z 394 " (cutoff:3.500A) Proline residue: z 401 - end of helix Processing helix chain 'z' and resid 412 through 435 Processing helix chain 'z' and resid 441 through 450 removed outlier: 3.840A pdb=" N LEU z 450 " --> pdb=" O ARG z 446 " (cutoff:3.500A) Processing helix chain 'z' and resid 454 through 469 Processing helix chain 'z' and resid 489 through 499 removed outlier: 5.047A pdb=" N ILE z 494 " --> pdb=" O GLU z 490 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS z 497 " --> pdb=" O ALA z 493 " (cutoff:3.500A) Processing helix chain 'z' and resid 500 through 505 Processing helix chain 'z' and resid 508 through 517 removed outlier: 4.041A pdb=" N LEU z 512 " --> pdb=" O TRP z 508 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLU z 515 " --> pdb=" O ASP z 511 " (cutoff:3.500A) Processing helix chain 'z' and resid 519 through 534 removed outlier: 4.139A pdb=" N LEU z 525 " --> pdb=" O GLN z 521 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR z 526 " --> pdb=" O ALA z 522 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ARG z 528 " --> pdb=" O ARG z 524 " (cutoff:3.500A) Processing helix chain 'z' and resid 546 through 560 removed outlier: 3.656A pdb=" N ILE z 550 " --> pdb=" O ARG z 546 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU z 552 " --> pdb=" O ASP z 548 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP z 559 " --> pdb=" O ASN z 555 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU z 560 " --> pdb=" O MET z 556 " (cutoff:3.500A) Processing helix chain 'z' and resid 569 through 576 removed outlier: 4.490A pdb=" N ARG z 573 " --> pdb=" O ALA z 569 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU z 576 " --> pdb=" O PHE z 572 " (cutoff:3.500A) Processing helix chain 'z' and resid 579 through 594 Processing helix chain 'C' and resid 10 through 16 removed outlier: 7.305A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL C 16 " --> pdb=" O ARG C 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 16' Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.513A pdb=" N ILE C 134 " --> pdb=" O PRO C 130 " (cutoff:3.500A) Proline residue: C 135 - end of helix No H-bonds generated for 'chain 'C' and resid 130 through 135' Processing helix chain 'C' and resid 206 through 214 removed outlier: 4.444A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.739A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ASN C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 225' Processing helix chain 'C' and resid 259 through 267 removed outlier: 6.792A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 267' Processing helix chain 'C' and resid 196 through 201 removed outlier: 4.272A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.514A pdb=" N VAL D 60 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 61' Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.942A pdb=" N HIS D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 97 through 104 removed outlier: 3.761A pdb=" N PHE D 101 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP D 103 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 104 " --> pdb=" O PHE D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.660A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 3.629A pdb=" N GLU E 111 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 removed outlier: 4.512A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 4.140A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 184 removed outlier: 3.821A pdb=" N LEU E 180 " --> pdb=" O ASP E 176 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ASP E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 removed outlier: 3.533A pdb=" N GLN E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU E 197 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU E 198 " --> pdb=" O LYS E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 21 removed outlier: 3.780A pdb=" N ARG E 21 " --> pdb=" O GLU E 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 16 through 21' Processing helix chain 'F' and resid 1 through 19 removed outlier: 3.682A pdb=" N ASP F 5 " --> pdb=" O ALA F 1 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR F 6 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP F 9 " --> pdb=" O ASP F 5 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL F 11 " --> pdb=" O TYR F 7 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.531A pdb=" N LYS F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 61 removed outlier: 4.625A pdb=" N ASN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE F 59 " --> pdb=" O ASP F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 4.070A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG F 101 " --> pdb=" O GLU F 97 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Proline residue: F 108 - end of helix Processing helix chain 'F' and resid 161 through 173 removed outlier: 3.867A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 removed outlier: 3.743A pdb=" N ILE F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Proline residue: F 138 - end of helix Processing helix chain 'G' and resid 1 through 6 removed outlier: 4.666A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 80 removed outlier: 3.520A pdb=" N ALA G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE G 76 " --> pdb=" O ASN G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 removed outlier: 4.519A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 30 removed outlier: 4.782A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY I 28 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN I 29 " --> pdb=" O PRO I 25 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLN I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 23 through 30' Processing helix chain 'I' and resid 33 through 49 removed outlier: 4.713A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N PHE I 41 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 82 removed outlier: 4.114A pdb=" N LEU I 78 " --> pdb=" O PRO I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 113 removed outlier: 4.586A pdb=" N LEU I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.647A pdb=" N SER I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY I 136 " --> pdb=" O ALA I 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 removed outlier: 3.624A pdb=" N ALA H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN H 28 " --> pdb=" O GLY H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 40 through 50 removed outlier: 5.832A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU H 45 " --> pdb=" O LYS H 41 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE H 46 " --> pdb=" O LYS H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 72 removed outlier: 5.177A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU H 70 " --> pdb=" O ASN H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.636A pdb=" N ALA H 105 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY H 107 " --> pdb=" O VAL H 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.712A pdb=" N THR J 30 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.921A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.014A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY J 107 " --> pdb=" O ILE J 103 " (cutoff:3.500A) removed outlier: 3.712A 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: 3.919A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 removed outlier: 3.613A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 61 Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.422A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.733A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 99 removed outlier: 6.427A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.606A pdb=" N GLU L 136 " --> pdb=" O ARG L 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.932A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.552A pdb=" N ARG M 114 " --> pdb=" O GLU M 110 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.600A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 58 removed outlier: 3.892A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.547A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 4.688A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 82 Processing helix chain 'N' and resid 83 through 89 removed outlier: 4.906A pdb=" N SER N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.691A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 3.504A pdb=" N ALA O 59 " --> pdb=" O GLU O 55 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 55 through 63' Processing helix chain 'O' and resid 67 through 86 removed outlier: 4.330A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.530A pdb=" N ALA O 107 " --> pdb=" O VAL O 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 13 removed outlier: 3.854A pdb=" N LYS P 5 " --> pdb=" O SER P 1 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN P 9 " --> pdb=" O LYS P 5 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET P 12 " --> pdb=" O GLU P 8 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LYS P 13 " --> pdb=" O GLN P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.641A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 96 through 103' Processing helix chain 'P' and resid 104 through 109 removed outlier: 5.628A pdb=" N ILE P 109 " --> pdb=" O LYS P 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 21 Processing helix chain 'Q' and resid 25 through 30 removed outlier: 4.152A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 36 removed outlier: 3.540A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 72 removed outlier: 4.234A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 removed outlier: 4.024A pdb=" N ASN Q 80 " --> pdb=" O SER Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 102 through 117 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.536A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 40 removed outlier: 4.319A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU S 36 " --> pdb=" O ALA S 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR S 39 " --> pdb=" O ILE S 35 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASN S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.787A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA S 58 " --> pdb=" O ALA S 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 1 through 11 removed outlier: 3.945A pdb=" N GLU T 5 " --> pdb=" O MET T 1 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 removed outlier: 3.527A pdb=" N MET T 24 " --> pdb=" O ALA T 20 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS T 26 " --> pdb=" O THR T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 removed outlier: 3.874A pdb=" N ALA T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 70 removed outlier: 4.040A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ALA U 70 " --> pdb=" O VAL U 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 65 through 70' Processing helix chain 'V' and resid 13 through 24 Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.692A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 60 removed outlier: 4.402A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU V 59 " --> pdb=" O GLU V 55 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL V 60 " --> pdb=" O PHE V 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 54 through 60' Processing helix chain 'X' and resid 51 through 62 removed outlier: 3.725A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLY X 62 " --> pdb=" O ILE X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 74 Processing helix chain 'Y' and resid 1 through 8 removed outlier: 4.619A pdb=" N GLU Y 5 " --> pdb=" O MET Y 1 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 23 removed outlier: 3.653A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU Y 17 " --> pdb=" O GLU Y 13 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 35 removed outlier: 4.360A pdb=" N ARG Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 61 removed outlier: 4.917A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.563A pdb=" N LEU Z 24 " --> pdb=" O LYS Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 removed outlier: 4.246A pdb=" N ALA Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 20 removed outlier: 4.523A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP 0 19 " --> pdb=" O ARG 0 15 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) Processing helix chain '1' and resid 25 through 30 Proline residue: 1 30 - end of helix Processing helix chain '2' and resid 8 through 16 removed outlier: 3.620A pdb=" N SER 2 15 " --> pdb=" O LYS 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 25 removed outlier: 5.003A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 removed outlier: 3.834A pdb=" N LEU 2 31 " --> pdb=" O GLY 2 27 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 13 Processing helix chain '3' and resid 31 through 36 removed outlier: 4.150A pdb=" N LYS 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ALA 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 31 through 36' Processing helix chain '3' and resid 37 through 45 Proline residue: 3 45 - end of helix Processing helix chain '3' and resid 51 through 62 removed outlier: 3.965A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA 3 59 " --> pdb=" O GLY 3 55 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '6' and resid 46 through 54 removed outlier: 3.881A pdb=" N ASP 6 50 " --> pdb=" O GLY 6 46 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLY 6 54 " --> pdb=" O ASP 6 50 " (cutoff:3.500A) Processing helix chain '6' and resid 55 through 65 removed outlier: 6.215A pdb=" N ARG 6 59 " --> pdb=" O GLY 6 55 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS 6 62 " --> pdb=" O ASP 6 58 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN 6 65 " --> pdb=" O ASN 6 61 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 88 through 91 removed outlier: 3.802A pdb=" N ALA b 159 " --> pdb=" O LYS b 65 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU b 160 " --> pdb=" O PRO b 181 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'c' and resid 18 through 21 removed outlier: 5.909A pdb=" N ASN c 18 " --> pdb=" O ILE c 54 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG c 58 " --> pdb=" O THR c 20 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 163 through 168 removed outlier: 3.535A pdb=" N GLY c 154 " --> pdb=" O ARG c 163 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLY c 196 " --> pdb=" O SER c 153 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR c 190 " --> pdb=" O GLY c 193 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP c 180 " --> pdb=" O LYS c 203 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'd' and resid 140 through 143 removed outlier: 3.527A pdb=" N ASP d 140 " --> pdb=" O PHE d 181 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'e' and resid 16 through 22 removed outlier: 3.529A pdb=" N ALA e 16 " --> pdb=" O LEU e 35 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE e 29 " --> pdb=" O LYS e 22 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA e 34 " --> pdb=" O GLY e 50 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLY e 50 " --> pdb=" O ALA e 34 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ARG e 44 " --> pdb=" O ASP e 40 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 82 through 87 removed outlier: 7.407A pdb=" N HIS e 82 " --> pdb=" O PRO e 97 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR e 127 " --> pdb=" O ARG e 92 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'f' and resid 39 through 42 removed outlier: 3.871A pdb=" N GLU f 40 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'f' and resid 43 through 47 removed outlier: 3.649A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'g' and resid 72 through 76 Processing sheet with id= 10, first strand: chain 'h' and resid 22 through 28 removed outlier: 6.217A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER h 28 " --> pdb=" O PRO h 56 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU h 51 " --> pdb=" O GLU h 57 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'h' and resid 73 through 76 removed outlier: 6.768A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'i' and resid 4 through 10 removed outlier: 3.805A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS i 26 " --> pdb=" O LEU i 60 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'j' and resid 37 through 41 removed outlier: 5.765A pdb=" N GLY j 38 " --> pdb=" O ASP j 75 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASP j 75 " --> pdb=" O GLY j 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU j 73 " --> pdb=" O ILE j 40 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL j 74 " --> pdb=" O ILE j 8 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE j 6 " --> pdb=" O ILE j 76 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 15, first strand: chain 'k' and resid 29 through 35 removed outlier: 4.350A pdb=" N ASN k 80 " --> pdb=" O SER k 16 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG k 105 " --> pdb=" O LYS k 79 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL k 83 " --> pdb=" O THR k 107 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'l' and resid 28 through 32 removed outlier: 3.589A pdb=" N ILE l 79 " --> pdb=" O GLY l 31 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'l' and resid 34 through 40 removed outlier: 3.793A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'p' and resid 4 through 10 removed outlier: 6.002A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL p 19 " --> pdb=" O GLY p 37 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY p 37 " --> pdb=" O VAL p 19 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'q' and resid 6 through 10 removed outlier: 4.519A pdb=" N GLY q 9 " --> pdb=" O VAL q 58 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL q 58 " --> pdb=" O GLY q 9 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'q' and resid 18 through 29 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 's' and resid 45 through 51 removed outlier: 4.212A pdb=" N LEU s 46 " --> pdb=" O VAL s 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE s 48 " --> pdb=" O VAL s 59 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'z' and resid 40 through 46 removed outlier: 4.053A pdb=" N ILE z 56 " --> pdb=" O ILE z 3 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL z 58 " --> pdb=" O THR z 5 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLY z 7 " --> pdb=" O VAL z 58 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY z 60 " --> pdb=" O GLY z 7 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N HIS z 8 " --> pdb=" O VAL z 81 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ALA z 83 " --> pdb=" O HIS z 8 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET z 106 " --> pdb=" O ASP z 76 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA z 110 " --> pdb=" O LEU z 80 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LYS z 142 " --> pdb=" O LEU z 107 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL z 109 " --> pdb=" O LYS z 142 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'z' and resid 175 through 179 removed outlier: 6.503A pdb=" N PHE z 175 " --> pdb=" O ALA z 258 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASP z 254 " --> pdb=" O ILE z 179 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TRP z 255 " --> pdb=" O THR z 210 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASP z 205 " --> pdb=" O VAL z 218 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN z 240 " --> pdb=" O ARG z 219 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE z 241 " --> pdb=" O LEU z 190 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU z 190 " --> pdb=" O ILE z 241 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'z' and resid 281 through 285 removed outlier: 6.407A pdb=" N ASN z 303 " --> pdb=" O LEU z 272 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE z 269 " --> pdb=" O VAL z 338 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASP z 319 " --> pdb=" O VAL z 337 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'z' and resid 471 through 474 Processing sheet with id= 26, first strand: chain 'z' and resid 596 through 599 Processing sheet with id= 27, first strand: chain 'C' and resid 74 through 77 removed outlier: 4.342A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'C' and resid 79 through 82 removed outlier: 3.874A pdb=" N ARG C 79 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'C' and resid 137 through 141 removed outlier: 4.843A pdb=" N SER C 138 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN C 162 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 175 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.557A pdb=" N VAL D 109 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 172 " --> pdb=" O VAL D 109 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 11 through 15 removed outlier: 5.365A pdb=" N ASN D 185 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 186 " --> pdb=" O ASP D 181 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 32 through 35 removed outlier: 3.669A pdb=" N ASN D 32 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 46 through 51 removed outlier: 6.134A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.515A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'E' and resid 1 through 5 removed outlier: 4.947A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'E' and resid 44 through 47 removed outlier: 7.305A pdb=" N ARG E 44 " --> pdb=" O PRO E 89 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA E 87 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'E' and resid 117 through 120 removed outlier: 3.979A pdb=" N LYS E 185 " --> pdb=" O ASP E 145 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU E 147 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 187 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'F' and resid 64 through 68 removed outlier: 3.901A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR F 34 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR F 154 " --> pdb=" O THR F 34 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'G' and resid 15 through 18 removed outlier: 3.573A pdb=" N ILE G 23 " --> pdb=" O ARG G 34 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'G' and resid 40 through 44 removed outlier: 3.542A pdb=" N THR G 50 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'G' and resid 82 through 88 removed outlier: 3.737A pdb=" N GLY G 134 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS G 84 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'G' and resid 93 through 97 removed outlier: 4.209A pdb=" N ALA G 96 " --> pdb=" O ASN G 103 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN G 103 " --> pdb=" O ALA G 96 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'H' and resid 3 through 6 removed outlier: 7.775A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'H' and resid 76 through 83 removed outlier: 7.379A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN H 133 " --> pdb=" O GLU H 114 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU H 114 " --> pdb=" O GLN H 133 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'J' and resid 52 through 57 removed outlier: 3.791A pdb=" N GLN J 138 " --> pdb=" O TRP J 15 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'J' and resid 74 through 77 Processing sheet with id= 47, first strand: chain 'K' and resid 6 through 10 removed outlier: 4.453A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'K' and resid 38 through 41 removed outlier: 3.948A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.181A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'L' and resid 88 through 91 Processing sheet with id= 51, first strand: chain 'M' and resid 62 through 66 removed outlier: 3.562A pdb=" N GLU M 104 " --> pdb=" O TRP M 64 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU M 102 " --> pdb=" O ARG M 66 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'O' and resid 49 through 53 removed outlier: 3.951A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE O 35 " --> pdb=" O THR O 53 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG O 25 " --> pdb=" O ILE O 40 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.559A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'P' and resid 48 through 52 removed outlier: 3.665A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ARG P 52 " --> pdb=" O HIS P 55 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N HIS P 55 " --> pdb=" O ARG P 52 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.552A pdb=" N PHE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL R 4 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.510A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE R 98 " --> pdb=" O GLN R 18 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'R' and resid 65 through 69 removed outlier: 4.002A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN R 91 " --> pdb=" O GLY R 69 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.587A pdb=" N THR S 3 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL S 107 " --> pdb=" O THR S 3 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL S 106 " --> pdb=" O THR S 72 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'S' and resid 73 through 79 removed outlier: 3.923A pdb=" N LYS S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'S' and resid 80 through 88 removed outlier: 3.648A pdb=" N THR S 100 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'T' and resid 12 through 15 removed outlier: 4.205A pdb=" N ALA T 13 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'U' and resid 39 through 44 removed outlier: 5.275A pdb=" N ASN U 39 " --> pdb=" O ALA U 62 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA U 62 " --> pdb=" O ASN U 39 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'U' and resid 81 through 86 removed outlier: 4.920A pdb=" N ARG U 81 " --> pdb=" O LYS U 96 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'V' and resid 69 through 72 removed outlier: 3.871A pdb=" N ARG V 9 " --> pdb=" O ALA V 39 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG V 93 " --> pdb=" O TYR V 31 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS V 88 " --> pdb=" O GLN V 78 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP V 90 " --> pdb=" O ASP V 76 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP V 76 " --> pdb=" O ASP V 90 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'W' and resid 46 through 50 removed outlier: 8.369A pdb=" N ASN W 46 " --> pdb=" O LYS W 58 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE W 56 " --> pdb=" O GLY W 48 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'W' and resid 61 through 67 Processing sheet with id= 67, first strand: chain 'X' and resid 11 through 17 removed outlier: 3.623A pdb=" N VAL X 12 " --> pdb=" O PHE X 28 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY X 14 " --> pdb=" O ARG X 26 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'X' and resid 34 through 40 Processing sheet with id= 69, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.337A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '0' and resid 27 through 30 No H-bonds generated for sheet with id= 70 Processing sheet with id= 71, first strand: chain '1' and resid 7 through 11 Processing sheet with id= 72, first strand: chain '1' and resid 33 through 39 removed outlier: 7.282A pdb=" N LEU 1 33 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU 1 50 " --> pdb=" O LEU 1 33 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU 1 35 " --> pdb=" O TYR 1 48 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain '3' and resid 21 through 24 removed outlier: 6.164A pdb=" N PHE 3 21 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain '4' and resid 13 through 19 removed outlier: 8.557A pdb=" N ASN 4 13 " --> pdb=" O SER 4 28 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER 4 28 " --> pdb=" O ASN 4 13 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL 4 25 " --> pdb=" O GLN 4 35 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N CYS 4 27 " --> pdb=" O HIS 4 33 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N HIS 4 33 " --> pdb=" O CYS 4 27 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain '6' and resid 11 through 16 removed outlier: 3.982A pdb=" N CYS 6 16 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN 6 20 " --> pdb=" O CYS 6 16 " (cutoff:3.500A) 1886 hydrogen bonds defined for protein. 5580 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4042 hydrogen bonds 6316 hydrogen bond angles 0 basepair planarities 1609 basepair parallelities 2438 stacking parallelities Total time for adding SS restraints: 218.15 Time building geometry restraints manager: 75.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.31: 15800 1.31 - 1.47: 86075 1.47 - 1.64: 63785 1.64 - 1.80: 234 1.80 - 1.96: 95 Bond restraints: 165989 Sorted by residual: bond pdb=" C4 5MU y 54 " pdb=" C5 5MU y 54 " ideal model delta sigma weight residual 1.802 1.479 0.323 2.00e-02 2.50e+03 2.61e+02 bond pdb=" C4 5MU A 747 " pdb=" C5 5MU A 747 " ideal model delta sigma weight residual 1.802 1.479 0.323 2.00e-02 2.50e+03 2.61e+02 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.802 1.479 0.323 2.00e-02 2.50e+03 2.61e+02 bond pdb=" C4 5MU v 54 " pdb=" C5 5MU v 54 " ideal model delta sigma weight residual 1.802 1.480 0.322 2.00e-02 2.50e+03 2.59e+02 bond pdb=" N1 5MU A 747 " pdb=" C6 5MU A 747 " ideal model delta sigma weight residual 1.635 1.336 0.299 2.00e-02 2.50e+03 2.23e+02 ... (remaining 165984 not shown) Histogram of bond angle deviations from ideal: 89.70 - 99.69: 66 99.69 - 109.68: 71271 109.68 - 119.67: 103182 119.67 - 129.66: 70112 129.66 - 139.64: 3226 Bond angle restraints: 247857 Sorted by residual: angle pdb=" C4' G A1071 " pdb=" C3' G A1071 " pdb=" O3' G A1071 " ideal model delta sigma weight residual 113.00 129.25 -16.25 1.50e+00 4.44e-01 1.17e+02 angle pdb=" C4' C A1044 " pdb=" C3' C A1044 " pdb=" O3' C A1044 " ideal model delta sigma weight residual 113.00 129.07 -16.07 1.50e+00 4.44e-01 1.15e+02 angle pdb=" C4' C A1072 " pdb=" C3' C A1072 " pdb=" O3' C A1072 " ideal model delta sigma weight residual 109.40 94.11 15.29 1.50e+00 4.44e-01 1.04e+02 angle pdb=" C3' G A1071 " pdb=" O3' G A1071 " pdb=" P C A1072 " ideal model delta sigma weight residual 120.20 105.69 14.51 1.50e+00 4.44e-01 9.35e+01 angle pdb=" C1' G7M A2069 " pdb=" N9 G7M A2069 " pdb=" C8 G7M A2069 " ideal model delta sigma weight residual 94.96 123.32 -28.36 3.00e+00 1.11e-01 8.94e+01 ... (remaining 247852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 94345 35.93 - 71.86: 10576 71.86 - 107.79: 1203 107.79 - 143.72: 15 143.72 - 179.65: 13 Dihedral angle restraints: 106152 sinusoidal: 87827 harmonic: 18325 Sorted by residual: dihedral pdb=" O4' G7M a 527 " pdb=" C4' G7M a 527 " pdb=" C3' G7M a 527 " pdb=" C2' G7M a 527 " ideal model delta sinusoidal sigma weight residual -35.00 40.53 -75.53 1 8.00e+00 1.56e-02 1.13e+02 dihedral pdb=" O4' G7M A2069 " pdb=" C4' G7M A2069 " pdb=" C3' G7M A2069 " pdb=" C2' G7M A2069 " ideal model delta sinusoidal sigma weight residual -35.00 36.88 -71.88 1 8.00e+00 1.56e-02 1.03e+02 dihedral pdb=" CA LYS H 8 " pdb=" C LYS H 8 " pdb=" N VAL H 9 " pdb=" CA VAL H 9 " ideal model delta harmonic sigma weight residual 180.00 -133.30 -46.70 0 5.00e+00 4.00e-02 8.72e+01 ... (remaining 106149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.944: 31474 0.944 - 1.887: 2 1.887 - 2.831: 0 2.831 - 3.775: 0 3.775 - 4.718: 4 Chirality restraints: 31480 Sorted by residual: chirality pdb=" C4' G7M A2069 " pdb=" C5' G7M A2069 " pdb=" O4' G7M A2069 " pdb=" C3' G7M A2069 " both_signs ideal model delta sigma weight residual False -2.50 2.22 -4.72 2.00e-01 2.50e+01 5.57e+02 chirality pdb=" C4' G7M a 527 " pdb=" C5' G7M a 527 " pdb=" O4' G7M a 527 " pdb=" C3' G7M a 527 " both_signs ideal model delta sigma weight residual False -2.50 1.98 -4.48 2.00e-01 2.50e+01 5.01e+02 chirality pdb=" C3' G7M a 527 " pdb=" C4' G7M a 527 " pdb=" O3' G7M a 527 " pdb=" C2' G7M a 527 " both_signs ideal model delta sigma weight residual False -2.48 1.72 -4.20 2.00e-01 2.50e+01 4.41e+02 ... (remaining 31477 not shown) Planarity restraints: 13686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1962 " -0.886 2.00e-02 2.50e+03 6.17e-01 8.56e+03 pdb=" C4' 5MC A1962 " 0.185 2.00e-02 2.50e+03 pdb=" O4' 5MC A1962 " 0.658 2.00e-02 2.50e+03 pdb=" C3' 5MC A1962 " -0.188 2.00e-02 2.50e+03 pdb=" O3' 5MC A1962 " 1.025 2.00e-02 2.50e+03 pdb=" C2' 5MC A1962 " -0.625 2.00e-02 2.50e+03 pdb=" O2' 5MC A1962 " -0.701 2.00e-02 2.50e+03 pdb=" C1' 5MC A1962 " 0.446 2.00e-02 2.50e+03 pdb=" N1 5MC A1962 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1407 " 0.049 2.00e-02 2.50e+03 5.93e-01 7.90e+03 pdb=" C4' 5MC a1407 " 0.459 2.00e-02 2.50e+03 pdb=" O4' 5MC a1407 " 0.633 2.00e-02 2.50e+03 pdb=" C3' 5MC a1407 " -0.582 2.00e-02 2.50e+03 pdb=" O3' 5MC a1407 " -0.637 2.00e-02 2.50e+03 pdb=" C2' 5MC a1407 " -0.186 2.00e-02 2.50e+03 pdb=" O2' 5MC a1407 " 0.950 2.00e-02 2.50e+03 pdb=" C1' 5MC a1407 " 0.220 2.00e-02 2.50e+03 pdb=" N1 5MC a1407 " -0.905 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' H2U v 20 " 0.833 2.00e-02 2.50e+03 5.86e-01 7.73e+03 pdb=" C4' H2U v 20 " -0.220 2.00e-02 2.50e+03 pdb=" O4' H2U v 20 " -0.560 2.00e-02 2.50e+03 pdb=" C3' H2U v 20 " 0.176 2.00e-02 2.50e+03 pdb=" O3' H2U v 20 " -0.984 2.00e-02 2.50e+03 pdb=" C2' H2U v 20 " 0.608 2.00e-02 2.50e+03 pdb=" O2' H2U v 20 " 0.678 2.00e-02 2.50e+03 pdb=" C1' H2U v 20 " -0.444 2.00e-02 2.50e+03 pdb=" N1 H2U v 20 " -0.087 2.00e-02 2.50e+03 ... (remaining 13683 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 1308 2.58 - 3.16: 118037 3.16 - 3.74: 323920 3.74 - 4.32: 414349 4.32 - 4.90: 554024 Nonbonded interactions: 1411638 Sorted by model distance: nonbonded pdb=" O1G GNP z 701 " pdb="MG MG z 702 " model vdw 1.994 2.170 nonbonded pdb=" OG1 THR z 14 " pdb="MG MG z 702 " model vdw 2.038 2.170 nonbonded pdb=" O2 U A 545 " pdb=" O6 G A 548 " model vdw 2.110 2.432 nonbonded pdb=" O1B GNP z 701 " pdb="MG MG z 702 " model vdw 2.119 2.170 nonbonded pdb=" OG SER D 97 " pdb=" OE1 GLU D 99 " model vdw 2.141 2.440 ... (remaining 1411633 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 10.470 Check model and map are aligned: 1.630 Set scattering table: 1.010 Process input model: 551.990 Find NCS groups from input model: 2.940 Set up NCS constraints: 0.360 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 572.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.323 165989 Z= 0.533 Angle : 1.211 28.360 247857 Z= 0.622 Chirality : 0.076 4.718 31480 Planarity : 0.023 0.617 13686 Dihedral : 22.135 179.652 94325 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 1.85 % Allowed : 5.72 % Favored : 92.43 % Rotamer: Outliers : 0.11 % Allowed : 1.59 % Favored : 98.30 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.10), residues: 6329 helix: -2.72 (0.08), residues: 1977 sheet: -2.22 (0.14), residues: 1014 loop : 0.31 (0.12), residues: 3338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.005 TRP z 419 HIS 0.038 0.004 HIS z 285 PHE 0.051 0.005 PHE k 51 TYR 0.069 0.005 TYR H 25 ARG 0.038 0.002 ARG V 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2667 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 2661 time to evaluate : 6.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 41 ASN cc_start: 0.9459 (t0) cc_final: 0.9151 (t0) REVERT: b 92 ASN cc_start: 0.9342 (p0) cc_final: 0.8984 (p0) REVERT: b 96 LEU cc_start: 0.8326 (tp) cc_final: 0.7955 (tp) REVERT: b 117 GLU cc_start: 0.8361 (pt0) cc_final: 0.7866 (pt0) REVERT: b 221 ARG cc_start: 0.7979 (mtt-85) cc_final: 0.7683 (ptm160) REVERT: c 18 ASN cc_start: 0.9354 (m-40) cc_final: 0.9040 (t0) REVERT: c 22 PHE cc_start: 0.7359 (t80) cc_final: 0.6934 (t80) REVERT: c 57 GLU cc_start: 0.8770 (pt0) cc_final: 0.8338 (pm20) REVERT: c 149 LYS cc_start: 0.9391 (ttmt) cc_final: 0.9113 (ttmt) REVERT: c 171 ARG cc_start: 0.8810 (mtp85) cc_final: 0.8269 (mmm160) REVERT: c 184 ASN cc_start: 0.8748 (t0) cc_final: 0.8110 (t0) REVERT: d 27 ILE cc_start: 0.5491 (tt) cc_final: 0.5269 (tt) REVERT: d 29 THR cc_start: 0.9176 (m) cc_final: 0.8955 (p) REVERT: d 44 LYS cc_start: 0.8661 (tptp) cc_final: 0.8289 (tmtt) REVERT: d 59 LYS cc_start: 0.9651 (ttpp) cc_final: 0.9408 (tptt) REVERT: d 74 TYR cc_start: 0.9138 (m-10) cc_final: 0.8755 (m-80) REVERT: d 81 LEU cc_start: 0.8988 (mp) cc_final: 0.8455 (tp) REVERT: d 82 LYS cc_start: 0.8498 (tptt) cc_final: 0.7984 (mttt) REVERT: d 99 ASN cc_start: 0.9306 (t0) cc_final: 0.9057 (t0) REVERT: d 109 THR cc_start: 0.7457 (p) cc_final: 0.6654 (p) REVERT: d 112 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8632 (mt-10) REVERT: d 134 TYR cc_start: 0.8855 (t80) cc_final: 0.8406 (t80) REVERT: d 136 VAL cc_start: 0.8104 (m) cc_final: 0.7897 (p) REVERT: d 139 ASN cc_start: 0.8911 (p0) cc_final: 0.8530 (m-40) REVERT: d 186 GLU cc_start: 0.8591 (pm20) cc_final: 0.8130 (pm20) REVERT: d 203 TYR cc_start: 0.7821 (m-80) cc_final: 0.7026 (m-80) REVERT: e 33 THR cc_start: 0.9228 (t) cc_final: 0.8789 (t) REVERT: e 63 MET cc_start: 0.9256 (mmp) cc_final: 0.8876 (mmp) REVERT: f 49 TYR cc_start: 0.8847 (p90) cc_final: 0.7651 (p90) REVERT: f 51 ILE cc_start: 0.8404 (mt) cc_final: 0.8191 (mp) REVERT: g 16 LYS cc_start: 0.8059 (ttpp) cc_final: 0.7761 (ttpt) REVERT: h 12 ARG cc_start: 0.8465 (tpp80) cc_final: 0.7708 (ttp-110) REVERT: h 58 LEU cc_start: 0.9209 (pp) cc_final: 0.8335 (pp) REVERT: h 111 THR cc_start: 0.8122 (p) cc_final: 0.7535 (p) REVERT: i 8 THR cc_start: 0.8521 (p) cc_final: 0.7795 (p) REVERT: i 83 THR cc_start: 0.9361 (t) cc_final: 0.9063 (t) REVERT: i 105 ARG cc_start: 0.6097 (ttt-90) cc_final: 0.4621 (tpt90) REVERT: i 114 LYS cc_start: 0.9283 (mmtm) cc_final: 0.9012 (mppt) REVERT: i 117 LEU cc_start: 0.8474 (pp) cc_final: 0.7680 (pp) REVERT: j 25 ILE cc_start: 0.8530 (tt) cc_final: 0.8318 (tp) REVERT: j 42 LEU cc_start: 0.9318 (mp) cc_final: 0.9097 (mp) REVERT: j 44 THR cc_start: 0.8431 (p) cc_final: 0.8194 (p) REVERT: j 52 LEU cc_start: 0.9224 (tt) cc_final: 0.9016 (tt) REVERT: j 63 ASP cc_start: 0.8710 (t0) cc_final: 0.8271 (t0) REVERT: j 64 GLN cc_start: 0.9269 (mm-40) cc_final: 0.8921 (mt0) REVERT: j 65 TYR cc_start: 0.7785 (m-80) cc_final: 0.6713 (m-10) REVERT: j 99 GLN cc_start: 0.8999 (mm110) cc_final: 0.8734 (mm110) REVERT: k 58 THR cc_start: 0.8152 (m) cc_final: 0.7714 (p) REVERT: k 73 VAL cc_start: 0.8591 (t) cc_final: 0.8324 (t) REVERT: k 80 ASN cc_start: 0.8803 (p0) cc_final: 0.8206 (t0) REVERT: k 82 GLU cc_start: 0.8739 (tp30) cc_final: 0.8535 (tp30) REVERT: l 48 LEU cc_start: 0.7883 (tp) cc_final: 0.7651 (tp) REVERT: l 52 CYS cc_start: 0.9267 (p) cc_final: 0.9037 (t) REVERT: l 55 ARG cc_start: 0.8955 (ttp-170) cc_final: 0.8681 (tpt-90) REVERT: m 70 ARG cc_start: 0.9212 (ttp-110) cc_final: 0.8939 (mmt180) REVERT: m 76 ILE cc_start: 0.9700 (mt) cc_final: 0.9243 (pt) REVERT: n 3 GLN cc_start: 0.9047 (pm20) cc_final: 0.8814 (pm20) REVERT: n 4 SER cc_start: 0.8927 (p) cc_final: 0.7985 (t) REVERT: n 9 GLU cc_start: 0.9530 (tm-30) cc_final: 0.9112 (tp30) REVERT: n 15 LEU cc_start: 0.8595 (tt) cc_final: 0.8151 (pp) REVERT: n 73 LEU cc_start: 0.9046 (mp) cc_final: 0.8804 (tp) REVERT: n 85 GLU cc_start: 0.9383 (tm-30) cc_final: 0.9065 (tm-30) REVERT: n 92 ILE cc_start: 0.9120 (mt) cc_final: 0.8896 (mm) REVERT: o 31 LEU cc_start: 0.9618 (mt) cc_final: 0.9343 (mt) REVERT: o 47 LYS cc_start: 0.9134 (mtmt) cc_final: 0.8519 (mtmm) REVERT: p 21 VAL cc_start: 0.8074 (t) cc_final: 0.7535 (t) REVERT: p 23 ASP cc_start: 0.8431 (t0) cc_final: 0.8213 (m-30) REVERT: p 35 ARG cc_start: 0.6859 (ttm170) cc_final: 0.5745 (ptm160) REVERT: p 39 PHE cc_start: 0.8987 (t80) cc_final: 0.8516 (t80) REVERT: p 66 THR cc_start: 0.7052 (m) cc_final: 0.6407 (m) REVERT: q 15 LYS cc_start: 0.8878 (tttt) cc_final: 0.8626 (tttt) REVERT: q 72 TRP cc_start: 0.8615 (m100) cc_final: 0.7991 (m100) REVERT: q 80 LYS cc_start: 0.8285 (mttm) cc_final: 0.7847 (tppt) REVERT: r 37 LYS cc_start: 0.9188 (mtpp) cc_final: 0.8939 (mtpt) REVERT: r 41 SER cc_start: 0.8374 (m) cc_final: 0.7813 (p) REVERT: r 51 GLN cc_start: 0.8960 (tp-100) cc_final: 0.8433 (tt0) REVERT: r 54 LEU cc_start: 0.9635 (tp) cc_final: 0.9354 (tp) REVERT: r 69 TYR cc_start: 0.6662 (m-80) cc_final: 0.6323 (m-10) REVERT: s 79 TYR cc_start: 0.5665 (t80) cc_final: 0.5120 (t80) REVERT: t 26 MET cc_start: 0.9415 (mmt) cc_final: 0.9101 (mmt) REVERT: t 30 PHE cc_start: 0.8404 (m-80) cc_final: 0.7909 (m-80) REVERT: t 31 ILE cc_start: 0.9573 (pt) cc_final: 0.9064 (pt) REVERT: t 81 GLN cc_start: 0.8825 (tt0) cc_final: 0.8471 (pt0) REVERT: u 13 VAL cc_start: 0.9112 (p) cc_final: 0.8887 (m) REVERT: u 53 LYS cc_start: 0.8992 (mptt) cc_final: 0.8576 (pttt) REVERT: z 1 MET cc_start: 0.2115 (mtm) cc_final: 0.1850 (ttm) REVERT: z 56 ILE cc_start: 0.6277 (mt) cc_final: 0.5920 (mp) REVERT: z 127 ARG cc_start: 0.7247 (mtt180) cc_final: 0.6859 (ptm-80) REVERT: z 167 ARG cc_start: 0.7651 (mmm160) cc_final: 0.6516 (mmt180) REVERT: z 348 ARG cc_start: 0.7637 (mtp85) cc_final: 0.6699 (mpt180) REVERT: z 382 ASP cc_start: 0.9512 (m-30) cc_final: 0.9169 (p0) REVERT: z 385 TRP cc_start: 0.8318 (t-100) cc_final: 0.7895 (t-100) REVERT: z 452 MET cc_start: 0.3247 (mtp) cc_final: 0.1805 (pmm) REVERT: z 466 ARG cc_start: 0.8930 (tpp80) cc_final: 0.8725 (tpm170) REVERT: z 475 HIS cc_start: 0.8675 (m90) cc_final: 0.8419 (m90) REVERT: C 37 SER cc_start: 0.8936 (m) cc_final: 0.8246 (t) REVERT: C 47 ARG cc_start: 0.8193 (mmt90) cc_final: 0.7818 (mmm-85) REVERT: C 76 VAL cc_start: 0.9361 (m) cc_final: 0.8903 (p) REVERT: C 94 LEU cc_start: 0.9188 (tt) cc_final: 0.8337 (tt) REVERT: C 143 VAL cc_start: 0.9263 (t) cc_final: 0.9026 (m) REVERT: C 145 MET cc_start: 0.8219 (mmp) cc_final: 0.7948 (mmm) REVERT: C 152 GLN cc_start: 0.7888 (mp10) cc_final: 0.7440 (mp10) REVERT: C 163 ILE cc_start: 0.8842 (mt) cc_final: 0.8328 (pt) REVERT: C 167 ASP cc_start: 0.8640 (p0) cc_final: 0.8120 (m-30) REVERT: C 173 LEU cc_start: 0.9717 (mt) cc_final: 0.9516 (mt) REVERT: C 182 LYS cc_start: 0.9460 (pttm) cc_final: 0.9212 (tttt) REVERT: C 194 VAL cc_start: 0.8748 (t) cc_final: 0.8542 (t) REVERT: C 239 PHE cc_start: 0.7987 (t80) cc_final: 0.6920 (t80) REVERT: D 11 MET cc_start: 0.8230 (mtp) cc_final: 0.7867 (mpp) REVERT: D 49 GLN cc_start: 0.7256 (pm20) cc_final: 0.6477 (pm20) REVERT: D 99 GLU cc_start: 0.9492 (mp0) cc_final: 0.9217 (pm20) REVERT: D 128 ARG cc_start: 0.5426 (tpt90) cc_final: 0.4402 (mmt180) REVERT: D 156 PHE cc_start: 0.8509 (m-80) cc_final: 0.7939 (p90) REVERT: D 172 VAL cc_start: 0.8596 (m) cc_final: 0.8318 (p) REVERT: E 30 GLN cc_start: 0.8721 (tt0) cc_final: 0.8502 (tt0) REVERT: E 111 GLU cc_start: 0.8709 (mp0) cc_final: 0.8313 (mm-30) REVERT: E 116 ASP cc_start: 0.9025 (m-30) cc_final: 0.8801 (p0) REVERT: E 176 ASP cc_start: 0.9116 (m-30) cc_final: 0.8273 (m-30) REVERT: E 179 SER cc_start: 0.8172 (p) cc_final: 0.7512 (p) REVERT: E 183 PHE cc_start: 0.8202 (m-80) cc_final: 0.7572 (m-10) REVERT: F 4 HIS cc_start: 0.9221 (t70) cc_final: 0.9002 (t70) REVERT: F 30 VAL cc_start: 0.8956 (m) cc_final: 0.7906 (m) REVERT: F 32 LYS cc_start: 0.9445 (mtmm) cc_final: 0.9105 (mtmm) REVERT: F 34 THR cc_start: 0.8705 (p) cc_final: 0.8279 (t) REVERT: F 37 MET cc_start: 0.5627 (mtp) cc_final: 0.5161 (mtp) REVERT: F 97 GLU cc_start: 0.8685 (tt0) cc_final: 0.8266 (pt0) REVERT: F 155 ILE cc_start: 0.9067 (mt) cc_final: 0.8694 (mp) REVERT: F 156 THR cc_start: 0.8622 (m) cc_final: 0.8327 (m) REVERT: F 169 LEU cc_start: 0.9049 (tt) cc_final: 0.8352 (pp) REVERT: G 68 ARG cc_start: 0.9460 (ttp80) cc_final: 0.9184 (ttp-110) REVERT: G 129 GLU cc_start: 0.9347 (tt0) cc_final: 0.9045 (tm-30) REVERT: G 150 TYR cc_start: 0.8820 (m-80) cc_final: 0.8536 (m-10) REVERT: G 156 TYR cc_start: 0.7575 (m-80) cc_final: 0.7373 (m-10) REVERT: I 71 LYS cc_start: 0.8598 (mtmm) cc_final: 0.8249 (pttp) REVERT: H 11 ASN cc_start: 0.8043 (t0) cc_final: 0.7565 (p0) REVERT: H 109 GLU cc_start: 0.8275 (pt0) cc_final: 0.8058 (mm-30) REVERT: J 14 ASP cc_start: 0.7706 (m-30) cc_final: 0.7441 (m-30) REVERT: J 25 LEU cc_start: 0.9518 (pp) cc_final: 0.9227 (pp) REVERT: J 52 ASP cc_start: 0.5461 (m-30) cc_final: 0.5224 (m-30) REVERT: J 53 TYR cc_start: 0.6898 (m-80) cc_final: 0.5887 (m-80) REVERT: J 89 PHE cc_start: 0.8817 (t80) cc_final: 0.8493 (t80) REVERT: J 122 LEU cc_start: 0.9196 (tt) cc_final: 0.8361 (pp) REVERT: J 124 VAL cc_start: 0.8642 (t) cc_final: 0.8125 (p) REVERT: K 8 LEU cc_start: 0.9623 (mt) cc_final: 0.8650 (mm) REVERT: K 13 ASN cc_start: 0.8964 (p0) cc_final: 0.8201 (p0) REVERT: K 109 SER cc_start: 0.8959 (m) cc_final: 0.8088 (p) REVERT: K 110 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7806 (pm20) REVERT: L 7 SER cc_start: 0.8504 (m) cc_final: 0.8005 (t) REVERT: L 55 MET cc_start: 0.8790 (tpt) cc_final: 0.7297 (tpt) REVERT: L 59 ARG cc_start: 0.9193 (ptm160) cc_final: 0.8667 (ptm160) REVERT: M 1 MET cc_start: 0.8611 (tpt) cc_final: 0.8192 (tmm) REVERT: M 60 GLN cc_start: 0.9489 (mp10) cc_final: 0.9083 (tp-100) REVERT: M 82 MET cc_start: 0.9154 (mmm) cc_final: 0.8910 (tpp) REVERT: M 132 THR cc_start: 0.8831 (p) cc_final: 0.8558 (p) REVERT: N 9 GLN cc_start: 0.8184 (pt0) cc_final: 0.7740 (pm20) REVERT: N 10 LEU cc_start: 0.9173 (mt) cc_final: 0.8902 (mp) REVERT: N 20 MET cc_start: 0.9590 (ttp) cc_final: 0.9311 (ttp) REVERT: N 24 MET cc_start: 0.9677 (ttt) cc_final: 0.9457 (tpp) REVERT: N 53 THR cc_start: 0.9468 (m) cc_final: 0.9229 (p) REVERT: N 75 ILE cc_start: 0.8380 (pp) cc_final: 0.7761 (pt) REVERT: N 83 LEU cc_start: 0.8746 (mp) cc_final: 0.8456 (mp) REVERT: O 29 HIS cc_start: 0.6947 (t-90) cc_final: 0.6548 (t-170) REVERT: O 31 THR cc_start: 0.8276 (t) cc_final: 0.7659 (p) REVERT: O 33 ARG cc_start: 0.8746 (ttm170) cc_final: 0.8411 (ptt-90) REVERT: P 6 GLN cc_start: 0.9326 (tt0) cc_final: 0.9112 (pt0) REVERT: P 55 HIS cc_start: 0.8234 (m90) cc_final: 0.8013 (m-70) REVERT: P 59 THR cc_start: 0.9413 (m) cc_final: 0.8905 (t) REVERT: P 84 SER cc_start: 0.9158 (m) cc_final: 0.8819 (t) REVERT: Q 10 ARG cc_start: 0.8594 (ptp90) cc_final: 0.7997 (ttp-170) REVERT: Q 14 LYS cc_start: 0.9483 (ttmt) cc_final: 0.9178 (tptt) REVERT: Q 15 LYS cc_start: 0.9499 (ttpt) cc_final: 0.9099 (tptt) REVERT: Q 46 TYR cc_start: 0.8235 (t80) cc_final: 0.8007 (t80) REVERT: Q 60 TRP cc_start: 0.8847 (m-90) cc_final: 0.8366 (m-90) REVERT: Q 70 GLN cc_start: 0.9348 (tt0) cc_final: 0.8791 (tm-30) REVERT: Q 109 VAL cc_start: 0.8948 (t) cc_final: 0.8649 (t) REVERT: R 40 MET cc_start: 0.8388 (tpt) cc_final: 0.7680 (tmm) REVERT: R 53 PHE cc_start: 0.8614 (m-10) cc_final: 0.8403 (m-10) REVERT: R 74 ILE cc_start: 0.9304 (mp) cc_final: 0.9016 (mp) REVERT: R 85 LYS cc_start: 0.8836 (pttp) cc_final: 0.8336 (tmtt) REVERT: S 9 HIS cc_start: 0.7919 (m90) cc_final: 0.6850 (m90) REVERT: S 49 LYS cc_start: 0.9406 (ptmt) cc_final: 0.8958 (tptm) REVERT: T 9 LYS cc_start: 0.9224 (mttt) cc_final: 0.8862 (mtpp) REVERT: T 10 VAL cc_start: 0.8103 (m) cc_final: 0.7440 (m) REVERT: T 18 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8385 (tm-30) REVERT: T 63 VAL cc_start: 0.8892 (t) cc_final: 0.8579 (t) REVERT: T 80 TRP cc_start: 0.8253 (p-90) cc_final: 0.7954 (p-90) REVERT: T 84 TYR cc_start: 0.9268 (m-80) cc_final: 0.8632 (m-10) REVERT: U 35 VAL cc_start: 0.9359 (t) cc_final: 0.9124 (p) REVERT: U 94 PHE cc_start: 0.8304 (t80) cc_final: 0.7987 (t80) REVERT: U 98 ASN cc_start: 0.8580 (t0) cc_final: 0.8354 (p0) REVERT: V 8 VAL cc_start: 0.9402 (t) cc_final: 0.8987 (m) REVERT: V 71 LYS cc_start: 0.9039 (mttm) cc_final: 0.8598 (mmtm) REVERT: V 83 LYS cc_start: 0.7835 (pttm) cc_final: 0.7627 (ptmm) REVERT: V 91 PHE cc_start: 0.9071 (m-80) cc_final: 0.8349 (m-80) REVERT: W 58 LYS cc_start: 0.8711 (ptpt) cc_final: 0.8173 (tppt) REVERT: W 73 ARG cc_start: 0.8864 (mtt180) cc_final: 0.8575 (mtt180) REVERT: X 36 ARG cc_start: 0.9038 (ttp80) cc_final: 0.8710 (ptt90) REVERT: X 45 PHE cc_start: 0.9491 (m-80) cc_final: 0.9115 (m-80) REVERT: X 67 LEU cc_start: 0.9618 (mp) cc_final: 0.9301 (pp) REVERT: Y 2 LYS cc_start: 0.7958 (ttpp) cc_final: 0.7283 (mmtt) REVERT: Y 39 GLN cc_start: 0.9237 (mt0) cc_final: 0.8716 (mp10) REVERT: Y 55 THR cc_start: 0.9240 (t) cc_final: 0.8816 (t) REVERT: Y 58 ASN cc_start: 0.9228 (t0) cc_final: 0.8950 (t0) REVERT: Z 4 ILE cc_start: 0.8546 (tt) cc_final: 0.8248 (pt) REVERT: Z 5 LYS cc_start: 0.9152 (ptpt) cc_final: 0.8704 (mtpp) REVERT: 2 19 ARG cc_start: 0.8823 (mtp85) cc_final: 0.8589 (mtp85) REVERT: 2 30 VAL cc_start: 0.9306 (m) cc_final: 0.9024 (t) REVERT: 2 34 ARG cc_start: 0.8803 (mtp85) cc_final: 0.8582 (ttm170) REVERT: 3 39 ARG cc_start: 0.9462 (mtp180) cc_final: 0.8907 (mtp85) REVERT: 3 42 HIS cc_start: 0.9506 (m90) cc_final: 0.9240 (m90) REVERT: 4 23 ILE cc_start: 0.9215 (pp) cc_final: 0.8876 (tp) outliers start: 6 outliers final: 2 residues processed: 2662 average time/residue: 1.4861 time to fit residues: 6480.3421 Evaluate side-chains 1650 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1648 time to evaluate : 6.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1095 random chunks: chunk 924 optimal weight: 0.9990 chunk 829 optimal weight: 20.0000 chunk 460 optimal weight: 8.9990 chunk 283 optimal weight: 30.0000 chunk 559 optimal weight: 20.0000 chunk 443 optimal weight: 7.9990 chunk 858 optimal weight: 7.9990 chunk 332 optimal weight: 10.0000 chunk 521 optimal weight: 30.0000 chunk 638 optimal weight: 30.0000 chunk 994 optimal weight: 20.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 88 GLN ** c 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 121 ASN g 67 ASN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 42 ASN ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 41 HIS ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN p 59 HIS s 13 HIS s 51 HIS s 68 HIS t 19 HIS ** t 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 18 GLN z 47 GLN ** z 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 400 GLN z 532 GLN D 32 ASN ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN D 164 GLN E 62 GLN E 90 GLN E 92 HIS ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN F 22 ASN F 26 GLN G 44 HIS ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN K 90 ASN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS Q 43 GLN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 42 HIS X 22 ASN ** X 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 HIS ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 165989 Z= 0.219 Angle : 0.723 22.146 247857 Z= 0.379 Chirality : 0.035 0.336 31480 Planarity : 0.007 0.165 13686 Dihedral : 23.247 179.798 81771 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.71 % Allowed : 5.01 % Favored : 94.28 % Rotamer: Outliers : 0.27 % Allowed : 4.61 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.56 (0.10), residues: 6329 helix: -1.33 (0.10), residues: 2050 sheet: -1.75 (0.14), residues: 1057 loop : -0.38 (0.11), residues: 3222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP F 96 HIS 0.023 0.002 HIS F 4 PHE 0.024 0.002 PHE c 36 TYR 0.045 0.003 TYR o 77 ARG 0.024 0.001 ARG S 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2049 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 2035 time to evaluate : 6.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 15 PHE cc_start: 0.8589 (p90) cc_final: 0.8300 (p90) REVERT: b 55 GLU cc_start: 0.8887 (tp30) cc_final: 0.8577 (tp30) REVERT: b 90 PHE cc_start: 0.9587 (p90) cc_final: 0.9371 (p90) REVERT: b 92 ASN cc_start: 0.9241 (p0) cc_final: 0.8892 (p0) REVERT: b 99 MET cc_start: 0.8108 (mmp) cc_final: 0.7789 (mmm) REVERT: b 119 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: b 138 ARG cc_start: 0.9262 (ttt180) cc_final: 0.9045 (tmt170) REVERT: b 168 GLU cc_start: 0.8079 (mp0) cc_final: 0.7791 (mp0) REVERT: b 174 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8623 (tt0) REVERT: c 5 HIS cc_start: 0.8628 (t70) cc_final: 0.8001 (t70) REVERT: c 24 ASN cc_start: 0.9355 (t0) cc_final: 0.9147 (p0) REVERT: c 128 MET cc_start: 0.6994 (tpp) cc_final: 0.6725 (mmm) REVERT: c 129 PHE cc_start: 0.8965 (p90) cc_final: 0.8648 (p90) REVERT: c 149 LYS cc_start: 0.9502 (ttmt) cc_final: 0.8889 (ttmt) REVERT: d 7 LYS cc_start: 0.9215 (ttpp) cc_final: 0.9008 (ttpt) REVERT: d 70 GLN cc_start: 0.8849 (pt0) cc_final: 0.8647 (pt0) REVERT: d 81 LEU cc_start: 0.9060 (mp) cc_final: 0.8530 (tp) REVERT: d 82 LYS cc_start: 0.8339 (tptt) cc_final: 0.7926 (mttp) REVERT: d 109 THR cc_start: 0.7456 (p) cc_final: 0.7153 (p) REVERT: d 134 TYR cc_start: 0.8835 (t80) cc_final: 0.8529 (t80) REVERT: d 139 ASN cc_start: 0.9040 (p0) cc_final: 0.8760 (m-40) REVERT: e 33 THR cc_start: 0.9361 (t) cc_final: 0.8860 (t) REVERT: e 35 LEU cc_start: 0.7546 (tt) cc_final: 0.7266 (pp) REVERT: e 147 ASN cc_start: 0.8316 (p0) cc_final: 0.7942 (p0) REVERT: f 9 MET cc_start: 0.8816 (mpp) cc_final: 0.8405 (mpp) REVERT: f 22 ILE cc_start: 0.9368 (pt) cc_final: 0.9044 (mt) REVERT: f 25 TYR cc_start: 0.9645 (m-10) cc_final: 0.9386 (m-10) REVERT: f 49 TYR cc_start: 0.8829 (p90) cc_final: 0.7546 (p90) REVERT: f 59 TYR cc_start: 0.7810 (m-80) cc_final: 0.7603 (m-80) REVERT: f 74 LEU cc_start: 0.9704 (tt) cc_final: 0.9469 (tt) REVERT: f 80 PHE cc_start: 0.9209 (m-10) cc_final: 0.8975 (m-80) REVERT: f 86 ARG cc_start: 0.8682 (mtp85) cc_final: 0.8346 (mmm-85) REVERT: g 3 ARG cc_start: 0.8614 (ptt-90) cc_final: 0.7850 (ptt-90) REVERT: g 101 ARG cc_start: 0.9104 (mtm180) cc_final: 0.8860 (mtt180) REVERT: h 32 LYS cc_start: 0.9207 (mtmm) cc_final: 0.8967 (mttt) REVERT: h 49 LYS cc_start: 0.9579 (mppt) cc_final: 0.9324 (mmtm) REVERT: h 75 GLN cc_start: 0.9456 (mp-120) cc_final: 0.9241 (mp-120) REVERT: h 88 LYS cc_start: 0.8430 (pttp) cc_final: 0.8126 (pttt) REVERT: h 111 THR cc_start: 0.8128 (p) cc_final: 0.7840 (p) REVERT: h 112 ASP cc_start: 0.8584 (m-30) cc_final: 0.8378 (m-30) REVERT: i 29 ILE cc_start: 0.8713 (mp) cc_final: 0.8196 (mp) REVERT: j 42 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9270 (mm) REVERT: j 44 THR cc_start: 0.8524 (p) cc_final: 0.8308 (p) REVERT: j 59 LYS cc_start: 0.7725 (pptt) cc_final: 0.7297 (ttpt) REVERT: j 63 ASP cc_start: 0.8789 (t0) cc_final: 0.8109 (t0) REVERT: j 64 GLN cc_start: 0.9267 (mm-40) cc_final: 0.9000 (mt0) REVERT: j 65 TYR cc_start: 0.7598 (m-80) cc_final: 0.6871 (m-80) REVERT: k 73 VAL cc_start: 0.8891 (t) cc_final: 0.8289 (p) REVERT: l 52 CYS cc_start: 0.9501 (p) cc_final: 0.9157 (p) REVERT: l 55 ARG cc_start: 0.9013 (ttp-170) cc_final: 0.8715 (tpt-90) REVERT: l 61 GLU cc_start: 0.7969 (pt0) cc_final: 0.7597 (pt0) REVERT: m 11 HIS cc_start: 0.8303 (m90) cc_final: 0.7916 (m-70) REVERT: m 71 GLU cc_start: 0.9601 (pp20) cc_final: 0.9381 (pp20) REVERT: n 4 SER cc_start: 0.9261 (p) cc_final: 0.9048 (t) REVERT: n 9 GLU cc_start: 0.9568 (tm-30) cc_final: 0.8986 (tp30) REVERT: n 73 LEU cc_start: 0.9105 (mp) cc_final: 0.8865 (tp) REVERT: n 88 MET cc_start: 0.9280 (mpp) cc_final: 0.9074 (mpp) REVERT: o 2 LEU cc_start: 0.8482 (mp) cc_final: 0.7903 (mt) REVERT: o 80 LEU cc_start: 0.8918 (tt) cc_final: 0.8361 (mt) REVERT: o 81 ILE cc_start: 0.8729 (mt) cc_final: 0.8433 (mt) REVERT: p 35 ARG cc_start: 0.7248 (ttm170) cc_final: 0.6975 (ptm-80) REVERT: p 39 PHE cc_start: 0.9223 (t80) cc_final: 0.8705 (t80) REVERT: q 25 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8408 (tp30) REVERT: q 52 CYS cc_start: 0.7516 (p) cc_final: 0.6617 (m) REVERT: q 72 TRP cc_start: 0.8625 (m100) cc_final: 0.8353 (m100) REVERT: q 80 LYS cc_start: 0.8204 (mttm) cc_final: 0.7808 (tptp) REVERT: r 37 LYS cc_start: 0.9199 (mtpp) cc_final: 0.8914 (tttm) REVERT: r 41 SER cc_start: 0.8222 (m) cc_final: 0.6869 (p) REVERT: r 51 GLN cc_start: 0.9047 (tp-100) cc_final: 0.8557 (tt0) REVERT: r 54 LEU cc_start: 0.9654 (tp) cc_final: 0.9398 (tp) REVERT: r 69 TYR cc_start: 0.6711 (m-80) cc_final: 0.6434 (m-10) REVERT: s 27 LYS cc_start: 0.7679 (mtmm) cc_final: 0.7419 (tptp) REVERT: s 33 TRP cc_start: 0.7524 (m100) cc_final: 0.7095 (m100) REVERT: s 42 ASN cc_start: 0.8563 (p0) cc_final: 0.8298 (t0) REVERT: s 43 MET cc_start: 0.8607 (mtp) cc_final: 0.8283 (mtt) REVERT: s 65 MET cc_start: 0.9216 (ttt) cc_final: 0.8167 (ttt) REVERT: s 68 HIS cc_start: 0.8722 (m90) cc_final: 0.8289 (m90) REVERT: s 73 PHE cc_start: 0.8797 (m-80) cc_final: 0.8110 (m-80) REVERT: t 81 GLN cc_start: 0.8819 (tt0) cc_final: 0.8401 (pt0) REVERT: t 82 ILE cc_start: 0.8783 (mt) cc_final: 0.8533 (tt) REVERT: u 30 GLU cc_start: 0.7581 (pm20) cc_final: 0.7307 (pm20) REVERT: u 53 LYS cc_start: 0.8999 (mptt) cc_final: 0.8542 (pttt) REVERT: z 36 MET cc_start: 0.5288 (tpt) cc_final: 0.4914 (tpt) REVERT: z 127 ARG cc_start: 0.7275 (mtt180) cc_final: 0.6978 (ptm-80) REVERT: z 167 ARG cc_start: 0.7608 (mmm160) cc_final: 0.6538 (mmt180) REVERT: z 320 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7469 (tpt170) REVERT: z 452 MET cc_start: 0.3481 (mtp) cc_final: 0.1969 (pmm) REVERT: z 475 HIS cc_start: 0.8697 (m90) cc_final: 0.8454 (m90) REVERT: C 23 LEU cc_start: 0.7943 (tt) cc_final: 0.7739 (tp) REVERT: C 24 HIS cc_start: 0.8607 (t70) cc_final: 0.8001 (t70) REVERT: C 47 ARG cc_start: 0.8280 (mmt90) cc_final: 0.7924 (mmm-85) REVERT: C 80 LEU cc_start: 0.9294 (tp) cc_final: 0.9012 (tp) REVERT: C 94 LEU cc_start: 0.9232 (tt) cc_final: 0.8981 (tt) REVERT: C 143 VAL cc_start: 0.9430 (t) cc_final: 0.9204 (m) REVERT: C 145 MET cc_start: 0.8154 (mmp) cc_final: 0.7858 (mmm) REVERT: C 152 GLN cc_start: 0.8308 (mp10) cc_final: 0.7834 (mp10) REVERT: C 194 VAL cc_start: 0.8712 (t) cc_final: 0.8446 (t) REVERT: C 211 ARG cc_start: 0.8385 (mmm-85) cc_final: 0.7872 (tpp80) REVERT: C 239 PHE cc_start: 0.7788 (t80) cc_final: 0.6430 (t80) REVERT: D 82 PHE cc_start: 0.6580 (t80) cc_final: 0.6312 (t80) REVERT: D 128 ARG cc_start: 0.5256 (tpt90) cc_final: 0.4130 (mmm-85) REVERT: D 129 THR cc_start: 0.8655 (m) cc_final: 0.8243 (m) REVERT: D 130 GLN cc_start: 0.8760 (mt0) cc_final: 0.8502 (tt0) REVERT: D 154 LYS cc_start: 0.8184 (mtmm) cc_final: 0.7190 (mtmm) REVERT: D 156 PHE cc_start: 0.8432 (m-80) cc_final: 0.7867 (p90) REVERT: D 172 VAL cc_start: 0.8828 (m) cc_final: 0.8622 (p) REVERT: D 185 ASN cc_start: 0.8227 (m-40) cc_final: 0.7935 (m110) REVERT: D 201 LEU cc_start: 0.9320 (mt) cc_final: 0.9113 (mt) REVERT: E 17 THR cc_start: 0.9305 (p) cc_final: 0.9041 (p) REVERT: E 19 PHE cc_start: 0.7850 (m-80) cc_final: 0.7593 (m-10) REVERT: E 21 ARG cc_start: 0.8734 (ptm160) cc_final: 0.8491 (ttp-110) REVERT: E 30 GLN cc_start: 0.8536 (tt0) cc_final: 0.8287 (mt0) REVERT: E 62 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8576 (mm-40) REVERT: E 63 LYS cc_start: 0.8393 (mttp) cc_final: 0.8136 (mttp) REVERT: E 105 LEU cc_start: 0.9707 (mp) cc_final: 0.9462 (pp) REVERT: E 162 ARG cc_start: 0.8907 (ptp-170) cc_final: 0.8520 (ptt180) REVERT: E 168 ASP cc_start: 0.9151 (p0) cc_final: 0.8889 (p0) REVERT: E 176 ASP cc_start: 0.8378 (m-30) cc_final: 0.8083 (m-30) REVERT: F 4 HIS cc_start: 0.9185 (t70) cc_final: 0.8766 (t70) REVERT: F 34 THR cc_start: 0.8928 (p) cc_final: 0.8548 (t) REVERT: F 37 MET cc_start: 0.6012 (mtp) cc_final: 0.5131 (mtm) REVERT: F 97 GLU cc_start: 0.8627 (tt0) cc_final: 0.8139 (pt0) REVERT: F 104 THR cc_start: 0.9178 (p) cc_final: 0.8897 (t) REVERT: F 124 ARG cc_start: 0.6978 (mmm160) cc_final: 0.6724 (tpt170) REVERT: F 129 MET cc_start: 0.6652 (pmm) cc_final: 0.6331 (pmm) REVERT: F 155 ILE cc_start: 0.9029 (mt) cc_final: 0.8829 (mp) REVERT: F 172 PHE cc_start: 0.7684 (m-80) cc_final: 0.7445 (m-80) REVERT: G 51 PHE cc_start: 0.7601 (m-10) cc_final: 0.7282 (m-10) REVERT: G 68 ARG cc_start: 0.9447 (ttp80) cc_final: 0.9116 (ptm-80) REVERT: G 105 SER cc_start: 0.9330 (m) cc_final: 0.9069 (t) REVERT: G 129 GLU cc_start: 0.9304 (tt0) cc_final: 0.9065 (tm-30) REVERT: G 157 LYS cc_start: 0.8441 (mttt) cc_final: 0.8163 (mmtp) REVERT: I 71 LYS cc_start: 0.8495 (mtmm) cc_final: 0.8194 (pttp) REVERT: I 95 ASP cc_start: 0.6330 (m-30) cc_final: 0.5639 (p0) REVERT: H 1 MET cc_start: 0.8590 (mmt) cc_final: 0.8266 (mmm) REVERT: H 11 ASN cc_start: 0.8036 (t0) cc_final: 0.7800 (p0) REVERT: H 47 PHE cc_start: 0.8095 (t80) cc_final: 0.7887 (t80) REVERT: J 2 LYS cc_start: 0.9258 (mmtt) cc_final: 0.8929 (pptt) REVERT: J 52 ASP cc_start: 0.5570 (m-30) cc_final: 0.5037 (m-30) REVERT: J 89 PHE cc_start: 0.9096 (t80) cc_final: 0.8678 (t80) REVERT: J 114 LEU cc_start: 0.9314 (tp) cc_final: 0.9041 (tp) REVERT: K 7 MET cc_start: 0.9191 (mmp) cc_final: 0.8928 (mmm) REVERT: K 8 LEU cc_start: 0.9465 (mt) cc_final: 0.9137 (mp) REVERT: K 13 ASN cc_start: 0.8512 (p0) cc_final: 0.8259 (p0) REVERT: K 23 LYS cc_start: 0.9327 (mtpp) cc_final: 0.8837 (mtpp) REVERT: K 71 ARG cc_start: 0.8653 (mmp80) cc_final: 0.8117 (mmp80) REVERT: K 104 THR cc_start: 0.8171 (t) cc_final: 0.7908 (t) REVERT: K 110 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7940 (pm20) REVERT: L 8 PRO cc_start: 0.8855 (Cg_endo) cc_final: 0.8650 (Cg_exo) REVERT: L 17 LYS cc_start: 0.7729 (ttpp) cc_final: 0.7434 (tmtt) REVERT: L 30 THR cc_start: 0.9265 (p) cc_final: 0.8899 (t) REVERT: L 55 MET cc_start: 0.8805 (tpt) cc_final: 0.7803 (tpt) REVERT: L 59 ARG cc_start: 0.9357 (ptm160) cc_final: 0.8647 (ptm160) REVERT: L 63 LYS cc_start: 0.8750 (ptmt) cc_final: 0.8410 (pttt) REVERT: L 84 LYS cc_start: 0.8977 (mttt) cc_final: 0.8649 (mmmt) REVERT: M 9 PHE cc_start: 0.9028 (m-80) cc_final: 0.8796 (m-80) REVERT: M 55 ARG cc_start: 0.8897 (mmp-170) cc_final: 0.8488 (tpp-160) REVERT: M 59 ARG cc_start: 0.9250 (mmp80) cc_final: 0.8958 (mmp80) REVERT: M 60 GLN cc_start: 0.9379 (mp10) cc_final: 0.9054 (tp-100) REVERT: M 68 PHE cc_start: 0.8937 (t80) cc_final: 0.8628 (t80) REVERT: M 70 ASP cc_start: 0.8763 (t0) cc_final: 0.8471 (t0) REVERT: M 82 MET cc_start: 0.9160 (mmm) cc_final: 0.8908 (tpt) REVERT: M 91 TYR cc_start: 0.8298 (p90) cc_final: 0.7751 (p90) REVERT: M 111 GLU cc_start: 0.9410 (pm20) cc_final: 0.9201 (pm20) REVERT: M 117 PHE cc_start: 0.8710 (m-10) cc_final: 0.8421 (m-10) REVERT: M 119 LEU cc_start: 0.8849 (mm) cc_final: 0.8518 (mm) REVERT: N 1 MET cc_start: 0.9212 (pmm) cc_final: 0.8791 (pmm) REVERT: N 9 GLN cc_start: 0.8618 (pt0) cc_final: 0.8199 (pm20) REVERT: N 24 MET cc_start: 0.9685 (ttt) cc_final: 0.9370 (tpp) REVERT: N 45 ARG cc_start: 0.9083 (mtm180) cc_final: 0.8456 (mtm180) REVERT: N 65 LEU cc_start: 0.9578 (tp) cc_final: 0.9247 (pp) REVERT: N 74 GLU cc_start: 0.9403 (tm-30) cc_final: 0.9173 (tm-30) REVERT: O 55 GLU cc_start: 0.8149 (tt0) cc_final: 0.7485 (mm-30) REVERT: O 115 LEU cc_start: 0.8517 (tp) cc_final: 0.8209 (tp) REVERT: P 6 GLN cc_start: 0.9389 (tt0) cc_final: 0.9118 (pt0) REVERT: P 55 HIS cc_start: 0.8773 (m-70) cc_final: 0.8410 (m170) REVERT: P 59 THR cc_start: 0.9536 (m) cc_final: 0.9027 (t) REVERT: P 84 SER cc_start: 0.9120 (m) cc_final: 0.8657 (t) REVERT: Q 10 ARG cc_start: 0.8703 (ptp90) cc_final: 0.8212 (ttp-170) REVERT: Q 14 LYS cc_start: 0.9528 (ttmt) cc_final: 0.9226 (tptt) REVERT: Q 15 LYS cc_start: 0.9432 (ttpt) cc_final: 0.9077 (tptm) REVERT: Q 23 TYR cc_start: 0.8371 (m-80) cc_final: 0.8155 (m-80) REVERT: Q 70 GLN cc_start: 0.9275 (tt0) cc_final: 0.8775 (tm-30) REVERT: R 35 PHE cc_start: 0.8374 (m-80) cc_final: 0.7630 (m-80) REVERT: R 40 MET cc_start: 0.8186 (tpt) cc_final: 0.6889 (tmm) REVERT: R 41 ILE cc_start: 0.9256 (mp) cc_final: 0.9012 (mp) REVERT: R 49 ILE cc_start: 0.7903 (pt) cc_final: 0.7649 (pt) REVERT: R 78 ARG cc_start: 0.9055 (mtp180) cc_final: 0.8727 (mtp180) REVERT: S 9 HIS cc_start: 0.7662 (m90) cc_final: 0.7271 (m90) REVERT: S 18 ARG cc_start: 0.9237 (tmt-80) cc_final: 0.8993 (tmt-80) REVERT: S 49 LYS cc_start: 0.9420 (ptmt) cc_final: 0.8915 (tptp) REVERT: S 86 MET cc_start: 0.8645 (tpt) cc_final: 0.8318 (tpp) REVERT: T 6 ARG cc_start: 0.8823 (tpm170) cc_final: 0.8533 (tpm170) REVERT: T 9 LYS cc_start: 0.9156 (mttt) cc_final: 0.8865 (mtpp) REVERT: T 15 HIS cc_start: 0.8117 (t70) cc_final: 0.7608 (t70) REVERT: T 18 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8337 (tm-30) REVERT: T 19 LYS cc_start: 0.8826 (ttpp) cc_final: 0.8582 (mttm) REVERT: T 33 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8511 (mmtt) REVERT: T 80 TRP cc_start: 0.8335 (p-90) cc_final: 0.7670 (p-90) REVERT: T 82 LYS cc_start: 0.9571 (ptmm) cc_final: 0.8717 (ptmm) REVERT: U 10 VAL cc_start: 0.8697 (t) cc_final: 0.8412 (t) REVERT: U 65 GLN cc_start: 0.8796 (mt0) cc_final: 0.8509 (mt0) REVERT: V 8 VAL cc_start: 0.9319 (t) cc_final: 0.8915 (m) REVERT: V 10 LYS cc_start: 0.9340 (mmtt) cc_final: 0.9134 (mmmm) REVERT: V 61 LEU cc_start: 0.9234 (pp) cc_final: 0.8708 (tt) REVERT: V 71 LYS cc_start: 0.8893 (mttm) cc_final: 0.8579 (mmtm) REVERT: V 91 PHE cc_start: 0.9260 (m-80) cc_final: 0.8919 (m-80) REVERT: W 21 ARG cc_start: 0.7589 (ptp90) cc_final: 0.7236 (mtm180) REVERT: W 46 ASN cc_start: 0.8984 (m-40) cc_final: 0.8168 (m-40) REVERT: W 58 LYS cc_start: 0.8926 (ptpt) cc_final: 0.8108 (tppt) REVERT: W 62 LYS cc_start: 0.9388 (mppt) cc_final: 0.8606 (mmtm) REVERT: W 73 ARG cc_start: 0.8961 (mtt180) cc_final: 0.8439 (mtt90) REVERT: W 79 GLU cc_start: 0.8441 (tp30) cc_final: 0.7399 (pp20) REVERT: X 37 PHE cc_start: 0.9275 (m-10) cc_final: 0.8951 (m-10) REVERT: X 45 PHE cc_start: 0.9479 (m-80) cc_final: 0.9220 (m-80) REVERT: X 63 ILE cc_start: 0.9365 (tp) cc_final: 0.9141 (mm) REVERT: X 71 ARG cc_start: 0.8642 (mpp-170) cc_final: 0.8192 (mmm160) REVERT: Y 2 LYS cc_start: 0.8097 (ttpp) cc_final: 0.7719 (ptpt) REVERT: Y 26 PHE cc_start: 0.9502 (t80) cc_final: 0.9239 (t80) REVERT: Y 39 GLN cc_start: 0.9220 (mt0) cc_final: 0.8991 (pm20) REVERT: Y 46 VAL cc_start: 0.9201 (m) cc_final: 0.8965 (p) REVERT: Y 55 THR cc_start: 0.8848 (t) cc_final: 0.8606 (t) REVERT: Z 29 ARG cc_start: 0.8582 (mtt180) cc_final: 0.8376 (mtt-85) REVERT: Z 57 GLU cc_start: 0.8107 (pp20) cc_final: 0.7811 (pm20) REVERT: 0 4 GLN cc_start: 0.8820 (pt0) cc_final: 0.8392 (pp30) REVERT: 0 6 LYS cc_start: 0.8704 (tmtt) cc_final: 0.8491 (tmtt) REVERT: 0 9 ARG cc_start: 0.8909 (mtp180) cc_final: 0.8577 (mtp180) REVERT: 0 11 LYS cc_start: 0.9529 (ttpt) cc_final: 0.9178 (ptpt) REVERT: 1 20 TYR cc_start: 0.8773 (m-80) cc_final: 0.8260 (m-10) REVERT: 1 26 LYS cc_start: 0.8641 (tptt) cc_final: 0.8050 (tppt) REVERT: 1 32 LYS cc_start: 0.7703 (tmtt) cc_final: 0.7245 (tmtt) REVERT: 1 37 LYS cc_start: 0.8307 (tttt) cc_final: 0.7634 (tptt) REVERT: 1 43 ARG cc_start: 0.7182 (mmm-85) cc_final: 0.6902 (mmm-85) REVERT: 2 13 ASN cc_start: 0.8863 (m110) cc_final: 0.7120 (t0) REVERT: 2 22 MET cc_start: 0.8914 (tpp) cc_final: 0.8542 (tpt) REVERT: 2 30 VAL cc_start: 0.9290 (m) cc_final: 0.9009 (t) REVERT: 3 25 HIS cc_start: 0.9357 (m90) cc_final: 0.9125 (m90) REVERT: 3 42 HIS cc_start: 0.9385 (m90) cc_final: 0.9125 (m90) REVERT: 4 23 ILE cc_start: 0.9053 (pt) cc_final: 0.8601 (tp) REVERT: 6 12 ILE cc_start: 0.8558 (pt) cc_final: 0.7940 (mp) outliers start: 14 outliers final: 4 residues processed: 2040 average time/residue: 1.4652 time to fit residues: 4962.8378 Evaluate side-chains 1544 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1537 time to evaluate : 6.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1095 random chunks: chunk 552 optimal weight: 50.0000 chunk 308 optimal weight: 9.9990 chunk 827 optimal weight: 40.0000 chunk 677 optimal weight: 50.0000 chunk 274 optimal weight: 0.6980 chunk 996 optimal weight: 20.0000 chunk 1076 optimal weight: 20.0000 chunk 887 optimal weight: 20.0000 chunk 987 optimal weight: 6.9990 chunk 339 optimal weight: 30.0000 chunk 799 optimal weight: 7.9990 overall best weight: 9.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 GLN g 67 ASN ** g 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 13 HIS s 56 HIS z 18 GLN z 213 ASN ** z 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 434 HIS E 62 GLN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN G 87 GLN K 9 ASN M 22 GLN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS R 66 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN Y 58 ASN 1 18 HIS ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 165989 Z= 0.237 Angle : 0.714 22.103 247857 Z= 0.377 Chirality : 0.035 0.355 31480 Planarity : 0.008 0.236 13686 Dihedral : 23.370 179.798 81771 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.78 % Favored : 93.59 % Rotamer: Outliers : 0.25 % Allowed : 5.13 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.52 (0.10), residues: 6329 helix: -0.99 (0.10), residues: 2022 sheet: -1.53 (0.14), residues: 1080 loop : -0.67 (0.11), residues: 3227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP z 419 HIS 0.015 0.002 HIS g 141 PHE 0.050 0.003 PHE F 121 TYR 0.035 0.003 TYR G 150 ARG 0.019 0.001 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1944 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1931 time to evaluate : 6.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 15 PHE cc_start: 0.8777 (p90) cc_final: 0.8465 (p90) REVERT: b 29 PHE cc_start: 0.8645 (m-10) cc_final: 0.8390 (m-10) REVERT: b 41 ASN cc_start: 0.9557 (t0) cc_final: 0.9238 (t0) REVERT: b 43 GLU cc_start: 0.7997 (pm20) cc_final: 0.7507 (pm20) REVERT: b 90 PHE cc_start: 0.9523 (p90) cc_final: 0.9054 (p90) REVERT: b 92 ASN cc_start: 0.9205 (p0) cc_final: 0.8746 (p0) REVERT: b 168 GLU cc_start: 0.8162 (mp0) cc_final: 0.7723 (mp0) REVERT: c 5 HIS cc_start: 0.8607 (t70) cc_final: 0.8090 (t70) REVERT: c 22 PHE cc_start: 0.7937 (t80) cc_final: 0.7601 (t80) REVERT: c 24 ASN cc_start: 0.9392 (t0) cc_final: 0.9043 (p0) REVERT: c 25 THR cc_start: 0.8483 (p) cc_final: 0.7811 (p) REVERT: c 129 PHE cc_start: 0.8939 (p90) cc_final: 0.8705 (p90) REVERT: c 169 GLU cc_start: 0.8705 (mp0) cc_final: 0.8367 (mp0) REVERT: c 191 THR cc_start: 0.5355 (p) cc_final: 0.4875 (t) REVERT: d 7 LYS cc_start: 0.9214 (ttpp) cc_final: 0.8984 (ttpt) REVERT: d 27 ILE cc_start: 0.5515 (tt) cc_final: 0.5295 (tt) REVERT: d 62 ARG cc_start: 0.9185 (mtt180) cc_final: 0.8507 (mmp80) REVERT: d 81 LEU cc_start: 0.9001 (mp) cc_final: 0.8596 (tp) REVERT: d 82 LYS cc_start: 0.8415 (tptt) cc_final: 0.8037 (mttt) REVERT: d 104 MET cc_start: 0.8534 (ttt) cc_final: 0.7885 (tmm) REVERT: d 183 ARG cc_start: 0.9606 (mmm160) cc_final: 0.9309 (mmm160) REVERT: d 186 GLU cc_start: 0.8754 (pm20) cc_final: 0.8315 (pm20) REVERT: d 196 GLU cc_start: 0.8666 (pm20) cc_final: 0.8156 (tm-30) REVERT: e 33 THR cc_start: 0.9377 (t) cc_final: 0.8839 (t) REVERT: e 51 LYS cc_start: 0.8479 (mtmt) cc_final: 0.7937 (mttt) REVERT: e 91 SER cc_start: 0.9330 (p) cc_final: 0.9116 (p) REVERT: e 95 MET cc_start: 0.8817 (pmm) cc_final: 0.8616 (pmm) REVERT: e 110 MET cc_start: 0.9331 (pmm) cc_final: 0.9075 (pmm) REVERT: e 127 TYR cc_start: 0.7071 (m-10) cc_final: 0.6612 (m-10) REVERT: e 134 ASN cc_start: 0.8471 (m-40) cc_final: 0.8153 (m-40) REVERT: e 147 ASN cc_start: 0.8171 (p0) cc_final: 0.7861 (p0) REVERT: f 1 MET cc_start: 0.8525 (tmm) cc_final: 0.8137 (tpp) REVERT: f 9 MET cc_start: 0.8765 (mpp) cc_final: 0.8488 (mpp) REVERT: f 49 TYR cc_start: 0.8781 (p90) cc_final: 0.7626 (p90) REVERT: f 80 PHE cc_start: 0.9250 (m-10) cc_final: 0.9009 (m-80) REVERT: f 86 ARG cc_start: 0.8646 (mtp85) cc_final: 0.8078 (mmt180) REVERT: g 3 ARG cc_start: 0.8727 (ptt-90) cc_final: 0.8100 (ptt-90) REVERT: g 57 GLU cc_start: 0.8254 (pm20) cc_final: 0.8053 (pm20) REVERT: g 101 ARG cc_start: 0.9112 (mtm180) cc_final: 0.8725 (mtt180) REVERT: h 49 LYS cc_start: 0.9518 (mppt) cc_final: 0.9311 (mmtm) REVERT: i 102 PHE cc_start: 0.7681 (m-10) cc_final: 0.7386 (m-80) REVERT: j 44 THR cc_start: 0.8582 (p) cc_final: 0.6397 (p) REVERT: j 63 ASP cc_start: 0.8968 (t0) cc_final: 0.8572 (t0) REVERT: j 64 GLN cc_start: 0.9332 (mm-40) cc_final: 0.9090 (mt0) REVERT: j 85 ASP cc_start: 0.9187 (m-30) cc_final: 0.8909 (m-30) REVERT: j 99 GLN cc_start: 0.8827 (mm110) cc_final: 0.8598 (mm-40) REVERT: k 73 VAL cc_start: 0.8870 (t) cc_final: 0.8385 (p) REVERT: l 52 CYS cc_start: 0.9506 (p) cc_final: 0.9190 (p) REVERT: l 55 ARG cc_start: 0.9158 (ttp-170) cc_final: 0.8772 (tpt-90) REVERT: l 56 LEU cc_start: 0.8840 (mm) cc_final: 0.8369 (mm) REVERT: l 61 GLU cc_start: 0.7937 (pt0) cc_final: 0.7661 (pt0) REVERT: m 11 HIS cc_start: 0.8572 (m90) cc_final: 0.8216 (m-70) REVERT: m 58 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8135 (pt0) REVERT: m 70 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.8880 (mmt180) REVERT: n 4 SER cc_start: 0.9381 (p) cc_final: 0.9110 (t) REVERT: n 9 GLU cc_start: 0.9557 (tm-30) cc_final: 0.9055 (tp30) REVERT: n 73 LEU cc_start: 0.9141 (mp) cc_final: 0.8641 (tp) REVERT: n 88 MET cc_start: 0.9285 (mpp) cc_final: 0.9081 (mpp) REVERT: o 14 PHE cc_start: 0.9146 (m-80) cc_final: 0.8668 (m-80) REVERT: o 27 GLN cc_start: 0.8956 (mm110) cc_final: 0.8551 (mm110) REVERT: o 47 LYS cc_start: 0.9038 (mtmt) cc_final: 0.8621 (pttt) REVERT: o 77 TYR cc_start: 0.8622 (t80) cc_final: 0.8045 (t80) REVERT: o 81 ILE cc_start: 0.8872 (mt) cc_final: 0.8407 (mm) REVERT: p 2 VAL cc_start: 0.7363 (m) cc_final: 0.6853 (p) REVERT: p 17 TYR cc_start: 0.8103 (m-80) cc_final: 0.7822 (m-80) REVERT: p 34 GLU cc_start: 0.8291 (pm20) cc_final: 0.7702 (pm20) REVERT: p 35 ARG cc_start: 0.7937 (ttm170) cc_final: 0.6781 (ttp80) REVERT: p 39 PHE cc_start: 0.9326 (t80) cc_final: 0.8777 (t80) REVERT: p 66 THR cc_start: 0.6967 (m) cc_final: 0.6026 (m) REVERT: p 79 ASN cc_start: 0.8675 (m110) cc_final: 0.8201 (t0) REVERT: q 24 ILE cc_start: 0.9274 (mm) cc_final: 0.9044 (mm) REVERT: q 25 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8254 (tp30) REVERT: q 52 CYS cc_start: 0.7509 (p) cc_final: 0.6954 (m) REVERT: q 72 TRP cc_start: 0.8828 (m100) cc_final: 0.8406 (m100) REVERT: q 80 LYS cc_start: 0.8154 (mttm) cc_final: 0.7802 (tptp) REVERT: r 41 SER cc_start: 0.7941 (m) cc_final: 0.6863 (p) REVERT: r 51 GLN cc_start: 0.9084 (tp-100) cc_final: 0.8460 (tt0) REVERT: r 54 LEU cc_start: 0.9633 (tp) cc_final: 0.9336 (tp) REVERT: r 69 TYR cc_start: 0.6974 (m-80) cc_final: 0.6727 (m-10) REVERT: s 27 LYS cc_start: 0.7719 (mtmm) cc_final: 0.7407 (tptp) REVERT: s 42 ASN cc_start: 0.8718 (p0) cc_final: 0.8291 (t0) REVERT: s 46 LEU cc_start: 0.8750 (mm) cc_final: 0.8515 (mm) REVERT: s 47 THR cc_start: 0.7792 (p) cc_final: 0.7510 (p) REVERT: s 65 MET cc_start: 0.8896 (ttt) cc_final: 0.8280 (ttt) REVERT: s 68 HIS cc_start: 0.8878 (m90) cc_final: 0.8624 (m-70) REVERT: t 77 ASN cc_start: 0.7963 (t0) cc_final: 0.7481 (t0) REVERT: t 81 GLN cc_start: 0.8843 (tt0) cc_final: 0.8421 (pt0) REVERT: t 83 ASN cc_start: 0.8880 (m-40) cc_final: 0.8569 (m-40) REVERT: u 6 ARG cc_start: 0.8745 (tpt90) cc_final: 0.7701 (tpt170) REVERT: u 12 ASP cc_start: 0.8627 (p0) cc_final: 0.8222 (p0) REVERT: u 30 GLU cc_start: 0.7735 (pm20) cc_final: 0.7401 (pm20) REVERT: u 53 LYS cc_start: 0.8955 (mptt) cc_final: 0.8518 (pttt) REVERT: z 127 ARG cc_start: 0.7385 (mtt180) cc_final: 0.6960 (ptm-80) REVERT: z 167 ARG cc_start: 0.7529 (mmm160) cc_final: 0.6591 (mpt180) REVERT: z 208 TRP cc_start: 0.7683 (t-100) cc_final: 0.7117 (t-100) REVERT: z 249 GLN cc_start: 0.8574 (mp10) cc_final: 0.8254 (mp10) REVERT: z 265 PHE cc_start: 0.8052 (p90) cc_final: 0.7652 (m-80) REVERT: z 320 ARG cc_start: 0.8120 (mtt90) cc_final: 0.7441 (tpt170) REVERT: z 348 ARG cc_start: 0.7993 (mtp85) cc_final: 0.6975 (mmt180) REVERT: z 382 ASP cc_start: 0.9504 (m-30) cc_final: 0.9242 (p0) REVERT: z 475 HIS cc_start: 0.8904 (m90) cc_final: 0.8627 (m90) REVERT: z 562 GLN cc_start: 0.8345 (mp10) cc_final: 0.7979 (mp10) REVERT: z 611 PHE cc_start: 0.6717 (t80) cc_final: 0.5981 (t80) REVERT: C 32 LEU cc_start: 0.9297 (pp) cc_final: 0.9052 (pp) REVERT: C 35 LYS cc_start: 0.8555 (ptmm) cc_final: 0.8269 (pttp) REVERT: C 64 VAL cc_start: 0.8069 (p) cc_final: 0.7708 (p) REVERT: C 94 LEU cc_start: 0.9143 (tt) cc_final: 0.8908 (tt) REVERT: C 143 VAL cc_start: 0.9352 (t) cc_final: 0.9011 (m) REVERT: C 145 MET cc_start: 0.8146 (mmp) cc_final: 0.7914 (mmm) REVERT: C 152 GLN cc_start: 0.8159 (mp10) cc_final: 0.7646 (mp10) REVERT: C 200 MET cc_start: 0.8240 (ptm) cc_final: 0.7373 (ptm) REVERT: C 211 ARG cc_start: 0.8439 (mmm-85) cc_final: 0.8053 (tpp80) REVERT: C 239 PHE cc_start: 0.8043 (t80) cc_final: 0.6566 (t80) REVERT: D 36 GLN cc_start: 0.8638 (mt0) cc_final: 0.7877 (mm-40) REVERT: D 82 PHE cc_start: 0.6907 (t80) cc_final: 0.6695 (t80) REVERT: D 128 ARG cc_start: 0.5458 (tpt90) cc_final: 0.3906 (mmm-85) REVERT: D 154 LYS cc_start: 0.8127 (mtmm) cc_final: 0.7378 (mtmm) REVERT: D 164 GLN cc_start: 0.8847 (tp40) cc_final: 0.8640 (tm-30) REVERT: D 172 VAL cc_start: 0.8905 (m) cc_final: 0.8626 (p) REVERT: D 201 LEU cc_start: 0.9298 (mt) cc_final: 0.9059 (mt) REVERT: D 202 ILE cc_start: 0.9533 (pt) cc_final: 0.9307 (mp) REVERT: E 17 THR cc_start: 0.9269 (p) cc_final: 0.9013 (p) REVERT: E 30 GLN cc_start: 0.8559 (tt0) cc_final: 0.8318 (mt0) REVERT: E 69 ARG cc_start: 0.8545 (mtm-85) cc_final: 0.7903 (mmm160) REVERT: E 101 TYR cc_start: 0.9611 (t80) cc_final: 0.9353 (t80) REVERT: E 105 LEU cc_start: 0.9746 (mp) cc_final: 0.9439 (pp) REVERT: E 147 LEU cc_start: 0.8900 (tp) cc_final: 0.8360 (tp) REVERT: E 154 ASP cc_start: 0.8171 (t70) cc_final: 0.7648 (p0) REVERT: E 166 LYS cc_start: 0.9462 (mptt) cc_final: 0.8915 (mptt) REVERT: E 168 ASP cc_start: 0.9131 (p0) cc_final: 0.8930 (p0) REVERT: E 176 ASP cc_start: 0.8655 (m-30) cc_final: 0.8386 (m-30) REVERT: F 34 THR cc_start: 0.8819 (p) cc_final: 0.8470 (t) REVERT: F 127 TYR cc_start: 0.8094 (t80) cc_final: 0.7794 (t80) REVERT: F 129 MET cc_start: 0.7024 (pmm) cc_final: 0.6663 (pmm) REVERT: F 153 ILE cc_start: 0.7772 (mp) cc_final: 0.7368 (mp) REVERT: F 155 ILE cc_start: 0.8978 (mt) cc_final: 0.8736 (mp) REVERT: G 18 ILE cc_start: 0.8115 (tt) cc_final: 0.7853 (mp) REVERT: G 87 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.6928 (pm20) REVERT: G 105 SER cc_start: 0.9298 (m) cc_final: 0.8972 (t) REVERT: G 129 GLU cc_start: 0.9318 (tt0) cc_final: 0.9016 (tm-30) REVERT: G 150 TYR cc_start: 0.8607 (m-80) cc_final: 0.8205 (m-80) REVERT: G 157 LYS cc_start: 0.8406 (mttt) cc_final: 0.7971 (mmtp) REVERT: G 172 GLU cc_start: 0.8393 (mp0) cc_final: 0.8169 (mp0) REVERT: I 71 LYS cc_start: 0.8427 (mtmm) cc_final: 0.8152 (pttp) REVERT: I 100 ILE cc_start: 0.6324 (tp) cc_final: 0.6096 (tp) REVERT: H 11 ASN cc_start: 0.8131 (t0) cc_final: 0.7716 (p0) REVERT: J 52 ASP cc_start: 0.5587 (m-30) cc_final: 0.5060 (m-30) REVERT: J 53 TYR cc_start: 0.7336 (m-80) cc_final: 0.6266 (m-80) REVERT: J 74 TYR cc_start: 0.9020 (m-80) cc_final: 0.8527 (m-80) REVERT: J 89 PHE cc_start: 0.9237 (t80) cc_final: 0.8887 (t80) REVERT: J 114 LEU cc_start: 0.9226 (tp) cc_final: 0.8894 (tp) REVERT: K 5 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8573 (tm-30) REVERT: K 8 LEU cc_start: 0.9428 (mt) cc_final: 0.9093 (mt) REVERT: K 9 ASN cc_start: 0.8905 (m-40) cc_final: 0.8092 (m110) REVERT: K 13 ASN cc_start: 0.8705 (p0) cc_final: 0.8399 (p0) REVERT: K 44 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8619 (mptt) REVERT: K 71 ARG cc_start: 0.8739 (mmp80) cc_final: 0.8003 (mmp-170) REVERT: K 73 ASP cc_start: 0.9061 (m-30) cc_final: 0.8854 (m-30) REVERT: K 97 THR cc_start: 0.9141 (p) cc_final: 0.8931 (p) REVERT: K 110 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8055 (pm20) REVERT: L 30 THR cc_start: 0.9139 (p) cc_final: 0.8779 (t) REVERT: L 55 MET cc_start: 0.8894 (tpt) cc_final: 0.8585 (tpt) REVERT: L 59 ARG cc_start: 0.9393 (ptm160) cc_final: 0.8958 (ptm160) REVERT: L 84 LYS cc_start: 0.8896 (mttt) cc_final: 0.8634 (mmmt) REVERT: L 107 PHE cc_start: 0.8292 (m-80) cc_final: 0.8063 (m-80) REVERT: L 111 ILE cc_start: 0.4776 (mm) cc_final: 0.4537 (mm) REVERT: M 9 PHE cc_start: 0.9078 (m-80) cc_final: 0.8796 (m-80) REVERT: M 10 ARG cc_start: 0.8982 (mmm160) cc_final: 0.8555 (mmp80) REVERT: M 12 MET cc_start: 0.9177 (tpt) cc_final: 0.8868 (tpp) REVERT: M 55 ARG cc_start: 0.9007 (mmp-170) cc_final: 0.8438 (tpp-160) REVERT: M 60 GLN cc_start: 0.9428 (mp10) cc_final: 0.9043 (tp-100) REVERT: M 68 PHE cc_start: 0.9123 (t80) cc_final: 0.8886 (t80) REVERT: M 70 ASP cc_start: 0.8800 (t0) cc_final: 0.8578 (t0) REVERT: M 82 MET cc_start: 0.9319 (mmm) cc_final: 0.8360 (tpp) REVERT: M 91 TYR cc_start: 0.8307 (p90) cc_final: 0.7660 (p90) REVERT: N 1 MET cc_start: 0.9283 (pmm) cc_final: 0.9038 (pmm) REVERT: N 9 GLN cc_start: 0.8717 (pt0) cc_final: 0.8327 (pm20) REVERT: N 10 LEU cc_start: 0.9260 (mp) cc_final: 0.9053 (mp) REVERT: N 20 MET cc_start: 0.9563 (ttp) cc_final: 0.9229 (ttp) REVERT: N 45 ARG cc_start: 0.8772 (mtm180) cc_final: 0.8133 (mtm-85) REVERT: N 46 ARG cc_start: 0.9290 (mtp85) cc_final: 0.8518 (mtt90) REVERT: N 49 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8690 (mt-10) REVERT: N 72 ASP cc_start: 0.9425 (t70) cc_final: 0.9220 (t0) REVERT: N 74 GLU cc_start: 0.9399 (tm-30) cc_final: 0.9178 (tm-30) REVERT: N 95 THR cc_start: 0.6876 (t) cc_final: 0.6632 (t) REVERT: O 34 HIS cc_start: 0.9068 (m-70) cc_final: 0.8773 (m-70) REVERT: O 115 LEU cc_start: 0.8482 (tp) cc_final: 0.8223 (tp) REVERT: P 6 GLN cc_start: 0.9372 (tt0) cc_final: 0.9070 (pt0) REVERT: P 55 HIS cc_start: 0.8963 (m-70) cc_final: 0.8760 (m-70) REVERT: P 59 THR cc_start: 0.9512 (m) cc_final: 0.9117 (p) REVERT: P 84 SER cc_start: 0.8965 (m) cc_final: 0.8639 (t) REVERT: Q 10 ARG cc_start: 0.8705 (ptp90) cc_final: 0.8314 (ttp-170) REVERT: Q 14 LYS cc_start: 0.9481 (ttmt) cc_final: 0.9159 (tptt) REVERT: Q 15 LYS cc_start: 0.9379 (ttpt) cc_final: 0.8953 (tptm) REVERT: Q 23 TYR cc_start: 0.8482 (m-80) cc_final: 0.8087 (m-80) REVERT: Q 70 GLN cc_start: 0.9265 (tt0) cc_final: 0.8785 (tm-30) REVERT: R 34 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8275 (mm-30) REVERT: R 40 MET cc_start: 0.8473 (tpt) cc_final: 0.7353 (tmm) REVERT: R 41 ILE cc_start: 0.9321 (mp) cc_final: 0.9116 (mp) REVERT: R 53 PHE cc_start: 0.8682 (m-10) cc_final: 0.8441 (m-10) REVERT: R 87 GLN cc_start: 0.9148 (pp30) cc_final: 0.8896 (pp30) REVERT: R 95 ASP cc_start: 0.8995 (m-30) cc_final: 0.8745 (m-30) REVERT: S 18 ARG cc_start: 0.9256 (tmt-80) cc_final: 0.8999 (tmt-80) REVERT: S 49 LYS cc_start: 0.9439 (ptmt) cc_final: 0.8932 (tptp) REVERT: S 86 MET cc_start: 0.8622 (tpt) cc_final: 0.8269 (tpp) REVERT: S 87 PRO cc_start: 0.9245 (Cg_exo) cc_final: 0.8740 (Cg_endo) REVERT: S 97 LEU cc_start: 0.9386 (mp) cc_final: 0.8959 (mp) REVERT: T 6 ARG cc_start: 0.9142 (tpm170) cc_final: 0.8768 (tpm170) REVERT: T 8 LEU cc_start: 0.8463 (pp) cc_final: 0.8251 (pp) REVERT: T 12 ARG cc_start: 0.9241 (mmm-85) cc_final: 0.8354 (mmm160) REVERT: T 18 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8412 (tm-30) REVERT: T 33 LYS cc_start: 0.9035 (mmtp) cc_final: 0.8231 (mmtp) REVERT: T 79 ASP cc_start: 0.9173 (t0) cc_final: 0.8892 (t0) REVERT: T 80 TRP cc_start: 0.8544 (p-90) cc_final: 0.7871 (p-90) REVERT: T 82 LYS cc_start: 0.9635 (ptmm) cc_final: 0.8498 (ptmm) REVERT: U 65 GLN cc_start: 0.8871 (mt0) cc_final: 0.8566 (mt0) REVERT: V 8 VAL cc_start: 0.9440 (t) cc_final: 0.8996 (m) REVERT: V 18 ARG cc_start: 0.8877 (mtt180) cc_final: 0.8524 (mmt90) REVERT: V 29 ILE cc_start: 0.8537 (pt) cc_final: 0.8086 (mm) REVERT: V 71 LYS cc_start: 0.8931 (mttm) cc_final: 0.8613 (mmtm) REVERT: V 91 PHE cc_start: 0.9226 (m-80) cc_final: 0.8521 (m-80) REVERT: W 13 GLU cc_start: 0.8776 (mp0) cc_final: 0.8449 (mp0) REVERT: W 46 ASN cc_start: 0.8949 (m-40) cc_final: 0.8221 (m-40) REVERT: W 47 VAL cc_start: 0.9406 (t) cc_final: 0.9036 (p) REVERT: W 58 LYS cc_start: 0.8768 (ptpt) cc_final: 0.7847 (tppt) REVERT: W 71 LYS cc_start: 0.8139 (ptmt) cc_final: 0.7540 (ptpt) REVERT: W 76 ILE cc_start: 0.9612 (mp) cc_final: 0.9172 (tp) REVERT: W 79 GLU cc_start: 0.8671 (tp30) cc_final: 0.7593 (pp20) REVERT: X 22 ASN cc_start: 0.8873 (m110) cc_final: 0.8282 (p0) REVERT: X 36 ARG cc_start: 0.9304 (ttp80) cc_final: 0.8731 (ptt90) REVERT: X 37 PHE cc_start: 0.9312 (m-10) cc_final: 0.8982 (m-10) REVERT: X 45 PHE cc_start: 0.9493 (m-80) cc_final: 0.9090 (m-80) REVERT: X 49 ARG cc_start: 0.7245 (mtt180) cc_final: 0.6997 (mtt180) REVERT: X 53 LYS cc_start: 0.8661 (ptpp) cc_final: 0.8395 (pttm) REVERT: X 71 ARG cc_start: 0.8722 (mpp-170) cc_final: 0.8513 (mmm160) REVERT: Y 2 LYS cc_start: 0.8142 (ttpp) cc_final: 0.7668 (ptpt) REVERT: Y 20 ASN cc_start: 0.9501 (m110) cc_final: 0.9083 (t0) REVERT: Y 39 GLN cc_start: 0.9269 (mt0) cc_final: 0.8795 (mp10) REVERT: Y 46 VAL cc_start: 0.9130 (m) cc_final: 0.8790 (p) REVERT: Y 55 THR cc_start: 0.8995 (t) cc_final: 0.8776 (t) REVERT: Z 39 ASP cc_start: 0.8814 (m-30) cc_final: 0.8562 (m-30) REVERT: 0 3 GLN cc_start: 0.8551 (pm20) cc_final: 0.8054 (pm20) REVERT: 0 6 LYS cc_start: 0.8708 (tmtt) cc_final: 0.8409 (tmtt) REVERT: 0 9 ARG cc_start: 0.8837 (mtp180) cc_final: 0.8364 (mtp180) REVERT: 0 11 LYS cc_start: 0.9536 (ttpt) cc_final: 0.9176 (ptpt) REVERT: 0 36 LYS cc_start: 0.9143 (mmmt) cc_final: 0.8689 (mmmt) REVERT: 0 45 ASP cc_start: 0.9377 (p0) cc_final: 0.9105 (p0) REVERT: 1 18 HIS cc_start: 0.8236 (t70) cc_final: 0.7881 (t70) REVERT: 1 20 TYR cc_start: 0.8972 (m-80) cc_final: 0.8438 (m-80) REVERT: 1 26 LYS cc_start: 0.8624 (tptt) cc_final: 0.8229 (tppt) REVERT: 1 32 LYS cc_start: 0.7584 (tmtt) cc_final: 0.7190 (tmtt) REVERT: 1 37 LYS cc_start: 0.8408 (tttt) cc_final: 0.7780 (tptt) REVERT: 2 22 MET cc_start: 0.8520 (tpp) cc_final: 0.8269 (tpp) REVERT: 3 25 HIS cc_start: 0.9562 (m90) cc_final: 0.9005 (m90) REVERT: 3 42 HIS cc_start: 0.9335 (m90) cc_final: 0.9050 (m90) REVERT: 4 23 ILE cc_start: 0.8854 (pt) cc_final: 0.8651 (tp) REVERT: 6 12 ILE cc_start: 0.8672 (pt) cc_final: 0.8134 (mp) outliers start: 13 outliers final: 1 residues processed: 1939 average time/residue: 1.4565 time to fit residues: 4711.0507 Evaluate side-chains 1516 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1513 time to evaluate : 6.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1095 random chunks: chunk 984 optimal weight: 7.9990 chunk 748 optimal weight: 30.0000 chunk 516 optimal weight: 30.0000 chunk 110 optimal weight: 40.0000 chunk 475 optimal weight: 30.0000 chunk 668 optimal weight: 30.0000 chunk 999 optimal weight: 30.0000 chunk 1058 optimal weight: 10.0000 chunk 522 optimal weight: 30.0000 chunk 947 optimal weight: 40.0000 chunk 285 optimal weight: 1.9990 overall best weight: 15.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 ASN b 88 GLN ** b 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS ** c 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 53 GLN ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN h 66 GLN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 37 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 18 GLN ** z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 67 HIS ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 ASN ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 HIS Y 58 ASN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.157 165989 Z= 0.353 Angle : 0.815 21.787 247857 Z= 0.426 Chirality : 0.040 0.321 31480 Planarity : 0.008 0.138 13686 Dihedral : 23.641 179.274 81771 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 34.88 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.34 % Favored : 93.11 % Rotamer: Outliers : 0.10 % Allowed : 4.67 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.10), residues: 6329 helix: -0.98 (0.10), residues: 2012 sheet: -1.56 (0.14), residues: 1068 loop : -1.06 (0.11), residues: 3249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP z 419 HIS 0.022 0.002 HIS b 14 PHE 0.035 0.003 PHE P 73 TYR 0.029 0.003 TYR c 167 ARG 0.031 0.001 ARG j 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1817 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1812 time to evaluate : 6.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 15 PHE cc_start: 0.8680 (p90) cc_final: 0.8403 (p90) REVERT: b 90 PHE cc_start: 0.9388 (p90) cc_final: 0.8889 (p90) REVERT: b 153 MET cc_start: 0.7725 (ppp) cc_final: 0.6672 (ppp) REVERT: b 180 ILE cc_start: 0.6545 (tp) cc_final: 0.6336 (tp) REVERT: c 5 HIS cc_start: 0.8582 (t70) cc_final: 0.8152 (t70) REVERT: c 22 PHE cc_start: 0.8173 (t80) cc_final: 0.7923 (t80) REVERT: c 24 ASN cc_start: 0.9311 (t0) cc_final: 0.8834 (p0) REVERT: c 58 ARG cc_start: 0.9542 (ttm110) cc_final: 0.8968 (ptp-110) REVERT: c 68 HIS cc_start: 0.8816 (m-70) cc_final: 0.8566 (m90) REVERT: c 149 LYS cc_start: 0.9580 (tmtt) cc_final: 0.9017 (tptp) REVERT: c 171 ARG cc_start: 0.8840 (mtp85) cc_final: 0.8462 (mtp85) REVERT: c 190 THR cc_start: 0.8722 (m) cc_final: 0.8447 (p) REVERT: d 59 LYS cc_start: 0.9543 (tttt) cc_final: 0.9243 (tptp) REVERT: d 62 ARG cc_start: 0.9203 (mtt180) cc_final: 0.8575 (mmp80) REVERT: d 70 GLN cc_start: 0.9094 (pt0) cc_final: 0.8868 (pt0) REVERT: d 81 LEU cc_start: 0.9182 (mp) cc_final: 0.8763 (tp) REVERT: d 94 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6958 (tt0) REVERT: d 99 ASN cc_start: 0.9136 (t0) cc_final: 0.8835 (t0) REVERT: d 109 THR cc_start: 0.7156 (p) cc_final: 0.6122 (p) REVERT: d 112 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8411 (mt-10) REVERT: d 134 TYR cc_start: 0.8580 (t80) cc_final: 0.8297 (t80) REVERT: d 196 GLU cc_start: 0.8618 (pm20) cc_final: 0.7935 (tm-30) REVERT: e 33 THR cc_start: 0.9420 (t) cc_final: 0.8958 (t) REVERT: e 51 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8113 (mttt) REVERT: e 71 ILE cc_start: 0.8714 (pt) cc_final: 0.8381 (mm) REVERT: e 95 MET cc_start: 0.8999 (pmm) cc_final: 0.8661 (pmm) REVERT: e 110 MET cc_start: 0.9264 (pmm) cc_final: 0.8894 (pmm) REVERT: e 127 TYR cc_start: 0.7235 (m-10) cc_final: 0.6030 (m-80) REVERT: f 5 GLU cc_start: 0.8873 (tt0) cc_final: 0.8371 (mm-30) REVERT: f 25 TYR cc_start: 0.9771 (m-10) cc_final: 0.9471 (m-10) REVERT: f 49 TYR cc_start: 0.8721 (p90) cc_final: 0.7873 (p90) REVERT: f 80 PHE cc_start: 0.9267 (m-10) cc_final: 0.9001 (m-80) REVERT: g 101 ARG cc_start: 0.8986 (mtm180) cc_final: 0.8316 (mtt180) REVERT: g 118 ARG cc_start: 0.8721 (mtp180) cc_final: 0.8467 (mtp-110) REVERT: h 49 LYS cc_start: 0.9571 (mppt) cc_final: 0.9344 (mmtm) REVERT: h 75 GLN cc_start: 0.9524 (mp-120) cc_final: 0.9229 (mp-120) REVERT: j 11 LYS cc_start: 0.8422 (pttm) cc_final: 0.8086 (pttm) REVERT: j 35 GLN cc_start: 0.8080 (tp40) cc_final: 0.7740 (tp40) REVERT: j 63 ASP cc_start: 0.9037 (t0) cc_final: 0.8695 (t0) REVERT: j 64 GLN cc_start: 0.9428 (mm-40) cc_final: 0.9151 (mt0) REVERT: j 66 GLU cc_start: 0.8826 (tp30) cc_final: 0.8563 (tp30) REVERT: j 99 GLN cc_start: 0.8876 (mm110) cc_final: 0.8403 (mp10) REVERT: k 73 VAL cc_start: 0.8954 (t) cc_final: 0.8684 (p) REVERT: l 52 CYS cc_start: 0.9476 (p) cc_final: 0.9147 (p) REVERT: l 55 ARG cc_start: 0.9257 (ttp-170) cc_final: 0.8871 (tpt-90) REVERT: l 56 LEU cc_start: 0.8958 (mm) cc_final: 0.8398 (mm) REVERT: m 11 HIS cc_start: 0.8829 (m90) cc_final: 0.8534 (m-70) REVERT: m 22 TYR cc_start: 0.8914 (t80) cc_final: 0.8662 (t80) REVERT: m 80 MET cc_start: 0.7744 (ttt) cc_final: 0.6165 (tmm) REVERT: n 4 SER cc_start: 0.9401 (p) cc_final: 0.8419 (t) REVERT: n 73 LEU cc_start: 0.9142 (mp) cc_final: 0.8590 (tp) REVERT: o 2 LEU cc_start: 0.8810 (mt) cc_final: 0.8569 (mt) REVERT: o 14 PHE cc_start: 0.9176 (m-80) cc_final: 0.8551 (m-80) REVERT: o 77 TYR cc_start: 0.8486 (t80) cc_final: 0.7840 (t80) REVERT: o 81 ILE cc_start: 0.9101 (mt) cc_final: 0.8694 (mm) REVERT: p 1 MET cc_start: 0.8742 (tpt) cc_final: 0.8393 (tpt) REVERT: p 21 VAL cc_start: 0.8113 (t) cc_final: 0.7835 (t) REVERT: p 34 GLU cc_start: 0.8728 (pm20) cc_final: 0.8046 (pm20) REVERT: p 39 PHE cc_start: 0.9271 (t80) cc_final: 0.8812 (t80) REVERT: p 56 ARG cc_start: 0.9313 (mtp85) cc_final: 0.8866 (mtp85) REVERT: p 66 THR cc_start: 0.7664 (m) cc_final: 0.7240 (m) REVERT: p 79 ASN cc_start: 0.8709 (m110) cc_final: 0.8256 (t0) REVERT: q 72 TRP cc_start: 0.8996 (m100) cc_final: 0.8567 (m100) REVERT: q 80 LYS cc_start: 0.8254 (mttm) cc_final: 0.7801 (tppt) REVERT: r 41 SER cc_start: 0.7661 (m) cc_final: 0.6724 (p) REVERT: r 51 GLN cc_start: 0.8949 (tp-100) cc_final: 0.8540 (tt0) REVERT: r 54 LEU cc_start: 0.9654 (tp) cc_final: 0.9451 (tp) REVERT: s 27 LYS cc_start: 0.7816 (mtmm) cc_final: 0.7603 (tptt) REVERT: s 46 LEU cc_start: 0.8841 (mm) cc_final: 0.8557 (mm) REVERT: s 47 THR cc_start: 0.7942 (p) cc_final: 0.7685 (p) REVERT: s 68 HIS cc_start: 0.8938 (m90) cc_final: 0.8498 (m-70) REVERT: s 73 PHE cc_start: 0.8782 (m-80) cc_final: 0.8276 (m-80) REVERT: t 83 ASN cc_start: 0.9048 (m-40) cc_final: 0.8745 (m-40) REVERT: u 30 GLU cc_start: 0.7726 (pm20) cc_final: 0.7501 (pm20) REVERT: u 53 LYS cc_start: 0.9087 (mptt) cc_final: 0.8654 (pttt) REVERT: z 89 MET cc_start: 0.7301 (tpt) cc_final: 0.6948 (ttm) REVERT: z 127 ARG cc_start: 0.7551 (mtt180) cc_final: 0.7088 (tmt170) REVERT: z 190 LEU cc_start: 0.8391 (tp) cc_final: 0.8058 (mm) REVERT: z 208 TRP cc_start: 0.7556 (t-100) cc_final: 0.7085 (t-100) REVERT: z 249 GLN cc_start: 0.8647 (mp10) cc_final: 0.8277 (mp10) REVERT: z 265 PHE cc_start: 0.8270 (p90) cc_final: 0.7965 (m-80) REVERT: z 320 ARG cc_start: 0.8047 (mtt90) cc_final: 0.7280 (tpt170) REVERT: z 382 ASP cc_start: 0.9567 (m-30) cc_final: 0.9329 (p0) REVERT: z 475 HIS cc_start: 0.8798 (m90) cc_final: 0.8478 (m90) REVERT: z 510 ARG cc_start: 0.7620 (tpp-160) cc_final: 0.7317 (tpp-160) REVERT: z 514 LYS cc_start: 0.4246 (mttt) cc_final: 0.3764 (pttp) REVERT: z 562 GLN cc_start: 0.8282 (mp10) cc_final: 0.7937 (mp10) REVERT: C 32 LEU cc_start: 0.9244 (pp) cc_final: 0.8702 (pp) REVERT: C 33 LEU cc_start: 0.9025 (mt) cc_final: 0.8525 (mt) REVERT: C 143 VAL cc_start: 0.9362 (t) cc_final: 0.8979 (m) REVERT: C 145 MET cc_start: 0.8235 (mmp) cc_final: 0.7901 (mmm) REVERT: C 152 GLN cc_start: 0.8150 (mp10) cc_final: 0.7774 (mp10) REVERT: C 180 MET cc_start: 0.8057 (mpp) cc_final: 0.7849 (mmm) REVERT: C 200 MET cc_start: 0.8389 (ptm) cc_final: 0.7561 (ptm) REVERT: C 239 PHE cc_start: 0.8211 (t80) cc_final: 0.6913 (t80) REVERT: C 241 LYS cc_start: 0.9066 (tptp) cc_final: 0.8759 (tptt) REVERT: D 18 ASP cc_start: 0.8820 (m-30) cc_final: 0.8535 (m-30) REVERT: D 27 ILE cc_start: 0.9344 (tp) cc_final: 0.9133 (tp) REVERT: D 35 THR cc_start: 0.9275 (p) cc_final: 0.8768 (p) REVERT: D 36 GLN cc_start: 0.8829 (mt0) cc_final: 0.8026 (mm-40) REVERT: D 77 ARG cc_start: 0.8644 (tmm160) cc_final: 0.8228 (ptm160) REVERT: D 82 PHE cc_start: 0.6711 (t80) cc_final: 0.6491 (t80) REVERT: D 128 ARG cc_start: 0.5834 (tpt90) cc_final: 0.4013 (mmm-85) REVERT: D 154 LYS cc_start: 0.8265 (mtmm) cc_final: 0.7615 (mtmm) REVERT: D 164 GLN cc_start: 0.8756 (tp40) cc_final: 0.8312 (tm-30) REVERT: D 201 LEU cc_start: 0.9283 (mt) cc_final: 0.8780 (pp) REVERT: D 202 ILE cc_start: 0.9508 (pt) cc_final: 0.9269 (tp) REVERT: E 19 PHE cc_start: 0.8513 (m-80) cc_final: 0.8210 (m-10) REVERT: E 30 GLN cc_start: 0.8666 (tt0) cc_final: 0.8411 (mt0) REVERT: E 63 LYS cc_start: 0.8525 (mttp) cc_final: 0.8265 (mttp) REVERT: E 166 LYS cc_start: 0.9445 (mptt) cc_final: 0.9120 (mmtt) REVERT: E 176 ASP cc_start: 0.8869 (m-30) cc_final: 0.8547 (m-30) REVERT: F 34 THR cc_start: 0.8824 (p) cc_final: 0.8468 (t) REVERT: F 37 MET cc_start: 0.6686 (mtp) cc_final: 0.6042 (mtm) REVERT: F 129 MET cc_start: 0.7070 (pmm) cc_final: 0.6712 (pmm) REVERT: F 135 ILE cc_start: 0.8821 (mm) cc_final: 0.8549 (mt) REVERT: F 155 ILE cc_start: 0.9060 (mt) cc_final: 0.8844 (mp) REVERT: G 18 ILE cc_start: 0.8311 (tt) cc_final: 0.8056 (mp) REVERT: G 68 ARG cc_start: 0.9381 (ttp80) cc_final: 0.9007 (tpt-90) REVERT: G 105 SER cc_start: 0.9348 (m) cc_final: 0.8980 (t) REVERT: G 129 GLU cc_start: 0.9245 (tt0) cc_final: 0.8854 (tm-30) REVERT: G 157 LYS cc_start: 0.8430 (mttt) cc_final: 0.7718 (mmtp) REVERT: G 172 GLU cc_start: 0.8290 (mp0) cc_final: 0.8079 (mp0) REVERT: I 71 LYS cc_start: 0.8557 (mtmm) cc_final: 0.8251 (pttp) REVERT: H 1 MET cc_start: 0.9115 (mmt) cc_final: 0.8863 (mmm) REVERT: J 14 ASP cc_start: 0.8081 (m-30) cc_final: 0.7878 (m-30) REVERT: J 19 ASP cc_start: 0.8382 (p0) cc_final: 0.8171 (t70) REVERT: J 52 ASP cc_start: 0.6043 (m-30) cc_final: 0.5591 (m-30) REVERT: J 74 TYR cc_start: 0.9138 (m-80) cc_final: 0.8585 (m-80) REVERT: J 89 PHE cc_start: 0.9530 (t80) cc_final: 0.9043 (t80) REVERT: J 108 MET cc_start: 0.7693 (mtm) cc_final: 0.6712 (mtm) REVERT: K 1 MET cc_start: 0.6173 (tpt) cc_final: 0.4710 (tpt) REVERT: K 13 ASN cc_start: 0.8785 (p0) cc_final: 0.8538 (p0) REVERT: K 38 ILE cc_start: 0.8878 (tp) cc_final: 0.8656 (tp) REVERT: K 44 LYS cc_start: 0.9201 (mmmt) cc_final: 0.8829 (mmtm) REVERT: K 71 ARG cc_start: 0.8889 (mmp80) cc_final: 0.8565 (mmp-170) REVERT: K 79 PHE cc_start: 0.8202 (m-10) cc_final: 0.7754 (m-10) REVERT: K 100 PHE cc_start: 0.8869 (m-80) cc_final: 0.8580 (m-80) REVERT: K 110 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8329 (pm20) REVERT: L 30 THR cc_start: 0.9268 (p) cc_final: 0.8935 (t) REVERT: L 48 ARG cc_start: 0.6415 (mtm180) cc_final: 0.5183 (ptp-110) REVERT: L 60 ARG cc_start: 0.9237 (ttt-90) cc_final: 0.8746 (ttt180) REVERT: L 135 ILE cc_start: 0.9478 (tp) cc_final: 0.9255 (tp) REVERT: M 10 ARG cc_start: 0.9031 (mmm160) cc_final: 0.8757 (mmm160) REVERT: M 36 VAL cc_start: 0.9012 (p) cc_final: 0.8573 (p) REVERT: M 55 ARG cc_start: 0.9210 (mmp-170) cc_final: 0.8655 (tpp-160) REVERT: M 60 GLN cc_start: 0.9486 (mp10) cc_final: 0.9119 (tp-100) REVERT: N 9 GLN cc_start: 0.8860 (pt0) cc_final: 0.8330 (pm20) REVERT: N 24 MET cc_start: 0.9481 (tpp) cc_final: 0.9167 (tpp) REVERT: N 45 ARG cc_start: 0.8696 (mtm180) cc_final: 0.8232 (mtm-85) REVERT: N 46 ARG cc_start: 0.9332 (mtp85) cc_final: 0.8653 (mtt90) REVERT: N 62 ASN cc_start: 0.9649 (m110) cc_final: 0.9422 (m110) REVERT: N 72 ASP cc_start: 0.9371 (t70) cc_final: 0.9144 (t0) REVERT: N 74 GLU cc_start: 0.9394 (tm-30) cc_final: 0.9156 (tm-30) REVERT: O 34 HIS cc_start: 0.9111 (m-70) cc_final: 0.8364 (m-70) REVERT: P 84 SER cc_start: 0.9098 (m) cc_final: 0.8853 (t) REVERT: Q 7 VAL cc_start: 0.8733 (m) cc_final: 0.8278 (m) REVERT: Q 10 ARG cc_start: 0.8770 (ptp90) cc_final: 0.8540 (mtm180) REVERT: Q 14 LYS cc_start: 0.9492 (ttmt) cc_final: 0.9258 (tptt) REVERT: Q 15 LYS cc_start: 0.9404 (ttpt) cc_final: 0.8953 (tptm) REVERT: Q 23 TYR cc_start: 0.8793 (m-80) cc_final: 0.8453 (m-80) REVERT: Q 70 GLN cc_start: 0.9304 (tt0) cc_final: 0.8790 (tm-30) REVERT: R 12 HIS cc_start: 0.9142 (m90) cc_final: 0.8070 (t-90) REVERT: R 35 PHE cc_start: 0.8292 (m-80) cc_final: 0.7980 (m-80) REVERT: R 40 MET cc_start: 0.8552 (tpt) cc_final: 0.7588 (tmm) REVERT: R 41 ILE cc_start: 0.9393 (mp) cc_final: 0.9168 (mp) REVERT: R 85 LYS cc_start: 0.8326 (tptp) cc_final: 0.7988 (tptp) REVERT: R 87 GLN cc_start: 0.9273 (pp30) cc_final: 0.8905 (pp30) REVERT: S 18 ARG cc_start: 0.9235 (tmt-80) cc_final: 0.9001 (tmt-80) REVERT: S 49 LYS cc_start: 0.9440 (ptmt) cc_final: 0.8972 (tptp) REVERT: S 88 ARG cc_start: 0.6509 (tpm170) cc_final: 0.6248 (tpt170) REVERT: T 6 ARG cc_start: 0.9173 (tpm170) cc_final: 0.8239 (tpm170) REVERT: T 9 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8490 (mtmm) REVERT: T 12 ARG cc_start: 0.9260 (mmm-85) cc_final: 0.8795 (tpp-160) REVERT: T 63 VAL cc_start: 0.9142 (t) cc_final: 0.8942 (t) REVERT: T 79 ASP cc_start: 0.8520 (t0) cc_final: 0.7827 (t0) REVERT: T 80 TRP cc_start: 0.8745 (p-90) cc_final: 0.7981 (p-90) REVERT: U 8 ASP cc_start: 0.8205 (m-30) cc_final: 0.7696 (m-30) REVERT: U 9 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8118 (tp30) REVERT: U 65 GLN cc_start: 0.8917 (mt0) cc_final: 0.8436 (mt0) REVERT: V 71 LYS cc_start: 0.8922 (mttm) cc_final: 0.8548 (mmtm) REVERT: V 82 TYR cc_start: 0.9375 (p90) cc_final: 0.8234 (p90) REVERT: V 87 GLN cc_start: 0.9566 (mm110) cc_final: 0.9356 (mm110) REVERT: V 91 PHE cc_start: 0.9234 (m-80) cc_final: 0.8660 (m-80) REVERT: W 13 GLU cc_start: 0.8776 (mp0) cc_final: 0.8460 (mp0) REVERT: W 21 ARG cc_start: 0.7517 (ptp90) cc_final: 0.7079 (mtm180) REVERT: W 58 LYS cc_start: 0.8761 (ptpt) cc_final: 0.7968 (tppt) REVERT: W 62 LYS cc_start: 0.9519 (mppt) cc_final: 0.8834 (mmtm) REVERT: W 76 ILE cc_start: 0.9684 (mp) cc_final: 0.9289 (tp) REVERT: W 79 GLU cc_start: 0.8810 (tp30) cc_final: 0.7643 (pp20) REVERT: X 15 ASN cc_start: 0.8629 (m-40) cc_final: 0.8400 (m-40) REVERT: X 36 ARG cc_start: 0.9321 (ttp80) cc_final: 0.8992 (ptt90) REVERT: X 45 PHE cc_start: 0.9447 (m-80) cc_final: 0.9243 (m-80) REVERT: X 64 ASP cc_start: 0.8625 (t0) cc_final: 0.8334 (t0) REVERT: X 71 ARG cc_start: 0.8789 (mpp-170) cc_final: 0.8314 (tpp-160) REVERT: Y 2 LYS cc_start: 0.8591 (ttpp) cc_final: 0.7999 (ptpt) REVERT: Y 9 LYS cc_start: 0.9528 (tttm) cc_final: 0.9286 (pttm) REVERT: Y 20 ASN cc_start: 0.9642 (m110) cc_final: 0.9267 (t0) REVERT: Y 26 PHE cc_start: 0.9392 (t80) cc_final: 0.9175 (t80) REVERT: Y 55 THR cc_start: 0.9012 (t) cc_final: 0.8807 (t) REVERT: Z 4 ILE cc_start: 0.9137 (tt) cc_final: 0.8929 (tt) REVERT: Z 39 ASP cc_start: 0.8827 (m-30) cc_final: 0.8492 (m-30) REVERT: 0 3 GLN cc_start: 0.8972 (pm20) cc_final: 0.8190 (pm20) REVERT: 0 9 ARG cc_start: 0.8984 (mtp180) cc_final: 0.8659 (mtp180) REVERT: 0 11 LYS cc_start: 0.9554 (ttpt) cc_final: 0.9188 (ptpp) REVERT: 0 47 TYR cc_start: 0.8858 (m-80) cc_final: 0.8408 (m-10) REVERT: 1 18 HIS cc_start: 0.8244 (t70) cc_final: 0.7890 (t70) REVERT: 1 20 TYR cc_start: 0.8817 (m-80) cc_final: 0.8564 (m-80) REVERT: 1 32 LYS cc_start: 0.7827 (tmtt) cc_final: 0.7386 (tmtt) REVERT: 2 5 PHE cc_start: 0.7517 (t80) cc_final: 0.7154 (t80) REVERT: 2 22 MET cc_start: 0.8629 (tpp) cc_final: 0.8375 (tpp) REVERT: 2 29 GLN cc_start: 0.9298 (pm20) cc_final: 0.9098 (pm20) REVERT: 3 21 PHE cc_start: 0.9215 (m-80) cc_final: 0.8894 (m-10) REVERT: 3 25 HIS cc_start: 0.9623 (m90) cc_final: 0.9092 (m170) REVERT: 3 31 ILE cc_start: 0.9204 (mt) cc_final: 0.8639 (tt) REVERT: 3 41 ARG cc_start: 0.9174 (ptp-110) cc_final: 0.8839 (mtm110) REVERT: 3 42 HIS cc_start: 0.9438 (m90) cc_final: 0.8707 (m90) REVERT: 3 51 LYS cc_start: 0.8378 (pttp) cc_final: 0.8151 (mtpt) REVERT: 3 61 LEU cc_start: 0.9040 (mt) cc_final: 0.8667 (mp) REVERT: 4 13 ASN cc_start: 0.9052 (t0) cc_final: 0.8769 (t0) REVERT: 6 12 ILE cc_start: 0.8926 (pt) cc_final: 0.8439 (mp) outliers start: 5 outliers final: 0 residues processed: 1815 average time/residue: 1.4765 time to fit residues: 4542.6789 Evaluate side-chains 1450 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1450 time to evaluate : 6.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1095 random chunks: chunk 881 optimal weight: 30.0000 chunk 600 optimal weight: 30.0000 chunk 15 optimal weight: 40.0000 chunk 788 optimal weight: 20.0000 chunk 436 optimal weight: 20.0000 chunk 903 optimal weight: 8.9990 chunk 731 optimal weight: 30.0000 chunk 1 optimal weight: 30.0000 chunk 540 optimal weight: 20.0000 chunk 950 optimal weight: 40.0000 chunk 267 optimal weight: 4.9990 overall best weight: 14.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 99 ASN g 67 ASN ** g 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN h 66 GLN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 37 GLN k 80 ASN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 65 GLN ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 18 GLN ** z 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 8 ASN W 53 HIS X 22 ASN Y 58 ASN 1 45 HIS ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 165989 Z= 0.325 Angle : 0.793 21.294 247857 Z= 0.416 Chirality : 0.039 0.372 31480 Planarity : 0.008 0.127 13686 Dihedral : 23.848 178.182 81771 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 34.70 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.52 % Favored : 91.96 % Rotamer: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % 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: -1.98 (0.10), residues: 6329 helix: -1.00 (0.10), residues: 2033 sheet: -1.51 (0.14), residues: 1061 loop : -1.38 (0.10), residues: 3235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP C 212 HIS 0.013 0.002 HIS 1 45 PHE 0.027 0.003 PHE W 22 TYR 0.046 0.003 TYR c 167 ARG 0.015 0.001 ARG X 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1764 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1759 time to evaluate : 6.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 15 PHE cc_start: 0.8797 (p90) cc_final: 0.8508 (p90) REVERT: b 29 PHE cc_start: 0.8859 (m-10) cc_final: 0.8541 (m-10) REVERT: b 41 ASN cc_start: 0.9567 (t0) cc_final: 0.9340 (t0) REVERT: b 90 PHE cc_start: 0.9484 (p90) cc_final: 0.9066 (p90) REVERT: b 95 TRP cc_start: 0.6386 (t-100) cc_final: 0.6050 (t-100) REVERT: b 153 MET cc_start: 0.8578 (ppp) cc_final: 0.8130 (ppp) REVERT: c 5 HIS cc_start: 0.8559 (t70) cc_final: 0.8187 (t70) REVERT: c 68 HIS cc_start: 0.8781 (m-70) cc_final: 0.8510 (m-70) REVERT: c 190 THR cc_start: 0.8808 (m) cc_final: 0.8489 (p) REVERT: c 191 THR cc_start: 0.5928 (p) cc_final: 0.5463 (t) REVERT: d 62 ARG cc_start: 0.9156 (mtt180) cc_final: 0.8568 (mmp80) REVERT: d 81 LEU cc_start: 0.9246 (mp) cc_final: 0.8921 (tp) REVERT: d 94 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6825 (tt0) REVERT: d 99 ASN cc_start: 0.9021 (t0) cc_final: 0.8782 (t0) REVERT: d 183 ARG cc_start: 0.9517 (mmm160) cc_final: 0.9137 (mmm160) REVERT: d 202 LEU cc_start: 0.8892 (tt) cc_final: 0.8629 (mt) REVERT: e 28 ARG cc_start: 0.8053 (mpp80) cc_final: 0.7835 (mtt90) REVERT: e 33 THR cc_start: 0.9485 (t) cc_final: 0.9039 (t) REVERT: e 51 LYS cc_start: 0.8512 (mtmt) cc_final: 0.8184 (mttt) REVERT: e 110 MET cc_start: 0.9294 (pmm) cc_final: 0.9006 (pmm) REVERT: e 127 TYR cc_start: 0.7165 (m-10) cc_final: 0.6047 (m-80) REVERT: f 49 TYR cc_start: 0.8376 (p90) cc_final: 0.8136 (p90) REVERT: f 74 LEU cc_start: 0.9707 (tt) cc_final: 0.9260 (tt) REVERT: f 80 PHE cc_start: 0.9332 (m-10) cc_final: 0.9019 (m-80) REVERT: g 98 LEU cc_start: 0.8867 (tp) cc_final: 0.8507 (tt) REVERT: g 101 ARG cc_start: 0.8928 (mtm180) cc_final: 0.8551 (mtt180) REVERT: h 6 ILE cc_start: 0.9447 (pt) cc_final: 0.9202 (pt) REVERT: h 8 ASP cc_start: 0.9481 (m-30) cc_final: 0.9225 (m-30) REVERT: h 41 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6112 (pp20) REVERT: h 47 ASP cc_start: 0.9136 (m-30) cc_final: 0.8855 (p0) REVERT: h 49 LYS cc_start: 0.9551 (mppt) cc_final: 0.9164 (mmtm) REVERT: h 75 GLN cc_start: 0.9550 (mp-120) cc_final: 0.9191 (mp-120) REVERT: h 76 ARG cc_start: 0.8155 (ttt-90) cc_final: 0.7153 (ttt-90) REVERT: h 83 ARG cc_start: 0.7494 (mmt180) cc_final: 0.6741 (mmt90) REVERT: h 110 MET cc_start: 0.8820 (ptp) cc_final: 0.8534 (ptp) REVERT: j 44 THR cc_start: 0.8234 (p) cc_final: 0.7883 (p) REVERT: j 63 ASP cc_start: 0.9220 (t0) cc_final: 0.8853 (t0) REVERT: j 64 GLN cc_start: 0.9450 (mm-40) cc_final: 0.9159 (mt0) REVERT: j 99 GLN cc_start: 0.8846 (mm110) cc_final: 0.8422 (mp10) REVERT: l 52 CYS cc_start: 0.9462 (p) cc_final: 0.9147 (p) REVERT: l 60 PHE cc_start: 0.8190 (m-10) cc_final: 0.7909 (m-10) REVERT: m 11 HIS cc_start: 0.8939 (m90) cc_final: 0.8657 (m90) REVERT: m 22 TYR cc_start: 0.8978 (t80) cc_final: 0.8511 (t80) REVERT: m 58 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8097 (mt-10) REVERT: n 4 SER cc_start: 0.9373 (p) cc_final: 0.9149 (t) REVERT: n 9 GLU cc_start: 0.9439 (pp20) cc_final: 0.9149 (tt0) REVERT: n 15 LEU cc_start: 0.9117 (tt) cc_final: 0.8900 (pp) REVERT: n 73 LEU cc_start: 0.9115 (mp) cc_final: 0.8732 (tp) REVERT: n 97 LYS cc_start: 0.9301 (tptm) cc_final: 0.8991 (tptm) REVERT: p 2 VAL cc_start: 0.8020 (m) cc_final: 0.7762 (m) REVERT: p 14 ARG cc_start: 0.8831 (mmm-85) cc_final: 0.8599 (mmm-85) REVERT: p 21 VAL cc_start: 0.8061 (t) cc_final: 0.7764 (t) REVERT: p 34 GLU cc_start: 0.8792 (pm20) cc_final: 0.8485 (pm20) REVERT: p 35 ARG cc_start: 0.7594 (ttm170) cc_final: 0.6093 (ttt180) REVERT: p 39 PHE cc_start: 0.9247 (t80) cc_final: 0.8798 (t80) REVERT: p 40 ASN cc_start: 0.8920 (t0) cc_final: 0.8667 (t0) REVERT: p 79 ASN cc_start: 0.8735 (m110) cc_final: 0.8370 (t0) REVERT: q 24 ILE cc_start: 0.9342 (mm) cc_final: 0.9107 (mm) REVERT: q 72 TRP cc_start: 0.9066 (m100) cc_final: 0.8607 (m100) REVERT: q 80 LYS cc_start: 0.8337 (mttm) cc_final: 0.7782 (tppt) REVERT: r 42 ARG cc_start: 0.9018 (mpt180) cc_final: 0.8806 (ptp-110) REVERT: s 27 LYS cc_start: 0.7850 (mtmm) cc_final: 0.7605 (tptt) REVERT: s 46 LEU cc_start: 0.8732 (mm) cc_final: 0.8447 (mm) REVERT: s 47 THR cc_start: 0.8178 (p) cc_final: 0.7959 (p) REVERT: s 65 MET cc_start: 0.8945 (ttt) cc_final: 0.8536 (ttt) REVERT: s 68 HIS cc_start: 0.9024 (m90) cc_final: 0.8614 (m-70) REVERT: s 73 PHE cc_start: 0.8866 (m-80) cc_final: 0.8419 (m-80) REVERT: t 12 GLN cc_start: 0.9566 (pt0) cc_final: 0.9354 (pt0) REVERT: t 26 MET cc_start: 0.9628 (mmp) cc_final: 0.9406 (mmp) REVERT: t 77 ASN cc_start: 0.8112 (t0) cc_final: 0.7659 (t0) REVERT: t 81 GLN cc_start: 0.9033 (tt0) cc_final: 0.8648 (pt0) REVERT: u 30 GLU cc_start: 0.7831 (pm20) cc_final: 0.7576 (pm20) REVERT: u 33 ARG cc_start: 0.8867 (ppt170) cc_final: 0.8649 (ppt170) REVERT: u 53 LYS cc_start: 0.9157 (mptt) cc_final: 0.8731 (pttm) REVERT: z 89 MET cc_start: 0.7101 (tpt) cc_final: 0.6547 (ttm) REVERT: z 127 ARG cc_start: 0.7387 (mtt180) cc_final: 0.6959 (tmt170) REVERT: z 265 PHE cc_start: 0.8460 (p90) cc_final: 0.8048 (m-80) REVERT: z 475 HIS cc_start: 0.8803 (m90) cc_final: 0.8440 (m90) REVERT: z 510 ARG cc_start: 0.7429 (tpp-160) cc_final: 0.7143 (tpp-160) REVERT: z 514 LYS cc_start: 0.4286 (mttt) cc_final: 0.3762 (pttp) REVERT: z 562 GLN cc_start: 0.8156 (mp10) cc_final: 0.7822 (mp10) REVERT: C 200 MET cc_start: 0.8444 (ptm) cc_final: 0.7577 (ptm) REVERT: C 239 PHE cc_start: 0.8374 (t80) cc_final: 0.6841 (t80) REVERT: C 241 LYS cc_start: 0.9116 (tptp) cc_final: 0.8691 (tptt) REVERT: D 36 GLN cc_start: 0.8983 (mt0) cc_final: 0.8170 (mm-40) REVERT: D 67 HIS cc_start: 0.8705 (t70) cc_final: 0.8477 (t-90) REVERT: D 82 PHE cc_start: 0.6556 (t80) cc_final: 0.6226 (t80) REVERT: D 128 ARG cc_start: 0.5534 (tpt90) cc_final: 0.3853 (mmm-85) REVERT: D 201 LEU cc_start: 0.9252 (mt) cc_final: 0.9017 (mt) REVERT: E 166 LYS cc_start: 0.9366 (mptt) cc_final: 0.9083 (mptt) REVERT: E 176 ASP cc_start: 0.8708 (m-30) cc_final: 0.8426 (m-30) REVERT: F 37 MET cc_start: 0.6668 (mtp) cc_final: 0.6219 (mtm) REVERT: F 129 MET cc_start: 0.6905 (pmm) cc_final: 0.6604 (pmm) REVERT: F 153 ILE cc_start: 0.7385 (mp) cc_final: 0.7072 (mp) REVERT: F 155 ILE cc_start: 0.9220 (mt) cc_final: 0.9008 (mm) REVERT: G 18 ILE cc_start: 0.8480 (tt) cc_final: 0.8207 (mp) REVERT: G 41 GLU cc_start: 0.8415 (pp20) cc_final: 0.7846 (pp20) REVERT: G 68 ARG cc_start: 0.9408 (ttp80) cc_final: 0.9039 (tpt-90) REVERT: G 82 PHE cc_start: 0.8040 (m-80) cc_final: 0.7689 (m-80) REVERT: G 116 LEU cc_start: 0.9558 (mt) cc_final: 0.9257 (mp) REVERT: G 129 GLU cc_start: 0.9225 (tt0) cc_final: 0.8843 (tm-30) REVERT: G 172 GLU cc_start: 0.8390 (mp0) cc_final: 0.8147 (mp0) REVERT: I 71 LYS cc_start: 0.8592 (mtmm) cc_final: 0.8322 (pttp) REVERT: H 1 MET cc_start: 0.9065 (mmt) cc_final: 0.8749 (mmm) REVERT: J 21 THR cc_start: 0.7479 (p) cc_final: 0.7252 (m) REVERT: J 53 TYR cc_start: 0.7815 (m-80) cc_final: 0.7184 (m-10) REVERT: J 74 TYR cc_start: 0.9021 (m-80) cc_final: 0.8318 (m-80) REVERT: J 89 PHE cc_start: 0.9537 (t80) cc_final: 0.9052 (t80) REVERT: J 108 MET cc_start: 0.7623 (mtm) cc_final: 0.6774 (mtm) REVERT: K 38 ILE cc_start: 0.8833 (tp) cc_final: 0.8553 (tp) REVERT: K 71 ARG cc_start: 0.8787 (mmp80) cc_final: 0.8402 (mmp-170) REVERT: K 100 PHE cc_start: 0.8743 (m-80) cc_final: 0.8443 (m-80) REVERT: K 110 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8631 (pm20) REVERT: L 30 THR cc_start: 0.9224 (p) cc_final: 0.8886 (t) REVERT: L 51 GLU cc_start: 0.8928 (pm20) cc_final: 0.8434 (pm20) REVERT: L 55 MET cc_start: 0.9029 (tpt) cc_final: 0.8763 (tpt) REVERT: L 61 LEU cc_start: 0.9607 (mt) cc_final: 0.9267 (mt) REVERT: M 22 GLN cc_start: 0.8000 (tt0) cc_final: 0.7544 (tt0) REVERT: M 36 VAL cc_start: 0.8963 (p) cc_final: 0.8592 (p) REVERT: M 60 GLN cc_start: 0.9324 (mp10) cc_final: 0.8983 (tp-100) REVERT: M 68 PHE cc_start: 0.9273 (t80) cc_final: 0.8989 (t80) REVERT: N 3 HIS cc_start: 0.8915 (m170) cc_final: 0.8612 (m170) REVERT: N 9 GLN cc_start: 0.8789 (pt0) cc_final: 0.8335 (pm20) REVERT: N 16 HIS cc_start: 0.8289 (t-170) cc_final: 0.7877 (t-90) REVERT: N 20 MET cc_start: 0.9637 (ttm) cc_final: 0.9402 (ttm) REVERT: N 46 ARG cc_start: 0.9418 (mtp85) cc_final: 0.8684 (mtt90) REVERT: N 62 ASN cc_start: 0.9683 (m110) cc_final: 0.9467 (m110) REVERT: N 72 ASP cc_start: 0.9405 (t70) cc_final: 0.9160 (t0) REVERT: N 74 GLU cc_start: 0.9408 (tm-30) cc_final: 0.9172 (tm-30) REVERT: N 110 MET cc_start: 0.8792 (mmp) cc_final: 0.8491 (mmm) REVERT: O 31 THR cc_start: 0.8731 (p) cc_final: 0.8400 (p) REVERT: O 33 ARG cc_start: 0.8723 (ttm170) cc_final: 0.8092 (ptt-90) REVERT: O 34 HIS cc_start: 0.9005 (m-70) cc_final: 0.8242 (m-70) REVERT: O 40 ILE cc_start: 0.7927 (mm) cc_final: 0.7680 (mm) REVERT: P 2 ASN cc_start: 0.9246 (t0) cc_final: 0.8448 (m-40) REVERT: P 15 ASP cc_start: 0.9420 (m-30) cc_final: 0.9133 (p0) REVERT: P 64 SER cc_start: 0.9321 (m) cc_final: 0.9012 (t) REVERT: P 96 LEU cc_start: 0.9569 (mp) cc_final: 0.9353 (mt) REVERT: P 97 TYR cc_start: 0.9436 (m-10) cc_final: 0.9112 (m-10) REVERT: P 98 TYR cc_start: 0.8985 (p90) cc_final: 0.8585 (p90) REVERT: Q 7 VAL cc_start: 0.8790 (m) cc_final: 0.8547 (m) REVERT: Q 10 ARG cc_start: 0.8780 (ptp90) cc_final: 0.8542 (ptt-90) REVERT: Q 14 LYS cc_start: 0.9523 (ttmt) cc_final: 0.9245 (tptt) REVERT: Q 15 LYS cc_start: 0.9428 (ttpt) cc_final: 0.9019 (tptt) REVERT: Q 23 TYR cc_start: 0.8999 (m-80) cc_final: 0.8506 (m-80) REVERT: Q 46 TYR cc_start: 0.8868 (t80) cc_final: 0.8546 (t80) REVERT: R 40 MET cc_start: 0.8635 (tpt) cc_final: 0.7869 (tmm) REVERT: R 85 LYS cc_start: 0.8243 (tmtt) cc_final: 0.7984 (tmtt) REVERT: R 87 GLN cc_start: 0.9348 (pp30) cc_final: 0.8937 (pp30) REVERT: S 18 ARG cc_start: 0.9292 (tmt-80) cc_final: 0.9041 (tmt-80) REVERT: S 49 LYS cc_start: 0.9458 (ptmt) cc_final: 0.8998 (tptp) REVERT: S 87 PRO cc_start: 0.8977 (Cg_exo) cc_final: 0.8717 (Cg_endo) REVERT: U 8 ASP cc_start: 0.8210 (m-30) cc_final: 0.7858 (m-30) REVERT: U 9 GLU cc_start: 0.8931 (mm-30) cc_final: 0.7939 (tp30) REVERT: U 65 GLN cc_start: 0.8913 (mt0) cc_final: 0.8627 (mt0) REVERT: U 84 PHE cc_start: 0.7852 (p90) cc_final: 0.7524 (p90) REVERT: V 8 VAL cc_start: 0.9538 (t) cc_final: 0.9269 (t) REVERT: V 70 ILE cc_start: 0.8377 (mp) cc_final: 0.7855 (mp) REVERT: V 71 LYS cc_start: 0.8819 (mttm) cc_final: 0.8464 (mmtm) REVERT: V 82 TYR cc_start: 0.9646 (p90) cc_final: 0.8733 (p90) REVERT: V 87 GLN cc_start: 0.9531 (mm110) cc_final: 0.9325 (mm110) REVERT: V 91 PHE cc_start: 0.9232 (m-80) cc_final: 0.8787 (m-10) REVERT: W 13 GLU cc_start: 0.8494 (mp0) cc_final: 0.8234 (mp0) REVERT: W 21 ARG cc_start: 0.7370 (ptp90) cc_final: 0.7059 (mtm180) REVERT: W 53 HIS cc_start: 0.8987 (m-70) cc_final: 0.8677 (m170) REVERT: W 58 LYS cc_start: 0.8717 (ptpt) cc_final: 0.7753 (tppt) REVERT: W 62 LYS cc_start: 0.9489 (mppt) cc_final: 0.8866 (mmtm) REVERT: W 76 ILE cc_start: 0.9680 (mp) cc_final: 0.9356 (tp) REVERT: W 79 GLU cc_start: 0.8785 (tp30) cc_final: 0.7652 (pp20) REVERT: X 15 ASN cc_start: 0.8586 (m-40) cc_final: 0.8259 (m-40) REVERT: X 22 ASN cc_start: 0.9124 (m110) cc_final: 0.8806 (m-40) REVERT: X 36 ARG cc_start: 0.9291 (ttp80) cc_final: 0.8728 (ptt90) REVERT: X 37 PHE cc_start: 0.9197 (m-10) cc_final: 0.8968 (m-10) REVERT: X 45 PHE cc_start: 0.9643 (m-80) cc_final: 0.9173 (m-80) REVERT: X 48 LEU cc_start: 0.8717 (mt) cc_final: 0.8144 (tt) REVERT: X 49 ARG cc_start: 0.7636 (mtp85) cc_final: 0.7404 (mtt180) REVERT: X 64 ASP cc_start: 0.8969 (t0) cc_final: 0.8704 (t0) REVERT: X 71 ARG cc_start: 0.8691 (mpp-170) cc_final: 0.8326 (tpp-160) REVERT: Y 1 MET cc_start: 0.7927 (mmp) cc_final: 0.6368 (mpp) REVERT: Y 2 LYS cc_start: 0.8619 (ttpp) cc_final: 0.7980 (ptpt) REVERT: Y 20 ASN cc_start: 0.9643 (m110) cc_final: 0.9316 (t0) REVERT: Y 55 THR cc_start: 0.9049 (t) cc_final: 0.8805 (t) REVERT: Z 19 HIS cc_start: 0.7595 (m170) cc_final: 0.7355 (m170) REVERT: Z 39 ASP cc_start: 0.8653 (m-30) cc_final: 0.8422 (m-30) REVERT: 0 3 GLN cc_start: 0.9023 (pm20) cc_final: 0.8395 (pm20) REVERT: 0 9 ARG cc_start: 0.8815 (mtp180) cc_final: 0.8491 (mtp180) REVERT: 0 11 LYS cc_start: 0.9573 (ttpt) cc_final: 0.9213 (ptpp) REVERT: 1 18 HIS cc_start: 0.8196 (t70) cc_final: 0.7802 (t70) REVERT: 1 20 TYR cc_start: 0.8883 (m-80) cc_final: 0.8607 (m-10) REVERT: 1 26 LYS cc_start: 0.8791 (tptt) cc_final: 0.8509 (tppt) REVERT: 1 32 LYS cc_start: 0.7901 (tmtt) cc_final: 0.7438 (tmtt) REVERT: 1 44 GLN cc_start: 0.9213 (pt0) cc_final: 0.8658 (mm-40) REVERT: 2 5 PHE cc_start: 0.7781 (t80) cc_final: 0.7337 (t80) REVERT: 2 22 MET cc_start: 0.8868 (tpp) cc_final: 0.8621 (tpp) REVERT: 3 25 HIS cc_start: 0.9613 (m90) cc_final: 0.9043 (m170) REVERT: 3 31 ILE cc_start: 0.9229 (mt) cc_final: 0.8702 (tt) REVERT: 3 42 HIS cc_start: 0.9407 (m90) cc_final: 0.8945 (m90) REVERT: 3 43 LEU cc_start: 0.9648 (mt) cc_final: 0.9313 (mt) REVERT: 3 51 LYS cc_start: 0.8477 (pttp) cc_final: 0.8155 (mtpt) REVERT: 3 61 LEU cc_start: 0.9027 (mt) cc_final: 0.8659 (mp) REVERT: 4 13 ASN cc_start: 0.9111 (t0) cc_final: 0.8770 (t0) REVERT: 6 12 ILE cc_start: 0.9014 (pt) cc_final: 0.8550 (mp) outliers start: 5 outliers final: 0 residues processed: 1762 average time/residue: 1.3922 time to fit residues: 4129.7780 Evaluate side-chains 1415 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1414 time to evaluate : 6.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1095 random chunks: chunk 356 optimal weight: 20.0000 chunk 953 optimal weight: 30.0000 chunk 209 optimal weight: 20.0000 chunk 621 optimal weight: 40.0000 chunk 261 optimal weight: 8.9990 chunk 1059 optimal weight: 7.9990 chunk 879 optimal weight: 40.0000 chunk 490 optimal weight: 40.0000 chunk 88 optimal weight: 30.0000 chunk 350 optimal weight: 10.0000 chunk 556 optimal weight: 30.0000 overall best weight: 13.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 99 ASN g 67 ASN ** g 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 37 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 51 GLN t 12 GLN z 18 GLN ** z 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS Y 58 ASN ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 165989 Z= 0.302 Angle : 0.781 20.725 247857 Z= 0.411 Chirality : 0.039 0.395 31480 Planarity : 0.007 0.125 13686 Dihedral : 23.946 178.498 81771 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 34.68 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.76 % Favored : 91.75 % Rotamer: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.02 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.10), residues: 6329 helix: -1.01 (0.10), residues: 2025 sheet: -1.54 (0.14), residues: 1083 loop : -1.53 (0.10), residues: 3221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP z 385 HIS 0.015 0.002 HIS 1 45 PHE 0.028 0.003 PHE f 78 TYR 0.036 0.003 TYR c 167 ARG 0.017 0.001 ARG J 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1735 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1732 time to evaluate : 6.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 15 PHE cc_start: 0.8936 (p90) cc_final: 0.8665 (p90) REVERT: b 29 PHE cc_start: 0.8998 (m-10) cc_final: 0.8666 (m-10) REVERT: b 41 ASN cc_start: 0.9550 (t0) cc_final: 0.9281 (t0) REVERT: b 99 MET cc_start: 0.8203 (mmp) cc_final: 0.7957 (mmm) REVERT: b 153 MET cc_start: 0.8492 (ppp) cc_final: 0.7567 (tmm) REVERT: c 5 HIS cc_start: 0.8589 (t70) cc_final: 0.8226 (t70) REVERT: c 171 ARG cc_start: 0.8574 (mtp85) cc_final: 0.8246 (mtt-85) REVERT: c 184 ASN cc_start: 0.8600 (t0) cc_final: 0.8022 (t0) REVERT: c 190 THR cc_start: 0.8776 (m) cc_final: 0.8458 (p) REVERT: c 191 THR cc_start: 0.5810 (p) cc_final: 0.5288 (t) REVERT: d 81 LEU cc_start: 0.9253 (mp) cc_final: 0.8891 (tp) REVERT: d 94 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6625 (tt0) REVERT: d 99 ASN cc_start: 0.8993 (t0) cc_final: 0.8705 (t0) REVERT: d 130 ASN cc_start: 0.7074 (t0) cc_final: 0.6161 (m110) REVERT: d 183 ARG cc_start: 0.9524 (mmm160) cc_final: 0.9116 (mmm160) REVERT: e 33 THR cc_start: 0.9488 (t) cc_final: 0.9086 (t) REVERT: e 51 LYS cc_start: 0.8605 (mtmt) cc_final: 0.8385 (mttt) REVERT: e 68 ARG cc_start: 0.9218 (ttm110) cc_final: 0.9014 (mmm160) REVERT: e 110 MET cc_start: 0.9210 (pmm) cc_final: 0.8992 (pmm) REVERT: e 127 TYR cc_start: 0.7110 (m-10) cc_final: 0.6716 (m-10) REVERT: f 5 GLU cc_start: 0.8897 (tt0) cc_final: 0.8509 (mp0) REVERT: f 49 TYR cc_start: 0.8313 (p90) cc_final: 0.8037 (p90) REVERT: f 80 PHE cc_start: 0.9302 (m-10) cc_final: 0.9006 (m-80) REVERT: g 47 GLU cc_start: 0.9485 (mp0) cc_final: 0.9257 (mp0) REVERT: g 98 LEU cc_start: 0.8809 (tp) cc_final: 0.8488 (tt) REVERT: g 101 ARG cc_start: 0.8929 (mtm180) cc_final: 0.8566 (mtt180) REVERT: h 8 ASP cc_start: 0.9494 (m-30) cc_final: 0.9208 (m-30) REVERT: h 47 ASP cc_start: 0.9106 (m-30) cc_final: 0.8862 (p0) REVERT: h 49 LYS cc_start: 0.9510 (mppt) cc_final: 0.9255 (mmtm) REVERT: h 75 GLN cc_start: 0.9546 (mp-120) cc_final: 0.9187 (mp-120) REVERT: h 83 ARG cc_start: 0.7248 (mmt180) cc_final: 0.6547 (mmt90) REVERT: j 44 THR cc_start: 0.8242 (p) cc_final: 0.7936 (p) REVERT: j 63 ASP cc_start: 0.9271 (t0) cc_final: 0.8975 (t0) REVERT: j 64 GLN cc_start: 0.9491 (mm-40) cc_final: 0.9209 (mt0) REVERT: j 99 GLN cc_start: 0.8767 (mm110) cc_final: 0.8359 (mp10) REVERT: l 52 CYS cc_start: 0.9423 (p) cc_final: 0.8618 (t) REVERT: m 11 HIS cc_start: 0.8948 (m90) cc_final: 0.8667 (m90) REVERT: m 22 TYR cc_start: 0.8939 (t80) cc_final: 0.8472 (t80) REVERT: n 9 GLU cc_start: 0.9458 (pp20) cc_final: 0.9178 (tt0) REVERT: n 15 LEU cc_start: 0.9183 (tt) cc_final: 0.8387 (pp) REVERT: n 64 ARG cc_start: 0.9466 (mtt180) cc_final: 0.9245 (mtp85) REVERT: n 73 LEU cc_start: 0.9074 (mp) cc_final: 0.8833 (tp) REVERT: o 1 SER cc_start: 0.7907 (p) cc_final: 0.7501 (m) REVERT: o 46 LYS cc_start: 0.8555 (ptpt) cc_final: 0.8347 (ptpp) REVERT: o 77 TYR cc_start: 0.8418 (t80) cc_final: 0.7761 (t80) REVERT: o 81 ILE cc_start: 0.8929 (mm) cc_final: 0.8416 (mm) REVERT: p 1 MET cc_start: 0.8875 (tpt) cc_final: 0.8586 (tpp) REVERT: p 2 VAL cc_start: 0.7419 (m) cc_final: 0.7129 (m) REVERT: p 14 ARG cc_start: 0.8959 (mmm-85) cc_final: 0.8742 (mmm-85) REVERT: p 34 GLU cc_start: 0.8879 (pm20) cc_final: 0.8322 (pm20) REVERT: p 35 ARG cc_start: 0.7479 (ttm170) cc_final: 0.6138 (ttt180) REVERT: p 39 PHE cc_start: 0.9220 (t80) cc_final: 0.8818 (t80) REVERT: p 79 ASN cc_start: 0.8749 (m110) cc_final: 0.8461 (t0) REVERT: q 33 TYR cc_start: 0.8780 (m-10) cc_final: 0.8343 (m-10) REVERT: q 72 TRP cc_start: 0.9096 (m100) cc_final: 0.8721 (m100) REVERT: q 80 LYS cc_start: 0.8332 (mttm) cc_final: 0.7762 (tppt) REVERT: r 73 HIS cc_start: 0.9005 (m-70) cc_final: 0.8777 (m-70) REVERT: s 27 LYS cc_start: 0.7947 (mtmm) cc_final: 0.7567 (tppt) REVERT: s 35 ARG cc_start: 0.9097 (mtp-110) cc_final: 0.8825 (mtp-110) REVERT: s 46 LEU cc_start: 0.8670 (mm) cc_final: 0.8358 (mm) REVERT: s 65 MET cc_start: 0.8994 (ttt) cc_final: 0.8755 (ttt) REVERT: s 68 HIS cc_start: 0.9029 (m90) cc_final: 0.8617 (m-70) REVERT: s 73 PHE cc_start: 0.8853 (m-80) cc_final: 0.8409 (m-80) REVERT: t 12 GLN cc_start: 0.9539 (pt0) cc_final: 0.9294 (pt0) REVERT: t 38 ILE cc_start: 0.9389 (mm) cc_final: 0.8980 (mm) REVERT: t 47 GLN cc_start: 0.9586 (mt0) cc_final: 0.9341 (mp10) REVERT: u 6 ARG cc_start: 0.8404 (tpt90) cc_final: 0.7556 (ttm-80) REVERT: u 30 GLU cc_start: 0.7873 (pm20) cc_final: 0.7652 (pm20) REVERT: u 53 LYS cc_start: 0.9222 (mptt) cc_final: 0.8822 (pttm) REVERT: z 89 MET cc_start: 0.7134 (tpt) cc_final: 0.6505 (ttm) REVERT: z 127 ARG cc_start: 0.6888 (mtt180) cc_final: 0.6541 (tmm-80) REVERT: z 216 MET cc_start: 0.5337 (mmm) cc_final: 0.4807 (mmm) REVERT: z 265 PHE cc_start: 0.8529 (p90) cc_final: 0.8049 (m-80) REVERT: z 514 LYS cc_start: 0.4458 (mttt) cc_final: 0.3908 (pttp) REVERT: z 562 GLN cc_start: 0.8169 (mp10) cc_final: 0.7832 (mp10) REVERT: C 145 MET cc_start: 0.8344 (mmp) cc_final: 0.7731 (mmm) REVERT: C 200 MET cc_start: 0.8512 (ptm) cc_final: 0.7659 (ptm) REVERT: C 239 PHE cc_start: 0.8448 (t80) cc_final: 0.6953 (t80) REVERT: C 241 LYS cc_start: 0.9054 (tptp) cc_final: 0.8603 (tptt) REVERT: D 36 GLN cc_start: 0.9022 (mt0) cc_final: 0.8202 (mm-40) REVERT: D 67 HIS cc_start: 0.8664 (t70) cc_final: 0.8416 (t-90) REVERT: D 82 PHE cc_start: 0.6600 (t80) cc_final: 0.6283 (t80) REVERT: D 126 ASN cc_start: 0.9629 (t0) cc_final: 0.9428 (t0) REVERT: D 128 ARG cc_start: 0.5634 (tpt90) cc_final: 0.3503 (mmm-85) REVERT: D 201 LEU cc_start: 0.9347 (mt) cc_final: 0.9006 (mt) REVERT: E 30 GLN cc_start: 0.8995 (mt0) cc_final: 0.8554 (mp10) REVERT: E 166 LYS cc_start: 0.9427 (mptt) cc_final: 0.9141 (mptt) REVERT: E 176 ASP cc_start: 0.8770 (m-30) cc_final: 0.8402 (m-30) REVERT: F 37 MET cc_start: 0.6578 (mtp) cc_final: 0.6087 (mtm) REVERT: F 129 MET cc_start: 0.6973 (pmm) cc_final: 0.6691 (pmm) REVERT: F 133 GLU cc_start: 0.6667 (tm-30) cc_final: 0.6445 (tm-30) REVERT: F 155 ILE cc_start: 0.9153 (mt) cc_final: 0.8922 (mm) REVERT: F 174 PHE cc_start: 0.7909 (m-10) cc_final: 0.7698 (m-10) REVERT: G 18 ILE cc_start: 0.8515 (tt) cc_final: 0.8246 (mp) REVERT: G 41 GLU cc_start: 0.8396 (pp20) cc_final: 0.7840 (pp20) REVERT: G 68 ARG cc_start: 0.9389 (ttp80) cc_final: 0.8996 (ptm-80) REVERT: G 116 LEU cc_start: 0.9491 (mt) cc_final: 0.9187 (mp) REVERT: G 172 GLU cc_start: 0.8381 (mp0) cc_final: 0.8123 (mp0) REVERT: I 71 LYS cc_start: 0.8579 (mtmm) cc_final: 0.8308 (pttp) REVERT: H 1 MET cc_start: 0.9142 (mmt) cc_final: 0.8769 (mmm) REVERT: J 52 ASP cc_start: 0.5965 (m-30) cc_final: 0.5758 (m-30) REVERT: J 53 TYR cc_start: 0.7567 (m-80) cc_final: 0.7016 (m-10) REVERT: J 74 TYR cc_start: 0.8978 (m-80) cc_final: 0.8298 (m-80) REVERT: J 89 PHE cc_start: 0.9542 (t80) cc_final: 0.9070 (t80) REVERT: J 108 MET cc_start: 0.7800 (mtm) cc_final: 0.7092 (mtm) REVERT: K 42 THR cc_start: 0.9734 (t) cc_final: 0.9423 (m) REVERT: K 44 LYS cc_start: 0.9225 (mmmt) cc_final: 0.8879 (mmtm) REVERT: K 100 PHE cc_start: 0.8727 (m-80) cc_final: 0.8427 (m-80) REVERT: K 110 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8761 (pm20) REVERT: L 30 THR cc_start: 0.9189 (p) cc_final: 0.8830 (t) REVERT: L 55 MET cc_start: 0.9118 (tpt) cc_final: 0.8914 (tpt) REVERT: L 73 ILE cc_start: 0.9593 (pt) cc_final: 0.9160 (pt) REVERT: L 106 GLU cc_start: 0.9082 (pt0) cc_final: 0.8455 (pm20) REVERT: L 107 PHE cc_start: 0.8477 (m-80) cc_final: 0.7983 (m-80) REVERT: M 22 GLN cc_start: 0.7836 (tt0) cc_final: 0.7495 (tt0) REVERT: M 59 ARG cc_start: 0.9158 (mmp80) cc_final: 0.8921 (mmp80) REVERT: M 60 GLN cc_start: 0.9281 (mp10) cc_final: 0.8995 (tp-100) REVERT: M 68 PHE cc_start: 0.9257 (t80) cc_final: 0.9030 (t80) REVERT: M 111 GLU cc_start: 0.9375 (pm20) cc_final: 0.9170 (pm20) REVERT: N 3 HIS cc_start: 0.8814 (m170) cc_final: 0.8497 (m170) REVERT: N 9 GLN cc_start: 0.8810 (pt0) cc_final: 0.8402 (pm20) REVERT: N 16 HIS cc_start: 0.8343 (t-170) cc_final: 0.7972 (t-90) REVERT: N 24 MET cc_start: 0.9489 (tpp) cc_final: 0.9236 (tpp) REVERT: N 46 ARG cc_start: 0.9325 (mtp85) cc_final: 0.8708 (mtt90) REVERT: N 49 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8736 (mt-10) REVERT: N 62 ASN cc_start: 0.9645 (m110) cc_final: 0.9332 (m110) REVERT: N 110 MET cc_start: 0.8772 (mmp) cc_final: 0.8423 (mmm) REVERT: O 31 THR cc_start: 0.8837 (p) cc_final: 0.8534 (p) REVERT: O 33 ARG cc_start: 0.8718 (ttm170) cc_final: 0.8030 (ptt-90) REVERT: O 34 HIS cc_start: 0.8881 (m-70) cc_final: 0.8201 (m90) REVERT: O 40 ILE cc_start: 0.7948 (mm) cc_final: 0.7724 (mm) REVERT: P 2 ASN cc_start: 0.9298 (t0) cc_final: 0.8540 (m110) REVERT: P 59 THR cc_start: 0.9628 (m) cc_final: 0.9284 (p) REVERT: P 64 SER cc_start: 0.9350 (m) cc_final: 0.9045 (t) REVERT: P 96 LEU cc_start: 0.9572 (mp) cc_final: 0.9291 (mp) REVERT: P 98 TYR cc_start: 0.9075 (p90) cc_final: 0.8630 (p90) REVERT: Q 2 ARG cc_start: 0.8469 (mtp180) cc_final: 0.8005 (mtm-85) REVERT: Q 14 LYS cc_start: 0.9513 (ttmt) cc_final: 0.9242 (tptt) REVERT: Q 15 LYS cc_start: 0.9394 (ttpt) cc_final: 0.8912 (tptm) REVERT: Q 23 TYR cc_start: 0.8971 (m-80) cc_final: 0.8403 (m-80) REVERT: Q 48 ASP cc_start: 0.7112 (m-30) cc_final: 0.6595 (m-30) REVERT: R 21 ARG cc_start: 0.9176 (mmt-90) cc_final: 0.8953 (mmp80) REVERT: R 34 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8561 (mm-30) REVERT: R 40 MET cc_start: 0.8611 (tpt) cc_final: 0.7893 (tmm) REVERT: R 53 PHE cc_start: 0.8877 (m-10) cc_final: 0.8523 (m-10) REVERT: R 74 ILE cc_start: 0.9403 (mm) cc_final: 0.9198 (mm) REVERT: R 85 LYS cc_start: 0.8283 (tmtt) cc_final: 0.7964 (tmtt) REVERT: R 87 GLN cc_start: 0.9377 (pp30) cc_final: 0.8918 (pp30) REVERT: R 95 ASP cc_start: 0.9207 (m-30) cc_final: 0.8944 (m-30) REVERT: S 18 ARG cc_start: 0.9313 (tmt-80) cc_final: 0.9008 (tmt-80) REVERT: S 49 LYS cc_start: 0.9500 (ptmt) cc_final: 0.9075 (tptp) REVERT: S 75 PHE cc_start: 0.8839 (p90) cc_final: 0.8540 (p90) REVERT: S 87 PRO cc_start: 0.8854 (Cg_exo) cc_final: 0.8449 (Cg_endo) REVERT: T 6 ARG cc_start: 0.9347 (tpm170) cc_final: 0.8569 (tpm170) REVERT: T 24 MET cc_start: 0.9424 (mtm) cc_final: 0.9060 (mtt) REVERT: T 63 VAL cc_start: 0.8955 (t) cc_final: 0.8750 (t) REVERT: T 64 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8211 (tmtt) REVERT: T 80 TRP cc_start: 0.8903 (p-90) cc_final: 0.7666 (p-90) REVERT: U 8 ASP cc_start: 0.8209 (m-30) cc_final: 0.7674 (m-30) REVERT: U 9 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8060 (tp30) REVERT: U 14 THR cc_start: 0.9066 (p) cc_final: 0.8565 (p) REVERT: V 44 HIS cc_start: 0.8350 (t-90) cc_final: 0.7745 (t-90) REVERT: V 70 ILE cc_start: 0.8506 (mp) cc_final: 0.8070 (mp) REVERT: V 71 LYS cc_start: 0.8710 (mttm) cc_final: 0.8486 (mmtm) REVERT: V 87 GLN cc_start: 0.9524 (mm110) cc_final: 0.9318 (mm110) REVERT: V 91 PHE cc_start: 0.9169 (m-80) cc_final: 0.8881 (m-80) REVERT: W 13 GLU cc_start: 0.8566 (mp0) cc_final: 0.8245 (mp0) REVERT: W 21 ARG cc_start: 0.7594 (ptp90) cc_final: 0.7166 (mtm180) REVERT: W 53 HIS cc_start: 0.9052 (m-70) cc_final: 0.8382 (m90) REVERT: W 58 LYS cc_start: 0.8623 (ptpt) cc_final: 0.7596 (tppt) REVERT: W 62 LYS cc_start: 0.9500 (mppt) cc_final: 0.8737 (mptt) REVERT: W 71 LYS cc_start: 0.8476 (ptpt) cc_final: 0.7785 (pttt) REVERT: W 73 ARG cc_start: 0.9539 (mtt180) cc_final: 0.9032 (mtt180) REVERT: W 76 ILE cc_start: 0.9689 (mp) cc_final: 0.9395 (tp) REVERT: W 79 GLU cc_start: 0.8816 (tp30) cc_final: 0.7632 (pp20) REVERT: X 28 PHE cc_start: 0.8751 (m-80) cc_final: 0.8544 (m-80) REVERT: X 36 ARG cc_start: 0.9333 (ttp80) cc_final: 0.9091 (ptt90) REVERT: X 37 PHE cc_start: 0.9275 (m-10) cc_final: 0.9038 (m-10) REVERT: X 45 PHE cc_start: 0.9653 (m-80) cc_final: 0.9196 (m-80) REVERT: X 48 LEU cc_start: 0.8713 (mt) cc_final: 0.8145 (tt) REVERT: X 49 ARG cc_start: 0.7618 (mtp85) cc_final: 0.7320 (mtt180) REVERT: X 64 ASP cc_start: 0.8947 (t0) cc_final: 0.8682 (t0) REVERT: X 71 ARG cc_start: 0.8778 (mpp-170) cc_final: 0.8539 (mmm160) REVERT: Y 1 MET cc_start: 0.7870 (mmp) cc_final: 0.6345 (mpp) REVERT: Y 2 LYS cc_start: 0.8680 (ttpp) cc_final: 0.8343 (ptmm) REVERT: Y 55 THR cc_start: 0.9056 (t) cc_final: 0.8834 (t) REVERT: Z 39 ASP cc_start: 0.8999 (m-30) cc_final: 0.8653 (m-30) REVERT: 0 3 GLN cc_start: 0.9009 (pm20) cc_final: 0.8448 (pm20) REVERT: 0 11 LYS cc_start: 0.9581 (ttpt) cc_final: 0.9294 (ptpt) REVERT: 0 14 MET cc_start: 0.8858 (tpt) cc_final: 0.8511 (tpp) REVERT: 0 47 TYR cc_start: 0.8913 (m-10) cc_final: 0.8477 (m-10) REVERT: 1 8 ILE cc_start: 0.8927 (mp) cc_final: 0.8657 (mp) REVERT: 1 18 HIS cc_start: 0.7960 (t70) cc_final: 0.7581 (t70) REVERT: 1 20 TYR cc_start: 0.8887 (m-80) cc_final: 0.8622 (m-10) REVERT: 1 24 LYS cc_start: 0.9114 (tmmt) cc_final: 0.8875 (tmtt) REVERT: 1 32 LYS cc_start: 0.8053 (tmtt) cc_final: 0.7595 (tmtt) REVERT: 1 44 GLN cc_start: 0.9115 (pt0) cc_final: 0.8606 (mm-40) REVERT: 1 52 LYS cc_start: 0.8639 (pttm) cc_final: 0.8305 (mmtm) REVERT: 2 5 PHE cc_start: 0.7878 (t80) cc_final: 0.7382 (t80) REVERT: 2 22 MET cc_start: 0.8889 (tpp) cc_final: 0.8627 (tpp) REVERT: 3 21 PHE cc_start: 0.9187 (m-80) cc_final: 0.8958 (m-10) REVERT: 3 25 HIS cc_start: 0.9615 (m90) cc_final: 0.9143 (m170) REVERT: 3 31 ILE cc_start: 0.9209 (mt) cc_final: 0.8687 (tt) REVERT: 3 42 HIS cc_start: 0.9357 (m90) cc_final: 0.8944 (m90) REVERT: 3 43 LEU cc_start: 0.9712 (mt) cc_final: 0.9405 (mt) REVERT: 3 61 LEU cc_start: 0.9021 (mt) cc_final: 0.8712 (mp) REVERT: 4 13 ASN cc_start: 0.9135 (t0) cc_final: 0.8815 (t0) REVERT: 4 32 LYS cc_start: 0.9337 (mmtp) cc_final: 0.8972 (tppt) REVERT: 6 12 ILE cc_start: 0.9109 (pt) cc_final: 0.8667 (mp) outliers start: 3 outliers final: 2 residues processed: 1733 average time/residue: 1.3843 time to fit residues: 4060.5057 Evaluate side-chains 1381 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1379 time to evaluate : 6.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1095 random chunks: chunk 1021 optimal weight: 7.9990 chunk 119 optimal weight: 30.0000 chunk 603 optimal weight: 30.0000 chunk 773 optimal weight: 6.9990 chunk 599 optimal weight: 30.0000 chunk 891 optimal weight: 30.0000 chunk 591 optimal weight: 30.0000 chunk 1055 optimal weight: 8.9990 chunk 660 optimal weight: 30.0000 chunk 643 optimal weight: 30.0000 chunk 487 optimal weight: 30.0000 overall best weight: 16.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS ** c 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 80 ASN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 18 GLN ** z 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 475 HIS ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 65 GLN Y 58 ASN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 165989 Z= 0.364 Angle : 0.848 19.973 247857 Z= 0.442 Chirality : 0.042 0.417 31480 Planarity : 0.008 0.127 13686 Dihedral : 24.165 178.016 81771 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 41.53 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.90 % Favored : 90.65 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.10), residues: 6329 helix: -1.16 (0.10), residues: 2034 sheet: -1.71 (0.14), residues: 1091 loop : -1.78 (0.10), residues: 3204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.004 TRP n 41 HIS 0.017 0.003 HIS C 52 PHE 0.031 0.003 PHE F 172 TYR 0.036 0.003 TYR z 42 ARG 0.013 0.001 ARG k 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1655 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1655 time to evaluate : 6.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 8 MET cc_start: 0.8269 (tpt) cc_final: 0.8007 (tpt) REVERT: b 15 PHE cc_start: 0.8850 (p90) cc_final: 0.8622 (p90) REVERT: b 29 PHE cc_start: 0.9011 (m-10) cc_final: 0.8764 (m-10) REVERT: b 41 ASN cc_start: 0.9529 (t0) cc_final: 0.9315 (t0) REVERT: b 88 GLN cc_start: 0.7131 (mp-120) cc_final: 0.6165 (mp10) REVERT: b 90 PHE cc_start: 0.9383 (p90) cc_final: 0.9015 (p90) REVERT: b 102 ASN cc_start: 0.8149 (t0) cc_final: 0.7776 (t0) REVERT: b 153 MET cc_start: 0.8507 (ppp) cc_final: 0.8141 (ppp) REVERT: c 7 ASN cc_start: 0.9249 (t0) cc_final: 0.9028 (t0) REVERT: c 68 HIS cc_start: 0.8817 (m-70) cc_final: 0.8609 (m90) REVERT: c 171 ARG cc_start: 0.8376 (mtp85) cc_final: 0.8017 (mtp85) REVERT: c 183 TYR cc_start: 0.8751 (t80) cc_final: 0.8366 (t80) REVERT: c 184 ASN cc_start: 0.8910 (t0) cc_final: 0.8430 (t0) REVERT: c 190 THR cc_start: 0.8614 (m) cc_final: 0.8334 (p) REVERT: d 3 TYR cc_start: 0.9301 (t80) cc_final: 0.8809 (t80) REVERT: d 49 ASP cc_start: 0.9110 (p0) cc_final: 0.8906 (p0) REVERT: d 62 ARG cc_start: 0.9144 (mtt180) cc_final: 0.8569 (mmp80) REVERT: d 70 GLN cc_start: 0.9183 (pt0) cc_final: 0.8939 (pt0) REVERT: d 81 LEU cc_start: 0.9353 (mp) cc_final: 0.8940 (tp) REVERT: d 94 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6736 (tt0) REVERT: d 99 ASN cc_start: 0.9192 (t0) cc_final: 0.8926 (t0) REVERT: d 123 MET cc_start: 0.6293 (mmt) cc_final: 0.5795 (mmt) REVERT: e 33 THR cc_start: 0.9464 (t) cc_final: 0.9205 (t) REVERT: e 95 MET cc_start: 0.8850 (pmm) cc_final: 0.8565 (pmm) REVERT: e 110 MET cc_start: 0.9266 (pmm) cc_final: 0.8915 (pmm) REVERT: e 127 TYR cc_start: 0.7477 (m-10) cc_final: 0.6808 (m-80) REVERT: f 5 GLU cc_start: 0.9044 (tt0) cc_final: 0.8527 (mp0) REVERT: f 49 TYR cc_start: 0.8303 (p90) cc_final: 0.8093 (p90) REVERT: f 80 PHE cc_start: 0.9301 (m-10) cc_final: 0.8966 (m-80) REVERT: f 86 ARG cc_start: 0.7486 (mmt180) cc_final: 0.7031 (mtt-85) REVERT: g 47 GLU cc_start: 0.9472 (mp0) cc_final: 0.9220 (mp0) REVERT: g 65 LEU cc_start: 0.9111 (pp) cc_final: 0.8884 (pp) REVERT: g 98 LEU cc_start: 0.8845 (tp) cc_final: 0.8528 (tt) REVERT: g 103 ILE cc_start: 0.8897 (tp) cc_final: 0.8674 (pt) REVERT: g 141 HIS cc_start: 0.9209 (m-70) cc_final: 0.9001 (m-70) REVERT: h 75 GLN cc_start: 0.9576 (mp-120) cc_final: 0.9228 (mp-120) REVERT: h 109 VAL cc_start: 0.9687 (t) cc_final: 0.9463 (p) REVERT: h 126 CYS cc_start: 0.8935 (p) cc_final: 0.8661 (p) REVERT: i 24 ASN cc_start: 0.8301 (t0) cc_final: 0.8024 (t0) REVERT: i 106 ASP cc_start: 0.8527 (t0) cc_final: 0.8283 (t0) REVERT: j 11 LYS cc_start: 0.7843 (pttt) cc_final: 0.7529 (pttt) REVERT: j 44 THR cc_start: 0.8167 (p) cc_final: 0.7897 (p) REVERT: j 63 ASP cc_start: 0.9270 (t0) cc_final: 0.8997 (t0) REVERT: j 64 GLN cc_start: 0.9528 (mm-40) cc_final: 0.9252 (mt0) REVERT: j 99 GLN cc_start: 0.8930 (mm110) cc_final: 0.8608 (mp10) REVERT: l 52 CYS cc_start: 0.9429 (p) cc_final: 0.9078 (p) REVERT: m 11 HIS cc_start: 0.9132 (m90) cc_final: 0.8875 (m90) REVERT: m 22 TYR cc_start: 0.8869 (t80) cc_final: 0.8358 (t80) REVERT: n 9 GLU cc_start: 0.9517 (pp20) cc_final: 0.9271 (tt0) REVERT: n 41 TRP cc_start: 0.8426 (m-10) cc_final: 0.8167 (t-100) REVERT: n 64 ARG cc_start: 0.9460 (mtt180) cc_final: 0.9204 (mmm160) REVERT: p 2 VAL cc_start: 0.7322 (m) cc_final: 0.7006 (m) REVERT: p 5 ARG cc_start: 0.7437 (ptt180) cc_final: 0.6821 (ptt180) REVERT: p 14 ARG cc_start: 0.8995 (mmm-85) cc_final: 0.8786 (mmm-85) REVERT: p 21 VAL cc_start: 0.8192 (t) cc_final: 0.7802 (t) REVERT: p 34 GLU cc_start: 0.8900 (pm20) cc_final: 0.8501 (pm20) REVERT: p 39 PHE cc_start: 0.9177 (t80) cc_final: 0.8806 (t80) REVERT: p 56 ARG cc_start: 0.9283 (mtp85) cc_final: 0.8894 (mtp85) REVERT: q 72 TRP cc_start: 0.9160 (m100) cc_final: 0.8895 (m100) REVERT: q 80 LYS cc_start: 0.8133 (mttm) cc_final: 0.7656 (tppt) REVERT: r 73 HIS cc_start: 0.9065 (m-70) cc_final: 0.8829 (m-70) REVERT: s 27 LYS cc_start: 0.7876 (mtmm) cc_final: 0.7361 (tppt) REVERT: s 35 ARG cc_start: 0.9160 (mtp-110) cc_final: 0.8923 (mtp-110) REVERT: s 46 LEU cc_start: 0.8740 (mm) cc_final: 0.8501 (mm) REVERT: s 68 HIS cc_start: 0.9053 (m90) cc_final: 0.8729 (m-70) REVERT: t 12 GLN cc_start: 0.9588 (pt0) cc_final: 0.9364 (pt0) REVERT: t 26 MET cc_start: 0.9602 (mmp) cc_final: 0.9325 (mmm) REVERT: u 6 ARG cc_start: 0.8418 (tpt90) cc_final: 0.7661 (ttt180) REVERT: u 34 ARG cc_start: 0.9264 (mtt-85) cc_final: 0.9055 (mtt180) REVERT: u 46 ARG cc_start: 0.9250 (mmt-90) cc_final: 0.8990 (ttp80) REVERT: u 53 LYS cc_start: 0.9304 (mptt) cc_final: 0.8912 (pttm) REVERT: z 68 MET cc_start: 0.6484 (ptp) cc_final: 0.6170 (ptp) REVERT: z 127 ARG cc_start: 0.6638 (mtt180) cc_final: 0.6239 (tmm-80) REVERT: z 265 PHE cc_start: 0.8386 (p90) cc_final: 0.8177 (m-80) REVERT: z 514 LYS cc_start: 0.4382 (mttt) cc_final: 0.3884 (pttp) REVERT: z 562 GLN cc_start: 0.8101 (mp10) cc_final: 0.7851 (mp10) REVERT: C 179 GLU cc_start: 0.8305 (tt0) cc_final: 0.7305 (tm-30) REVERT: C 200 MET cc_start: 0.8667 (ptm) cc_final: 0.7765 (ptm) REVERT: D 36 GLN cc_start: 0.9029 (mt0) cc_final: 0.8186 (mm-40) REVERT: D 67 HIS cc_start: 0.8793 (t-90) cc_final: 0.8481 (t-90) REVERT: D 82 PHE cc_start: 0.6714 (t80) cc_final: 0.6228 (t80) REVERT: D 116 LYS cc_start: 0.9255 (mtmm) cc_final: 0.8957 (mtmm) REVERT: D 148 GLN cc_start: 0.8405 (tt0) cc_final: 0.6734 (tm-30) REVERT: E 30 GLN cc_start: 0.9035 (mt0) cc_final: 0.8600 (mp10) REVERT: E 166 LYS cc_start: 0.9434 (mptt) cc_final: 0.9128 (mptt) REVERT: E 176 ASP cc_start: 0.8744 (m-30) cc_final: 0.8464 (m-30) REVERT: F 127 TYR cc_start: 0.8474 (t80) cc_final: 0.8225 (t80) REVERT: F 129 MET cc_start: 0.6727 (pmm) cc_final: 0.6397 (pmm) REVERT: F 135 ILE cc_start: 0.8868 (mm) cc_final: 0.8590 (mm) REVERT: F 174 PHE cc_start: 0.8099 (m-10) cc_final: 0.7775 (m-80) REVERT: G 18 ILE cc_start: 0.8606 (tt) cc_final: 0.8330 (mp) REVERT: G 41 GLU cc_start: 0.8449 (pp20) cc_final: 0.7829 (pp20) REVERT: G 68 ARG cc_start: 0.9385 (ttp80) cc_final: 0.9000 (ptm-80) REVERT: G 116 LEU cc_start: 0.9504 (mt) cc_final: 0.9226 (mp) REVERT: G 129 GLU cc_start: 0.9570 (mt-10) cc_final: 0.9193 (mm-30) REVERT: G 151 ARG cc_start: 0.9256 (mmm160) cc_final: 0.9048 (mmm160) REVERT: G 172 GLU cc_start: 0.8326 (mp0) cc_final: 0.8061 (mp0) REVERT: I 71 LYS cc_start: 0.8665 (mtmm) cc_final: 0.8408 (pttp) REVERT: H 1 MET cc_start: 0.9066 (mmt) cc_final: 0.8677 (mmm) REVERT: H 128 HIS cc_start: 0.7522 (m-70) cc_final: 0.7146 (m-70) REVERT: J 14 ASP cc_start: 0.8025 (m-30) cc_final: 0.7777 (m-30) REVERT: J 53 TYR cc_start: 0.7681 (m-80) cc_final: 0.7156 (m-10) REVERT: J 74 TYR cc_start: 0.9028 (m-80) cc_final: 0.8462 (m-80) REVERT: J 89 PHE cc_start: 0.9552 (t80) cc_final: 0.9118 (t80) REVERT: J 108 MET cc_start: 0.7622 (mtm) cc_final: 0.6960 (mtm) REVERT: K 1 MET cc_start: 0.7653 (tpp) cc_final: 0.7082 (tpt) REVERT: K 100 PHE cc_start: 0.8717 (m-80) cc_final: 0.8454 (m-80) REVERT: K 110 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8853 (pm20) REVERT: L 30 THR cc_start: 0.9222 (p) cc_final: 0.8878 (t) REVERT: L 55 MET cc_start: 0.9140 (tpt) cc_final: 0.8908 (tpt) REVERT: L 73 ILE cc_start: 0.9575 (pt) cc_final: 0.9118 (pt) REVERT: L 106 GLU cc_start: 0.9038 (pt0) cc_final: 0.8428 (pm20) REVERT: L 107 PHE cc_start: 0.8459 (m-80) cc_final: 0.7919 (m-80) REVERT: M 22 GLN cc_start: 0.7801 (tt0) cc_final: 0.7461 (tt0) REVERT: M 59 ARG cc_start: 0.9098 (mmp80) cc_final: 0.8890 (mmp80) REVERT: M 60 GLN cc_start: 0.9291 (mp10) cc_final: 0.8920 (tp-100) REVERT: M 68 PHE cc_start: 0.9248 (t80) cc_final: 0.9030 (t80) REVERT: N 3 HIS cc_start: 0.8874 (m170) cc_final: 0.8062 (m170) REVERT: N 5 LYS cc_start: 0.8582 (mmmt) cc_final: 0.8290 (mmmt) REVERT: N 9 GLN cc_start: 0.8769 (pt0) cc_final: 0.8340 (pm20) REVERT: N 16 HIS cc_start: 0.8372 (t-170) cc_final: 0.7946 (t-90) REVERT: N 24 MET cc_start: 0.9519 (tpp) cc_final: 0.9233 (tpp) REVERT: N 74 GLU cc_start: 0.9336 (tm-30) cc_final: 0.9120 (tm-30) REVERT: N 110 MET cc_start: 0.8825 (mmp) cc_final: 0.8492 (mmm) REVERT: O 34 HIS cc_start: 0.8817 (m-70) cc_final: 0.8201 (m90) REVERT: O 40 ILE cc_start: 0.7999 (mm) cc_final: 0.7762 (mm) REVERT: P 2 ASN cc_start: 0.9344 (t0) cc_final: 0.8571 (m110) REVERT: P 64 SER cc_start: 0.9341 (m) cc_final: 0.9078 (t) REVERT: P 96 LEU cc_start: 0.9572 (mp) cc_final: 0.9349 (mp) REVERT: P 98 TYR cc_start: 0.8993 (p90) cc_final: 0.8484 (p90) REVERT: Q 2 ARG cc_start: 0.8689 (mtp180) cc_final: 0.8230 (mtm-85) REVERT: Q 14 LYS cc_start: 0.9487 (ttmt) cc_final: 0.9238 (tptt) REVERT: Q 15 LYS cc_start: 0.9466 (ttpt) cc_final: 0.8915 (tptt) REVERT: Q 23 TYR cc_start: 0.9110 (m-80) cc_final: 0.8449 (m-80) REVERT: Q 46 TYR cc_start: 0.8857 (t80) cc_final: 0.8606 (t80) REVERT: R 13 ARG cc_start: 0.8877 (ttp80) cc_final: 0.8537 (ttp80) REVERT: R 40 MET cc_start: 0.8733 (tpt) cc_final: 0.8252 (tmm) REVERT: R 84 ARG cc_start: 0.9167 (mtp-110) cc_final: 0.8916 (mtp-110) REVERT: R 85 LYS cc_start: 0.8387 (tmtt) cc_final: 0.8098 (tmtt) REVERT: R 87 GLN cc_start: 0.9403 (pp30) cc_final: 0.8940 (pp30) REVERT: S 8 ARG cc_start: 0.8671 (ptm160) cc_final: 0.8449 (mtm-85) REVERT: S 18 ARG cc_start: 0.9279 (tmt-80) cc_final: 0.9050 (tmt-80) REVERT: S 34 ASP cc_start: 0.9753 (p0) cc_final: 0.9397 (p0) REVERT: S 38 TYR cc_start: 0.8863 (m-80) cc_final: 0.8578 (m-80) REVERT: S 49 LYS cc_start: 0.9483 (ptmt) cc_final: 0.9049 (tptp) REVERT: S 86 MET cc_start: 0.8341 (tpp) cc_final: 0.8107 (tpp) REVERT: T 24 MET cc_start: 0.9304 (mtm) cc_final: 0.8979 (mtt) REVERT: T 64 LYS cc_start: 0.9016 (mmmt) cc_final: 0.8556 (tttt) REVERT: T 80 TRP cc_start: 0.8934 (p-90) cc_final: 0.7863 (p-90) REVERT: U 8 ASP cc_start: 0.7917 (m-30) cc_final: 0.7560 (m-30) REVERT: U 9 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8049 (tp30) REVERT: U 68 ASN cc_start: 0.9158 (m-40) cc_final: 0.8826 (m-40) REVERT: U 91 LYS cc_start: 0.8043 (tttt) cc_final: 0.7824 (tttt) REVERT: V 5 ASN cc_start: 0.8099 (m-40) cc_final: 0.7348 (t0) REVERT: V 44 HIS cc_start: 0.8107 (t-90) cc_final: 0.7903 (t-90) REVERT: V 70 ILE cc_start: 0.8509 (mp) cc_final: 0.8039 (mp) REVERT: V 71 LYS cc_start: 0.8574 (mttm) cc_final: 0.8321 (mmtm) REVERT: V 87 GLN cc_start: 0.9527 (mm110) cc_final: 0.9326 (mm-40) REVERT: V 91 PHE cc_start: 0.9074 (m-80) cc_final: 0.8848 (m-10) REVERT: W 21 ARG cc_start: 0.7642 (ptp90) cc_final: 0.7148 (mtm180) REVERT: W 51 ARG cc_start: 0.9202 (ptm-80) cc_final: 0.8859 (ttp-110) REVERT: W 53 HIS cc_start: 0.9087 (m-70) cc_final: 0.8447 (m90) REVERT: W 58 LYS cc_start: 0.8551 (ptpt) cc_final: 0.7578 (tppt) REVERT: W 62 LYS cc_start: 0.9533 (mppt) cc_final: 0.9310 (mmtm) REVERT: W 71 LYS cc_start: 0.8436 (ptpt) cc_final: 0.7841 (pttt) REVERT: W 73 ARG cc_start: 0.9528 (mtt180) cc_final: 0.9135 (mtt180) REVERT: W 76 ILE cc_start: 0.9710 (mp) cc_final: 0.9475 (tp) REVERT: X 15 ASN cc_start: 0.8659 (m-40) cc_final: 0.7563 (p0) REVERT: X 48 LEU cc_start: 0.8739 (mt) cc_final: 0.8199 (tt) REVERT: X 49 ARG cc_start: 0.7669 (mtp85) cc_final: 0.7437 (mtt180) REVERT: X 71 ARG cc_start: 0.8786 (mpp-170) cc_final: 0.8501 (tpp-160) REVERT: Y 1 MET cc_start: 0.7952 (mmp) cc_final: 0.6563 (mpp) REVERT: Y 2 LYS cc_start: 0.8813 (ttpp) cc_final: 0.8492 (ptmm) REVERT: Y 55 THR cc_start: 0.9252 (t) cc_final: 0.9045 (t) REVERT: Z 39 ASP cc_start: 0.9109 (m-30) cc_final: 0.8750 (m-30) REVERT: 0 3 GLN cc_start: 0.9228 (pm20) cc_final: 0.8787 (pm20) REVERT: 0 9 ARG cc_start: 0.9116 (mtp180) cc_final: 0.8811 (mtp180) REVERT: 0 11 LYS cc_start: 0.9602 (ttpt) cc_final: 0.9320 (ptpt) REVERT: 0 14 MET cc_start: 0.8837 (tpt) cc_final: 0.8568 (tpp) REVERT: 0 47 TYR cc_start: 0.8898 (m-10) cc_final: 0.8474 (m-10) REVERT: 1 18 HIS cc_start: 0.8077 (t70) cc_final: 0.7672 (t70) REVERT: 1 20 TYR cc_start: 0.8860 (m-80) cc_final: 0.8560 (m-10) REVERT: 1 26 LYS cc_start: 0.8724 (tptt) cc_final: 0.8282 (tppt) REVERT: 1 32 LYS cc_start: 0.8069 (tmtt) cc_final: 0.7568 (tmtt) REVERT: 1 44 GLN cc_start: 0.9191 (pt0) cc_final: 0.8569 (mm-40) REVERT: 1 52 LYS cc_start: 0.8644 (pttm) cc_final: 0.8256 (mmtm) REVERT: 2 5 PHE cc_start: 0.8015 (t80) cc_final: 0.7692 (t80) REVERT: 2 22 MET cc_start: 0.8945 (tpp) cc_final: 0.8683 (tpp) REVERT: 3 25 HIS cc_start: 0.9605 (m90) cc_final: 0.9249 (m170) REVERT: 3 31 ILE cc_start: 0.9171 (mt) cc_final: 0.8698 (tt) REVERT: 3 42 HIS cc_start: 0.9357 (m90) cc_final: 0.8954 (m90) REVERT: 3 61 LEU cc_start: 0.9041 (mt) cc_final: 0.8720 (mp) REVERT: 4 13 ASN cc_start: 0.9098 (t0) cc_final: 0.8769 (t0) REVERT: 6 12 ILE cc_start: 0.9121 (pt) cc_final: 0.8682 (mp) REVERT: 6 64 PHE cc_start: 0.6909 (t80) cc_final: 0.6337 (t80) outliers start: 0 outliers final: 0 residues processed: 1655 average time/residue: 1.4971 time to fit residues: 4238.0342 Evaluate side-chains 1362 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1362 time to evaluate : 6.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1095 random chunks: chunk 652 optimal weight: 20.0000 chunk 421 optimal weight: 50.0000 chunk 630 optimal weight: 30.0000 chunk 317 optimal weight: 6.9990 chunk 207 optimal weight: 0.0870 chunk 204 optimal weight: 9.9990 chunk 670 optimal weight: 30.0000 chunk 719 optimal weight: 30.0000 chunk 521 optimal weight: 30.0000 chunk 98 optimal weight: 40.0000 chunk 829 optimal weight: 3.9990 overall best weight: 8.2168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 17 HIS ** c 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 67 ASN ** g 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 51 GLN t 69 ASN z 18 GLN ** z 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 420 GLN ** z 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS E 46 GLN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 ASN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 42 HIS ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN 2 26 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 165989 Z= 0.219 Angle : 0.725 19.120 247857 Z= 0.384 Chirality : 0.036 0.437 31480 Planarity : 0.007 0.123 13686 Dihedral : 24.052 179.823 81771 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 29.44 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.39 % Favored : 92.21 % Rotamer: Outliers : 0.02 % Allowed : 1.57 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.10), residues: 6329 helix: -0.96 (0.10), residues: 2026 sheet: -1.49 (0.15), residues: 1072 loop : -1.67 (0.10), residues: 3231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP z 208 HIS 0.013 0.002 HIS b 38 PHE 0.059 0.003 PHE u 36 TYR 0.039 0.002 TYR o 77 ARG 0.021 0.001 ARG V 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1710 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1709 time to evaluate : 6.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 8 MET cc_start: 0.8183 (tpt) cc_final: 0.7875 (tpt) REVERT: b 15 PHE cc_start: 0.8860 (p90) cc_final: 0.8510 (p90) REVERT: b 29 PHE cc_start: 0.8967 (m-10) cc_final: 0.8687 (m-10) REVERT: b 41 ASN cc_start: 0.9528 (t0) cc_final: 0.9312 (t0) REVERT: b 90 PHE cc_start: 0.9438 (p90) cc_final: 0.9092 (p90) REVERT: b 96 LEU cc_start: 0.9304 (tp) cc_final: 0.8833 (tp) REVERT: b 99 MET cc_start: 0.8077 (mmp) cc_final: 0.7738 (mmp) REVERT: b 102 ASN cc_start: 0.8120 (t0) cc_final: 0.7744 (t0) REVERT: b 119 GLN cc_start: 0.8420 (pp30) cc_final: 0.8205 (pp30) REVERT: b 137 THR cc_start: 0.8487 (m) cc_final: 0.8226 (p) REVERT: b 153 MET cc_start: 0.8377 (ppp) cc_final: 0.7892 (ppp) REVERT: b 168 GLU cc_start: 0.8215 (pm20) cc_final: 0.7941 (pm20) REVERT: c 5 HIS cc_start: 0.8185 (t70) cc_final: 0.7809 (t70) REVERT: c 68 HIS cc_start: 0.8784 (m-70) cc_final: 0.8572 (m90) REVERT: c 106 ARG cc_start: 0.8376 (tpp-160) cc_final: 0.8111 (tmt-80) REVERT: c 183 TYR cc_start: 0.8499 (t80) cc_final: 0.7730 (t80) REVERT: c 184 ASN cc_start: 0.8765 (t0) cc_final: 0.8109 (t0) REVERT: c 185 THR cc_start: 0.8497 (p) cc_final: 0.8127 (p) REVERT: c 190 THR cc_start: 0.8707 (m) cc_final: 0.8405 (p) REVERT: d 3 TYR cc_start: 0.9259 (t80) cc_final: 0.8804 (t80) REVERT: d 69 ARG cc_start: 0.9463 (ttm110) cc_final: 0.8837 (tpt-90) REVERT: d 75 TYR cc_start: 0.8819 (t80) cc_final: 0.8456 (t80) REVERT: d 81 LEU cc_start: 0.9276 (mp) cc_final: 0.8881 (tp) REVERT: d 94 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6769 (tt0) REVERT: d 99 ASN cc_start: 0.9143 (t0) cc_final: 0.8843 (t0) REVERT: d 109 THR cc_start: 0.7177 (p) cc_final: 0.6277 (p) REVERT: d 112 GLU cc_start: 0.9281 (tm-30) cc_final: 0.7855 (mt-10) REVERT: d 153 ARG cc_start: 0.8574 (ttm170) cc_final: 0.7339 (ttm170) REVERT: d 183 ARG cc_start: 0.9480 (mmm160) cc_final: 0.9101 (mmm160) REVERT: e 68 ARG cc_start: 0.9284 (ttm110) cc_final: 0.9059 (mmm160) REVERT: e 110 MET cc_start: 0.9217 (pmm) cc_final: 0.8906 (pmm) REVERT: e 127 TYR cc_start: 0.7420 (m-10) cc_final: 0.6841 (m-80) REVERT: f 5 GLU cc_start: 0.8757 (tt0) cc_final: 0.8425 (mp0) REVERT: f 23 GLU cc_start: 0.9302 (mp0) cc_final: 0.9007 (pp20) REVERT: f 24 ARG cc_start: 0.9483 (ptp-170) cc_final: 0.9225 (ptp-170) REVERT: f 49 TYR cc_start: 0.8126 (p90) cc_final: 0.7894 (p90) REVERT: f 80 PHE cc_start: 0.9276 (m-10) cc_final: 0.8996 (m-80) REVERT: g 35 LYS cc_start: 0.8800 (ttpt) cc_final: 0.8280 (ptmt) REVERT: g 65 LEU cc_start: 0.9021 (pp) cc_final: 0.8811 (pp) REVERT: g 103 ILE cc_start: 0.8831 (tp) cc_final: 0.8589 (pt) REVERT: g 150 PHE cc_start: 0.7833 (m-80) cc_final: 0.7611 (m-80) REVERT: h 8 ASP cc_start: 0.9488 (m-30) cc_final: 0.9202 (m-30) REVERT: h 109 VAL cc_start: 0.9629 (t) cc_final: 0.9366 (p) REVERT: i 24 ASN cc_start: 0.8080 (t0) cc_final: 0.7878 (t0) REVERT: i 93 LEU cc_start: 0.8736 (tt) cc_final: 0.8525 (tt) REVERT: j 44 THR cc_start: 0.8201 (p) cc_final: 0.7944 (p) REVERT: j 59 LYS cc_start: 0.7030 (pptt) cc_final: 0.6784 (pptt) REVERT: j 64 GLN cc_start: 0.9557 (mm-40) cc_final: 0.9264 (mt0) REVERT: j 99 GLN cc_start: 0.8814 (mm110) cc_final: 0.8331 (mp10) REVERT: k 23 HIS cc_start: 0.8262 (t70) cc_final: 0.7916 (t-170) REVERT: l 52 CYS cc_start: 0.9490 (p) cc_final: 0.8762 (t) REVERT: m 11 HIS cc_start: 0.9080 (m90) cc_final: 0.8713 (m90) REVERT: m 22 TYR cc_start: 0.8880 (t80) cc_final: 0.8434 (t80) REVERT: n 15 LEU cc_start: 0.9121 (tt) cc_final: 0.8613 (pp) REVERT: o 1 SER cc_start: 0.7816 (m) cc_final: 0.7556 (m) REVERT: o 64 LYS cc_start: 0.9426 (ptpp) cc_final: 0.9123 (ptpp) REVERT: p 5 ARG cc_start: 0.6789 (ptt180) cc_final: 0.6277 (ptt180) REVERT: p 14 ARG cc_start: 0.8993 (mmm-85) cc_final: 0.8762 (mmm-85) REVERT: p 21 VAL cc_start: 0.8198 (t) cc_final: 0.7859 (t) REVERT: p 34 GLU cc_start: 0.8909 (pm20) cc_final: 0.8529 (pm20) REVERT: p 39 PHE cc_start: 0.9200 (t80) cc_final: 0.8794 (t80) REVERT: p 79 ASN cc_start: 0.8756 (m110) cc_final: 0.8437 (t0) REVERT: q 33 TYR cc_start: 0.8723 (m-10) cc_final: 0.8506 (m-10) REVERT: q 72 TRP cc_start: 0.9174 (m100) cc_final: 0.8838 (m100) REVERT: q 80 LYS cc_start: 0.8207 (mttm) cc_final: 0.7698 (tppt) REVERT: r 73 HIS cc_start: 0.9030 (m-70) cc_final: 0.8768 (m-70) REVERT: s 27 LYS cc_start: 0.7906 (mtmm) cc_final: 0.7479 (tppt) REVERT: s 35 ARG cc_start: 0.9148 (mtp-110) cc_final: 0.8893 (mtp-110) REVERT: s 46 LEU cc_start: 0.8687 (mm) cc_final: 0.8381 (mm) REVERT: s 47 THR cc_start: 0.8392 (p) cc_final: 0.8064 (p) REVERT: s 68 HIS cc_start: 0.9062 (m90) cc_final: 0.8719 (m-70) REVERT: s 73 PHE cc_start: 0.8828 (m-80) cc_final: 0.8456 (m-80) REVERT: t 12 GLN cc_start: 0.9587 (pt0) cc_final: 0.9348 (pt0) REVERT: t 47 GLN cc_start: 0.9604 (mt0) cc_final: 0.9386 (mp10) REVERT: u 6 ARG cc_start: 0.8436 (tpt90) cc_final: 0.7490 (ttm170) REVERT: u 53 LYS cc_start: 0.9286 (mptt) cc_final: 0.8954 (pttt) REVERT: z 68 MET cc_start: 0.6258 (ptp) cc_final: 0.5887 (ptp) REVERT: z 89 MET cc_start: 0.7610 (tpt) cc_final: 0.7211 (ttm) REVERT: z 127 ARG cc_start: 0.6711 (mtt180) cc_final: 0.6288 (tmm-80) REVERT: z 176 ARG cc_start: 0.7386 (ttm170) cc_final: 0.6055 (tpt170) REVERT: z 265 PHE cc_start: 0.8213 (p90) cc_final: 0.7973 (m-80) REVERT: z 465 MET cc_start: 0.8156 (mmp) cc_final: 0.7826 (mmm) REVERT: z 562 GLN cc_start: 0.8102 (mp10) cc_final: 0.7802 (mp10) REVERT: C 64 VAL cc_start: 0.8689 (p) cc_final: 0.8462 (p) REVERT: C 200 MET cc_start: 0.8610 (ptm) cc_final: 0.7720 (ptm) REVERT: D 36 GLN cc_start: 0.9041 (mt0) cc_final: 0.8327 (mm-40) REVERT: D 67 HIS cc_start: 0.8740 (t-90) cc_final: 0.8385 (t-90) REVERT: D 82 PHE cc_start: 0.6727 (t80) cc_final: 0.6153 (t80) REVERT: D 126 ASN cc_start: 0.9437 (t0) cc_final: 0.9143 (t0) REVERT: D 128 ARG cc_start: 0.5662 (tpt90) cc_final: 0.4119 (mmm160) REVERT: D 161 MET cc_start: 0.7983 (ptp) cc_final: 0.7623 (ptp) REVERT: D 164 GLN cc_start: 0.8782 (tp40) cc_final: 0.8269 (tm-30) REVERT: E 30 GLN cc_start: 0.8950 (mt0) cc_final: 0.8553 (mp10) REVERT: E 166 LYS cc_start: 0.9385 (mptt) cc_final: 0.9025 (mmtt) REVERT: E 176 ASP cc_start: 0.8808 (m-30) cc_final: 0.8480 (m-30) REVERT: F 78 ILE cc_start: 0.8762 (pt) cc_final: 0.8067 (tp) REVERT: F 129 MET cc_start: 0.6571 (pmm) cc_final: 0.6278 (pmm) REVERT: F 135 ILE cc_start: 0.8837 (mm) cc_final: 0.8614 (mt) REVERT: G 18 ILE cc_start: 0.8607 (tt) cc_final: 0.8341 (mp) REVERT: G 41 GLU cc_start: 0.8452 (pp20) cc_final: 0.7740 (pp20) REVERT: G 55 ASP cc_start: 0.6735 (m-30) cc_final: 0.6528 (m-30) REVERT: G 68 ARG cc_start: 0.9324 (ttp80) cc_final: 0.8976 (ptm-80) REVERT: G 116 LEU cc_start: 0.9453 (mt) cc_final: 0.9168 (mp) REVERT: G 129 GLU cc_start: 0.9590 (mt-10) cc_final: 0.9212 (mm-30) REVERT: G 151 ARG cc_start: 0.9243 (mmm160) cc_final: 0.9028 (mmm160) REVERT: G 172 GLU cc_start: 0.8340 (mp0) cc_final: 0.8056 (mp0) REVERT: I 71 LYS cc_start: 0.8627 (mtmm) cc_final: 0.8397 (pttp) REVERT: H 1 MET cc_start: 0.9050 (mmt) cc_final: 0.8617 (mmm) REVERT: H 3 VAL cc_start: 0.8586 (m) cc_final: 0.8349 (p) REVERT: J 14 ASP cc_start: 0.7869 (m-30) cc_final: 0.7650 (m-30) REVERT: J 53 TYR cc_start: 0.7455 (m-80) cc_final: 0.6797 (m-10) REVERT: J 74 TYR cc_start: 0.9028 (m-80) cc_final: 0.8437 (m-80) REVERT: J 89 PHE cc_start: 0.9496 (t80) cc_final: 0.9073 (t80) REVERT: J 108 MET cc_start: 0.7535 (mtm) cc_final: 0.6795 (mtm) REVERT: K 1 MET cc_start: 0.7569 (tpp) cc_final: 0.7057 (tpt) REVERT: K 8 LEU cc_start: 0.9221 (tp) cc_final: 0.8974 (tp) REVERT: K 13 ASN cc_start: 0.9097 (p0) cc_final: 0.8866 (p0) REVERT: K 38 ILE cc_start: 0.8695 (tp) cc_final: 0.8434 (tp) REVERT: K 110 GLU cc_start: 0.9217 (tm-30) cc_final: 0.8859 (pm20) REVERT: L 30 THR cc_start: 0.9081 (p) cc_final: 0.8694 (t) REVERT: L 55 MET cc_start: 0.9088 (tpt) cc_final: 0.8823 (tpt) REVERT: L 73 ILE cc_start: 0.9545 (pt) cc_final: 0.9102 (pt) REVERT: L 106 GLU cc_start: 0.9028 (pt0) cc_final: 0.8474 (pm20) REVERT: L 107 PHE cc_start: 0.8410 (m-80) cc_final: 0.7877 (m-80) REVERT: M 22 GLN cc_start: 0.7600 (tt0) cc_final: 0.7084 (tt0) REVERT: M 59 ARG cc_start: 0.9037 (mmp80) cc_final: 0.8777 (mmp80) REVERT: M 60 GLN cc_start: 0.9282 (mp10) cc_final: 0.9026 (tp-100) REVERT: M 68 PHE cc_start: 0.9306 (t80) cc_final: 0.9089 (t80) REVERT: M 97 GLN cc_start: 0.9184 (mp10) cc_final: 0.8843 (mm110) REVERT: M 111 GLU cc_start: 0.9295 (pm20) cc_final: 0.9052 (pm20) REVERT: N 3 HIS cc_start: 0.8891 (m170) cc_final: 0.8064 (m170) REVERT: N 5 LYS cc_start: 0.8528 (mmmt) cc_final: 0.8117 (mmmt) REVERT: N 9 GLN cc_start: 0.8547 (pt0) cc_final: 0.8309 (pm20) REVERT: N 16 HIS cc_start: 0.8307 (t-170) cc_final: 0.7819 (t70) REVERT: N 24 MET cc_start: 0.9480 (tpp) cc_final: 0.9109 (tpp) REVERT: N 107 ASN cc_start: 0.9329 (t160) cc_final: 0.9110 (t0) REVERT: N 110 MET cc_start: 0.8785 (mmp) cc_final: 0.8515 (mmm) REVERT: O 34 HIS cc_start: 0.8762 (m-70) cc_final: 0.8102 (m-70) REVERT: O 40 ILE cc_start: 0.7243 (mm) cc_final: 0.7040 (mm) REVERT: P 2 ASN cc_start: 0.9317 (t0) cc_final: 0.8554 (m110) REVERT: P 64 SER cc_start: 0.9271 (m) cc_final: 0.8989 (t) REVERT: Q 2 ARG cc_start: 0.8419 (mtp180) cc_final: 0.7970 (mtm-85) REVERT: Q 14 LYS cc_start: 0.9485 (ttmt) cc_final: 0.9174 (mmtt) REVERT: Q 15 LYS cc_start: 0.9362 (ttpt) cc_final: 0.8891 (tptt) REVERT: Q 23 TYR cc_start: 0.9234 (m-80) cc_final: 0.8539 (m-80) REVERT: Q 60 TRP cc_start: 0.8680 (m-10) cc_final: 0.8249 (m-90) REVERT: R 5 PHE cc_start: 0.9603 (p90) cc_final: 0.9334 (p90) REVERT: R 40 MET cc_start: 0.8532 (tpt) cc_final: 0.8102 (tmm) REVERT: R 87 GLN cc_start: 0.9337 (pp30) cc_final: 0.9024 (pp30) REVERT: S 18 ARG cc_start: 0.9194 (tmt-80) cc_final: 0.8994 (tmt-80) REVERT: S 34 ASP cc_start: 0.9782 (p0) cc_final: 0.9551 (p0) REVERT: S 49 LYS cc_start: 0.9484 (ptmt) cc_final: 0.9087 (tptp) REVERT: T 24 MET cc_start: 0.9291 (mtm) cc_final: 0.9003 (mtt) REVERT: T 64 LYS cc_start: 0.9045 (mmmt) cc_final: 0.8567 (tttt) REVERT: T 80 TRP cc_start: 0.8949 (p-90) cc_final: 0.7959 (p-90) REVERT: U 8 ASP cc_start: 0.7974 (m-30) cc_final: 0.7678 (m-30) REVERT: U 9 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8038 (tp30) REVERT: U 14 THR cc_start: 0.8975 (p) cc_final: 0.8566 (p) REVERT: U 44 HIS cc_start: 0.9082 (m-70) cc_final: 0.8310 (m-70) REVERT: U 68 ASN cc_start: 0.9081 (m-40) cc_final: 0.8832 (m-40) REVERT: V 9 ARG cc_start: 0.9337 (mtp180) cc_final: 0.9129 (mtp180) REVERT: V 29 ILE cc_start: 0.8903 (pt) cc_final: 0.8526 (mm) REVERT: V 70 ILE cc_start: 0.8514 (mp) cc_final: 0.8034 (mp) REVERT: V 71 LYS cc_start: 0.8521 (mttm) cc_final: 0.8267 (mmtm) REVERT: V 76 ASP cc_start: 0.8107 (t70) cc_final: 0.7297 (t70) REVERT: V 91 PHE cc_start: 0.9079 (m-80) cc_final: 0.8863 (m-10) REVERT: W 13 GLU cc_start: 0.8376 (mp0) cc_final: 0.7981 (mp0) REVERT: W 21 ARG cc_start: 0.7565 (ptp90) cc_final: 0.7181 (mtm180) REVERT: W 46 ASN cc_start: 0.9157 (m-40) cc_final: 0.8765 (m-40) REVERT: W 54 THR cc_start: 0.8082 (p) cc_final: 0.7602 (p) REVERT: W 58 LYS cc_start: 0.8540 (ptpt) cc_final: 0.7460 (mmmt) REVERT: W 62 LYS cc_start: 0.9491 (mppt) cc_final: 0.9240 (mmtm) REVERT: W 73 ARG cc_start: 0.9411 (mtt180) cc_final: 0.9124 (mtt180) REVERT: W 74 LYS cc_start: 0.9574 (mmpt) cc_final: 0.9361 (mtpt) REVERT: W 76 ILE cc_start: 0.9713 (mp) cc_final: 0.9418 (tp) REVERT: X 15 ASN cc_start: 0.8713 (m-40) cc_final: 0.7605 (p0) REVERT: X 45 PHE cc_start: 0.9575 (m-80) cc_final: 0.9285 (m-80) REVERT: X 48 LEU cc_start: 0.8800 (mt) cc_final: 0.8275 (tt) REVERT: X 71 ARG cc_start: 0.8843 (mpp-170) cc_final: 0.8628 (mmm160) REVERT: Y 2 LYS cc_start: 0.8672 (ttpp) cc_final: 0.8390 (ptmm) REVERT: Z 39 ASP cc_start: 0.9080 (m-30) cc_final: 0.8627 (m-30) REVERT: Z 52 PHE cc_start: 0.8695 (p90) cc_final: 0.7871 (p90) REVERT: Z 53 MET cc_start: 0.9396 (mpp) cc_final: 0.9121 (mmm) REVERT: 0 3 GLN cc_start: 0.8970 (pm20) cc_final: 0.8613 (pm20) REVERT: 0 11 LYS cc_start: 0.9599 (ttpt) cc_final: 0.9271 (ptpt) REVERT: 0 14 MET cc_start: 0.8850 (tpt) cc_final: 0.8506 (tpp) REVERT: 1 18 HIS cc_start: 0.7964 (t70) cc_final: 0.7578 (t70) REVERT: 1 20 TYR cc_start: 0.8873 (m-80) cc_final: 0.8576 (m-10) REVERT: 1 26 LYS cc_start: 0.8736 (tptt) cc_final: 0.8282 (tppt) REVERT: 1 32 LYS cc_start: 0.8073 (tmtt) cc_final: 0.7577 (tmtt) REVERT: 1 44 GLN cc_start: 0.9178 (pt0) cc_final: 0.8566 (tp40) REVERT: 1 52 LYS cc_start: 0.8715 (pttm) cc_final: 0.8245 (mmtm) REVERT: 2 5 PHE cc_start: 0.7954 (t80) cc_final: 0.7312 (t80) REVERT: 2 22 MET cc_start: 0.9059 (tpp) cc_final: 0.8829 (tpp) REVERT: 3 3 ILE cc_start: 0.6694 (mm) cc_final: 0.6489 (mm) REVERT: 3 25 HIS cc_start: 0.9614 (m90) cc_final: 0.9279 (m90) REVERT: 3 31 ILE cc_start: 0.9135 (mt) cc_final: 0.8618 (tt) REVERT: 3 42 HIS cc_start: 0.9317 (m90) cc_final: 0.8917 (m90) REVERT: 4 13 ASN cc_start: 0.9125 (t0) cc_final: 0.8726 (t0) REVERT: 6 12 ILE cc_start: 0.9052 (pt) cc_final: 0.8654 (mp) REVERT: 6 64 PHE cc_start: 0.7104 (t80) cc_final: 0.6550 (t80) outliers start: 1 outliers final: 1 residues processed: 1709 average time/residue: 1.4868 time to fit residues: 4338.8938 Evaluate side-chains 1417 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1416 time to evaluate : 6.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1095 random chunks: chunk 960 optimal weight: 20.0000 chunk 1011 optimal weight: 40.0000 chunk 922 optimal weight: 30.0000 chunk 983 optimal weight: 7.9990 chunk 1010 optimal weight: 30.0000 chunk 591 optimal weight: 30.0000 chunk 428 optimal weight: 9.9990 chunk 772 optimal weight: 7.9990 chunk 301 optimal weight: 0.9990 chunk 888 optimal weight: 20.0000 chunk 930 optimal weight: 30.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 17 HIS b 88 GLN ** c 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 18 ASN ** c 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 18 GLN ** z 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 420 GLN ** z 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN E 46 GLN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 ASN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 HIS ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 HIS W 53 HIS ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN 6 20 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 165989 Z= 0.238 Angle : 0.732 18.316 247857 Z= 0.388 Chirality : 0.036 0.421 31480 Planarity : 0.007 0.124 13686 Dihedral : 24.024 179.657 81771 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 31.69 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.47 % Favored : 91.20 % Rotamer: Outliers : 0.02 % Allowed : 1.26 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % 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: -2.17 (0.10), residues: 6329 helix: -0.94 (0.10), residues: 2021 sheet: -1.51 (0.15), residues: 1073 loop : -1.71 (0.10), residues: 3235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP z 208 HIS 0.013 0.002 HIS b 38 PHE 0.036 0.003 PHE g 25 TYR 0.030 0.002 TYR G 150 ARG 0.020 0.001 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1660 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1659 time to evaluate : 6.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 8 MET cc_start: 0.8252 (tpt) cc_final: 0.7899 (tpt) REVERT: b 15 PHE cc_start: 0.8755 (p90) cc_final: 0.8407 (p90) REVERT: b 29 PHE cc_start: 0.8984 (m-10) cc_final: 0.8706 (m-10) REVERT: b 41 ASN cc_start: 0.9547 (t0) cc_final: 0.9238 (t0) REVERT: b 90 PHE cc_start: 0.9402 (p90) cc_final: 0.9044 (p90) REVERT: b 102 ASN cc_start: 0.8338 (t0) cc_final: 0.7892 (t0) REVERT: b 136 ARG cc_start: 0.8478 (mtm180) cc_final: 0.8190 (ptt180) REVERT: b 137 THR cc_start: 0.8521 (m) cc_final: 0.8201 (p) REVERT: b 153 MET cc_start: 0.8399 (ppp) cc_final: 0.7963 (ppp) REVERT: b 168 GLU cc_start: 0.7925 (pm20) cc_final: 0.7689 (pm20) REVERT: b 174 GLU cc_start: 0.8761 (pp20) cc_final: 0.8527 (pp20) REVERT: c 5 HIS cc_start: 0.8334 (t70) cc_final: 0.7899 (t70) REVERT: c 22 PHE cc_start: 0.8208 (t80) cc_final: 0.7984 (t80) REVERT: c 24 ASN cc_start: 0.8815 (t0) cc_final: 0.8546 (t0) REVERT: c 68 HIS cc_start: 0.8845 (m-70) cc_final: 0.8541 (m-70) REVERT: c 106 ARG cc_start: 0.8312 (tpp-160) cc_final: 0.8066 (tmt-80) REVERT: c 171 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7936 (mtp85) REVERT: c 183 TYR cc_start: 0.8415 (t80) cc_final: 0.7777 (t80) REVERT: c 190 THR cc_start: 0.8603 (m) cc_final: 0.8322 (p) REVERT: d 3 TYR cc_start: 0.9268 (t80) cc_final: 0.8736 (t80) REVERT: d 27 ILE cc_start: 0.5573 (tt) cc_final: 0.5366 (tt) REVERT: d 94 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6879 (tt0) REVERT: d 99 ASN cc_start: 0.9145 (t0) cc_final: 0.8839 (t0) REVERT: d 109 THR cc_start: 0.7019 (p) cc_final: 0.6140 (p) REVERT: d 112 GLU cc_start: 0.9287 (tm-30) cc_final: 0.7891 (mt-10) REVERT: d 130 ASN cc_start: 0.6380 (t0) cc_final: 0.5848 (m110) REVERT: d 153 ARG cc_start: 0.8665 (ttm170) cc_final: 0.7425 (ttm170) REVERT: d 183 ARG cc_start: 0.9496 (mmm160) cc_final: 0.9083 (mmm160) REVERT: e 64 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8775 (mt-10) REVERT: e 68 ARG cc_start: 0.9208 (ttm110) cc_final: 0.8981 (mmm160) REVERT: e 127 TYR cc_start: 0.7458 (m-10) cc_final: 0.6624 (m-80) REVERT: f 5 GLU cc_start: 0.8876 (tt0) cc_final: 0.8439 (mp0) REVERT: f 80 PHE cc_start: 0.9245 (m-10) cc_final: 0.8973 (m-80) REVERT: f 91 ARG cc_start: 0.7652 (mmm-85) cc_final: 0.6573 (mmm-85) REVERT: g 35 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8301 (pttm) REVERT: g 57 GLU cc_start: 0.8347 (pm20) cc_final: 0.7962 (pp20) REVERT: g 103 ILE cc_start: 0.8806 (tp) cc_final: 0.8552 (pt) REVERT: h 8 ASP cc_start: 0.9476 (m-30) cc_final: 0.9219 (m-30) REVERT: h 109 VAL cc_start: 0.9622 (t) cc_final: 0.9385 (p) REVERT: i 26 LYS cc_start: 0.7088 (tptp) cc_final: 0.6737 (tppt) REVERT: i 93 LEU cc_start: 0.8798 (tt) cc_final: 0.8495 (tt) REVERT: j 59 LYS cc_start: 0.7090 (pptt) cc_final: 0.6817 (pptt) REVERT: j 63 ASP cc_start: 0.9229 (t0) cc_final: 0.8567 (t0) REVERT: j 64 GLN cc_start: 0.9556 (mm-40) cc_final: 0.9279 (mt0) REVERT: j 65 TYR cc_start: 0.8096 (m-80) cc_final: 0.7665 (m-80) REVERT: j 99 GLN cc_start: 0.8915 (mm110) cc_final: 0.8426 (mp10) REVERT: l 52 CYS cc_start: 0.9505 (p) cc_final: 0.8711 (t) REVERT: m 11 HIS cc_start: 0.9093 (m90) cc_final: 0.8756 (m90) REVERT: m 22 TYR cc_start: 0.8902 (t80) cc_final: 0.8425 (t80) REVERT: n 9 GLU cc_start: 0.9397 (pp20) cc_final: 0.9077 (tt0) REVERT: n 15 LEU cc_start: 0.9086 (tt) cc_final: 0.8842 (tt) REVERT: n 18 LYS cc_start: 0.8490 (pttt) cc_final: 0.7900 (pttt) REVERT: o 1 SER cc_start: 0.7709 (m) cc_final: 0.7405 (m) REVERT: o 63 ARG cc_start: 0.9165 (tpt90) cc_final: 0.8545 (tpm170) REVERT: o 64 LYS cc_start: 0.9419 (ptpp) cc_final: 0.9050 (ptpp) REVERT: o 66 LEU cc_start: 0.9268 (tp) cc_final: 0.8956 (tp) REVERT: p 5 ARG cc_start: 0.7066 (ptt180) cc_final: 0.6455 (ptt180) REVERT: p 21 VAL cc_start: 0.8174 (t) cc_final: 0.7866 (t) REVERT: p 34 GLU cc_start: 0.8829 (pm20) cc_final: 0.8441 (pm20) REVERT: p 39 PHE cc_start: 0.9216 (t80) cc_final: 0.8863 (t80) REVERT: p 79 ASN cc_start: 0.8757 (m110) cc_final: 0.8461 (t0) REVERT: q 15 LYS cc_start: 0.8805 (tttp) cc_final: 0.8605 (tttm) REVERT: q 16 MET cc_start: 0.7535 (mmm) cc_final: 0.6790 (mmm) REVERT: q 72 TRP cc_start: 0.9198 (m100) cc_final: 0.8931 (m100) REVERT: q 80 LYS cc_start: 0.8159 (mttm) cc_final: 0.7679 (tppt) REVERT: r 73 HIS cc_start: 0.9046 (m-70) cc_final: 0.8817 (m-70) REVERT: s 27 LYS cc_start: 0.7939 (mtmm) cc_final: 0.7369 (tppt) REVERT: s 46 LEU cc_start: 0.8463 (mm) cc_final: 0.8175 (mm) REVERT: s 65 MET cc_start: 0.9022 (ttt) cc_final: 0.8807 (tmm) REVERT: t 12 GLN cc_start: 0.9575 (pt0) cc_final: 0.9365 (pt0) REVERT: t 47 GLN cc_start: 0.9604 (mt0) cc_final: 0.9391 (mp10) REVERT: u 6 ARG cc_start: 0.8438 (tpt90) cc_final: 0.7781 (ttt180) REVERT: u 12 ASP cc_start: 0.8733 (p0) cc_final: 0.8356 (p0) REVERT: u 30 GLU cc_start: 0.7893 (pm20) cc_final: 0.7507 (pm20) REVERT: u 53 LYS cc_start: 0.9301 (mptt) cc_final: 0.8971 (pttt) REVERT: z 68 MET cc_start: 0.6210 (ptp) cc_final: 0.5892 (ptp) REVERT: z 89 MET cc_start: 0.7724 (tpt) cc_final: 0.7338 (ttm) REVERT: z 127 ARG cc_start: 0.6716 (mtt180) cc_final: 0.6485 (ttt-90) REVERT: z 265 PHE cc_start: 0.8217 (p90) cc_final: 0.7979 (m-80) REVERT: z 465 MET cc_start: 0.8177 (mmp) cc_final: 0.7838 (mmm) REVERT: z 510 ARG cc_start: 0.7406 (tpp-160) cc_final: 0.7087 (tpp-160) REVERT: z 514 LYS cc_start: 0.3810 (mttt) cc_final: 0.3238 (pttp) REVERT: z 562 GLN cc_start: 0.7998 (mp10) cc_final: 0.7719 (mp10) REVERT: C 64 VAL cc_start: 0.8503 (p) cc_final: 0.8250 (p) REVERT: C 131 MET cc_start: 0.9330 (mmp) cc_final: 0.8845 (mmm) REVERT: C 160 TYR cc_start: 0.7880 (p90) cc_final: 0.7666 (p90) REVERT: C 200 MET cc_start: 0.8577 (ptm) cc_final: 0.7729 (ptm) REVERT: D 18 ASP cc_start: 0.8649 (m-30) cc_final: 0.8435 (m-30) REVERT: D 36 GLN cc_start: 0.9057 (mt0) cc_final: 0.8367 (mm-40) REVERT: D 67 HIS cc_start: 0.8764 (t-90) cc_final: 0.8462 (t-90) REVERT: D 82 PHE cc_start: 0.6709 (t80) cc_final: 0.6073 (t80) REVERT: D 126 ASN cc_start: 0.9411 (t0) cc_final: 0.9096 (t0) REVERT: D 161 MET cc_start: 0.7994 (ptp) cc_final: 0.7625 (ptp) REVERT: D 165 MET cc_start: 0.8461 (ttt) cc_final: 0.8058 (mtp) REVERT: E 30 GLN cc_start: 0.8957 (mt0) cc_final: 0.8569 (mp10) REVERT: E 49 ARG cc_start: 0.9238 (ttm-80) cc_final: 0.8936 (mtm110) REVERT: E 166 LYS cc_start: 0.9396 (mptt) cc_final: 0.9082 (mptt) REVERT: E 176 ASP cc_start: 0.8827 (m-30) cc_final: 0.8522 (m-30) REVERT: F 129 MET cc_start: 0.6592 (pmm) cc_final: 0.6238 (pmm) REVERT: F 135 ILE cc_start: 0.8812 (mm) cc_final: 0.8501 (mm) REVERT: F 172 PHE cc_start: 0.8467 (m-80) cc_final: 0.8219 (m-80) REVERT: F 174 PHE cc_start: 0.7243 (m-80) cc_final: 0.6955 (m-80) REVERT: G 18 ILE cc_start: 0.8621 (tt) cc_final: 0.8331 (mp) REVERT: G 41 GLU cc_start: 0.8463 (pp20) cc_final: 0.7849 (pp20) REVERT: G 68 ARG cc_start: 0.9334 (ttp80) cc_final: 0.8963 (ptm-80) REVERT: G 70 LEU cc_start: 0.9564 (pp) cc_final: 0.9305 (pp) REVERT: G 116 LEU cc_start: 0.9462 (mt) cc_final: 0.9185 (mp) REVERT: G 129 GLU cc_start: 0.9583 (mt-10) cc_final: 0.9178 (mm-30) REVERT: G 151 ARG cc_start: 0.9158 (mmm160) cc_final: 0.8908 (mmm160) REVERT: G 172 GLU cc_start: 0.8297 (mp0) cc_final: 0.8007 (mp0) REVERT: I 71 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8370 (pttp) REVERT: H 1 MET cc_start: 0.9016 (mmt) cc_final: 0.8563 (mmm) REVERT: H 3 VAL cc_start: 0.8565 (m) cc_final: 0.8346 (p) REVERT: H 70 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7140 (tp30) REVERT: J 14 ASP cc_start: 0.7872 (m-30) cc_final: 0.7656 (m-30) REVERT: J 52 ASP cc_start: 0.6041 (m-30) cc_final: 0.5813 (m-30) REVERT: J 53 TYR cc_start: 0.7477 (m-80) cc_final: 0.6814 (m-10) REVERT: J 74 TYR cc_start: 0.9068 (m-80) cc_final: 0.8488 (m-80) REVERT: J 89 PHE cc_start: 0.9509 (t80) cc_final: 0.9073 (t80) REVERT: J 108 MET cc_start: 0.7669 (mtm) cc_final: 0.6899 (mtm) REVERT: K 1 MET cc_start: 0.7557 (tpp) cc_final: 0.7077 (tpt) REVERT: K 8 LEU cc_start: 0.9200 (tp) cc_final: 0.8917 (tp) REVERT: K 13 ASN cc_start: 0.9036 (p0) cc_final: 0.8818 (p0) REVERT: K 20 MET cc_start: 0.8875 (mmp) cc_final: 0.8530 (mmm) REVERT: K 38 ILE cc_start: 0.8740 (tp) cc_final: 0.8514 (tp) REVERT: K 42 THR cc_start: 0.9768 (m) cc_final: 0.9103 (p) REVERT: K 44 LYS cc_start: 0.9214 (mmmt) cc_final: 0.8818 (mmtm) REVERT: K 110 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8851 (pm20) REVERT: L 30 THR cc_start: 0.9082 (p) cc_final: 0.8715 (t) REVERT: L 55 MET cc_start: 0.9130 (tpt) cc_final: 0.8860 (tpt) REVERT: L 73 ILE cc_start: 0.9538 (pt) cc_final: 0.9072 (pt) REVERT: L 106 GLU cc_start: 0.8991 (pt0) cc_final: 0.8399 (pm20) REVERT: L 107 PHE cc_start: 0.8457 (m-80) cc_final: 0.7920 (m-80) REVERT: M 12 MET cc_start: 0.9349 (tpt) cc_final: 0.9069 (tpp) REVERT: M 22 GLN cc_start: 0.7538 (tt0) cc_final: 0.7076 (tt0) REVERT: M 59 ARG cc_start: 0.9062 (mmp80) cc_final: 0.8833 (mmp80) REVERT: M 60 GLN cc_start: 0.9305 (mp10) cc_final: 0.9062 (tp40) REVERT: M 68 PHE cc_start: 0.9276 (t80) cc_final: 0.9074 (t80) REVERT: M 97 GLN cc_start: 0.9189 (mp10) cc_final: 0.8841 (mm110) REVERT: N 3 HIS cc_start: 0.8858 (m170) cc_final: 0.8068 (m170) REVERT: N 5 LYS cc_start: 0.8530 (mmmt) cc_final: 0.8150 (mmmt) REVERT: N 6 SER cc_start: 0.8470 (m) cc_final: 0.8263 (m) REVERT: N 16 HIS cc_start: 0.8394 (t-170) cc_final: 0.7992 (t70) REVERT: N 24 MET cc_start: 0.9506 (tpp) cc_final: 0.9125 (tpp) REVERT: N 46 ARG cc_start: 0.9279 (mtp85) cc_final: 0.8503 (mtt90) REVERT: N 110 MET cc_start: 0.8895 (mmp) cc_final: 0.8582 (mmm) REVERT: O 34 HIS cc_start: 0.8788 (m-70) cc_final: 0.8112 (m-70) REVERT: O 40 ILE cc_start: 0.7177 (mm) cc_final: 0.6965 (mm) REVERT: O 63 LYS cc_start: 0.8553 (pttp) cc_final: 0.7903 (mmpt) REVERT: P 2 ASN cc_start: 0.9315 (t0) cc_final: 0.8521 (m110) REVERT: P 55 HIS cc_start: 0.9386 (m-70) cc_final: 0.9037 (m-70) REVERT: P 64 SER cc_start: 0.9206 (m) cc_final: 0.8832 (t) REVERT: Q 2 ARG cc_start: 0.8458 (mtp180) cc_final: 0.8029 (mtm-85) REVERT: Q 14 LYS cc_start: 0.9472 (ttmt) cc_final: 0.9153 (mmtt) REVERT: Q 15 LYS cc_start: 0.9362 (ttpt) cc_final: 0.8842 (tptt) REVERT: Q 23 TYR cc_start: 0.9265 (m-80) cc_final: 0.8489 (m-80) REVERT: Q 60 TRP cc_start: 0.8753 (m-10) cc_final: 0.8426 (m-90) REVERT: R 5 PHE cc_start: 0.9606 (p90) cc_final: 0.9270 (p90) REVERT: R 40 MET cc_start: 0.8700 (tpt) cc_final: 0.8216 (tmm) REVERT: R 87 GLN cc_start: 0.9218 (pp30) cc_final: 0.8778 (pp30) REVERT: S 49 LYS cc_start: 0.9492 (ptmt) cc_final: 0.9107 (tptp) REVERT: S 86 MET cc_start: 0.8721 (tpt) cc_final: 0.8443 (tpp) REVERT: T 12 ARG cc_start: 0.9181 (mmm-85) cc_final: 0.7877 (mmm160) REVERT: T 24 MET cc_start: 0.9305 (mtm) cc_final: 0.9001 (mtt) REVERT: T 64 LYS cc_start: 0.9063 (mmmt) cc_final: 0.8589 (tmtt) REVERT: T 80 TRP cc_start: 0.8936 (p-90) cc_final: 0.7947 (p-90) REVERT: U 6 ARG cc_start: 0.8709 (mmm160) cc_final: 0.8234 (mmt90) REVERT: U 8 ASP cc_start: 0.7894 (m-30) cc_final: 0.7575 (m-30) REVERT: U 9 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8080 (tp30) REVERT: U 14 THR cc_start: 0.9024 (p) cc_final: 0.8691 (p) REVERT: U 68 ASN cc_start: 0.9100 (m-40) cc_final: 0.8848 (m-40) REVERT: V 5 ASN cc_start: 0.8151 (m-40) cc_final: 0.7561 (t0) REVERT: V 29 ILE cc_start: 0.8945 (pt) cc_final: 0.8593 (mm) REVERT: V 70 ILE cc_start: 0.8398 (mp) cc_final: 0.7983 (mp) REVERT: V 87 GLN cc_start: 0.9259 (mp-120) cc_final: 0.8584 (mp10) REVERT: V 91 PHE cc_start: 0.9050 (m-80) cc_final: 0.8833 (m-10) REVERT: W 21 ARG cc_start: 0.7421 (ptp90) cc_final: 0.7193 (ptp90) REVERT: W 46 ASN cc_start: 0.9157 (m-40) cc_final: 0.8785 (m-40) REVERT: W 58 LYS cc_start: 0.8572 (ptpt) cc_final: 0.7517 (mmmt) REVERT: W 62 LYS cc_start: 0.9399 (mppt) cc_final: 0.9186 (mmtm) REVERT: W 73 ARG cc_start: 0.9429 (mtt180) cc_final: 0.9066 (mtt180) REVERT: W 76 ILE cc_start: 0.9725 (mp) cc_final: 0.9447 (tp) REVERT: X 15 ASN cc_start: 0.8748 (m-40) cc_final: 0.7447 (p0) REVERT: X 28 PHE cc_start: 0.8764 (m-10) cc_final: 0.8459 (m-80) REVERT: X 48 LEU cc_start: 0.8912 (mt) cc_final: 0.8350 (tt) REVERT: X 64 ASP cc_start: 0.8943 (t0) cc_final: 0.8659 (t0) REVERT: X 71 ARG cc_start: 0.8783 (mpp-170) cc_final: 0.8373 (tpp-160) REVERT: Y 2 LYS cc_start: 0.8727 (ttpp) cc_final: 0.8489 (ptmm) REVERT: Z 39 ASP cc_start: 0.8951 (m-30) cc_final: 0.8626 (m-30) REVERT: Z 52 PHE cc_start: 0.8688 (p90) cc_final: 0.8430 (p90) REVERT: 0 3 GLN cc_start: 0.9025 (pm20) cc_final: 0.8629 (pm20) REVERT: 0 5 ASN cc_start: 0.9310 (m110) cc_final: 0.9068 (m-40) REVERT: 0 11 LYS cc_start: 0.9600 (ttpt) cc_final: 0.9262 (ptpt) REVERT: 0 14 MET cc_start: 0.8796 (tpt) cc_final: 0.8380 (tpp) REVERT: 0 16 ARG cc_start: 0.9184 (mtt90) cc_final: 0.8962 (mtt90) REVERT: 0 45 ASP cc_start: 0.9378 (p0) cc_final: 0.9127 (p0) REVERT: 0 47 TYR cc_start: 0.8487 (m-80) cc_final: 0.8163 (m-80) REVERT: 1 18 HIS cc_start: 0.8001 (t70) cc_final: 0.7600 (t70) REVERT: 1 20 TYR cc_start: 0.8855 (m-80) cc_final: 0.8573 (m-10) REVERT: 1 26 LYS cc_start: 0.8710 (tptt) cc_final: 0.8232 (tppt) REVERT: 1 32 LYS cc_start: 0.8103 (tmtt) cc_final: 0.7629 (tmtt) REVERT: 1 44 GLN cc_start: 0.9217 (pt0) cc_final: 0.8571 (tp40) REVERT: 1 52 LYS cc_start: 0.8649 (pttm) cc_final: 0.8177 (mmtm) REVERT: 2 22 MET cc_start: 0.9013 (tpp) cc_final: 0.8754 (tpp) REVERT: 3 25 HIS cc_start: 0.9595 (m90) cc_final: 0.9258 (m90) REVERT: 3 31 ILE cc_start: 0.9131 (mt) cc_final: 0.8629 (tt) REVERT: 3 42 HIS cc_start: 0.9347 (m90) cc_final: 0.8938 (m90) REVERT: 4 1 MET cc_start: 0.6606 (ptt) cc_final: 0.6254 (pmm) REVERT: 4 13 ASN cc_start: 0.9166 (t0) cc_final: 0.8747 (t0) REVERT: 4 37 GLN cc_start: 0.7588 (pm20) cc_final: 0.7249 (pm20) REVERT: 6 12 ILE cc_start: 0.9143 (pt) cc_final: 0.8740 (mp) outliers start: 1 outliers final: 0 residues processed: 1659 average time/residue: 1.3825 time to fit residues: 3900.8529 Evaluate side-chains 1372 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1372 time to evaluate : 5.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1095 random chunks: chunk 980 optimal weight: 30.0000 chunk 645 optimal weight: 30.0000 chunk 1039 optimal weight: 50.0000 chunk 634 optimal weight: 30.0000 chunk 493 optimal weight: 40.0000 chunk 722 optimal weight: 20.0000 chunk 1090 optimal weight: 0.0670 chunk 1004 optimal weight: 7.9990 chunk 868 optimal weight: 0.0570 chunk 90 optimal weight: 20.0000 chunk 670 optimal weight: 30.0000 overall best weight: 9.6246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 20 ASN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 34 GLN ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 68 HIS ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 18 GLN ** z 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 420 GLN z 474 HIS C 57 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 165989 Z= 0.236 Angle : 0.729 17.596 247857 Z= 0.386 Chirality : 0.036 0.428 31480 Planarity : 0.007 0.123 13686 Dihedral : 24.032 179.845 81771 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 31.17 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.14 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.10), residues: 6329 helix: -0.94 (0.11), residues: 2012 sheet: -1.51 (0.15), residues: 1058 loop : -1.73 (0.10), residues: 3259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP z 385 HIS 0.011 0.002 HIS b 38 PHE 0.029 0.003 PHE g 25 TYR 0.037 0.002 TYR o 77 ARG 0.016 0.001 ARG p 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12658 Ramachandran restraints generated. 6329 Oldfield, 0 Emsley, 6329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1653 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1653 time to evaluate : 6.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 15 PHE cc_start: 0.8720 (p90) cc_final: 0.8316 (p90) REVERT: b 29 PHE cc_start: 0.8934 (m-10) cc_final: 0.8657 (m-10) REVERT: b 41 ASN cc_start: 0.9569 (t0) cc_final: 0.9294 (t0) REVERT: b 73 ARG cc_start: 0.8515 (ttm170) cc_final: 0.8116 (mpt180) REVERT: b 90 PHE cc_start: 0.9376 (p90) cc_final: 0.9041 (p90) REVERT: b 136 ARG cc_start: 0.8478 (mtm180) cc_final: 0.8144 (ptt180) REVERT: b 137 THR cc_start: 0.8523 (m) cc_final: 0.8186 (p) REVERT: b 153 MET cc_start: 0.8448 (ppp) cc_final: 0.7982 (ppp) REVERT: c 5 HIS cc_start: 0.8402 (t70) cc_final: 0.7945 (t70) REVERT: c 22 PHE cc_start: 0.8207 (t80) cc_final: 0.7987 (t80) REVERT: c 68 HIS cc_start: 0.8872 (m-70) cc_final: 0.8569 (m90) REVERT: c 106 ARG cc_start: 0.8264 (tpp-160) cc_final: 0.8061 (tmt-80) REVERT: c 171 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7886 (mtp85) REVERT: c 183 TYR cc_start: 0.8435 (t80) cc_final: 0.7932 (t80) REVERT: c 190 THR cc_start: 0.8593 (m) cc_final: 0.8303 (p) REVERT: c 200 TRP cc_start: 0.8162 (m-90) cc_final: 0.7692 (m-90) REVERT: d 3 TYR cc_start: 0.9296 (t80) cc_final: 0.8694 (t80) REVERT: d 50 TYR cc_start: 0.9321 (t80) cc_final: 0.9105 (t80) REVERT: d 99 ASN cc_start: 0.9153 (t0) cc_final: 0.8827 (t0) REVERT: d 109 THR cc_start: 0.7104 (p) cc_final: 0.6315 (p) REVERT: d 112 GLU cc_start: 0.9314 (tm-30) cc_final: 0.7938 (mt-10) REVERT: d 130 ASN cc_start: 0.6225 (t0) cc_final: 0.5848 (m110) REVERT: d 134 TYR cc_start: 0.8585 (t80) cc_final: 0.8321 (t80) REVERT: d 153 ARG cc_start: 0.8583 (ttm170) cc_final: 0.7301 (ttm170) REVERT: d 183 ARG cc_start: 0.9469 (mmm160) cc_final: 0.9072 (mmm160) REVERT: e 68 ARG cc_start: 0.9229 (ttm110) cc_final: 0.9020 (mmm160) REVERT: e 92 ARG cc_start: 0.9511 (mmm160) cc_final: 0.8978 (mmm-85) REVERT: e 127 TYR cc_start: 0.7413 (m-10) cc_final: 0.6358 (m-80) REVERT: f 5 GLU cc_start: 0.8850 (tt0) cc_final: 0.8480 (mp0) REVERT: f 49 TYR cc_start: 0.8442 (p90) cc_final: 0.8220 (p90) REVERT: f 80 PHE cc_start: 0.9222 (m-10) cc_final: 0.8903 (m-80) REVERT: g 35 LYS cc_start: 0.8819 (ttpt) cc_final: 0.8293 (pttm) REVERT: g 57 GLU cc_start: 0.8262 (pm20) cc_final: 0.7887 (pp20) REVERT: g 89 GLU cc_start: 0.9462 (mp0) cc_final: 0.9246 (mm-30) REVERT: g 103 ILE cc_start: 0.8814 (tp) cc_final: 0.8559 (pt) REVERT: h 8 ASP cc_start: 0.9485 (m-30) cc_final: 0.9224 (m-30) REVERT: h 109 VAL cc_start: 0.9616 (t) cc_final: 0.9401 (p) REVERT: i 24 ASN cc_start: 0.8238 (t0) cc_final: 0.8035 (t0) REVERT: j 35 GLN cc_start: 0.7522 (tt0) cc_final: 0.7299 (tt0) REVERT: j 59 LYS cc_start: 0.7071 (pptt) cc_final: 0.6752 (pptt) REVERT: j 63 ASP cc_start: 0.9283 (t0) cc_final: 0.8743 (t0) REVERT: j 64 GLN cc_start: 0.9569 (mm-40) cc_final: 0.9291 (mt0) REVERT: j 65 TYR cc_start: 0.8072 (m-80) cc_final: 0.7602 (m-80) REVERT: j 99 GLN cc_start: 0.8937 (mm110) cc_final: 0.8507 (mp10) REVERT: l 48 LEU cc_start: 0.8041 (tp) cc_final: 0.7839 (tp) REVERT: l 52 CYS cc_start: 0.9499 (p) cc_final: 0.8722 (t) REVERT: m 11 HIS cc_start: 0.9132 (m90) cc_final: 0.8819 (m90) REVERT: m 22 TYR cc_start: 0.8853 (t80) cc_final: 0.8050 (t80) REVERT: m 70 ARG cc_start: 0.9200 (pmt-80) cc_final: 0.8924 (pmt-80) REVERT: m 74 MET cc_start: 0.9620 (ptp) cc_final: 0.9357 (mpp) REVERT: n 64 ARG cc_start: 0.9419 (mtt180) cc_final: 0.9104 (mmm160) REVERT: n 70 HIS cc_start: 0.8877 (m170) cc_final: 0.8595 (m170) REVERT: p 5 ARG cc_start: 0.6653 (ptt180) cc_final: 0.6101 (ptt180) REVERT: p 21 VAL cc_start: 0.8145 (t) cc_final: 0.7805 (t) REVERT: p 34 GLU cc_start: 0.8836 (pm20) cc_final: 0.8415 (pm20) REVERT: p 39 PHE cc_start: 0.9226 (t80) cc_final: 0.8919 (t80) REVERT: p 79 ASN cc_start: 0.8748 (m110) cc_final: 0.8449 (t0) REVERT: q 16 MET cc_start: 0.7771 (mmm) cc_final: 0.7043 (mmm) REVERT: q 32 ILE cc_start: 0.8388 (tt) cc_final: 0.8187 (tt) REVERT: q 80 LYS cc_start: 0.8197 (mttm) cc_final: 0.7720 (tppt) REVERT: r 73 HIS cc_start: 0.9050 (m-70) cc_final: 0.8803 (m-70) REVERT: s 20 LYS cc_start: 0.9212 (mmmt) cc_final: 0.8894 (mmmt) REVERT: s 27 LYS cc_start: 0.7808 (mtmm) cc_final: 0.7159 (tppt) REVERT: s 68 HIS cc_start: 0.9027 (m90) cc_final: 0.8792 (m-70) REVERT: t 12 GLN cc_start: 0.9594 (pt0) cc_final: 0.9355 (pt0) REVERT: t 47 GLN cc_start: 0.9598 (mt0) cc_final: 0.9371 (mp10) REVERT: u 6 ARG cc_start: 0.8309 (tpt90) cc_final: 0.7619 (ttt180) REVERT: u 12 ASP cc_start: 0.8674 (p0) cc_final: 0.8290 (p0) REVERT: u 30 GLU cc_start: 0.7800 (pm20) cc_final: 0.7340 (pm20) REVERT: u 53 LYS cc_start: 0.9310 (mptt) cc_final: 0.9053 (pttt) REVERT: z 36 MET cc_start: 0.6146 (tpt) cc_final: 0.5893 (tpt) REVERT: z 68 MET cc_start: 0.6024 (ptp) cc_final: 0.5811 (ptp) REVERT: z 89 MET cc_start: 0.7767 (tpt) cc_final: 0.7374 (ttm) REVERT: z 127 ARG cc_start: 0.6759 (mtt180) cc_final: 0.6411 (ttp80) REVERT: z 265 PHE cc_start: 0.8233 (p90) cc_final: 0.7990 (m-80) REVERT: z 465 MET cc_start: 0.8142 (mmp) cc_final: 0.7878 (mmm) REVERT: z 510 ARG cc_start: 0.7383 (tpp-160) cc_final: 0.7066 (tpp-160) REVERT: z 514 LYS cc_start: 0.3749 (mttt) cc_final: 0.3156 (pttp) REVERT: z 562 GLN cc_start: 0.7992 (mp10) cc_final: 0.7729 (mp10) REVERT: C 131 MET cc_start: 0.9277 (mmp) cc_final: 0.8761 (mmm) REVERT: C 160 TYR cc_start: 0.8075 (p90) cc_final: 0.7870 (p90) REVERT: C 200 MET cc_start: 0.8575 (ptm) cc_final: 0.7727 (ptm) REVERT: D 36 GLN cc_start: 0.9036 (mt0) cc_final: 0.8348 (mm-40) REVERT: D 67 HIS cc_start: 0.8774 (t-90) cc_final: 0.8418 (t-90) REVERT: D 82 PHE cc_start: 0.6712 (t80) cc_final: 0.6082 (t80) REVERT: D 126 ASN cc_start: 0.9365 (t0) cc_final: 0.9051 (t0) REVERT: D 161 MET cc_start: 0.7980 (ptp) cc_final: 0.7514 (ptp) REVERT: E 30 GLN cc_start: 0.8960 (mt0) cc_final: 0.8574 (mp10) REVERT: E 88 ARG cc_start: 0.9223 (mpp80) cc_final: 0.8559 (mpp80) REVERT: E 166 LYS cc_start: 0.9359 (mptt) cc_final: 0.9007 (mptt) REVERT: E 176 ASP cc_start: 0.8877 (m-30) cc_final: 0.8579 (m-30) REVERT: F 78 ILE cc_start: 0.8880 (pt) cc_final: 0.8202 (tp) REVERT: F 129 MET cc_start: 0.6178 (pmm) cc_final: 0.5887 (pmm) REVERT: F 135 ILE cc_start: 0.8765 (mm) cc_final: 0.8551 (mt) REVERT: F 172 PHE cc_start: 0.8449 (m-80) cc_final: 0.8201 (m-80) REVERT: F 174 PHE cc_start: 0.7619 (m-80) cc_final: 0.7318 (m-80) REVERT: G 18 ILE cc_start: 0.8612 (tt) cc_final: 0.8325 (mp) REVERT: G 41 GLU cc_start: 0.8606 (pp20) cc_final: 0.7925 (pp20) REVERT: G 68 ARG cc_start: 0.9373 (ttp80) cc_final: 0.8820 (ptm-80) REVERT: G 86 LEU cc_start: 0.9016 (mp) cc_final: 0.7875 (mp) REVERT: G 116 LEU cc_start: 0.9439 (mt) cc_final: 0.9162 (mp) REVERT: G 129 GLU cc_start: 0.9602 (mt-10) cc_final: 0.9215 (mm-30) REVERT: G 136 ASP cc_start: 0.9311 (t0) cc_final: 0.9069 (t0) REVERT: G 151 ARG cc_start: 0.9188 (mmm160) cc_final: 0.8947 (mmm160) REVERT: G 172 GLU cc_start: 0.8268 (mp0) cc_final: 0.7972 (mp0) REVERT: I 71 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8354 (pttp) REVERT: H 1 MET cc_start: 0.9010 (mmt) cc_final: 0.8533 (mmm) REVERT: H 3 VAL cc_start: 0.8759 (m) cc_final: 0.8537 (p) REVERT: H 70 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7193 (tp30) REVERT: J 14 ASP cc_start: 0.7841 (m-30) cc_final: 0.7610 (m-30) REVERT: J 52 ASP cc_start: 0.6002 (m-30) cc_final: 0.5754 (m-30) REVERT: J 53 TYR cc_start: 0.7505 (m-80) cc_final: 0.6732 (m-10) REVERT: J 74 TYR cc_start: 0.9051 (m-80) cc_final: 0.8450 (m-80) REVERT: J 89 PHE cc_start: 0.9488 (t80) cc_final: 0.9093 (t80) REVERT: J 108 MET cc_start: 0.7640 (mtm) cc_final: 0.6895 (mtm) REVERT: K 1 MET cc_start: 0.7276 (tpp) cc_final: 0.5293 (tmm) REVERT: K 3 GLN cc_start: 0.8516 (mt0) cc_final: 0.8199 (mp10) REVERT: K 8 LEU cc_start: 0.9253 (tp) cc_final: 0.8942 (tp) REVERT: K 13 ASN cc_start: 0.9038 (p0) cc_final: 0.8822 (p0) REVERT: K 38 ILE cc_start: 0.8625 (tp) cc_final: 0.8374 (tp) REVERT: K 42 THR cc_start: 0.9755 (m) cc_final: 0.9279 (m) REVERT: K 44 LYS cc_start: 0.9229 (mmmt) cc_final: 0.8820 (mmtm) REVERT: K 71 ARG cc_start: 0.9000 (mmp80) cc_final: 0.8782 (mmp80) REVERT: K 80 ASP cc_start: 0.9406 (p0) cc_final: 0.8736 (p0) REVERT: K 110 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8867 (pm20) REVERT: L 30 THR cc_start: 0.9028 (p) cc_final: 0.8653 (t) REVERT: L 55 MET cc_start: 0.9118 (tpt) cc_final: 0.8822 (tpt) REVERT: L 103 ILE cc_start: 0.9245 (pt) cc_final: 0.8973 (mm) REVERT: M 12 MET cc_start: 0.9251 (tpt) cc_final: 0.8989 (tpp) REVERT: M 22 GLN cc_start: 0.7746 (tt0) cc_final: 0.7275 (tt0) REVERT: M 36 VAL cc_start: 0.8892 (p) cc_final: 0.8623 (p) REVERT: M 57 VAL cc_start: 0.8050 (p) cc_final: 0.7553 (p) REVERT: M 59 ARG cc_start: 0.9069 (mmp80) cc_final: 0.8812 (mmp80) REVERT: M 68 PHE cc_start: 0.9300 (t80) cc_final: 0.9098 (t80) REVERT: M 97 GLN cc_start: 0.9233 (mp10) cc_final: 0.8929 (mm110) REVERT: N 3 HIS cc_start: 0.8800 (m170) cc_final: 0.8042 (m170) REVERT: N 5 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8153 (mmmt) REVERT: N 16 HIS cc_start: 0.8717 (t-170) cc_final: 0.8271 (t70) REVERT: N 24 MET cc_start: 0.9483 (tpp) cc_final: 0.9123 (tpp) REVERT: N 46 ARG cc_start: 0.9238 (mtp85) cc_final: 0.8456 (mtt90) REVERT: N 79 LEU cc_start: 0.9510 (mp) cc_final: 0.9304 (mp) REVERT: N 110 MET cc_start: 0.8741 (mmp) cc_final: 0.8457 (mmm) REVERT: O 34 HIS cc_start: 0.8799 (m-70) cc_final: 0.8061 (m-70) REVERT: O 40 ILE cc_start: 0.7254 (mm) cc_final: 0.7029 (mm) REVERT: O 63 LYS cc_start: 0.8563 (pttp) cc_final: 0.7940 (mmpt) REVERT: P 2 ASN cc_start: 0.9344 (t0) cc_final: 0.8723 (m110) REVERT: P 3 ILE cc_start: 0.8936 (tp) cc_final: 0.8575 (tp) REVERT: P 6 GLN cc_start: 0.9475 (pt0) cc_final: 0.9233 (pp30) REVERT: P 7 LEU cc_start: 0.8851 (pp) cc_final: 0.8565 (pp) REVERT: P 55 HIS cc_start: 0.9377 (m-70) cc_final: 0.9049 (m-70) REVERT: P 64 SER cc_start: 0.9260 (m) cc_final: 0.8984 (t) REVERT: Q 2 ARG cc_start: 0.8432 (mtp180) cc_final: 0.8003 (mtm-85) REVERT: Q 14 LYS cc_start: 0.9452 (ttmt) cc_final: 0.9116 (mmtt) REVERT: Q 15 LYS cc_start: 0.9376 (ttpt) cc_final: 0.8880 (tptt) REVERT: Q 23 TYR cc_start: 0.9265 (m-80) cc_final: 0.8911 (m-80) REVERT: Q 56 PHE cc_start: 0.8817 (m-10) cc_final: 0.8119 (m-80) REVERT: Q 60 TRP cc_start: 0.8770 (m-10) cc_final: 0.8449 (m-90) REVERT: R 5 PHE cc_start: 0.9600 (p90) cc_final: 0.9228 (p90) REVERT: R 12 HIS cc_start: 0.9123 (m-70) cc_final: 0.8847 (m-70) REVERT: R 40 MET cc_start: 0.8715 (tpt) cc_final: 0.8273 (tmm) REVERT: R 74 ILE cc_start: 0.9305 (mm) cc_final: 0.9101 (mm) REVERT: R 87 GLN cc_start: 0.9161 (pp30) cc_final: 0.8742 (pp30) REVERT: S 49 LYS cc_start: 0.9490 (ptmt) cc_final: 0.9107 (tptp) REVERT: S 86 MET cc_start: 0.8775 (tpt) cc_final: 0.8484 (tpp) REVERT: T 6 ARG cc_start: 0.9520 (tpm170) cc_final: 0.9232 (tpm170) REVERT: T 12 ARG cc_start: 0.9164 (mmm-85) cc_final: 0.7779 (mmm160) REVERT: T 24 MET cc_start: 0.9277 (mtm) cc_final: 0.8896 (mtp) REVERT: T 25 GLU cc_start: 0.8821 (mp0) cc_final: 0.8616 (mp0) REVERT: T 64 LYS cc_start: 0.8924 (mmmt) cc_final: 0.8484 (tmtt) REVERT: T 80 TRP cc_start: 0.8958 (p-90) cc_final: 0.8041 (p-90) REVERT: U 6 ARG cc_start: 0.8681 (mmm160) cc_final: 0.8190 (mmt90) REVERT: U 8 ASP cc_start: 0.7757 (m-30) cc_final: 0.7447 (m-30) REVERT: U 9 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8072 (tp30) REVERT: U 68 ASN cc_start: 0.9084 (m-40) cc_final: 0.8800 (m-40) REVERT: V 5 ASN cc_start: 0.8178 (m-40) cc_final: 0.7488 (t0) REVERT: V 29 ILE cc_start: 0.8905 (pt) cc_final: 0.8604 (mm) REVERT: V 44 HIS cc_start: 0.8384 (t-90) cc_final: 0.7975 (t70) REVERT: V 82 TYR cc_start: 0.9680 (p90) cc_final: 0.9471 (p90) REVERT: V 87 GLN cc_start: 0.9290 (mp-120) cc_final: 0.8608 (mp10) REVERT: W 21 ARG cc_start: 0.7922 (ptp90) cc_final: 0.7659 (ptp90) REVERT: W 53 HIS cc_start: 0.8906 (m90) cc_final: 0.8280 (m-70) REVERT: W 62 LYS cc_start: 0.9429 (mppt) cc_final: 0.9226 (mmtm) REVERT: W 76 ILE cc_start: 0.9701 (mp) cc_final: 0.9478 (tp) REVERT: X 48 LEU cc_start: 0.8954 (mt) cc_final: 0.8648 (tt) REVERT: X 64 ASP cc_start: 0.9032 (t0) cc_final: 0.8794 (t0) REVERT: X 71 ARG cc_start: 0.8776 (mpp-170) cc_final: 0.8393 (tpp-160) REVERT: Y 1 MET cc_start: 0.7704 (mmp) cc_final: 0.7498 (mmm) REVERT: Y 2 LYS cc_start: 0.8657 (ttpp) cc_final: 0.8141 (ptmm) REVERT: Z 39 ASP cc_start: 0.9026 (m-30) cc_final: 0.8757 (m-30) REVERT: 0 3 GLN cc_start: 0.8937 (pm20) cc_final: 0.8591 (pm20) REVERT: 0 11 LYS cc_start: 0.9605 (ttpt) cc_final: 0.9261 (ptpt) REVERT: 0 14 MET cc_start: 0.8824 (tpt) cc_final: 0.8394 (tpp) REVERT: 0 16 ARG cc_start: 0.9220 (mtt90) cc_final: 0.8972 (mtt90) REVERT: 0 51 ARG cc_start: 0.8948 (mpp-170) cc_final: 0.8548 (mpp80) REVERT: 1 18 HIS cc_start: 0.7969 (t70) cc_final: 0.7566 (t70) REVERT: 1 20 TYR cc_start: 0.8860 (m-80) cc_final: 0.8574 (m-10) REVERT: 1 26 LYS cc_start: 0.8685 (tptt) cc_final: 0.8183 (tppt) REVERT: 1 32 LYS cc_start: 0.8087 (tmtt) cc_final: 0.7612 (tmtt) REVERT: 1 44 GLN cc_start: 0.9224 (pt0) cc_final: 0.8554 (tp40) REVERT: 1 52 LYS cc_start: 0.8567 (pttm) cc_final: 0.8211 (mmtm) REVERT: 2 22 MET cc_start: 0.9053 (tpp) cc_final: 0.8817 (tpp) REVERT: 3 3 ILE cc_start: 0.6709 (mm) cc_final: 0.6509 (mm) REVERT: 3 25 HIS cc_start: 0.9579 (m90) cc_final: 0.9252 (m90) REVERT: 3 31 ILE cc_start: 0.9143 (mt) cc_final: 0.8640 (tt) REVERT: 3 42 HIS cc_start: 0.9338 (m90) cc_final: 0.8935 (m90) REVERT: 4 13 ASN cc_start: 0.9217 (t0) cc_final: 0.8792 (t0) REVERT: 4 18 LYS cc_start: 0.9268 (tmtt) cc_final: 0.9067 (tmtt) REVERT: 6 12 ILE cc_start: 0.9075 (pt) cc_final: 0.8679 (mp) REVERT: 6 64 PHE cc_start: 0.6989 (t80) cc_final: 0.6540 (t80) outliers start: 0 outliers final: 0 residues processed: 1653 average time/residue: 1.4903 time to fit residues: 4226.2388 Evaluate side-chains 1377 residues out of total 5252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1377 time to evaluate : 6.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1095 random chunks: chunk 532 optimal weight: 30.0000 chunk 690 optimal weight: 30.0000 chunk 925 optimal weight: 6.9990 chunk 266 optimal weight: 9.9990 chunk 800 optimal weight: 30.0000 chunk 128 optimal weight: 50.0000 chunk 241 optimal weight: 6.9990 chunk 870 optimal weight: 6.9990 chunk 364 optimal weight: 7.9990 chunk 893 optimal weight: 40.0000 chunk 110 optimal weight: 40.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN h 17 GLN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 34 GLN ** o 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 51 GLN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 18 GLN ** z 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 420 GLN C 57 HIS ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.062936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.052911 restraints weight = 1050868.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.054798 restraints weight = 445601.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.055918 restraints weight = 239398.399| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 165989 Z= 0.210 Angle : 0.703 16.998 247857 Z= 0.373 Chirality : 0.035 0.423 31480 Planarity : 0.007 0.123 13686 Dihedral : 23.990 179.448 81771 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 29.22 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.28 % Favored : 91.42 % Rotamer: Outliers : 0.02 % Allowed : 0.36 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.10), residues: 6329 helix: -0.84 (0.11), residues: 1995 sheet: -1.48 (0.15), residues: 1060 loop : -1.70 (0.10), residues: 3274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP z 385 HIS 0.014 0.002 HIS J 47 PHE 0.036 0.002 PHE f 78 TYR 0.030 0.002 TYR o 77 ARG 0.037 0.001 ARG K 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 54498.77 seconds wall clock time: 947 minutes 51.80 seconds (56871.80 seconds total)