Starting phenix.real_space_refine on Sun Mar 24 12:25:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lze_4125/03_2024/5lze_4125_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lze_4125/03_2024/5lze_4125.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lze_4125/03_2024/5lze_4125_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lze_4125/03_2024/5lze_4125_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lze_4125/03_2024/5lze_4125_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lze_4125/03_2024/5lze_4125.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lze_4125/03_2024/5lze_4125.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lze_4125/03_2024/5lze_4125_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lze_4125/03_2024/5lze_4125_updated.pdb" } resolution = 3.5 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= 0.015 sd= 0.273 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4782 5.49 5 S 151 5.16 5 C 74201 2.51 5 N 27541 2.21 5 O 41341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 107": "NH1" <-> "NH2" Residue "b PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 125": "NH1" <-> "NH2" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 135": "NH1" <-> "NH2" Residue "d PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "k TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "n TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "q PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "I PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 60": "NH1" <-> "NH2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" 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 TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 75": "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 "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 39": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 43": "NH1" <-> "NH2" 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 PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 31": "OD1" <-> "OD2" Residue "6 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 148018 Number of models: 1 Model: "" Number of chains: 59 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': 107, 'rna2p_pyr': 68, 'rna3p': 10, 'rna3p_pur': 761, 'rna3p_pyr': 592} Link IDs: {'rna2p': 175, 'rna3p': 1363} 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: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p': 3, 'rna3p_pur': 35, 'rna3p_pyr': 32} Link IDs: {'rna2p': 6, 'rna3p': 70} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 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': 5, 'rna2p_pyr': 5, 'rna3p_pur': 20, 'rna3p_pyr': 18} Link IDs: {'rna2p': 9, 'rna3p': 38} 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': 11, 'rna3p': 3, 'rna3p_pur': 38, 'rna3p_pyr': 35} Link IDs: {'rna2p': 18, 'rna3p': 76} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 62274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2900, 62274 Classifications: {'RNA': 2900} Modifications used: {'p5*END': 1, 'rna2p': 7, 'rna2p_pur': 224, 'rna2p_pyr': 108, 'rna3p': 17, 'rna3p_pur': 1442, 'rna3p_pyr': 1102} Link IDs: {'rna2p': 339, 'rna3p': 2560} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen planarities: 1 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': 6, 'rna2p_pyr': 3, 'rna3p_pur': 58, 'rna3p_pyr': 53} Link IDs: {'rna2p': 9, 'rna3p': 110} 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: "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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A10G7 SG CYS 4 14 179.530 99.361 136.236 1.00114.73 S ATOM A10P5 SG CYS 6 16 114.070 107.170 228.386 1.00194.30 S ATOM A10TF SG CYS 6 37 117.340 107.398 226.831 1.00148.41 S ATOM A10U0 SG CYS 6 40 115.831 103.808 225.331 1.00193.31 S Time building chain proxies: 54.27, per 1000 atoms: 0.37 Number of scatterers: 148018 At special positions: 0 Unit cell: (237.8, 265.64, 248.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 151 16.00 P 4782 15.00 O 41341 8.00 N 27541 7.00 C 74201 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=0, symmetry=0 Time building additional restraints: 60.86 Conformation dependent library (CDL) restraints added in 6.5 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 40 " pdb="ZN ZN 6 100 " - pdb=" SG CYS 6 16 " pdb="ZN ZN 6 100 " - pdb=" SG CYS 6 37 " 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10684 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: 176 helices and 66 sheets defined 38.1% alpha, 17.5% beta 1558 base pairs and 2451 stacking pairs defined. Time for finding SS restraints: 69.84 Creating SS restraints... Processing helix chain 'b' and resid 42 through 63 Proline residue: b 47 - end of helix removed outlier: 3.602A pdb=" N LYS b 63 " --> pdb=" O ILE b 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 87 removed outlier: 4.758A pdb=" N GLU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER b 85 " --> pdb=" O ASP b 81 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N CYS b 86 " --> pdb=" O ALA b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 3.663A pdb=" N THR b 118 " --> pdb=" O LYS b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 128 removed outlier: 4.440A pdb=" N LYS b 127 " --> pdb=" O GLY b 123 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 Processing helix chain 'b' and resid 164 through 169 removed outlier: 4.011A pdb=" N GLU b 168 " --> pdb=" O ASP b 164 " (cutoff:3.500A) removed outlier: 4.054A 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: 3.866A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY b 179 " --> pdb=" O ALA b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 191 through 196 removed outlier: 4.433A pdb=" N VAL b 195 " --> pdb=" O ASP b 191 " (cutoff:3.500A) removed outlier: 4.739A 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 225 removed outlier: 3.710A pdb=" N ARG b 221 " --> pdb=" O ALA b 217 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU b 222 " --> pdb=" O ALA b 218 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 11 removed outlier: 3.821A pdb=" N ILE c 9 " --> pdb=" O HIS c 5 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 47 removed outlier: 4.132A pdb=" N ALA c 29 " --> pdb=" O THR c 25 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASP c 30 " --> pdb=" O LYS c 26 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.599A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.725A pdb=" N LYS c 85 " --> pdb=" O GLU c 81 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY c 95 " --> pdb=" O ALA c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 removed outlier: 3.777A pdb=" N ASP c 111 " --> pdb=" O LYS c 107 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ALA c 112 " --> pdb=" O PRO c 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 107 through 112' Processing helix chain 'c' and resid 113 through 126 Processing helix chain 'c' and resid 128 through 144 Processing helix chain 'd' and resid 6 through 15 removed outlier: 3.972A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 3.884A 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: 3.664A pdb=" N ARG d 80 " --> pdb=" O LYS d 76 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU d 81 " --> pdb=" O GLU d 77 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 removed outlier: 3.666A pdb=" N ARG d 96 " --> pdb=" O LEU d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 105 Processing helix chain 'd' and resid 109 through 120 removed outlier: 4.318A pdb=" N HIS d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) Processing helix chain 'd' and resid 151 through 165 removed outlier: 6.351A pdb=" N LYS d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU d 159 " --> pdb=" O LYS d 155 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU d 160 " --> pdb=" O ALA d 156 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLU d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 191 removed outlier: 3.947A pdb=" N SER d 191 " --> pdb=" O ARG d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 205 removed outlier: 4.342A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.609A pdb=" N GLN e 60 " --> pdb=" O PRO e 56 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 5.826A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 removed outlier: 3.735A pdb=" N ARG e 137 " --> pdb=" O ILE e 133 " (cutoff:3.500A) removed outlier: 4.019A 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 Processing helix chain 'f' and resid 11 through 19 removed outlier: 3.722A pdb=" N SER f 15 " --> pdb=" O HIS f 11 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLU f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLN f 17 " --> pdb=" O ASP f 13 " (cutoff:3.500A) Proline residue: f 19 - end of helix Processing helix chain 'f' and resid 20 through 33 Processing helix chain 'f' and resid 67 through 81 Processing helix chain 'g' and resid 19 through 30 removed outlier: 3.844A pdb=" N LEU g 29 " --> pdb=" O PHE g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 54 removed outlier: 3.539A pdb=" N GLN g 51 " --> pdb=" O GLU g 47 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG g 52 " --> pdb=" O THR g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 69 removed outlier: 3.697A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 111 removed outlier: 3.925A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS g 109 " --> pdb=" O GLU g 105 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 5.631A 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 removed outlier: 3.854A pdb=" N GLU g 145 " --> pdb=" O HIS g 141 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA g 146 " --> pdb=" O ARG g 142 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN g 147 " --> pdb=" O MET g 143 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYS g 148 " --> pdb=" O ALA g 144 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 111 through 119 Processing helix chain 'i' and resid 33 through 38 Processing helix chain 'i' and resid 45 through 55 Proline residue: i 50 - end of helix removed outlier: 3.664A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP i 55 " --> pdb=" O LEU i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 87 removed outlier: 4.679A pdb=" N MET i 87 " --> pdb=" O THR i 83 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 98 removed outlier: 4.997A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.326A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA j 21 " --> pdb=" O LEU j 17 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.971A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 4.247A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 74 removed outlier: 3.615A pdb=" N ASP k 71 " --> pdb=" O GLU k 67 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL k 73 " --> pdb=" O CYS k 69 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS k 74 " --> pdb=" O ALA k 70 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 103 removed outlier: 4.183A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG k 97 " --> pdb=" O GLU k 93 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA k 98 " --> pdb=" O SER k 94 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU k 99 " --> pdb=" O THR k 95 " (cutoff:3.500A) removed outlier: 3.507A 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: 4.897A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY l 117 " --> pdb=" O ARG l 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 112 through 117' Processing helix chain 'm' and resid 13 through 21 removed outlier: 3.812A pdb=" N SER m 20 " --> pdb=" O ILE m 16 " (cutoff:3.500A) removed outlier: 4.858A 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 48 through 63 removed outlier: 3.779A pdb=" N ASP m 57 " --> pdb=" O ASP m 53 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 removed outlier: 3.555A pdb=" N GLY m 83 " --> pdb=" O LEU m 79 " (cutoff:3.500A) Processing helix chain 'm' and resid 84 through 93 Processing helix chain 'm' and resid 105 through 110 Processing helix chain 'n' and resid 2 through 20 Processing helix chain 'n' and resid 23 through 29 removed outlier: 4.914A pdb=" N LYS n 27 " --> pdb=" O ARG n 23 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 50 removed outlier: 3.658A pdb=" N TRP n 41 " --> pdb=" O ASP n 37 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR n 49 " --> pdb=" O LEU n 45 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU n 50 " --> pdb=" O LYS n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 79 through 90 removed outlier: 3.743A pdb=" N ARG n 89 " --> pdb=" O GLU n 85 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 15 Processing helix chain 'o' and resid 23 through 43 removed outlier: 4.171A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 removed outlier: 3.577A pdb=" N MET o 58 " --> pdb=" O GLY o 54 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 85 removed outlier: 3.589A pdb=" N GLN o 79 " --> pdb=" O ALA o 75 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.790A pdb=" N ILE p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 79 removed outlier: 5.064A pdb=" N ASN p 79 " --> pdb=" O ILE p 75 " (cutoff:3.500A) Processing helix chain 'r' and resid 11 through 16 removed outlier: 6.237A pdb=" N GLU r 15 " --> pdb=" O ARG r 11 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 33 removed outlier: 5.157A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N THR r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 removed outlier: 3.783A 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: 4.369A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 3.592A 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: 4.720A pdb=" N ALA t 10 " --> pdb=" O ALA t 6 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS t 15 " --> pdb=" O ILE t 11 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) Processing helix chain 't' and resid 42 through 64 Proline residue: t 55 - end of helix Processing helix chain 't' and resid 67 through 86 Processing helix chain 'u' and resid 16 through 23 removed outlier: 4.346A pdb=" N ARG u 20 " --> pdb=" O ARG u 16 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N CYS u 22 " --> pdb=" O PHE u 18 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU u 23 " --> pdb=" O LYS u 19 " (cutoff:3.500A) Processing helix chain 'u' and resid 24 through 34 removed outlier: 4.381A pdb=" N LEU u 28 " --> pdb=" O LYS u 24 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ARG u 33 " --> pdb=" O ALA u 29 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ARG u 34 " --> pdb=" O GLU u 30 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 62 removed outlier: 4.176A pdb=" N THR u 42 " --> pdb=" O GLU u 38 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU u 62 " --> pdb=" O LYS u 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 16 removed outlier: 7.157A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL C 16 " --> pdb=" O ARG C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 4.710A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLU C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 29 through 34' Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.690A 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: 4.348A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.602A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.088A 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: 5.625A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.411A 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 'D' and resid 61 through 72 removed outlier: 3.765A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.230A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.529A pdb=" N VAL E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 removed outlier: 4.115A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 3.724A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 189 through 201 removed outlier: 3.719A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 19 removed outlier: 4.411A pdb=" N ASP F 5 " --> pdb=" O ALA F 1 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR F 6 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL F 11 " --> pdb=" O TYR F 7 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 Processing helix chain 'F' and resid 47 through 60 removed outlier: 4.989A pdb=" N ASN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 4.043A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 4.544A 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 Processing helix chain 'F' and resid 133 through 138 removed outlier: 4.192A 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 7 removed outlier: 4.029A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Proline residue: G 7 - end of helix Processing helix chain 'G' and resid 59 through 80 Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.743A pdb=" N ALA G 144 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 29 removed outlier: 4.689A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 49 removed outlier: 4.233A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS I 39 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N PHE I 41 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP I 46 " --> pdb=" O ASN I 42 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 83 removed outlier: 4.082A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 114 removed outlier: 4.500A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.550A pdb=" N GLY I 136 " --> pdb=" O ALA I 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 40 through 50 removed outlier: 4.897A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 72 removed outlier: 5.561A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.792A pdb=" N ALA H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY H 107 " --> pdb=" O VAL H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 removed outlier: 4.277A pdb=" N VAL H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ARG H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 111 through 116' Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.620A pdb=" N GLY J 38 " --> pdb=" O ARG J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.131A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.786A 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: 3.838A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 120 removed outlier: 4.807A pdb=" N MET K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LYS K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ILE K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Proline residue: K 120 - end of helix Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.835A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.117A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.851A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 99 removed outlier: 4.387A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 removed outlier: 4.370A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.958A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 58 removed outlier: 4.155A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.301A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASP N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 4.315A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 82 removed outlier: 4.401A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 88 Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.088A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 5.069A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 4.041A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 1 through 12 removed outlier: 3.702A pdb=" N LYS P 5 " --> pdb=" O SER P 1 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 103 removed outlier: 3.956A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N THR P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 98 through 103' Processing helix chain 'Q' and resid 5 through 21 removed outlier: 3.650A pdb=" N LYS Q 21 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 4.209A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 60 removed outlier: 3.677A pdb=" N ARG Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 72 Processing helix chain 'Q' and resid 74 through 86 removed outlier: 3.661A pdb=" N ALA Q 85 " --> pdb=" O GLY Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 102 through 117 removed outlier: 3.619A pdb=" N ALA Q 117 " --> pdb=" O LYS Q 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.619A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 4.013A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 62 removed outlier: 4.243A pdb=" N ASN S 61 " --> pdb=" O ASN S 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 1 through 11 removed outlier: 4.061A pdb=" N GLU T 5 " --> pdb=" O MET T 1 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 removed outlier: 3.534A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 removed outlier: 3.745A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.929A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 4.901A 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 removed outlier: 3.731A pdb=" N ARG V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 4.188A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 3.819A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 61 removed outlier: 3.881A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 74 Processing helix chain 'Y' and resid 1 through 7 removed outlier: 3.722A pdb=" N LEU Y 6 " --> pdb=" O LYS Y 2 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 23 Processing helix chain 'Y' and resid 25 through 35 removed outlier: 3.922A pdb=" N ARG Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 62 removed outlier: 4.058A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 51 Processing helix chain '0' and resid 8 through 20 removed outlier: 3.892A pdb=" N ARG 0 16 " --> pdb=" O ARG 0 12 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASP 0 19 " --> pdb=" O ARG 0 15 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 24 removed outlier: 4.356A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 38 Processing helix chain '3' and resid 6 through 13 Processing helix chain '3' and resid 31 through 36 removed outlier: 4.991A pdb=" N LYS 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 5.726A 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 50 through 62 removed outlier: 4.159A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '6' and resid 45 through 54 removed outlier: 4.192A pdb=" N ARG 6 49 " --> pdb=" O THR 6 45 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP 6 50 " --> pdb=" O GLY 6 46 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY 6 54 " --> pdb=" O ASP 6 50 " (cutoff:3.500A) Processing helix chain '6' and resid 55 through 65 removed outlier: 5.901A pdb=" N ARG 6 59 " --> pdb=" O GLY 6 55 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 29 through 33 removed outlier: 7.103A pdb=" N PHE b 29 " --> pdb=" O ASN b 41 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE b 39 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL b 37 " --> pdb=" O ALA b 33 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'b' and resid 66 through 70 removed outlier: 3.810A pdb=" N PHE b 183 " --> pdb=" O LEU b 160 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL b 162 " --> pdb=" O PHE b 183 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 53 through 58 Processing sheet with id= 4, first strand: chain 'c' and resid 163 through 170 removed outlier: 3.539A pdb=" N GLY c 154 " --> pdb=" O ARG c 163 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY c 196 " --> pdb=" O SER c 153 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR c 190 " --> pdb=" O GLY c 193 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP c 180 " --> pdb=" O LYS c 203 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'd' and resid 170 through 173 removed outlier: 5.047A pdb=" N ASP d 173 " --> pdb=" O GLU d 178 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU d 178 " --> pdb=" O ASP d 173 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 10 through 15 removed outlier: 3.967A pdb=" N GLN e 11 " --> pdb=" O GLY e 39 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY e 39 " --> pdb=" O GLN e 11 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 82 through 87 removed outlier: 7.551A pdb=" N HIS e 82 " --> pdb=" O PRO e 97 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR e 127 " --> pdb=" O ARG e 92 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'f' and resid 39 through 42 removed outlier: 4.477A pdb=" N GLU f 40 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TRP f 42 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET f 90 " --> pdb=" O GLU f 5 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'f' and resid 43 through 47 removed outlier: 3.696A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU f 47 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'g' and resid 72 through 76 Processing sheet with id= 11, first strand: chain 'h' and resid 22 through 27 removed outlier: 6.315A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS h 49 " --> pdb=" O GLU h 59 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP h 47 " --> pdb=" O THR h 61 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'h' and resid 73 through 76 removed outlier: 6.855A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'i' and resid 4 through 10 removed outlier: 4.057A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS i 67 " --> pdb=" O ALA i 15 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'j' and resid 44 through 52 removed outlier: 3.526A pdb=" N ARG j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU j 47 " --> pdb=" O ILE j 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE j 67 " --> pdb=" O GLU j 47 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN j 99 " --> pdb=" O ARG j 9 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'k' and resid 29 through 34 Processing sheet with id= 16, first strand: chain 'l' and resid 28 through 31 removed outlier: 5.081A pdb=" N LEU l 80 " --> pdb=" O VAL l 97 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'l' and resid 35 through 40 removed outlier: 4.744A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 5.328A 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: 5.898A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL p 19 " --> pdb=" O GLY p 37 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY p 37 " --> pdb=" O VAL p 19 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLY p 49 " --> pdb=" O ASN p 40 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'q' and resid 6 through 10 removed outlier: 4.675A pdb=" N GLY q 9 " --> pdb=" O VAL q 58 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL q 58 " --> pdb=" O GLY q 9 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL q 75 " --> pdb=" O GLU q 59 " (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 46 through 51 removed outlier: 4.710A pdb=" N LEU s 46 " --> pdb=" O VAL s 61 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C' and resid 79 through 82 removed outlier: 4.001A pdb=" N ARG C 79 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'C' and resid 161 through 164 removed outlier: 6.802A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C' and resid 90 through 95 removed outlier: 4.448A pdb=" N GLU C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'D' and resid 3 through 8 removed outlier: 4.560A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU D 168 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'D' and resid 11 through 16 removed outlier: 4.405A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 189 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'D' and resid 79 through 84 removed outlier: 6.008A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.501A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'E' and resid 1 through 5 No H-bonds generated for sheet with id= 29 Processing sheet with id= 30, first strand: chain 'E' and resid 44 through 47 removed outlier: 7.419A pdb=" N ARG E 44 " --> pdb=" O PRO E 89 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ALA E 87 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.653A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 147 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL E 187 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE E 149 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'F' and resid 64 through 68 removed outlier: 3.566A pdb=" N VAL F 88 " --> pdb=" O LEU F 35 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN F 36 " --> pdb=" O ASP F 152 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLY F 38 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLY F 150 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU F 151 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THR F 157 " --> pdb=" O GLY F 125 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY F 125 " --> pdb=" O THR F 157 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'G' and resid 15 through 18 Processing sheet with id= 34, first strand: chain 'G' and resid 40 through 44 Processing sheet with id= 35, first strand: chain 'G' and resid 81 through 88 removed outlier: 6.438A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'G' and resid 93 through 97 removed outlier: 3.550A pdb=" N ALA G 96 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'H' and resid 2 through 6 removed outlier: 5.466A pdb=" N GLN H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ALA H 39 " --> pdb=" O GLN H 2 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'H' and resid 76 through 81 removed outlier: 6.813A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.877A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.258A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU K 86 " --> pdb=" O ALA K 11 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 41 Processing sheet with id= 42, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.502A pdb=" N ASP M 106 " --> pdb=" O LYS M 62 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.510A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.651A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'O' and resid 49 through 53 removed outlier: 4.123A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE O 35 " --> pdb=" O THR O 53 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'P' and resid 37 through 44 removed outlier: 5.983A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'P' and resid 56 through 63 removed outlier: 8.064A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.559A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'R' and resid 18 through 21 removed outlier: 3.948A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL R 72 " --> pdb=" O HIS R 89 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLN R 91 " --> pdb=" O GLU R 70 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLU R 70 " --> pdb=" O GLN R 91 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE R 93 " --> pdb=" O ARG R 68 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ARG R 68 " --> pdb=" O PHE R 93 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'R' and resid 32 through 36 Processing sheet with id= 51, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.322A pdb=" N THR S 3 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL S 107 " --> pdb=" O THR S 3 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'T' and resid 29 through 33 removed outlier: 5.038A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'U' and resid 39 through 44 removed outlier: 4.582A pdb=" N ASN U 39 " --> pdb=" O ALA U 62 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'U' and resid 81 through 86 removed outlier: 5.004A pdb=" N ARG U 81 " --> pdb=" O LYS U 96 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'V' and resid 69 through 73 removed outlier: 7.157A pdb=" N PHE V 2 " --> pdb=" O VAL V 60 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR V 62 " --> pdb=" O PHE V 2 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA V 6 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG V 9 " --> pdb=" O ALA V 39 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS V 88 " --> pdb=" O GLN V 78 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'W' and resid 47 through 50 removed outlier: 4.296A pdb=" N THR W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'W' and resid 61 through 67 Processing sheet with id= 58, first strand: chain 'X' and resid 11 through 18 removed outlier: 3.611A pdb=" N VAL X 12 " --> pdb=" O PHE X 28 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG X 26 " --> pdb=" O GLY X 14 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER X 18 " --> pdb=" O ASN X 22 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN X 22 " --> pdb=" O SER X 18 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'X' and resid 34 through 40 Processing sheet with id= 60, first strand: chain 'Z' and resid 33 through 38 removed outlier: 4.930A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN Z 8 " --> pdb=" O HIS Z 33 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU Z 57 " --> pdb=" O LYS Z 5 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain '0' and resid 27 through 30 removed outlier: 6.277A pdb=" N SER 0 28 " --> pdb=" O LYS 0 36 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS 0 36 " --> pdb=" O SER 0 28 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP 0 30 " --> pdb=" O GLY 0 34 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain '1' and resid 6 through 11 Processing sheet with id= 63, first strand: chain '1' and resid 33 through 36 removed outlier: 6.636A pdb=" N LEU 1 33 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU 1 50 " --> pdb=" O LEU 1 33 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU 1 35 " --> pdb=" O TYR 1 48 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain '3' and resid 21 through 24 removed outlier: 5.662A pdb=" N PHE 3 21 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain '4' and resid 23 through 27 removed outlier: 6.911A pdb=" N ILE 4 23 " --> pdb=" O GLN 4 37 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N CYS 4 27 " --> pdb=" O HIS 4 33 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N HIS 4 33 " --> pdb=" O CYS 4 27 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain '6' and resid 20 through 25 removed outlier: 4.097A pdb=" N ASN 6 20 " --> pdb=" O CYS 6 16 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS 6 16 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) 1683 hydrogen bonds defined for protein. 4998 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3922 hydrogen bonds 6242 hydrogen bond angles 0 basepair planarities 1558 basepair parallelities 2451 stacking parallelities Total time for adding SS restraints: 210.96 Time building geometry restraints manager: 65.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.53: 148098 1.53 - 1.90: 12816 1.90 - 2.26: 2 2.26 - 2.63: 0 2.63 - 3.00: 4 Bond restraints: 160920 Sorted by residual: bond pdb=" O3' U y 67A" pdb=" P C y 68 " ideal model delta sigma weight residual 1.607 2.997 -1.390 1.50e-02 4.44e+03 8.59e+03 bond pdb=" O3' G y 5 " pdb=" P A y 5A" ideal model delta sigma weight residual 1.607 2.992 -1.385 1.50e-02 4.44e+03 8.53e+03 bond pdb=" O3' A y 67 " pdb=" P U y 67A" ideal model delta sigma weight residual 1.607 2.991 -1.384 1.50e-02 4.44e+03 8.52e+03 bond pdb=" O3' G y 47 " pdb=" P G y 47A" ideal model delta sigma weight residual 1.607 2.967 -1.360 1.50e-02 4.44e+03 8.22e+03 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.802 1.469 0.333 2.00e-02 2.50e+03 2.78e+02 ... (remaining 160915 not shown) Histogram of bond angle deviations from ideal: 69.27 - 83.57: 12 83.57 - 97.87: 18 97.87 - 112.17: 110010 112.17 - 126.48: 116513 126.48 - 140.78: 14409 Bond angle restraints: 240962 Sorted by residual: angle pdb=" O3' U y 67A" pdb=" P C y 68 " pdb=" O5' C y 68 " ideal model delta sigma weight residual 104.00 71.70 32.30 1.50e+00 4.44e-01 4.64e+02 angle pdb=" O3' G y 5 " pdb=" P A y 5A" pdb=" O5' A y 5A" ideal model delta sigma weight residual 104.00 73.08 30.92 1.50e+00 4.44e-01 4.25e+02 angle pdb=" O3' A y 67 " pdb=" P U y 67A" pdb=" O5' U y 67A" ideal model delta sigma weight residual 104.00 76.44 27.56 1.50e+00 4.44e-01 3.38e+02 angle pdb=" O3' G y 47 " pdb=" P G y 47A" pdb=" O5' G y 47A" ideal model delta sigma weight residual 104.00 79.25 24.75 1.50e+00 4.44e-01 2.72e+02 angle pdb=" O3' A y 67 " pdb=" P U y 67A" pdb=" OP1 U y 67A" ideal model delta sigma weight residual 108.00 69.27 38.73 3.00e+00 1.11e-01 1.67e+02 ... (remaining 240957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 90813 35.91 - 71.81: 10946 71.81 - 107.72: 1261 107.72 - 143.63: 34 143.63 - 179.54: 23 Dihedral angle restraints: 103077 sinusoidal: 86515 harmonic: 16562 Sorted by residual: dihedral pdb=" CA ILE m 3 " pdb=" C ILE m 3 " pdb=" N ALA m 4 " pdb=" CA ALA m 4 " ideal model delta harmonic sigma weight residual 180.00 -120.88 -59.12 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA HIS 3 30 " pdb=" C HIS 3 30 " pdb=" N ILE 3 31 " pdb=" CA ILE 3 31 " ideal model delta harmonic sigma weight residual -180.00 -126.94 -53.06 0 5.00e+00 4.00e-02 1.13e+02 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 39.75 -74.75 1 8.00e+00 1.56e-02 1.11e+02 ... (remaining 103074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.946: 30720 0.946 - 1.891: 0 1.891 - 2.837: 0 2.837 - 3.782: 0 3.782 - 4.728: 4 Chirality restraints: 30724 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 2.23 -4.73 2.00e-01 2.50e+01 5.59e+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 2.05 -4.55 2.00e-01 2.50e+01 5.17e+02 chirality pdb=" C3' G7M A2069 " pdb=" C4' G7M A2069 " pdb=" O3' G7M A2069 " pdb=" C2' G7M A2069 " both_signs ideal model delta sigma weight residual False -2.48 1.77 -4.25 2.00e-01 2.50e+01 4.51e+02 ... (remaining 30721 not shown) Planarity restraints: 12791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2251 " 0.089 2.00e-02 2.50e+03 6.21e-01 8.67e+03 pdb=" C4' OMG A2251 " 0.430 2.00e-02 2.50e+03 pdb=" O4' OMG A2251 " 0.609 2.00e-02 2.50e+03 pdb=" C3' OMG A2251 " -0.612 2.00e-02 2.50e+03 pdb=" O3' OMG A2251 " -0.691 2.00e-02 2.50e+03 pdb=" C2' OMG A2251 " -0.158 2.00e-02 2.50e+03 pdb=" O2' OMG A2251 " 1.062 2.00e-02 2.50e+03 pdb=" C1' OMG A2251 " 0.197 2.00e-02 2.50e+03 pdb=" N9 OMG A2251 " -0.928 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1407 " 0.073 2.00e-02 2.50e+03 6.08e-01 8.33e+03 pdb=" C4' 5MC a1407 " 0.440 2.00e-02 2.50e+03 pdb=" O4' 5MC a1407 " 0.575 2.00e-02 2.50e+03 pdb=" C3' 5MC a1407 " -0.589 2.00e-02 2.50e+03 pdb=" O3' 5MC a1407 " -0.688 2.00e-02 2.50e+03 pdb=" C2' 5MC a1407 " -0.140 2.00e-02 2.50e+03 pdb=" O2' 5MC a1407 " 1.028 2.00e-02 2.50e+03 pdb=" C1' 5MC a1407 " 0.228 2.00e-02 2.50e+03 pdb=" N1 5MC a1407 " -0.925 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1207 " -0.041 2.00e-02 2.50e+03 5.91e-01 7.86e+03 pdb=" C4' 2MG a1207 " -0.461 2.00e-02 2.50e+03 pdb=" O4' 2MG a1207 " -0.708 2.00e-02 2.50e+03 pdb=" C3' 2MG a1207 " 0.584 2.00e-02 2.50e+03 pdb=" O3' 2MG a1207 " 0.590 2.00e-02 2.50e+03 pdb=" C2' 2MG a1207 " 0.224 2.00e-02 2.50e+03 pdb=" O2' 2MG a1207 " -0.896 2.00e-02 2.50e+03 pdb=" C1' 2MG a1207 " -0.209 2.00e-02 2.50e+03 pdb=" N9 2MG a1207 " 0.918 2.00e-02 2.50e+03 ... (remaining 12788 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 12535 2.71 - 3.25: 132462 3.25 - 3.80: 309715 3.80 - 4.35: 387829 4.35 - 4.90: 508462 Nonbonded interactions: 1351003 Sorted by model distance: nonbonded pdb=" O2' U a 407 " pdb=" OE1 GLU d 112 " model vdw 2.158 2.440 nonbonded pdb=" O2' C a1097 " pdb=" O2' A a1169 " model vdw 2.175 2.440 nonbonded pdb=" N2 G A1171 " pdb=" O2 C A1178 " model vdw 2.178 2.496 nonbonded pdb=" OG SER r 35 " pdb=" OE2 GLU u 23 " model vdw 2.200 2.440 nonbonded pdb=" O2' A a 749 " pdb=" OD1 ASN o 19 " model vdw 2.202 2.440 ... (remaining 1350998 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: 0.880 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: 9.810 Check model and map are aligned: 1.420 Set scattering table: 0.920 Process input model: 516.290 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.330 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:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 534.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 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 : 0.012 1.390 160920 Z= 0.720 Angle : 1.238 38.729 240962 Z= 0.642 Chirality : 0.077 4.728 30724 Planarity : 0.022 0.621 12791 Dihedral : 22.969 179.537 92390 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 2.22 % Allowed : 7.68 % Favored : 90.10 % Rotamer: Outliers : 0.72 % Allowed : 2.47 % Favored : 96.81 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.10), residues: 5717 helix: -2.77 (0.09), residues: 1820 sheet: -3.26 (0.13), residues: 957 loop : -1.31 (0.11), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP s 33 HIS 0.033 0.004 HIS o 45 PHE 0.064 0.005 PHE I 37 TYR 0.040 0.004 TYR i 5 ARG 0.028 0.001 ARG R 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2325 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 2291 time to evaluate : 6.021 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: b 66 ILE cc_start: 0.8620 (mm) cc_final: 0.8381 (mm) REVERT: b 81 ASP cc_start: 0.8237 (m-30) cc_final: 0.7765 (m-30) REVERT: b 90 PHE cc_start: 0.8613 (p90) cc_final: 0.8159 (p90) REVERT: b 91 VAL cc_start: 0.9314 (t) cc_final: 0.8971 (p) REVERT: b 118 THR cc_start: 0.8411 (m) cc_final: 0.8127 (m) REVERT: b 168 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7160 (tp30) REVERT: b 172 ILE cc_start: 0.7917 (mt) cc_final: 0.7595 (mt) REVERT: b 202 ASN cc_start: 0.7779 (t0) cc_final: 0.7576 (t0) REVERT: b 210 THR cc_start: 0.8492 (p) cc_final: 0.8248 (p) REVERT: c 24 ASN cc_start: 0.6393 (p0) cc_final: 0.5730 (p0) REVERT: c 48 LYS cc_start: 0.8516 (mttt) cc_final: 0.7768 (pttm) REVERT: c 56 ILE cc_start: 0.8573 (mm) cc_final: 0.8297 (mt) REVERT: c 105 VAL cc_start: 0.8614 (t) cc_final: 0.8390 (m) REVERT: c 130 ARG cc_start: 0.8715 (tpp80) cc_final: 0.8497 (mmt-90) REVERT: c 134 LYS cc_start: 0.8844 (mttt) cc_final: 0.8476 (tmmt) REVERT: c 135 ARG cc_start: 0.8525 (ttt180) cc_final: 0.8020 (tpp-160) REVERT: c 139 ASN cc_start: 0.8747 (m-40) cc_final: 0.8215 (m-40) REVERT: c 187 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8447 (mt-10) REVERT: d 9 LYS cc_start: 0.6742 (tttt) cc_final: 0.6223 (mmtp) REVERT: d 13 ARG cc_start: 0.7379 (ttm-80) cc_final: 0.7063 (tpp-160) REVERT: d 46 ARG cc_start: 0.8060 (ttm110) cc_final: 0.7453 (tpm170) REVERT: d 57 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8187 (tppt) REVERT: d 59 LYS cc_start: 0.7494 (tttt) cc_final: 0.7281 (ttpp) REVERT: d 61 ARG cc_start: 0.7700 (ttp80) cc_final: 0.7467 (ttp80) REVERT: d 62 ARG cc_start: 0.7611 (mmt180) cc_final: 0.7104 (tpm170) REVERT: d 69 ARG cc_start: 0.8782 (tpp-160) cc_final: 0.8097 (ptt180) REVERT: d 92 LEU cc_start: 0.6809 (mt) cc_final: 0.6539 (mt) REVERT: d 96 ARG cc_start: 0.8570 (mtp85) cc_final: 0.8356 (mtp-110) REVERT: d 131 ILE cc_start: 0.7688 (mm) cc_final: 0.7222 (pt) REVERT: e 145 ASN cc_start: 0.8856 (m-40) cc_final: 0.8389 (m110) REVERT: f 2 ARG cc_start: 0.7534 (mtt180) cc_final: 0.6282 (mtp85) REVERT: f 19 PRO cc_start: 0.8341 (Cg_exo) cc_final: 0.8019 (Cg_endo) REVERT: f 21 MET cc_start: 0.7717 (mtp) cc_final: 0.7465 (mmm) REVERT: g 11 ILE cc_start: 0.8578 (pt) cc_final: 0.7500 (pt) REVERT: g 55 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7693 (mmtp) REVERT: g 77 ARG cc_start: 0.6741 (ttt90) cc_final: 0.6010 (mtp180) REVERT: g 129 ASN cc_start: 0.8284 (p0) cc_final: 0.8013 (p0) REVERT: h 2 MET cc_start: 0.8661 (ptp) cc_final: 0.8451 (tpp) REVERT: h 21 LYS cc_start: 0.8141 (mtpp) cc_final: 0.7840 (mtpp) REVERT: h 59 GLU cc_start: 0.7904 (pm20) cc_final: 0.7632 (pm20) REVERT: h 78 SER cc_start: 0.9013 (t) cc_final: 0.8761 (p) REVERT: h 87 ARG cc_start: 0.8634 (mtt-85) cc_final: 0.8362 (mtm180) REVERT: h 93 LYS cc_start: 0.7242 (mtpp) cc_final: 0.7032 (mmtt) REVERT: h 120 LEU cc_start: 0.7683 (pp) cc_final: 0.7462 (pp) REVERT: i 17 ARG cc_start: 0.8333 (mtp-110) cc_final: 0.7936 (ptm160) REVERT: i 30 ASN cc_start: 0.9295 (m-40) cc_final: 0.9090 (m110) REVERT: j 44 THR cc_start: 0.9406 (m) cc_final: 0.9168 (p) REVERT: j 45 ARG cc_start: 0.8159 (mmm-85) cc_final: 0.7711 (ttt-90) REVERT: j 63 ASP cc_start: 0.8201 (t0) cc_final: 0.7496 (t0) REVERT: j 68 ARG cc_start: 0.8929 (mtt180) cc_final: 0.8653 (mtt180) REVERT: j 69 THR cc_start: 0.9326 (m) cc_final: 0.9051 (p) REVERT: k 34 THR cc_start: 0.8422 (p) cc_final: 0.8063 (t) REVERT: k 39 ASN cc_start: 0.8660 (m-40) cc_final: 0.8373 (m110) REVERT: k 51 PHE cc_start: 0.7127 (m-10) cc_final: 0.6651 (m-10) REVERT: k 76 TYR cc_start: 0.8156 (m-80) cc_final: 0.7857 (m-10) REVERT: k 82 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8093 (mm-30) REVERT: k 104 PHE cc_start: 0.8650 (m-80) cc_final: 0.8332 (m-80) REVERT: k 105 ARG cc_start: 0.7607 (mtp-110) cc_final: 0.7202 (mtp85) REVERT: k 107 THR cc_start: 0.8334 (m) cc_final: 0.7918 (p) REVERT: k 108 ASN cc_start: 0.9016 (p0) cc_final: 0.8479 (p0) REVERT: k 110 THR cc_start: 0.8538 (p) cc_final: 0.8314 (t) REVERT: k 111 ASP cc_start: 0.8296 (t70) cc_final: 0.7885 (t70) REVERT: l 8 ARG cc_start: 0.8512 (ttm110) cc_final: 0.8072 (tpm170) REVERT: l 88 ASP cc_start: 0.7785 (t70) cc_final: 0.7270 (t0) REVERT: l 111 GLN cc_start: 0.7680 (mt0) cc_final: 0.7433 (mt0) REVERT: m 22 TYR cc_start: 0.8619 (t80) cc_final: 0.8402 (t80) REVERT: m 77 LYS cc_start: 0.8163 (tttm) cc_final: 0.7941 (tppt) REVERT: n 12 ARG cc_start: 0.8527 (mtt90) cc_final: 0.8080 (mtt-85) REVERT: n 25 GLU cc_start: 0.8648 (pm20) cc_final: 0.8410 (pm20) REVERT: n 53 ASP cc_start: 0.8604 (m-30) cc_final: 0.8219 (m-30) REVERT: p 9 HIS cc_start: 0.6923 (m-70) cc_final: 0.6551 (m-70) REVERT: p 63 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8189 (mm-40) REVERT: q 46 HIS cc_start: 0.8145 (t70) cc_final: 0.7924 (t70) REVERT: q 61 ARG cc_start: 0.7734 (ptt90) cc_final: 0.7309 (ttp80) REVERT: q 72 TRP cc_start: 0.8033 (m100) cc_final: 0.7678 (m100) REVERT: r 71 ASP cc_start: 0.7500 (p0) cc_final: 0.6802 (p0) REVERT: s 9 PHE cc_start: 0.8454 (t80) cc_final: 0.8180 (t80) REVERT: s 19 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7879 (tm-30) REVERT: s 56 HIS cc_start: 0.8207 (m90) cc_final: 0.7686 (m-70) REVERT: s 57 VAL cc_start: 0.9195 (p) cc_final: 0.8949 (p) REVERT: s 62 THR cc_start: 0.8463 (m) cc_final: 0.8142 (p) REVERT: s 65 MET cc_start: 0.8163 (mtm) cc_final: 0.7961 (mtm) REVERT: t 35 TYR cc_start: 0.8510 (m-80) cc_final: 0.7995 (m-80) REVERT: t 43 LYS cc_start: 0.8062 (pttt) cc_final: 0.7531 (tttt) REVERT: t 51 ASN cc_start: 0.8223 (m-40) cc_final: 0.7967 (m-40) REVERT: t 54 GLN cc_start: 0.8779 (tt0) cc_final: 0.8560 (tt0) REVERT: u 39 LYS cc_start: 0.7943 (mtpt) cc_final: 0.7626 (mtpt) REVERT: u 46 ARG cc_start: 0.7519 (mtp85) cc_final: 0.7180 (mtp85) REVERT: C 17 LYS cc_start: 0.8704 (mtmt) cc_final: 0.8362 (mtpp) REVERT: C 61 TYR cc_start: 0.8923 (t80) cc_final: 0.8629 (t80) REVERT: C 65 ASP cc_start: 0.8733 (t70) cc_final: 0.8493 (t0) REVERT: C 81 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8410 (mm-30) REVERT: C 101 ARG cc_start: 0.8152 (mtt180) cc_final: 0.7913 (mtt-85) REVERT: C 113 ASP cc_start: 0.7666 (m-30) cc_final: 0.7203 (t0) REVERT: C 142 ASN cc_start: 0.9253 (t0) cc_final: 0.8944 (t0) REVERT: C 152 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8195 (mm-40) REVERT: C 176 ARG cc_start: 0.9034 (tpt170) cc_final: 0.8749 (tpt-90) REVERT: C 212 TRP cc_start: 0.8874 (p90) cc_final: 0.8408 (p90) REVERT: C 268 ARG cc_start: 0.8842 (mmt180) cc_final: 0.8553 (mmm-85) REVERT: D 16 THR cc_start: 0.7990 (p) cc_final: 0.7639 (t) REVERT: D 30 GLU cc_start: 0.8100 (mp0) cc_final: 0.7672 (mm-30) REVERT: D 77 ARG cc_start: 0.7888 (ptt90) cc_final: 0.7654 (ptt90) REVERT: D 95 SER cc_start: 0.7965 (m) cc_final: 0.7759 (p) REVERT: D 109 VAL cc_start: 0.9282 (t) cc_final: 0.9059 (p) REVERT: E 7 ASP cc_start: 0.7740 (p0) cc_final: 0.5996 (p0) REVERT: E 111 GLU cc_start: 0.8537 (tp30) cc_final: 0.8270 (tp30) REVERT: E 116 ASP cc_start: 0.7978 (m-30) cc_final: 0.7522 (t0) REVERT: E 171 ASP cc_start: 0.8235 (t70) cc_final: 0.7842 (t70) REVERT: E 185 LYS cc_start: 0.8330 (mmmt) cc_final: 0.7975 (mmmt) REVERT: F 10 GLU cc_start: 0.7877 (mp0) cc_final: 0.7599 (mp0) REVERT: F 19 PHE cc_start: 0.8736 (m-80) cc_final: 0.8397 (m-10) REVERT: F 79 ARG cc_start: 0.7642 (mtm110) cc_final: 0.7085 (mmm160) REVERT: F 127 TYR cc_start: 0.8473 (t80) cc_final: 0.8163 (t80) REVERT: F 144 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7632 (mmtm) REVERT: F 146 ASP cc_start: 0.7434 (p0) cc_final: 0.6950 (m-30) REVERT: F 163 GLU cc_start: 0.7735 (tp30) cc_final: 0.7498 (tp30) REVERT: F 169 LEU cc_start: 0.8899 (mt) cc_final: 0.7900 (pp) REVERT: F 176 PHE cc_start: 0.7927 (m-10) cc_final: 0.6661 (m-10) REVERT: G 19 ASN cc_start: 0.7180 (t0) cc_final: 0.6960 (t0) REVERT: G 114 HIS cc_start: 0.8414 (t70) cc_final: 0.8174 (t70) REVERT: G 120 ILE cc_start: 0.8084 (mm) cc_final: 0.7797 (mm) REVERT: I 16 MET cc_start: 0.4203 (mmp) cc_final: 0.3962 (ptp) REVERT: I 34 ILE cc_start: 0.3616 (OUTLIER) cc_final: 0.3405 (mm) REVERT: I 116 MET cc_start: 0.3000 (mmp) cc_final: 0.2086 (ttm) REVERT: I 135 MET cc_start: 0.0491 (mmt) cc_final: -0.1247 (ppp) REVERT: J 35 ARG cc_start: 0.8753 (mmt90) cc_final: 0.8520 (mmt90) REVERT: J 44 TYR cc_start: 0.8870 (t80) cc_final: 0.8655 (t80) REVERT: J 58 ASN cc_start: 0.8133 (t0) cc_final: 0.7816 (t0) REVERT: J 80 HIS cc_start: 0.8108 (t-90) cc_final: 0.7563 (m170) REVERT: J 81 ILE cc_start: 0.8289 (tt) cc_final: 0.8081 (tt) REVERT: J 130 HIS cc_start: 0.9317 (p90) cc_final: 0.8632 (p90) REVERT: K 20 MET cc_start: 0.8730 (ttp) cc_final: 0.8357 (ttm) REVERT: K 59 LYS cc_start: 0.8755 (mttt) cc_final: 0.8466 (mttm) REVERT: L 18 ARG cc_start: 0.8715 (mtp-110) cc_final: 0.8442 (ttp-110) REVERT: L 55 MET cc_start: 0.8873 (tpp) cc_final: 0.8627 (tpp) REVERT: L 69 ARG cc_start: 0.8512 (ttm-80) cc_final: 0.8259 (mmm-85) REVERT: L 112 LEU cc_start: 0.8567 (tp) cc_final: 0.8252 (mt) REVERT: L 121 THR cc_start: 0.8173 (m) cc_final: 0.7682 (p) REVERT: L 132 ARG cc_start: 0.8254 (ttm-80) cc_final: 0.7780 (ttm-80) REVERT: M 30 SER cc_start: 0.8853 (m) cc_final: 0.8234 (p) REVERT: M 47 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8535 (mm-30) REVERT: M 73 ILE cc_start: 0.9505 (mm) cc_final: 0.9250 (mm) REVERT: M 105 MET cc_start: 0.8950 (ttm) cc_final: 0.8718 (ttm) REVERT: M 108 VAL cc_start: 0.8984 (m) cc_final: 0.8644 (p) REVERT: N 74 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8520 (tp30) REVERT: N 94 TYR cc_start: 0.9122 (m-80) cc_final: 0.8223 (m-80) REVERT: N 114 GLU cc_start: 0.8397 (pm20) cc_final: 0.7970 (pm20) REVERT: N 117 ASP cc_start: 0.8191 (m-30) cc_final: 0.7969 (m-30) REVERT: O 58 ILE cc_start: 0.8662 (mm) cc_final: 0.8459 (mm) REVERT: O 64 TYR cc_start: 0.7415 (t80) cc_final: 0.7159 (t80) REVERT: O 115 LEU cc_start: 0.8620 (tp) cc_final: 0.8386 (tp) REVERT: P 6 GLN cc_start: 0.8521 (tt0) cc_final: 0.8213 (tp40) REVERT: P 10 GLU cc_start: 0.8885 (pt0) cc_final: 0.8484 (mp0) REVERT: P 13 LYS cc_start: 0.7244 (ptpt) cc_final: 0.7000 (ptpt) REVERT: P 28 LYS cc_start: 0.9098 (ttmm) cc_final: 0.8573 (mttt) REVERT: P 86 LYS cc_start: 0.8502 (mmtm) cc_final: 0.8256 (mptt) REVERT: P 97 TYR cc_start: 0.8740 (m-80) cc_final: 0.8424 (m-10) REVERT: P 105 LYS cc_start: 0.8783 (mmmt) cc_final: 0.8543 (mmmm) REVERT: Q 23 TYR cc_start: 0.9196 (m-10) cc_final: 0.8941 (m-10) REVERT: Q 46 TYR cc_start: 0.9301 (t80) cc_final: 0.8838 (t80) REVERT: Q 83 LYS cc_start: 0.8797 (ttpp) cc_final: 0.8317 (mptt) REVERT: Q 101 ASP cc_start: 0.8094 (t70) cc_final: 0.7759 (t0) REVERT: R 19 THR cc_start: 0.9212 (t) cc_final: 0.8947 (m) REVERT: S 3 THR cc_start: 0.8538 (m) cc_final: 0.7646 (p) REVERT: S 15 GLN cc_start: 0.8923 (tt0) cc_final: 0.8345 (mt0) REVERT: S 95 ARG cc_start: 0.8494 (mtp-110) cc_final: 0.8284 (ttm170) REVERT: S 107 VAL cc_start: 0.9202 (m) cc_final: 0.8605 (p) REVERT: T 33 LYS cc_start: 0.8721 (ptmt) cc_final: 0.8464 (pttt) REVERT: T 44 LYS cc_start: 0.8632 (tttm) cc_final: 0.8171 (tmmt) REVERT: T 49 LYS cc_start: 0.8726 (mtmt) cc_final: 0.8297 (mmtp) REVERT: T 80 TRP cc_start: 0.9130 (p-90) cc_final: 0.8928 (p-90) REVERT: U 18 LYS cc_start: 0.8905 (ttmt) cc_final: 0.8435 (tttp) REVERT: U 85 ARG cc_start: 0.8263 (ptp90) cc_final: 0.8020 (ptt90) REVERT: V 1 MET cc_start: 0.5577 (ptm) cc_final: 0.4964 (mmp) REVERT: V 10 LYS cc_start: 0.7794 (pttm) cc_final: 0.7138 (mmmt) REVERT: V 14 LYS cc_start: 0.8088 (ttmm) cc_final: 0.7795 (pttp) REVERT: V 29 ILE cc_start: 0.9142 (tp) cc_final: 0.8870 (tp) REVERT: V 31 TYR cc_start: 0.8767 (p90) cc_final: 0.8541 (p90) REVERT: V 38 LEU cc_start: 0.8422 (tp) cc_final: 0.8139 (tp) REVERT: W 7 ARG cc_start: 0.7914 (tpp80) cc_final: 0.7668 (mpt180) REVERT: W 64 LYS cc_start: 0.8951 (tptm) cc_final: 0.8664 (tmmt) REVERT: W 65 PHE cc_start: 0.9153 (m-80) cc_final: 0.8943 (m-80) REVERT: W 66 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8155 (mt-10) REVERT: W 68 LYS cc_start: 0.8301 (mtpt) cc_final: 0.7991 (mtpt) REVERT: X 2 ARG cc_start: 0.8614 (mtt90) cc_final: 0.8386 (mtm-85) REVERT: X 34 SER cc_start: 0.8968 (m) cc_final: 0.8664 (t) REVERT: X 43 LYS cc_start: 0.8964 (mttt) cc_final: 0.8712 (tppt) REVERT: X 45 PHE cc_start: 0.8710 (m-10) cc_final: 0.7716 (m-10) REVERT: X 65 THR cc_start: 0.8505 (m) cc_final: 0.8297 (p) REVERT: Y 4 LYS cc_start: 0.8781 (mtmt) cc_final: 0.8446 (tmtt) REVERT: Y 45 GLN cc_start: 0.8598 (pt0) cc_final: 0.8298 (pt0) REVERT: Y 50 VAL cc_start: 0.9030 (t) cc_final: 0.8721 (p) REVERT: Y 53 VAL cc_start: 0.8540 (t) cc_final: 0.8298 (t) REVERT: Z 3 THR cc_start: 0.8495 (m) cc_final: 0.8261 (t) REVERT: Z 4 ILE cc_start: 0.8954 (tt) cc_final: 0.8733 (pt) REVERT: Z 30 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.8138 (ptp-110) REVERT: 0 12 ARG cc_start: 0.8522 (ttp80) cc_final: 0.7981 (ttm170) REVERT: 0 51 ARG cc_start: 0.8933 (ptp-170) cc_final: 0.8651 (ptp-110) REVERT: 1 7 LYS cc_start: 0.7943 (ptpt) cc_final: 0.7667 (ptpt) REVERT: 1 9 LYS cc_start: 0.7678 (ttpt) cc_final: 0.7476 (tttt) REVERT: 1 48 TYR cc_start: 0.8689 (m-80) cc_final: 0.7914 (m-80) REVERT: 2 33 ARG cc_start: 0.8964 (mtm-85) cc_final: 0.8433 (mtm180) REVERT: 4 3 VAL cc_start: 0.9501 (m) cc_final: 0.9124 (t) REVERT: 6 8 LYS cc_start: 0.8132 (ptpt) cc_final: 0.7643 (tptm) REVERT: 6 9 TYR cc_start: 0.8370 (t80) cc_final: 0.8046 (t80) REVERT: 6 30 HIS cc_start: 0.6934 (OUTLIER) cc_final: 0.6353 (p-80) REVERT: 6 59 ARG cc_start: 0.8677 (ptt90) cc_final: 0.7520 (tpt90) REVERT: 6 61 ASN cc_start: 0.7366 (p0) cc_final: 0.7142 (m-40) outliers start: 34 outliers final: 10 residues processed: 2312 average time/residue: 1.5500 time to fit residues: 5996.7785 Evaluate side-chains 1661 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1649 time to evaluate : 6.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 6 residue 16 CYS Chi-restraints excluded: chain 6 residue 30 HIS Chi-restraints excluded: chain 6 residue 32 LEU Chi-restraints excluded: chain 6 residue 66 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 873 optimal weight: 7.9990 chunk 783 optimal weight: 20.0000 chunk 434 optimal weight: 10.0000 chunk 267 optimal weight: 5.9990 chunk 528 optimal weight: 0.9990 chunk 418 optimal weight: 20.0000 chunk 810 optimal weight: 7.9990 chunk 313 optimal weight: 10.0000 chunk 492 optimal weight: 10.0000 chunk 603 optimal weight: 0.9990 chunk 938 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 176 ASN c 40 GLN c 175 HIS d 53 GLN d 58 GLN e 18 ASN ** i 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 GLN i 125 GLN j 58 ASN k 37 GLN l 4 ASN l 5 GLN l 19 ASN n 65 GLN p 9 HIS p 18 GLN ** s 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS t 47 GLN t 74 HIS C 69 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 238 ASN D 32 ASN D 150 GLN D 185 ASN E 24 ASN E 41 GLN E 195 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN H 20 ASN H 73 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN N 31 HIS O 29 HIS O 34 HIS P 14 GLN Q 43 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN Y 20 ASN Y 31 GLN Y 36 GLN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 41 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 160920 Z= 0.229 Angle : 0.725 15.565 240962 Z= 0.384 Chirality : 0.037 0.360 30724 Planarity : 0.007 0.132 12791 Dihedral : 23.562 179.844 81032 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.33 % Favored : 92.93 % Rotamer: Outliers : 3.79 % Allowed : 14.51 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.11), residues: 5717 helix: -0.51 (0.11), residues: 1863 sheet: -2.68 (0.13), residues: 1042 loop : -1.01 (0.12), residues: 2812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 212 HIS 0.012 0.001 HIS k 117 PHE 0.045 0.002 PHE u 36 TYR 0.039 0.002 TYR d 75 ARG 0.011 0.001 ARG O 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1976 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1797 time to evaluate : 6.179 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: b 45 THR cc_start: 0.8213 (m) cc_final: 0.7909 (m) REVERT: b 81 ASP cc_start: 0.7934 (m-30) cc_final: 0.7504 (m-30) REVERT: b 90 PHE cc_start: 0.8554 (p90) cc_final: 0.7905 (p90) REVERT: b 117 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6730 (pp20) REVERT: b 141 GLU cc_start: 0.7642 (mt-10) cc_final: 0.6800 (mt-10) REVERT: b 168 GLU cc_start: 0.7557 (mt-10) cc_final: 0.6776 (tp30) REVERT: b 178 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6343 (pt) REVERT: b 202 ASN cc_start: 0.7724 (t0) cc_final: 0.7310 (t0) REVERT: b 222 GLU cc_start: 0.7874 (tp30) cc_final: 0.7643 (mm-30) REVERT: c 7 ASN cc_start: 0.8664 (m-40) cc_final: 0.8372 (t0) REVERT: c 41 TYR cc_start: 0.8746 (t80) cc_final: 0.8524 (t80) REVERT: c 87 ARG cc_start: 0.8421 (mtt180) cc_final: 0.8141 (ttp-170) REVERT: c 134 LYS cc_start: 0.8832 (mttt) cc_final: 0.8623 (tmmt) REVERT: c 135 ARG cc_start: 0.8474 (ttt180) cc_final: 0.7890 (tpp-160) REVERT: c 139 ASN cc_start: 0.8588 (m-40) cc_final: 0.8201 (m-40) REVERT: c 156 LEU cc_start: 0.8739 (mt) cc_final: 0.8084 (mt) REVERT: c 169 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8594 (mp0) REVERT: c 187 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8287 (mt-10) REVERT: d 13 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7142 (tpm170) REVERT: d 46 ARG cc_start: 0.8161 (ttm110) cc_final: 0.7763 (tpm170) REVERT: d 69 ARG cc_start: 0.8922 (tpp-160) cc_final: 0.8200 (ptt180) REVERT: d 84 ASN cc_start: 0.7600 (t0) cc_final: 0.6505 (m-40) REVERT: d 131 ILE cc_start: 0.7783 (mm) cc_final: 0.7337 (pt) REVERT: e 119 VAL cc_start: 0.7973 (t) cc_final: 0.7725 (m) REVERT: e 148 SER cc_start: 0.8525 (m) cc_final: 0.8080 (p) REVERT: f 17 GLN cc_start: 0.7370 (tm-30) cc_final: 0.7011 (pp30) REVERT: g 20 GLU cc_start: 0.7753 (pp20) cc_final: 0.7284 (pp20) REVERT: g 57 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7406 (mt-10) REVERT: g 62 GLU cc_start: 0.8195 (tp30) cc_final: 0.7939 (tp30) REVERT: g 66 GLU cc_start: 0.7833 (tp30) cc_final: 0.7599 (tp30) REVERT: g 77 ARG cc_start: 0.6855 (ttt90) cc_final: 0.6464 (tpp80) REVERT: g 122 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6492 (tp30) REVERT: g 129 ASN cc_start: 0.8346 (p0) cc_final: 0.7990 (p0) REVERT: h 2 MET cc_start: 0.8764 (ptp) cc_final: 0.8397 (tpp) REVERT: h 59 GLU cc_start: 0.7463 (pm20) cc_final: 0.6954 (pm20) REVERT: h 78 SER cc_start: 0.8717 (t) cc_final: 0.8437 (p) REVERT: i 30 ASN cc_start: 0.9098 (m-40) cc_final: 0.8859 (m-40) REVERT: j 24 GLU cc_start: 0.8688 (tp30) cc_final: 0.7807 (tm-30) REVERT: j 28 THR cc_start: 0.8208 (m) cc_final: 0.7672 (t) REVERT: j 45 ARG cc_start: 0.8097 (mmm-85) cc_final: 0.7606 (ttm-80) REVERT: j 63 ASP cc_start: 0.8037 (t0) cc_final: 0.7714 (t0) REVERT: j 68 ARG cc_start: 0.8976 (mtt180) cc_final: 0.8720 (mtt180) REVERT: j 69 THR cc_start: 0.9207 (m) cc_final: 0.8817 (p) REVERT: k 34 THR cc_start: 0.8626 (p) cc_final: 0.8153 (t) REVERT: k 39 ASN cc_start: 0.8621 (m-40) cc_final: 0.8420 (m110) REVERT: k 52 ARG cc_start: 0.8078 (tpp-160) cc_final: 0.7869 (mmm160) REVERT: k 68 ARG cc_start: 0.8180 (ttm110) cc_final: 0.7663 (mtt180) REVERT: k 69 CYS cc_start: 0.8992 (t) cc_final: 0.8378 (t) REVERT: k 104 PHE cc_start: 0.8501 (m-80) cc_final: 0.8143 (m-80) REVERT: k 105 ARG cc_start: 0.7410 (mtp-110) cc_final: 0.7085 (mtp85) REVERT: k 110 THR cc_start: 0.8501 (p) cc_final: 0.8215 (t) REVERT: k 111 ASP cc_start: 0.8166 (t70) cc_final: 0.7868 (t70) REVERT: l 8 ARG cc_start: 0.8344 (ttm110) cc_final: 0.8092 (tpm170) REVERT: l 18 SER cc_start: 0.8655 (t) cc_final: 0.8203 (p) REVERT: l 88 ASP cc_start: 0.7193 (t70) cc_final: 0.6814 (t0) REVERT: l 111 GLN cc_start: 0.7556 (mt0) cc_final: 0.7277 (mt0) REVERT: m 77 LYS cc_start: 0.8517 (tttm) cc_final: 0.8168 (tptt) REVERT: n 25 GLU cc_start: 0.8612 (pm20) cc_final: 0.8357 (pm20) REVERT: o 44 GLU cc_start: 0.8460 (pm20) cc_final: 0.8195 (pm20) REVERT: p 31 ARG cc_start: 0.8359 (ttm170) cc_final: 0.7965 (ttp-170) REVERT: p 54 LEU cc_start: 0.8482 (pt) cc_final: 0.8131 (pp) REVERT: p 63 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8018 (tp40) REVERT: q 18 LYS cc_start: 0.8134 (tttm) cc_final: 0.7802 (tptm) REVERT: q 30 HIS cc_start: 0.8764 (t-90) cc_final: 0.8525 (t-90) REVERT: q 61 ARG cc_start: 0.7715 (ptt90) cc_final: 0.7170 (ttp80) REVERT: q 72 TRP cc_start: 0.8131 (m100) cc_final: 0.7803 (m100) REVERT: r 39 VAL cc_start: 0.9524 (t) cc_final: 0.9309 (p) REVERT: s 19 GLU cc_start: 0.8407 (mm-30) cc_final: 0.7725 (tm-30) REVERT: s 62 THR cc_start: 0.8596 (m) cc_final: 0.8065 (p) REVERT: s 68 HIS cc_start: 0.8368 (m90) cc_final: 0.8151 (m90) REVERT: t 28 ARG cc_start: 0.8548 (ptm160) cc_final: 0.8037 (ttm110) REVERT: t 35 TYR cc_start: 0.8270 (m-80) cc_final: 0.8067 (m-80) REVERT: t 39 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7081 (mm-30) REVERT: t 43 LYS cc_start: 0.8217 (pttt) cc_final: 0.7719 (tttt) REVERT: t 47 GLN cc_start: 0.8724 (tp40) cc_final: 0.8335 (tp-100) REVERT: u 39 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7660 (mtpt) REVERT: C 33 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8812 (mp) REVERT: C 123 ILE cc_start: 0.8977 (mm) cc_final: 0.8775 (mm) REVERT: C 142 ASN cc_start: 0.9298 (t0) cc_final: 0.8914 (t0) REVERT: C 152 GLN cc_start: 0.8612 (mm-40) cc_final: 0.7974 (mm-40) REVERT: C 212 TRP cc_start: 0.8792 (p90) cc_final: 0.8561 (p90) REVERT: C 268 ARG cc_start: 0.8591 (mmt180) cc_final: 0.8292 (mmm-85) REVERT: D 16 THR cc_start: 0.7999 (p) cc_final: 0.7684 (t) REVERT: D 88 GLU cc_start: 0.8349 (pm20) cc_final: 0.8019 (pm20) REVERT: D 99 GLU cc_start: 0.8049 (pm20) cc_final: 0.7828 (mp0) REVERT: D 109 VAL cc_start: 0.8829 (t) cc_final: 0.8525 (p) REVERT: E 7 ASP cc_start: 0.7977 (p0) cc_final: 0.7764 (p0) REVERT: E 35 TYR cc_start: 0.8678 (t80) cc_final: 0.8455 (t80) REVERT: E 116 ASP cc_start: 0.8013 (m-30) cc_final: 0.7599 (t0) REVERT: E 136 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7252 (tm-30) REVERT: F 10 GLU cc_start: 0.7952 (mp0) cc_final: 0.7643 (mp0) REVERT: F 31 GLU cc_start: 0.8523 (mt-10) cc_final: 0.7823 (mp0) REVERT: F 55 ASP cc_start: 0.7805 (m-30) cc_final: 0.7556 (m-30) REVERT: F 79 ARG cc_start: 0.7712 (mtm110) cc_final: 0.7099 (mmm160) REVERT: F 136 ILE cc_start: 0.8782 (pp) cc_final: 0.8456 (mp) REVERT: F 144 LYS cc_start: 0.7877 (mmtt) cc_final: 0.7641 (mmtm) REVERT: F 146 ASP cc_start: 0.7481 (p0) cc_final: 0.6184 (m-30) REVERT: F 163 GLU cc_start: 0.7557 (tp30) cc_final: 0.7338 (tp30) REVERT: F 176 PHE cc_start: 0.7739 (m-10) cc_final: 0.7415 (m-10) REVERT: G 19 ASN cc_start: 0.7200 (t0) cc_final: 0.6969 (t0) REVERT: G 94 ARG cc_start: 0.8503 (mtt180) cc_final: 0.8230 (mtp180) REVERT: G 114 HIS cc_start: 0.8497 (t70) cc_final: 0.8247 (t70) REVERT: I 16 MET cc_start: 0.4383 (mmp) cc_final: 0.3980 (ptp) REVERT: I 116 MET cc_start: 0.3113 (mmp) cc_final: 0.2599 (tpp) REVERT: H 42 LYS cc_start: 0.8035 (ptmt) cc_final: 0.7675 (tptm) REVERT: J 58 ASN cc_start: 0.8190 (t0) cc_final: 0.7641 (t0) REVERT: J 61 LYS cc_start: 0.8572 (mmmt) cc_final: 0.8096 (mptt) REVERT: J 130 HIS cc_start: 0.9139 (p90) cc_final: 0.8634 (p90) REVERT: K 17 ARG cc_start: 0.8775 (tpp80) cc_final: 0.8459 (mmm-85) REVERT: L 55 MET cc_start: 0.8897 (tpp) cc_final: 0.8676 (tpp) REVERT: L 63 LYS cc_start: 0.9331 (ptmt) cc_final: 0.8980 (pttt) REVERT: L 132 ARG cc_start: 0.8054 (ttm-80) cc_final: 0.7643 (ttm-80) REVERT: L 136 GLU cc_start: 0.8691 (pt0) cc_final: 0.8298 (mt-10) REVERT: M 30 SER cc_start: 0.8753 (m) cc_final: 0.8369 (p) REVERT: M 108 VAL cc_start: 0.8840 (m) cc_final: 0.8573 (m) REVERT: N 24 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8871 (mtm) REVERT: N 74 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8686 (tp30) REVERT: N 114 GLU cc_start: 0.8234 (pm20) cc_final: 0.7940 (pm20) REVERT: N 117 ASP cc_start: 0.8054 (m-30) cc_final: 0.7646 (m-30) REVERT: O 64 TYR cc_start: 0.7382 (t80) cc_final: 0.6890 (t80) REVERT: P 28 LYS cc_start: 0.8910 (ttmm) cc_final: 0.8513 (mttt) REVERT: P 81 ASP cc_start: 0.8345 (t0) cc_final: 0.7986 (t0) REVERT: P 87 ARG cc_start: 0.7982 (mtp-110) cc_final: 0.7546 (ttt180) REVERT: P 95 LYS cc_start: 0.9054 (mptt) cc_final: 0.8494 (mmmt) REVERT: P 105 LYS cc_start: 0.8594 (mmmt) cc_final: 0.8314 (mmmm) REVERT: Q 46 TYR cc_start: 0.9258 (t80) cc_final: 0.8803 (t80) REVERT: Q 83 LYS cc_start: 0.8601 (ttpp) cc_final: 0.7929 (mptt) REVERT: R 11 GLN cc_start: 0.8917 (mp10) cc_final: 0.8650 (mp10) REVERT: R 19 THR cc_start: 0.9133 (t) cc_final: 0.8794 (m) REVERT: S 3 THR cc_start: 0.8516 (m) cc_final: 0.7530 (p) REVERT: S 15 GLN cc_start: 0.8706 (tt0) cc_final: 0.8471 (mt0) REVERT: S 65 ASP cc_start: 0.8211 (t0) cc_final: 0.7762 (t0) REVERT: S 84 ARG cc_start: 0.8525 (mmt-90) cc_final: 0.8111 (mmt180) REVERT: S 96 ILE cc_start: 0.9096 (pp) cc_final: 0.8815 (pt) REVERT: S 107 VAL cc_start: 0.9177 (m) cc_final: 0.8610 (p) REVERT: T 1 MET cc_start: 0.5843 (ptm) cc_final: 0.5262 (ttp) REVERT: T 44 LYS cc_start: 0.8479 (tttm) cc_final: 0.8007 (tmmt) REVERT: U 85 ARG cc_start: 0.7992 (ptp90) cc_final: 0.7544 (ptt-90) REVERT: V 1 MET cc_start: 0.5929 (ptm) cc_final: 0.5164 (mmp) REVERT: V 10 LYS cc_start: 0.7785 (pttm) cc_final: 0.7261 (mmmt) REVERT: V 29 ILE cc_start: 0.9217 (tp) cc_final: 0.8876 (tp) REVERT: V 31 TYR cc_start: 0.8518 (p90) cc_final: 0.8195 (p90) REVERT: V 38 LEU cc_start: 0.8381 (tp) cc_final: 0.8065 (tp) REVERT: W 7 ARG cc_start: 0.7860 (tpp80) cc_final: 0.7640 (mtm-85) REVERT: W 25 GLU cc_start: 0.8680 (tt0) cc_final: 0.8453 (tt0) REVERT: W 64 LYS cc_start: 0.8923 (tptm) cc_final: 0.8712 (tmmt) REVERT: X 18 SER cc_start: 0.8992 (p) cc_final: 0.8767 (m) REVERT: X 34 SER cc_start: 0.8840 (m) cc_final: 0.8617 (t) REVERT: Y 20 ASN cc_start: 0.9109 (m-40) cc_final: 0.8844 (m110) REVERT: Y 39 GLN cc_start: 0.8377 (pt0) cc_final: 0.8024 (pt0) REVERT: Y 45 GLN cc_start: 0.8518 (pt0) cc_final: 0.8268 (pt0) REVERT: 0 30 ASP cc_start: 0.7887 (t70) cc_final: 0.7456 (t70) REVERT: 0 51 ARG cc_start: 0.9017 (ptp-170) cc_final: 0.8737 (ptp-110) REVERT: 1 7 LYS cc_start: 0.7999 (ptpt) cc_final: 0.7731 (ptpt) REVERT: 1 48 TYR cc_start: 0.8648 (m-80) cc_final: 0.8407 (m-10) REVERT: 2 33 ARG cc_start: 0.8923 (mtm-85) cc_final: 0.8295 (mtm180) REVERT: 4 30 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8107 (tm-30) REVERT: 6 4 ASP cc_start: 0.7442 (p0) cc_final: 0.7213 (p0) REVERT: 6 16 CYS cc_start: 0.5631 (OUTLIER) cc_final: 0.5177 (t) REVERT: 6 59 ARG cc_start: 0.8625 (ptt90) cc_final: 0.7303 (tpt90) REVERT: 6 66 ILE cc_start: 0.1818 (OUTLIER) cc_final: 0.1297 (mp) outliers start: 179 outliers final: 113 residues processed: 1856 average time/residue: 1.3353 time to fit residues: 4213.4316 Evaluate side-chains 1759 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1639 time to evaluate : 6.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 117 GLU Chi-restraints excluded: chain b residue 145 ASN Chi-restraints excluded: chain b residue 150 ILE Chi-restraints excluded: chain b residue 166 ASP Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain c residue 107 LYS Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain c residue 194 VAL Chi-restraints excluded: chain c residue 206 ILE Chi-restraints excluded: chain d residue 82 LYS Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 178 GLU Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 87 SER Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain i residue 8 THR Chi-restraints excluded: chain i residue 27 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 67 LYS Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 71 SER Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 61 VAL Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain u residue 30 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 17 SER Chi-restraints excluded: chain 0 residue 43 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 6 residue 16 CYS Chi-restraints excluded: chain 6 residue 39 LYS Chi-restraints excluded: chain 6 residue 66 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 521 optimal weight: 10.0000 chunk 291 optimal weight: 0.7980 chunk 781 optimal weight: 0.0270 chunk 639 optimal weight: 10.0000 chunk 259 optimal weight: 8.9990 chunk 940 optimal weight: 10.0000 chunk 1016 optimal weight: 9.9990 chunk 837 optimal weight: 8.9990 chunk 932 optimal weight: 5.9990 chunk 320 optimal weight: 20.0000 chunk 754 optimal weight: 0.9990 overall best weight: 3.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 175 HIS ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 58 GLN ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 GLN j 58 ASN k 37 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 19 ASN o 41 HIS p 9 HIS p 18 GLN ** t 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 54 GLN C 116 GLN C 133 ASN E 195 GLN ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN I 42 ASN J 131 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN 0 3 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 160920 Z= 0.185 Angle : 0.646 14.215 240962 Z= 0.348 Chirality : 0.034 0.336 30724 Planarity : 0.006 0.133 12791 Dihedral : 23.453 179.403 81019 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.73 % Favored : 92.67 % Rotamer: Outliers : 4.29 % Allowed : 17.51 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.11), residues: 5717 helix: 0.20 (0.12), residues: 1873 sheet: -2.27 (0.14), residues: 1035 loop : -0.92 (0.12), residues: 2809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 212 HIS 0.009 0.001 HIS f 11 PHE 0.042 0.002 PHE s 40 TYR 0.052 0.002 TYR b 212 ARG 0.020 0.001 ARG F 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1935 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1732 time to evaluate : 6.268 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: b 45 THR cc_start: 0.8174 (m) cc_final: 0.7843 (m) REVERT: b 55 GLU cc_start: 0.8133 (tp30) cc_final: 0.7554 (tp30) REVERT: b 81 ASP cc_start: 0.7847 (m-30) cc_final: 0.7491 (m-30) REVERT: b 90 PHE cc_start: 0.8585 (p90) cc_final: 0.7706 (p90) REVERT: b 92 ASN cc_start: 0.8562 (p0) cc_final: 0.8285 (p0) REVERT: b 107 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7911 (mtm180) REVERT: b 168 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6963 (tp30) REVERT: b 178 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6304 (pt) REVERT: c 41 TYR cc_start: 0.8786 (t80) cc_final: 0.8445 (t80) REVERT: c 87 ARG cc_start: 0.8333 (mtt180) cc_final: 0.8086 (ttp-170) REVERT: c 134 LYS cc_start: 0.8799 (mttt) cc_final: 0.8542 (tmmt) REVERT: c 135 ARG cc_start: 0.8460 (ttt180) cc_final: 0.7858 (tpp-160) REVERT: c 139 ASN cc_start: 0.8689 (m-40) cc_final: 0.8365 (m-40) REVERT: c 187 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8219 (mt-10) REVERT: d 13 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7054 (tpp-160) REVERT: d 46 ARG cc_start: 0.8214 (ttm110) cc_final: 0.7782 (tpm170) REVERT: d 69 ARG cc_start: 0.8888 (tpp-160) cc_final: 0.8155 (ptt180) REVERT: d 84 ASN cc_start: 0.7769 (t0) cc_final: 0.6797 (m-40) REVERT: d 103 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7448 (mpt-90) REVERT: e 38 VAL cc_start: 0.9107 (m) cc_final: 0.8775 (p) REVERT: f 17 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7354 (pp30) REVERT: f 45 ARG cc_start: 0.7183 (ptm160) cc_final: 0.6630 (ptt180) REVERT: f 46 GLN cc_start: 0.7837 (tt0) cc_final: 0.7623 (tp40) REVERT: f 65 GLU cc_start: 0.8240 (tp30) cc_final: 0.7691 (tp30) REVERT: g 20 GLU cc_start: 0.7837 (pp20) cc_final: 0.7612 (pp20) REVERT: g 43 TYR cc_start: 0.8203 (m-80) cc_final: 0.7741 (m-80) REVERT: g 67 ASN cc_start: 0.8182 (m-40) cc_final: 0.7711 (t0) REVERT: g 77 ARG cc_start: 0.6905 (ttt90) cc_final: 0.6624 (ttm-80) REVERT: g 122 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6553 (tp30) REVERT: g 128 GLU cc_start: 0.8652 (mt-10) cc_final: 0.7577 (tm-30) REVERT: g 129 ASN cc_start: 0.8235 (p0) cc_final: 0.7985 (p0) REVERT: h 2 MET cc_start: 0.8778 (ptp) cc_final: 0.8340 (tpp) REVERT: h 42 GLU cc_start: 0.8526 (tp30) cc_final: 0.8252 (tp30) REVERT: h 59 GLU cc_start: 0.7305 (pm20) cc_final: 0.6795 (pm20) REVERT: h 78 SER cc_start: 0.8642 (t) cc_final: 0.8310 (p) REVERT: h 120 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7215 (pt) REVERT: i 32 ARG cc_start: 0.8809 (mmm-85) cc_final: 0.8462 (mmm-85) REVERT: i 67 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8741 (mtmt) REVERT: j 24 GLU cc_start: 0.8696 (tp30) cc_final: 0.7891 (tm-30) REVERT: j 28 THR cc_start: 0.8387 (m) cc_final: 0.8041 (m) REVERT: j 63 ASP cc_start: 0.8128 (t0) cc_final: 0.7716 (t0) REVERT: j 66 GLU cc_start: 0.8424 (pt0) cc_final: 0.8164 (pt0) REVERT: j 68 ARG cc_start: 0.8946 (mtt180) cc_final: 0.8601 (mtt180) REVERT: j 69 THR cc_start: 0.9150 (m) cc_final: 0.8665 (p) REVERT: k 34 THR cc_start: 0.8720 (p) cc_final: 0.8281 (t) REVERT: k 36 ARG cc_start: 0.8377 (tpp80) cc_final: 0.8094 (tpp80) REVERT: k 37 GLN cc_start: 0.8610 (mt0) cc_final: 0.8296 (mp-120) REVERT: k 52 ARG cc_start: 0.8033 (tpp-160) cc_final: 0.7792 (mmm160) REVERT: k 68 ARG cc_start: 0.8217 (ttm110) cc_final: 0.7556 (mtt180) REVERT: k 69 CYS cc_start: 0.9052 (t) cc_final: 0.8543 (t) REVERT: k 104 PHE cc_start: 0.8556 (m-80) cc_final: 0.8212 (m-80) REVERT: k 105 ARG cc_start: 0.7310 (mtp-110) cc_final: 0.7011 (mtp85) REVERT: k 110 THR cc_start: 0.8450 (p) cc_final: 0.8168 (t) REVERT: k 111 ASP cc_start: 0.8071 (t70) cc_final: 0.7822 (t70) REVERT: l 8 ARG cc_start: 0.8255 (ttm110) cc_final: 0.8002 (tpm170) REVERT: l 37 TYR cc_start: 0.7766 (p90) cc_final: 0.7357 (p90) REVERT: l 81 ILE cc_start: 0.9146 (tp) cc_final: 0.8936 (tp) REVERT: l 111 GLN cc_start: 0.7635 (mt0) cc_final: 0.7331 (mt0) REVERT: m 77 LYS cc_start: 0.8567 (tttm) cc_final: 0.8250 (tptt) REVERT: n 25 GLU cc_start: 0.8543 (pm20) cc_final: 0.8110 (pm20) REVERT: o 39 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7721 (tt0) REVERT: p 5 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7396 (ptt-90) REVERT: p 63 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7895 (tp-100) REVERT: q 17 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7634 (tp30) REVERT: q 30 HIS cc_start: 0.8809 (t-90) cc_final: 0.8515 (t-90) REVERT: q 41 THR cc_start: 0.9093 (t) cc_final: 0.8882 (t) REVERT: q 43 LEU cc_start: 0.8768 (mt) cc_final: 0.8561 (mp) REVERT: q 61 ARG cc_start: 0.7652 (ptt90) cc_final: 0.7210 (ttp-170) REVERT: q 72 TRP cc_start: 0.8105 (m100) cc_final: 0.7892 (m100) REVERT: r 20 ILE cc_start: 0.7030 (mm) cc_final: 0.6559 (mm) REVERT: s 19 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7678 (tm-30) REVERT: s 23 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7221 (mt-10) REVERT: s 30 LEU cc_start: 0.7182 (mp) cc_final: 0.6846 (mm) REVERT: s 36 ARG cc_start: 0.7817 (ptp-170) cc_final: 0.7526 (ptt180) REVERT: s 62 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8095 (p) REVERT: t 35 TYR cc_start: 0.8188 (m-80) cc_final: 0.7987 (m-80) REVERT: t 39 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7181 (mm-30) REVERT: t 43 LYS cc_start: 0.8274 (pttt) cc_final: 0.7850 (tttt) REVERT: t 47 GLN cc_start: 0.8750 (tp40) cc_final: 0.8472 (tp40) REVERT: t 82 ILE cc_start: 0.8522 (pt) cc_final: 0.8239 (mt) REVERT: C 33 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8745 (mp) REVERT: C 113 ASP cc_start: 0.7949 (m-30) cc_final: 0.7347 (t0) REVERT: C 142 ASN cc_start: 0.9318 (t0) cc_final: 0.8958 (t0) REVERT: C 152 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8026 (mm-40) REVERT: C 180 MET cc_start: 0.8360 (mmt) cc_final: 0.7998 (mmt) REVERT: C 268 ARG cc_start: 0.8473 (mmt180) cc_final: 0.8159 (mmm-85) REVERT: D 16 THR cc_start: 0.8154 (p) cc_final: 0.7810 (t) REVERT: D 28 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8614 (tm-30) REVERT: D 30 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7818 (mp0) REVERT: D 165 MET cc_start: 0.8899 (ttm) cc_final: 0.8674 (ttt) REVERT: D 189 VAL cc_start: 0.9179 (m) cc_final: 0.8811 (p) REVERT: E 116 ASP cc_start: 0.8061 (m-30) cc_final: 0.7699 (t0) REVERT: E 122 GLU cc_start: 0.6300 (pm20) cc_final: 0.6100 (pm20) REVERT: E 127 GLU cc_start: 0.6757 (pm20) cc_final: 0.6371 (pm20) REVERT: E 136 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7496 (tm-30) REVERT: E 154 ASP cc_start: 0.4631 (m-30) cc_final: 0.4153 (m-30) REVERT: E 156 ASN cc_start: 0.8072 (t0) cc_final: 0.7604 (p0) REVERT: E 171 ASP cc_start: 0.8046 (t70) cc_final: 0.7824 (t70) REVERT: E 176 ASP cc_start: 0.6156 (t0) cc_final: 0.5086 (p0) REVERT: F 10 GLU cc_start: 0.7976 (mp0) cc_final: 0.7735 (mp0) REVERT: F 79 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7138 (mmm160) REVERT: F 127 TYR cc_start: 0.8444 (t80) cc_final: 0.8178 (t80) REVERT: F 144 LYS cc_start: 0.7852 (mmtt) cc_final: 0.7577 (mmtm) REVERT: F 163 GLU cc_start: 0.7755 (tp30) cc_final: 0.7470 (tp30) REVERT: G 19 ASN cc_start: 0.7083 (t0) cc_final: 0.6844 (t0) REVERT: G 37 ASN cc_start: 0.7000 (t0) cc_final: 0.6697 (p0) REVERT: G 94 ARG cc_start: 0.8477 (mtt180) cc_final: 0.8271 (mtp180) REVERT: G 127 GLN cc_start: 0.7845 (tt0) cc_final: 0.7271 (tt0) REVERT: I 16 MET cc_start: 0.4477 (mmp) cc_final: 0.3995 (ptp) REVERT: I 116 MET cc_start: 0.3368 (mmp) cc_final: 0.2684 (tpp) REVERT: H 30 LEU cc_start: 0.8213 (mt) cc_final: 0.7993 (mt) REVERT: J 34 ARG cc_start: 0.9079 (mmm-85) cc_final: 0.8738 (ttt-90) REVERT: J 58 ASN cc_start: 0.8133 (t0) cc_final: 0.7639 (t0) REVERT: J 99 ARG cc_start: 0.8624 (mmm-85) cc_final: 0.8174 (mmm-85) REVERT: J 128 ASN cc_start: 0.8404 (t0) cc_final: 0.7418 (m110) REVERT: L 63 LYS cc_start: 0.9384 (ptmt) cc_final: 0.9051 (pttt) REVERT: L 78 ARG cc_start: 0.8155 (mtt90) cc_final: 0.7851 (mtt90) REVERT: M 30 SER cc_start: 0.8840 (m) cc_final: 0.8405 (p) REVERT: N 24 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8896 (mtm) REVERT: N 74 GLU cc_start: 0.9214 (tm-30) cc_final: 0.8717 (tp30) REVERT: N 114 GLU cc_start: 0.8292 (pm20) cc_final: 0.7897 (pm20) REVERT: O 56 LYS cc_start: 0.6537 (pttm) cc_final: 0.6183 (ttmm) REVERT: O 111 ARG cc_start: 0.8004 (mmm160) cc_final: 0.7724 (mmt180) REVERT: P 28 LYS cc_start: 0.8803 (ttmm) cc_final: 0.8493 (mttt) REVERT: P 81 ASP cc_start: 0.8340 (t0) cc_final: 0.8009 (t0) REVERT: P 84 SER cc_start: 0.8291 (m) cc_final: 0.8018 (p) REVERT: P 87 ARG cc_start: 0.7932 (mtp-110) cc_final: 0.7433 (ttp-170) REVERT: P 95 LYS cc_start: 0.8986 (mptt) cc_final: 0.8533 (mmmt) REVERT: Q 46 TYR cc_start: 0.9287 (t80) cc_final: 0.8825 (t80) REVERT: Q 83 LYS cc_start: 0.8588 (ttpp) cc_final: 0.7826 (mptt) REVERT: Q 101 ASP cc_start: 0.8205 (t0) cc_final: 0.7915 (t0) REVERT: R 34 GLU cc_start: 0.8517 (mm-30) cc_final: 0.7937 (pm20) REVERT: R 55 ASP cc_start: 0.7943 (t0) cc_final: 0.7682 (t0) REVERT: S 3 THR cc_start: 0.8349 (m) cc_final: 0.7451 (p) REVERT: S 62 ASP cc_start: 0.8655 (m-30) cc_final: 0.8130 (m-30) REVERT: S 65 ASP cc_start: 0.8139 (t0) cc_final: 0.7754 (t0) REVERT: S 66 ILE cc_start: 0.8456 (mp) cc_final: 0.8156 (mt) REVERT: S 84 ARG cc_start: 0.8479 (mmt-90) cc_final: 0.8088 (mmt180) REVERT: S 107 VAL cc_start: 0.9240 (m) cc_final: 0.8600 (p) REVERT: T 44 LYS cc_start: 0.8107 (tttm) cc_final: 0.7807 (tttm) REVERT: T 52 GLU cc_start: 0.8420 (pp20) cc_final: 0.8026 (mt-10) REVERT: U 6 ARG cc_start: 0.8425 (tpp-160) cc_final: 0.8196 (tpp-160) REVERT: U 25 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7699 (tttt) REVERT: V 1 MET cc_start: 0.5387 (ptm) cc_final: 0.4923 (mmt) REVERT: V 7 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7804 (pp20) REVERT: V 29 ILE cc_start: 0.9195 (tp) cc_final: 0.8842 (tp) REVERT: V 38 LEU cc_start: 0.8428 (tp) cc_final: 0.8113 (tp) REVERT: V 48 MET cc_start: 0.8650 (tpp) cc_final: 0.8307 (tpp) REVERT: V 56 PHE cc_start: 0.9108 (t80) cc_final: 0.8800 (t80) REVERT: W 7 ARG cc_start: 0.7982 (tpp80) cc_final: 0.7617 (mtm-85) REVERT: X 18 SER cc_start: 0.9011 (p) cc_final: 0.8734 (m) REVERT: X 34 SER cc_start: 0.8858 (m) cc_final: 0.8619 (t) REVERT: Y 4 LYS cc_start: 0.8308 (tmtt) cc_final: 0.8039 (tptt) REVERT: Y 39 GLN cc_start: 0.8345 (pt0) cc_final: 0.7932 (pt0) REVERT: Y 50 VAL cc_start: 0.9055 (t) cc_final: 0.8837 (p) REVERT: 0 12 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7762 (ttp-170) REVERT: 0 51 ARG cc_start: 0.9047 (ptp-170) cc_final: 0.8753 (ptp-110) REVERT: 1 9 LYS cc_start: 0.7819 (ttpt) cc_final: 0.7511 (tttt) REVERT: 1 18 HIS cc_start: 0.8269 (t70) cc_final: 0.8044 (t-90) REVERT: 6 8 LYS cc_start: 0.8261 (tptt) cc_final: 0.7904 (tptp) REVERT: 6 59 ARG cc_start: 0.8485 (ptt90) cc_final: 0.7142 (tpt90) REVERT: 6 66 ILE cc_start: 0.2004 (OUTLIER) cc_final: 0.1583 (mp) outliers start: 203 outliers final: 122 residues processed: 1807 average time/residue: 1.3332 time to fit residues: 4120.0832 Evaluate side-chains 1740 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1608 time to evaluate : 5.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 145 ASN Chi-restraints excluded: chain b residue 147 LEU Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 107 LYS Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 160 GLU Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 82 LYS Chi-restraints excluded: chain e residue 21 SER Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 87 SER Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 42 VAL Chi-restraints excluded: chain g residue 53 SER Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 105 GLU Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 27 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 67 LYS Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 11 VAL Chi-restraints excluded: chain q residue 17 GLU Chi-restraints excluded: chain q residue 45 VAL Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 62 THR Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 39 LYS Chi-restraints excluded: chain 6 residue 66 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 929 optimal weight: 3.9990 chunk 707 optimal weight: 0.8980 chunk 488 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 448 optimal weight: 10.0000 chunk 631 optimal weight: 20.0000 chunk 944 optimal weight: 1.9990 chunk 999 optimal weight: 6.9990 chunk 493 optimal weight: 10.0000 chunk 894 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 175 HIS ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 53 GLN ** d 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 GLN f 14 GLN i 30 ASN i 109 GLN j 58 ASN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 19 ASN p 18 GLN ** q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 74 HIS D 36 GLN E 195 GLN ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN 0 3 GLN ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 160920 Z= 0.170 Angle : 0.622 14.044 240962 Z= 0.338 Chirality : 0.033 0.336 30724 Planarity : 0.006 0.125 12791 Dihedral : 23.383 179.897 81018 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.21 % Favored : 93.21 % Rotamer: Outliers : 4.46 % Allowed : 18.91 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.11), residues: 5717 helix: 0.52 (0.12), residues: 1855 sheet: -1.99 (0.14), residues: 1027 loop : -0.85 (0.12), residues: 2835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 212 HIS 0.008 0.001 HIS f 11 PHE 0.027 0.002 PHE t 50 TYR 0.036 0.002 TYR b 212 ARG 0.008 0.001 ARG N 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1902 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1691 time to evaluate : 6.164 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: b 45 THR cc_start: 0.8126 (m) cc_final: 0.7843 (m) REVERT: b 81 ASP cc_start: 0.7803 (m-30) cc_final: 0.7546 (m-30) REVERT: b 90 PHE cc_start: 0.8630 (p90) cc_final: 0.8193 (p90) REVERT: b 92 ASN cc_start: 0.8628 (p0) cc_final: 0.8372 (p0) REVERT: b 107 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7888 (mtm180) REVERT: b 160 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7972 (tt) REVERT: b 168 GLU cc_start: 0.7603 (mt-10) cc_final: 0.6783 (tp30) REVERT: b 178 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6287 (pt) REVERT: c 134 LYS cc_start: 0.8772 (mttt) cc_final: 0.8528 (tmmt) REVERT: c 135 ARG cc_start: 0.8595 (ttt180) cc_final: 0.7948 (tpp-160) REVERT: c 139 ASN cc_start: 0.8752 (m-40) cc_final: 0.8477 (m-40) REVERT: d 9 LYS cc_start: 0.6928 (tttt) cc_final: 0.6415 (mmtp) REVERT: d 13 ARG cc_start: 0.7499 (ttm-80) cc_final: 0.7159 (tpp-160) REVERT: d 43 ARG cc_start: 0.7467 (mmt180) cc_final: 0.6768 (ttt90) REVERT: d 46 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7638 (tpm170) REVERT: d 71 PHE cc_start: 0.8935 (t80) cc_final: 0.8726 (t80) REVERT: d 84 ASN cc_start: 0.7881 (t0) cc_final: 0.7113 (m-40) REVERT: d 103 ARG cc_start: 0.8106 (mmm-85) cc_final: 0.7594 (mpt-90) REVERT: d 169 TRP cc_start: 0.7108 (p90) cc_final: 0.6197 (p90) REVERT: e 119 VAL cc_start: 0.7891 (t) cc_final: 0.7515 (m) REVERT: e 127 TYR cc_start: 0.8789 (m-10) cc_final: 0.8584 (m-10) REVERT: e 134 ASN cc_start: 0.8717 (m-40) cc_final: 0.8310 (m110) REVERT: f 1 MET cc_start: 0.7483 (mmm) cc_final: 0.7133 (tpt) REVERT: f 36 ILE cc_start: 0.8359 (mm) cc_final: 0.8141 (mm) REVERT: f 65 GLU cc_start: 0.8089 (tp30) cc_final: 0.7515 (tp30) REVERT: g 43 TYR cc_start: 0.8212 (m-80) cc_final: 0.7850 (m-10) REVERT: g 67 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7782 (t0) REVERT: g 122 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6626 (tp30) REVERT: g 128 GLU cc_start: 0.8536 (mt-10) cc_final: 0.7468 (tm-30) REVERT: g 129 ASN cc_start: 0.8146 (p0) cc_final: 0.7831 (p0) REVERT: h 2 MET cc_start: 0.8745 (ptp) cc_final: 0.8290 (tpp) REVERT: h 42 GLU cc_start: 0.8447 (tp30) cc_final: 0.8149 (tp30) REVERT: h 59 GLU cc_start: 0.7077 (pm20) cc_final: 0.6632 (pm20) REVERT: h 78 SER cc_start: 0.8577 (t) cc_final: 0.8228 (p) REVERT: h 117 GLN cc_start: 0.8412 (tp40) cc_final: 0.8112 (mm-40) REVERT: h 120 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7218 (pt) REVERT: i 5 TYR cc_start: 0.6644 (m-10) cc_final: 0.6208 (m-10) REVERT: i 32 ARG cc_start: 0.8768 (mmm-85) cc_final: 0.8442 (mmm-85) REVERT: i 67 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8715 (mtmt) REVERT: j 24 GLU cc_start: 0.8672 (tp30) cc_final: 0.7881 (tm-30) REVERT: j 66 GLU cc_start: 0.8426 (pt0) cc_final: 0.8062 (pt0) REVERT: j 68 ARG cc_start: 0.8884 (mtt180) cc_final: 0.8527 (mtt180) REVERT: j 69 THR cc_start: 0.9217 (m) cc_final: 0.8683 (p) REVERT: k 34 THR cc_start: 0.8766 (p) cc_final: 0.8344 (t) REVERT: k 36 ARG cc_start: 0.8441 (tpp80) cc_final: 0.8146 (tpp80) REVERT: k 51 PHE cc_start: 0.6802 (m-80) cc_final: 0.6572 (m-80) REVERT: k 52 ARG cc_start: 0.8079 (tpp-160) cc_final: 0.7842 (mmm160) REVERT: k 104 PHE cc_start: 0.8550 (m-80) cc_final: 0.8213 (m-80) REVERT: k 110 THR cc_start: 0.8424 (p) cc_final: 0.8179 (t) REVERT: l 8 ARG cc_start: 0.8238 (ttm110) cc_final: 0.8015 (tpm170) REVERT: l 37 TYR cc_start: 0.7896 (p90) cc_final: 0.7675 (p90) REVERT: l 111 GLN cc_start: 0.7629 (mt0) cc_final: 0.7315 (mt0) REVERT: m 77 LYS cc_start: 0.8625 (tttm) cc_final: 0.8352 (tptt) REVERT: n 25 GLU cc_start: 0.8584 (pm20) cc_final: 0.8105 (pm20) REVERT: n 78 LEU cc_start: 0.8909 (mt) cc_final: 0.8664 (mt) REVERT: p 63 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8119 (mm-40) REVERT: q 17 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7634 (tp30) REVERT: q 61 ARG cc_start: 0.7618 (ptt90) cc_final: 0.6987 (ttp-110) REVERT: q 72 TRP cc_start: 0.8193 (m100) cc_final: 0.7942 (m100) REVERT: r 20 ILE cc_start: 0.6938 (mm) cc_final: 0.6681 (mm) REVERT: r 30 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.7805 (t0) REVERT: s 16 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8221 (mmtm) REVERT: s 19 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7617 (tm-30) REVERT: s 23 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7001 (mt-10) REVERT: s 30 LEU cc_start: 0.7303 (mp) cc_final: 0.6750 (mm) REVERT: s 62 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8293 (p) REVERT: t 39 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7213 (mm-30) REVERT: t 43 LYS cc_start: 0.8440 (pttt) cc_final: 0.7925 (tttt) REVERT: t 47 GLN cc_start: 0.8717 (tp40) cc_final: 0.8507 (tp-100) REVERT: C 33 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8707 (mp) REVERT: C 86 ARG cc_start: 0.8849 (mtt-85) cc_final: 0.8139 (ptp-110) REVERT: C 113 ASP cc_start: 0.7957 (m-30) cc_final: 0.7363 (t0) REVERT: C 142 ASN cc_start: 0.9334 (t0) cc_final: 0.8947 (t0) REVERT: C 152 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8036 (mm-40) REVERT: C 180 MET cc_start: 0.8324 (mmt) cc_final: 0.7989 (mmt) REVERT: D 28 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8359 (tm-30) REVERT: D 30 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7809 (mp0) REVERT: D 99 GLU cc_start: 0.7929 (pm20) cc_final: 0.7472 (mp0) REVERT: D 203 VAL cc_start: 0.9168 (t) cc_final: 0.8923 (m) REVERT: E 74 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8775 (mtmm) REVERT: E 116 ASP cc_start: 0.8160 (m-30) cc_final: 0.7728 (t0) REVERT: E 127 GLU cc_start: 0.6838 (pm20) cc_final: 0.6389 (pm20) REVERT: E 136 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7581 (tm-30) REVERT: E 156 ASN cc_start: 0.8110 (t0) cc_final: 0.7630 (p0) REVERT: E 171 ASP cc_start: 0.7971 (t70) cc_final: 0.7615 (t70) REVERT: E 176 ASP cc_start: 0.6605 (t0) cc_final: 0.5643 (p0) REVERT: E 198 GLU cc_start: 0.8302 (tp30) cc_final: 0.7235 (tt0) REVERT: F 16 MET cc_start: 0.8026 (mmt) cc_final: 0.7761 (mmp) REVERT: F 36 ASN cc_start: 0.7489 (t0) cc_final: 0.7162 (t0) REVERT: F 79 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7122 (mmm160) REVERT: F 100 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8517 (tm-30) REVERT: F 128 SER cc_start: 0.9074 (OUTLIER) cc_final: 0.8285 (p) REVERT: F 163 GLU cc_start: 0.7745 (tp30) cc_final: 0.7469 (tp30) REVERT: G 19 ASN cc_start: 0.7164 (t0) cc_final: 0.6879 (t0) REVERT: G 94 ARG cc_start: 0.8462 (mtt180) cc_final: 0.8143 (mtp180) REVERT: G 127 GLN cc_start: 0.7835 (tt0) cc_final: 0.7290 (tt0) REVERT: G 152 ARG cc_start: 0.8744 (ttm110) cc_final: 0.8515 (ttm110) REVERT: I 16 MET cc_start: 0.4529 (mmp) cc_final: 0.4058 (ptp) REVERT: I 116 MET cc_start: 0.3180 (mmp) cc_final: 0.2547 (tpp) REVERT: J 34 ARG cc_start: 0.9075 (mmm-85) cc_final: 0.8757 (ttp80) REVERT: J 58 ASN cc_start: 0.7962 (t0) cc_final: 0.7498 (t0) REVERT: J 91 GLU cc_start: 0.8520 (tp30) cc_final: 0.8278 (tp30) REVERT: J 92 MET cc_start: 0.9594 (mmm) cc_final: 0.9376 (mmt) REVERT: J 99 ARG cc_start: 0.8624 (mmm-85) cc_final: 0.8368 (mmm-85) REVERT: J 128 ASN cc_start: 0.8385 (t0) cc_final: 0.7294 (m110) REVERT: J 131 ASN cc_start: 0.7941 (t0) cc_final: 0.7673 (t0) REVERT: L 14 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7781 (mmmm) REVERT: L 55 MET cc_start: 0.8796 (tpp) cc_final: 0.8564 (tpp) REVERT: L 63 LYS cc_start: 0.9420 (ptmt) cc_final: 0.9082 (pttt) REVERT: L 78 ARG cc_start: 0.8256 (mtt90) cc_final: 0.8035 (mtt90) REVERT: M 30 SER cc_start: 0.8858 (m) cc_final: 0.8414 (p) REVERT: M 31 PHE cc_start: 0.8605 (m-10) cc_final: 0.8397 (m-10) REVERT: N 74 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8672 (tp30) REVERT: N 114 GLU cc_start: 0.8249 (pm20) cc_final: 0.7885 (pm20) REVERT: O 15 ARG cc_start: 0.8905 (tpp80) cc_final: 0.8314 (ttm-80) REVERT: O 56 LYS cc_start: 0.6711 (pttm) cc_final: 0.6272 (ttmm) REVERT: O 108 ASP cc_start: 0.8382 (m-30) cc_final: 0.8174 (m-30) REVERT: P 28 LYS cc_start: 0.8723 (ttmm) cc_final: 0.8498 (mttt) REVERT: P 52 ARG cc_start: 0.8516 (mmt-90) cc_final: 0.8222 (mmt-90) REVERT: P 84 SER cc_start: 0.8349 (m) cc_final: 0.7937 (p) REVERT: P 95 LYS cc_start: 0.9013 (mptt) cc_final: 0.8552 (mmmt) REVERT: P 108 ARG cc_start: 0.8653 (mtm180) cc_final: 0.8442 (mtm110) REVERT: Q 46 TYR cc_start: 0.9324 (t80) cc_final: 0.8871 (t80) REVERT: Q 83 LYS cc_start: 0.8539 (ttpp) cc_final: 0.7854 (mptt) REVERT: Q 101 ASP cc_start: 0.8232 (t0) cc_final: 0.7926 (t0) REVERT: R 34 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7896 (pm20) REVERT: R 86 GLN cc_start: 0.9126 (tt0) cc_final: 0.8910 (tt0) REVERT: S 3 THR cc_start: 0.8402 (m) cc_final: 0.7652 (p) REVERT: S 62 ASP cc_start: 0.8504 (m-30) cc_final: 0.8016 (m-30) REVERT: S 65 ASP cc_start: 0.8077 (t0) cc_final: 0.7623 (t0) REVERT: S 107 VAL cc_start: 0.9286 (m) cc_final: 0.8887 (m) REVERT: T 4 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7869 (tm-30) REVERT: T 52 GLU cc_start: 0.8376 (pp20) cc_final: 0.8043 (mt-10) REVERT: U 25 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7750 (tttt) REVERT: V 7 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7954 (pp20) REVERT: V 24 ASN cc_start: 0.8082 (t0) cc_final: 0.7786 (t0) REVERT: V 29 ILE cc_start: 0.9143 (tp) cc_final: 0.8781 (tp) REVERT: V 38 LEU cc_start: 0.8500 (tp) cc_final: 0.8158 (tp) REVERT: V 56 PHE cc_start: 0.9100 (t80) cc_final: 0.8729 (t80) REVERT: V 68 LYS cc_start: 0.7606 (mmtm) cc_final: 0.7398 (mppt) REVERT: W 7 ARG cc_start: 0.7976 (tpp80) cc_final: 0.7617 (mtm-85) REVERT: W 12 SER cc_start: 0.9249 (m) cc_final: 0.9033 (p) REVERT: X 18 SER cc_start: 0.9017 (p) cc_final: 0.8689 (m) REVERT: X 34 SER cc_start: 0.8832 (m) cc_final: 0.8600 (t) REVERT: X 60 LYS cc_start: 0.8448 (ttmt) cc_final: 0.8100 (ttpp) REVERT: Y 19 LEU cc_start: 0.8814 (mm) cc_final: 0.8324 (pp) REVERT: Z 36 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7655 (mm-30) REVERT: 0 4 GLN cc_start: 0.8941 (tp40) cc_final: 0.8639 (tp40) REVERT: 0 51 ARG cc_start: 0.9084 (ptp-170) cc_final: 0.8762 (ptp-110) REVERT: 1 9 LYS cc_start: 0.7698 (ttpt) cc_final: 0.7450 (tttt) REVERT: 1 18 HIS cc_start: 0.8255 (t70) cc_final: 0.8043 (t-90) REVERT: 2 28 ARG cc_start: 0.9001 (mtm-85) cc_final: 0.8775 (mtm110) REVERT: 4 30 GLU cc_start: 0.8265 (tm-30) cc_final: 0.8057 (tm-30) REVERT: 4 36 ARG cc_start: 0.9048 (ttt90) cc_final: 0.8813 (ttt-90) REVERT: 6 8 LYS cc_start: 0.8309 (tptt) cc_final: 0.7969 (tptp) REVERT: 6 59 ARG cc_start: 0.8334 (ptt90) cc_final: 0.6975 (tpt90) REVERT: 6 66 ILE cc_start: 0.1653 (OUTLIER) cc_final: 0.1234 (mp) outliers start: 211 outliers final: 140 residues processed: 1774 average time/residue: 1.3477 time to fit residues: 4100.2820 Evaluate side-chains 1757 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1603 time to evaluate : 6.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 147 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 107 LYS Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 48 SER Chi-restraints excluded: chain d residue 82 LYS Chi-restraints excluded: chain e residue 21 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 47 PHE Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 87 SER Chi-restraints excluded: chain g residue 16 LYS Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 40 SER Chi-restraints excluded: chain g residue 53 SER Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 67 ASN Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 27 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 67 LYS Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 17 GLU Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain r residue 30 ASN Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain s residue 62 THR Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain W residue 52 ASP Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 17 SER Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 39 LYS Chi-restraints excluded: chain 6 residue 66 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 832 optimal weight: 40.0000 chunk 567 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 744 optimal weight: 0.0370 chunk 412 optimal weight: 20.0000 chunk 852 optimal weight: 0.9990 chunk 690 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 510 optimal weight: 50.0000 chunk 897 optimal weight: 9.9990 chunk 252 optimal weight: 30.0000 overall best weight: 6.2070 ------------------------------------------------------------------------------- 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 175 HIS ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 53 GLN ** d 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 GLN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 30 ASN i 36 GLN j 58 ASN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 19 ASN p 59 HIS t 74 HIS E 195 GLN ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN J 58 ASN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 33 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 160920 Z= 0.274 Angle : 0.674 14.065 240962 Z= 0.361 Chirality : 0.036 0.354 30724 Planarity : 0.007 0.131 12791 Dihedral : 23.375 179.815 81018 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.21 % Favored : 92.25 % Rotamer: Outliers : 5.77 % Allowed : 19.42 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.03 (0.11), residues: 5717 helix: 0.46 (0.12), residues: 1855 sheet: -1.77 (0.15), residues: 1011 loop : -0.97 (0.12), residues: 2851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 212 HIS 0.009 0.001 HIS f 58 PHE 0.026 0.002 PHE b 49 TYR 0.040 0.002 TYR d 75 ARG 0.008 0.001 ARG U 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1925 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1652 time to evaluate : 6.245 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: b 45 THR cc_start: 0.8166 (m) cc_final: 0.7883 (m) REVERT: b 48 MET cc_start: 0.7687 (mmm) cc_final: 0.7463 (mmm) REVERT: b 81 ASP cc_start: 0.7801 (m-30) cc_final: 0.7557 (m-30) REVERT: b 90 PHE cc_start: 0.8716 (p90) cc_final: 0.8220 (p90) REVERT: b 92 ASN cc_start: 0.8674 (p0) cc_final: 0.8361 (p0) REVERT: b 168 GLU cc_start: 0.7725 (mt-10) cc_final: 0.6928 (tp30) REVERT: b 178 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6319 (pt) REVERT: b 212 TYR cc_start: 0.8256 (m-80) cc_final: 0.7947 (m-80) REVERT: c 134 LYS cc_start: 0.8772 (mttt) cc_final: 0.8507 (tmmt) REVERT: c 135 ARG cc_start: 0.8565 (ttt180) cc_final: 0.7919 (tpp-160) REVERT: c 138 GLN cc_start: 0.9055 (tp40) cc_final: 0.8706 (tt0) REVERT: c 139 ASN cc_start: 0.8761 (m-40) cc_final: 0.8412 (m-40) REVERT: c 169 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8612 (mp0) REVERT: d 9 LYS cc_start: 0.7097 (tttt) cc_final: 0.6509 (mmtp) REVERT: d 43 ARG cc_start: 0.7519 (mmt180) cc_final: 0.6808 (ttt90) REVERT: d 46 ARG cc_start: 0.8264 (ttm110) cc_final: 0.7872 (mmp-170) REVERT: d 53 GLN cc_start: 0.8297 (mp-120) cc_final: 0.7867 (mp-120) REVERT: d 84 ASN cc_start: 0.7838 (t0) cc_final: 0.7324 (m-40) REVERT: d 103 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7722 (mpt-90) REVERT: d 169 TRP cc_start: 0.7246 (p90) cc_final: 0.6497 (p90) REVERT: e 110 MET cc_start: 0.9199 (mmm) cc_final: 0.8791 (mmm) REVERT: e 119 VAL cc_start: 0.8024 (t) cc_final: 0.7723 (m) REVERT: e 127 TYR cc_start: 0.8973 (m-10) cc_final: 0.8752 (m-10) REVERT: f 44 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7451 (ttm-80) REVERT: f 59 TYR cc_start: 0.8353 (m-10) cc_final: 0.7794 (m-80) REVERT: g 16 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7945 (tttt) REVERT: g 43 TYR cc_start: 0.8295 (m-80) cc_final: 0.7729 (m-10) REVERT: g 67 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7880 (t0) REVERT: g 77 ARG cc_start: 0.6588 (ttt180) cc_final: 0.4758 (tmm160) REVERT: g 122 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6278 (tp30) REVERT: g 128 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7458 (tm-30) REVERT: g 129 ASN cc_start: 0.8280 (p0) cc_final: 0.7948 (p0) REVERT: h 2 MET cc_start: 0.8737 (ptp) cc_final: 0.8261 (tpp) REVERT: h 42 GLU cc_start: 0.8473 (tp30) cc_final: 0.8194 (tp30) REVERT: h 117 GLN cc_start: 0.8447 (tp40) cc_final: 0.8160 (mm-40) REVERT: h 120 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7218 (pt) REVERT: i 32 ARG cc_start: 0.8734 (mmm-85) cc_final: 0.8430 (mmm-85) REVERT: j 24 GLU cc_start: 0.8613 (tp30) cc_final: 0.7924 (tm-30) REVERT: j 65 TYR cc_start: 0.8752 (m-80) cc_final: 0.8547 (m-80) REVERT: j 68 ARG cc_start: 0.8814 (mtt180) cc_final: 0.8534 (mtt180) REVERT: j 69 THR cc_start: 0.9223 (m) cc_final: 0.8713 (p) REVERT: k 34 THR cc_start: 0.8769 (p) cc_final: 0.8331 (t) REVERT: k 68 ARG cc_start: 0.8487 (ttm110) cc_final: 0.7648 (mtt-85) REVERT: k 69 CYS cc_start: 0.9101 (t) cc_final: 0.8677 (t) REVERT: k 104 PHE cc_start: 0.8537 (m-80) cc_final: 0.8108 (m-80) REVERT: k 105 ARG cc_start: 0.6433 (ttp-110) cc_final: 0.5865 (tmm160) REVERT: k 124 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7505 (pttm) REVERT: l 111 GLN cc_start: 0.7503 (mt0) cc_final: 0.7159 (mt0) REVERT: m 77 LYS cc_start: 0.8763 (tttm) cc_final: 0.8470 (tptt) REVERT: m 82 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8647 (tt) REVERT: n 25 GLU cc_start: 0.8634 (pm20) cc_final: 0.8073 (pm20) REVERT: o 39 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7771 (tt0) REVERT: o 82 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8633 (mt-10) REVERT: p 63 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7624 (tp-100) REVERT: q 4 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7068 (tp) REVERT: r 20 ILE cc_start: 0.7111 (mm) cc_final: 0.6832 (mm) REVERT: r 28 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8638 (mp) REVERT: s 11 ASP cc_start: 0.8601 (m-30) cc_final: 0.8394 (m-30) REVERT: s 16 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8206 (mmtm) REVERT: s 19 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7675 (tm-30) REVERT: s 30 LEU cc_start: 0.7373 (mp) cc_final: 0.6873 (mm) REVERT: s 62 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8221 (p) REVERT: s 79 TYR cc_start: 0.8402 (t80) cc_final: 0.7967 (t80) REVERT: t 35 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7227 (t80) REVERT: t 47 GLN cc_start: 0.8864 (tp40) cc_final: 0.8663 (tp-100) REVERT: C 33 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8780 (mp) REVERT: C 86 ARG cc_start: 0.8936 (mtt-85) cc_final: 0.8132 (ptp-110) REVERT: C 142 ASN cc_start: 0.9399 (t0) cc_final: 0.9083 (t0) REVERT: C 152 GLN cc_start: 0.8914 (mm-40) cc_final: 0.7915 (mm-40) REVERT: C 180 MET cc_start: 0.8340 (mmt) cc_final: 0.8051 (mmt) REVERT: D 99 GLU cc_start: 0.7788 (pm20) cc_final: 0.7368 (mp0) REVERT: E 198 GLU cc_start: 0.8273 (tp30) cc_final: 0.7171 (tt0) REVERT: F 16 MET cc_start: 0.8090 (mmt) cc_final: 0.7805 (mmp) REVERT: F 79 ARG cc_start: 0.7752 (mtm110) cc_final: 0.7053 (mmm160) REVERT: F 128 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8068 (p) REVERT: G 94 ARG cc_start: 0.8588 (mtt180) cc_final: 0.8194 (mtp180) REVERT: G 127 GLN cc_start: 0.7937 (tt0) cc_final: 0.7521 (tt0) REVERT: I 16 MET cc_start: 0.4308 (mmp) cc_final: 0.3815 (ptp) REVERT: I 116 MET cc_start: 0.3228 (mmp) cc_final: 0.2301 (tpp) REVERT: J 17 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.9125 (p) REVERT: J 34 ARG cc_start: 0.9100 (mmm-85) cc_final: 0.8873 (mtp85) REVERT: J 58 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7590 (t0) REVERT: J 91 GLU cc_start: 0.8573 (tp30) cc_final: 0.8329 (tp30) REVERT: J 99 ARG cc_start: 0.8831 (mmm-85) cc_final: 0.8514 (mmm-85) REVERT: J 128 ASN cc_start: 0.8562 (t0) cc_final: 0.7547 (m110) REVERT: J 131 ASN cc_start: 0.7989 (t0) cc_final: 0.7586 (t160) REVERT: L 14 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7830 (mmmm) REVERT: L 63 LYS cc_start: 0.9443 (ptmt) cc_final: 0.9106 (pttt) REVERT: L 106 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7208 (tp30) REVERT: M 30 SER cc_start: 0.8871 (m) cc_final: 0.8528 (p) REVERT: M 45 GLN cc_start: 0.8839 (mt0) cc_final: 0.8549 (mt0) REVERT: M 78 LEU cc_start: 0.8864 (tt) cc_final: 0.8530 (mp) REVERT: N 74 GLU cc_start: 0.9235 (tm-30) cc_final: 0.8612 (tp30) REVERT: N 114 GLU cc_start: 0.8382 (pm20) cc_final: 0.7610 (pm20) REVERT: O 15 ARG cc_start: 0.8860 (tpp80) cc_final: 0.8306 (ttm-80) REVERT: O 56 LYS cc_start: 0.7003 (pttm) cc_final: 0.6606 (ttmm) REVERT: O 108 ASP cc_start: 0.8533 (m-30) cc_final: 0.8290 (m-30) REVERT: P 12 MET cc_start: 0.8108 (ttm) cc_final: 0.7888 (ttp) REVERT: P 28 LYS cc_start: 0.8813 (ttmm) cc_final: 0.8563 (mttt) REVERT: P 87 ARG cc_start: 0.8067 (mtp-110) cc_final: 0.7380 (ttp-170) REVERT: P 95 LYS cc_start: 0.9033 (mptt) cc_final: 0.8649 (mmmt) REVERT: Q 46 TYR cc_start: 0.9405 (t80) cc_final: 0.8993 (t80) REVERT: Q 83 LYS cc_start: 0.8536 (ttpp) cc_final: 0.7872 (mptt) REVERT: R 18 GLN cc_start: 0.8113 (pt0) cc_final: 0.7838 (pt0) REVERT: R 34 GLU cc_start: 0.8524 (mm-30) cc_final: 0.7991 (pm20) REVERT: R 55 ASP cc_start: 0.7701 (t0) cc_final: 0.7463 (t0) REVERT: S 3 THR cc_start: 0.8473 (m) cc_final: 0.7706 (p) REVERT: S 65 ASP cc_start: 0.8184 (t0) cc_final: 0.7731 (t0) REVERT: S 107 VAL cc_start: 0.9280 (m) cc_final: 0.8856 (m) REVERT: T 4 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7952 (tm-30) REVERT: T 52 GLU cc_start: 0.8565 (pp20) cc_final: 0.8027 (mt-10) REVERT: T 92 ASN cc_start: 0.7891 (p0) cc_final: 0.7633 (p0) REVERT: U 25 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7868 (tttt) REVERT: V 7 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7909 (pp20) REVERT: V 24 ASN cc_start: 0.8128 (t0) cc_final: 0.7813 (t0) REVERT: V 29 ILE cc_start: 0.9186 (tp) cc_final: 0.8873 (tp) REVERT: V 38 LEU cc_start: 0.8563 (tp) cc_final: 0.8251 (tp) REVERT: V 48 MET cc_start: 0.8629 (tpp) cc_final: 0.8228 (tpp) REVERT: V 56 PHE cc_start: 0.9149 (t80) cc_final: 0.8796 (t80) REVERT: V 68 LYS cc_start: 0.7642 (mmtm) cc_final: 0.7430 (mppt) REVERT: V 93 ARG cc_start: 0.7314 (mtm-85) cc_final: 0.7049 (mtm-85) REVERT: W 7 ARG cc_start: 0.8055 (tpp80) cc_final: 0.7604 (mpt180) REVERT: W 12 SER cc_start: 0.9335 (m) cc_final: 0.9097 (p) REVERT: X 18 SER cc_start: 0.9121 (p) cc_final: 0.8898 (m) REVERT: X 34 SER cc_start: 0.8886 (m) cc_final: 0.8651 (t) REVERT: Y 4 LYS cc_start: 0.7880 (tptp) cc_final: 0.7441 (tptt) REVERT: Y 5 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8702 (mm-30) REVERT: Y 18 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8172 (tt) REVERT: Z 36 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7491 (mm-30) REVERT: 0 51 ARG cc_start: 0.9080 (ptp-170) cc_final: 0.8715 (ptm-80) REVERT: 1 50 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6709 (tp30) REVERT: 6 59 ARG cc_start: 0.8354 (ptt90) cc_final: 0.7005 (tpt90) REVERT: 6 66 ILE cc_start: 0.1621 (OUTLIER) cc_final: 0.1056 (mp) outliers start: 273 outliers final: 189 residues processed: 1760 average time/residue: 1.3319 time to fit residues: 4026.8453 Evaluate side-chains 1815 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1605 time to evaluate : 6.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 145 ASN Chi-restraints excluded: chain b residue 147 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 211 LEU Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 107 LYS Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 125 ARG Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 44 LYS Chi-restraints excluded: chain d residue 48 SER Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 82 LYS Chi-restraints excluded: chain e residue 47 PHE Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 44 ARG Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 87 SER Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 16 LYS Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 53 SER Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 67 ASN Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 96 ASN Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 27 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 82 GLU Chi-restraints excluded: chain k residue 124 LYS Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 92 ILE Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 30 LEU Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 11 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain r residue 28 LEU Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain s residue 62 THR Chi-restraints excluded: chain t residue 35 TYR Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain u residue 32 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 114 HIS Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 52 ASP Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 0 residue 17 SER Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 1 residue 50 GLU Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 4 residue 23 ILE Chi-restraints excluded: chain 6 residue 21 VAL Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 36 VAL Chi-restraints excluded: chain 6 residue 39 LYS Chi-restraints excluded: chain 6 residue 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 336 optimal weight: 5.9990 chunk 900 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 586 optimal weight: 10.0000 chunk 246 optimal weight: 0.9990 chunk 1000 optimal weight: 9.9990 chunk 830 optimal weight: 0.0030 chunk 463 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 330 optimal weight: 8.9990 chunk 525 optimal weight: 20.0000 overall best weight: 5.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 38 HIS c 175 HIS ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 GLN i 30 ASN j 58 ASN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 19 ASN n 48 GLN ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 30 HIS r 30 ASN ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 74 HIS D 36 GLN E 195 GLN ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN L 38 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN Y 39 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 160920 Z= 0.232 Angle : 0.648 14.087 240962 Z= 0.349 Chirality : 0.035 0.373 30724 Planarity : 0.006 0.127 12791 Dihedral : 23.380 179.741 81018 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.89 % Favored : 92.57 % Rotamer: Outliers : 5.50 % Allowed : 21.66 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.11), residues: 5717 helix: 0.54 (0.12), residues: 1857 sheet: -1.61 (0.15), residues: 1005 loop : -1.00 (0.12), residues: 2855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 212 HIS 0.006 0.001 HIS f 11 PHE 0.032 0.002 PHE c 129 TYR 0.027 0.002 TYR b 212 ARG 0.011 0.001 ARG G 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1919 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1659 time to evaluate : 6.265 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: b 45 THR cc_start: 0.8173 (m) cc_final: 0.7875 (m) REVERT: b 81 ASP cc_start: 0.7761 (m-30) cc_final: 0.7513 (m-30) REVERT: b 90 PHE cc_start: 0.8723 (p90) cc_final: 0.8221 (p90) REVERT: b 92 ASN cc_start: 0.8674 (p0) cc_final: 0.8368 (p0) REVERT: b 168 GLU cc_start: 0.7707 (mt-10) cc_final: 0.6985 (tp30) REVERT: b 178 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6085 (pp) REVERT: b 212 TYR cc_start: 0.8254 (m-80) cc_final: 0.7881 (m-80) REVERT: c 22 PHE cc_start: 0.8857 (t80) cc_final: 0.8637 (t80) REVERT: c 88 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7941 (mtmm) REVERT: c 134 LYS cc_start: 0.8755 (mttt) cc_final: 0.8505 (tmmt) REVERT: c 135 ARG cc_start: 0.8607 (ttt180) cc_final: 0.7922 (tpp-160) REVERT: c 138 GLN cc_start: 0.9034 (tp40) cc_final: 0.8670 (tt0) REVERT: c 139 ASN cc_start: 0.8766 (m-40) cc_final: 0.8429 (m-40) REVERT: c 169 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8495 (mp0) REVERT: d 9 LYS cc_start: 0.7066 (tttt) cc_final: 0.6451 (mttp) REVERT: d 13 ARG cc_start: 0.7394 (ttm-80) cc_final: 0.7110 (tpp-160) REVERT: d 43 ARG cc_start: 0.7524 (mmt180) cc_final: 0.6841 (ttt90) REVERT: d 46 ARG cc_start: 0.8268 (ttm110) cc_final: 0.7857 (mmp-170) REVERT: d 84 ASN cc_start: 0.7741 (t0) cc_final: 0.7144 (m-40) REVERT: d 103 ARG cc_start: 0.8157 (mmm-85) cc_final: 0.7670 (mpt-90) REVERT: d 169 TRP cc_start: 0.7255 (p90) cc_final: 0.6616 (p90) REVERT: e 110 MET cc_start: 0.9190 (mmm) cc_final: 0.8870 (mmm) REVERT: e 119 VAL cc_start: 0.8126 (t) cc_final: 0.7752 (m) REVERT: e 120 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7082 (m90) REVERT: e 127 TYR cc_start: 0.8994 (m-10) cc_final: 0.8719 (m-10) REVERT: f 1 MET cc_start: 0.7642 (tpt) cc_final: 0.7364 (tpt) REVERT: f 65 GLU cc_start: 0.8058 (tp30) cc_final: 0.7072 (tm-30) REVERT: g 17 PHE cc_start: 0.7764 (p90) cc_final: 0.7534 (p90) REVERT: g 43 TYR cc_start: 0.8316 (m-80) cc_final: 0.7754 (m-10) REVERT: g 67 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7855 (t0) REVERT: g 77 ARG cc_start: 0.6544 (ttt180) cc_final: 0.4708 (tmm160) REVERT: g 122 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6305 (tp30) REVERT: g 128 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7449 (tm-30) REVERT: g 129 ASN cc_start: 0.8287 (p0) cc_final: 0.7971 (p0) REVERT: h 2 MET cc_start: 0.8681 (ptp) cc_final: 0.8202 (tpp) REVERT: h 42 GLU cc_start: 0.8497 (tp30) cc_final: 0.8273 (tp30) REVERT: h 117 GLN cc_start: 0.8450 (tp40) cc_final: 0.8197 (mm-40) REVERT: h 120 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7191 (pt) REVERT: i 32 ARG cc_start: 0.8734 (mmm-85) cc_final: 0.8445 (mmm-85) REVERT: i 67 LYS cc_start: 0.8876 (mtmm) cc_final: 0.8623 (mtmt) REVERT: i 98 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7632 (ttm170) REVERT: j 24 GLU cc_start: 0.8603 (tp30) cc_final: 0.7907 (tm-30) REVERT: j 68 ARG cc_start: 0.8824 (mtt180) cc_final: 0.8554 (mtt180) REVERT: j 69 THR cc_start: 0.9153 (m) cc_final: 0.8592 (p) REVERT: k 34 THR cc_start: 0.8774 (p) cc_final: 0.8378 (t) REVERT: k 82 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8243 (mm-30) REVERT: k 104 PHE cc_start: 0.8567 (m-80) cc_final: 0.8251 (m-80) REVERT: k 105 ARG cc_start: 0.6649 (ttp-110) cc_final: 0.6157 (tmm160) REVERT: k 108 ASN cc_start: 0.9035 (p0) cc_final: 0.8580 (p0) REVERT: k 124 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7500 (pttm) REVERT: l 8 ARG cc_start: 0.7980 (tpm170) cc_final: 0.7701 (tpm170) REVERT: l 111 GLN cc_start: 0.7532 (mt0) cc_final: 0.7212 (mt0) REVERT: m 77 LYS cc_start: 0.8767 (tttm) cc_final: 0.8392 (tptt) REVERT: m 81 ASP cc_start: 0.8493 (m-30) cc_final: 0.8153 (p0) REVERT: m 82 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8466 (tp) REVERT: m 106 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7513 (mmp-170) REVERT: m 109 LYS cc_start: 0.8872 (ttmt) cc_final: 0.8610 (mtmt) REVERT: n 25 GLU cc_start: 0.8678 (pm20) cc_final: 0.8169 (pm20) REVERT: o 39 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7833 (tt0) REVERT: o 67 ASP cc_start: 0.8437 (m-30) cc_final: 0.8154 (m-30) REVERT: o 82 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8578 (mt-10) REVERT: p 63 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7344 (tp-100) REVERT: q 4 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7560 (tp) REVERT: r 20 ILE cc_start: 0.7096 (mm) cc_final: 0.6827 (mm) REVERT: r 28 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8662 (mp) REVERT: r 60 ARG cc_start: 0.8532 (mtt90) cc_final: 0.7798 (mtm-85) REVERT: s 5 LYS cc_start: 0.5824 (OUTLIER) cc_final: 0.5090 (pttp) REVERT: s 19 GLU cc_start: 0.8508 (mm-30) cc_final: 0.7702 (tm-30) REVERT: s 23 GLU cc_start: 0.7317 (mt-10) cc_final: 0.7044 (mt-10) REVERT: s 30 LEU cc_start: 0.7434 (mp) cc_final: 0.7025 (mm) REVERT: s 62 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8224 (p) REVERT: s 79 TYR cc_start: 0.8464 (t80) cc_final: 0.7799 (t80) REVERT: t 35 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.7288 (t80) REVERT: C 33 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8761 (mp) REVERT: C 86 ARG cc_start: 0.8955 (mtt-85) cc_final: 0.8133 (ptp-110) REVERT: C 130 PRO cc_start: 0.9016 (Cg_exo) cc_final: 0.8705 (Cg_endo) REVERT: C 131 MET cc_start: 0.8923 (mpp) cc_final: 0.8094 (mpp) REVERT: C 132 ARG cc_start: 0.9169 (ttp-110) cc_final: 0.8842 (tpp-160) REVERT: C 142 ASN cc_start: 0.9389 (t0) cc_final: 0.9087 (t0) REVERT: C 152 GLN cc_start: 0.8966 (mm-40) cc_final: 0.7954 (mm-40) REVERT: C 180 MET cc_start: 0.8306 (mmt) cc_final: 0.7995 (mmt) REVERT: C 186 ASP cc_start: 0.8338 (m-30) cc_final: 0.8092 (m-30) REVERT: D 36 GLN cc_start: 0.9047 (pt0) cc_final: 0.8789 (pt0) REVERT: D 99 GLU cc_start: 0.7870 (pm20) cc_final: 0.7435 (mp0) REVERT: E 116 ASP cc_start: 0.8495 (m-30) cc_final: 0.7979 (t0) REVERT: E 127 GLU cc_start: 0.7045 (pm20) cc_final: 0.6684 (pm20) REVERT: E 156 ASN cc_start: 0.8131 (t0) cc_final: 0.7665 (p0) REVERT: E 198 GLU cc_start: 0.8276 (tp30) cc_final: 0.7231 (tt0) REVERT: F 79 ARG cc_start: 0.7803 (mtm110) cc_final: 0.7059 (mmm160) REVERT: F 128 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.7909 (p) REVERT: F 129 MET cc_start: 0.8089 (tmm) cc_final: 0.7834 (ptt) REVERT: F 176 PHE cc_start: 0.8073 (m-10) cc_final: 0.7831 (m-10) REVERT: G 94 ARG cc_start: 0.8525 (mtt180) cc_final: 0.8110 (mtp180) REVERT: G 127 GLN cc_start: 0.7979 (tt0) cc_final: 0.7317 (tt0) REVERT: I 16 MET cc_start: 0.4326 (mmp) cc_final: 0.3889 (ptp) REVERT: I 116 MET cc_start: 0.3352 (mmp) cc_final: 0.2418 (tpp) REVERT: J 17 VAL cc_start: 0.9356 (OUTLIER) cc_final: 0.9141 (p) REVERT: J 99 ARG cc_start: 0.8855 (mmm-85) cc_final: 0.8573 (mmm-85) REVERT: J 128 ASN cc_start: 0.8402 (t0) cc_final: 0.7379 (m110) REVERT: J 131 ASN cc_start: 0.7872 (t0) cc_final: 0.7530 (t0) REVERT: L 14 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7844 (mmmm) REVERT: L 55 MET cc_start: 0.8739 (tpp) cc_final: 0.8471 (tpp) REVERT: L 63 LYS cc_start: 0.9459 (ptmt) cc_final: 0.9124 (pttt) REVERT: M 17 ASN cc_start: 0.8809 (t160) cc_final: 0.8592 (t0) REVERT: M 30 SER cc_start: 0.8913 (m) cc_final: 0.8532 (p) REVERT: M 45 GLN cc_start: 0.8819 (mt0) cc_final: 0.8485 (mt0) REVERT: M 78 LEU cc_start: 0.8861 (tt) cc_final: 0.8533 (mp) REVERT: M 82 MET cc_start: 0.9491 (OUTLIER) cc_final: 0.8987 (mpp) REVERT: N 74 GLU cc_start: 0.9263 (tm-30) cc_final: 0.8612 (tp30) REVERT: N 114 GLU cc_start: 0.8363 (pm20) cc_final: 0.7606 (pm20) REVERT: O 15 ARG cc_start: 0.8879 (tpp80) cc_final: 0.8220 (ttm-80) REVERT: O 56 LYS cc_start: 0.6959 (pttm) cc_final: 0.6591 (ttmm) REVERT: O 108 ASP cc_start: 0.8534 (m-30) cc_final: 0.8296 (m-30) REVERT: P 87 ARG cc_start: 0.8029 (mtp-110) cc_final: 0.7327 (ttp-170) REVERT: P 95 LYS cc_start: 0.8965 (mptt) cc_final: 0.8631 (mmmt) REVERT: Q 46 TYR cc_start: 0.9407 (t80) cc_final: 0.9083 (t80) REVERT: Q 83 LYS cc_start: 0.8500 (ttpp) cc_final: 0.7833 (mptt) REVERT: Q 90 ASP cc_start: 0.9045 (p0) cc_final: 0.8746 (p0) REVERT: R 18 GLN cc_start: 0.8158 (pt0) cc_final: 0.7917 (pt0) REVERT: R 24 LYS cc_start: 0.8899 (ttmm) cc_final: 0.8683 (ttmm) REVERT: R 34 GLU cc_start: 0.8540 (mm-30) cc_final: 0.7945 (pm20) REVERT: S 3 THR cc_start: 0.8524 (m) cc_final: 0.7837 (p) REVERT: S 57 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.8176 (p0) REVERT: S 65 ASP cc_start: 0.8121 (t0) cc_final: 0.7648 (t0) REVERT: S 66 ILE cc_start: 0.8636 (mp) cc_final: 0.8399 (mp) REVERT: S 107 VAL cc_start: 0.9256 (m) cc_final: 0.8833 (m) REVERT: T 4 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7989 (tm-30) REVERT: T 52 GLU cc_start: 0.8572 (pp20) cc_final: 0.8049 (mt-10) REVERT: T 92 ASN cc_start: 0.7771 (p0) cc_final: 0.7359 (p0) REVERT: U 25 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7987 (tttt) REVERT: V 5 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7689 (p0) REVERT: V 7 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7963 (pp20) REVERT: V 24 ASN cc_start: 0.8241 (t0) cc_final: 0.7981 (t0) REVERT: V 29 ILE cc_start: 0.9187 (tp) cc_final: 0.8860 (tp) REVERT: V 38 LEU cc_start: 0.8528 (tp) cc_final: 0.8204 (tp) REVERT: V 56 PHE cc_start: 0.9126 (t80) cc_final: 0.8716 (t80) REVERT: V 68 LYS cc_start: 0.7690 (mmtm) cc_final: 0.7461 (mppt) REVERT: W 7 ARG cc_start: 0.8098 (tpp80) cc_final: 0.7710 (mtm-85) REVERT: W 12 SER cc_start: 0.9304 (m) cc_final: 0.9096 (p) REVERT: W 72 ASN cc_start: 0.7791 (t0) cc_final: 0.7577 (t0) REVERT: X 18 SER cc_start: 0.9095 (p) cc_final: 0.8823 (m) REVERT: X 34 SER cc_start: 0.8871 (m) cc_final: 0.8640 (t) REVERT: X 60 LYS cc_start: 0.8421 (ttmm) cc_final: 0.8058 (ttpp) REVERT: X 75 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8458 (mm-30) REVERT: Y 4 LYS cc_start: 0.7846 (tptp) cc_final: 0.7341 (tptt) REVERT: Y 5 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8597 (mm-30) REVERT: Y 18 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8173 (tt) REVERT: Z 4 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8763 (pt) REVERT: Z 36 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7476 (mm-30) REVERT: 1 9 LYS cc_start: 0.8096 (ttpt) cc_final: 0.7860 (tttt) REVERT: 1 18 HIS cc_start: 0.8419 (t-90) cc_final: 0.8201 (t-90) REVERT: 1 50 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6874 (tp30) REVERT: 2 28 ARG cc_start: 0.9047 (mtm-85) cc_final: 0.8845 (mtm110) REVERT: 6 59 ARG cc_start: 0.8336 (ptt90) cc_final: 0.6967 (tpt90) REVERT: 6 66 ILE cc_start: 0.1307 (OUTLIER) cc_final: 0.0918 (mp) outliers start: 260 outliers final: 189 residues processed: 1756 average time/residue: 1.3149 time to fit residues: 3979.8526 Evaluate side-chains 1806 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1591 time to evaluate : 6.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 145 ASN Chi-restraints excluded: chain b residue 147 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain c residue 107 LYS Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 125 ARG Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 165 GLU Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 44 LYS Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 82 LYS Chi-restraints excluded: chain e residue 21 SER Chi-restraints excluded: chain e residue 47 PHE Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 87 SER Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 16 LYS Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 67 ASN Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 96 ASN Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 8 THR Chi-restraints excluded: chain i residue 27 ILE Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 78 ILE Chi-restraints excluded: chain k residue 82 GLU Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 124 LYS Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 106 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 30 LEU Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 45 VAL Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain r residue 28 LEU Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 62 THR Chi-restraints excluded: chain t residue 35 TYR Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 52 ASP Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 17 SER Chi-restraints excluded: chain 1 residue 37 LYS Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 1 residue 50 GLU Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 23 ILE Chi-restraints excluded: chain 6 residue 21 VAL Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 39 LYS Chi-restraints excluded: chain 6 residue 66 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 964 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 570 optimal weight: 10.0000 chunk 730 optimal weight: 8.9990 chunk 566 optimal weight: 10.0000 chunk 842 optimal weight: 5.9990 chunk 558 optimal weight: 10.0000 chunk 996 optimal weight: 20.0000 chunk 623 optimal weight: 20.0000 chunk 607 optimal weight: 10.0000 chunk 460 optimal weight: 10.0000 overall best weight: 8.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 GLN ** d 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 GLN e 121 ASN i 30 ASN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 37 GLN ** k 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 19 ASN o 34 GLN p 9 HIS t 74 HIS D 185 ASN E 195 GLN ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 26 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 160920 Z= 0.381 Angle : 0.747 14.131 240962 Z= 0.393 Chirality : 0.040 0.392 30724 Planarity : 0.007 0.133 12791 Dihedral : 23.430 179.922 81018 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.92 % Favored : 91.55 % Rotamer: Outliers : 5.94 % Allowed : 22.42 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.11), residues: 5717 helix: 0.30 (0.12), residues: 1860 sheet: -1.55 (0.15), residues: 1015 loop : -1.21 (0.12), residues: 2842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP g 102 HIS 0.009 0.002 HIS q 46 PHE 0.031 0.002 PHE c 129 TYR 0.038 0.002 TYR d 75 ARG 0.010 0.001 ARG G 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1905 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1624 time to evaluate : 6.195 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: b 81 ASP cc_start: 0.7751 (m-30) cc_final: 0.7404 (m-30) REVERT: b 90 PHE cc_start: 0.8730 (p90) cc_final: 0.8196 (p90) REVERT: b 92 ASN cc_start: 0.8724 (p0) cc_final: 0.8398 (p0) REVERT: b 168 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7214 (tp30) REVERT: b 178 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6106 (pp) REVERT: b 212 TYR cc_start: 0.8328 (m-80) cc_final: 0.8001 (m-80) REVERT: c 40 GLN cc_start: 0.8625 (tt0) cc_final: 0.8415 (tt0) REVERT: c 134 LYS cc_start: 0.8747 (mttt) cc_final: 0.8481 (tmmt) REVERT: c 135 ARG cc_start: 0.8670 (ttt180) cc_final: 0.7904 (tpp-160) REVERT: c 139 ASN cc_start: 0.8846 (m-40) cc_final: 0.8371 (m-40) REVERT: c 169 GLU cc_start: 0.8881 (mp0) cc_final: 0.8669 (mp0) REVERT: c 205 GLU cc_start: 0.7808 (tt0) cc_final: 0.7579 (tt0) REVERT: d 9 LYS cc_start: 0.7058 (tttt) cc_final: 0.6401 (mttp) REVERT: d 13 ARG cc_start: 0.7329 (ttm-80) cc_final: 0.7128 (tpm170) REVERT: d 43 ARG cc_start: 0.7561 (mmt180) cc_final: 0.6912 (ttt90) REVERT: d 46 ARG cc_start: 0.8290 (ttm110) cc_final: 0.7857 (mmp-170) REVERT: d 84 ASN cc_start: 0.7805 (t0) cc_final: 0.7284 (m-40) REVERT: e 110 MET cc_start: 0.9235 (mmm) cc_final: 0.8922 (mmm) REVERT: e 119 VAL cc_start: 0.8225 (t) cc_final: 0.7885 (m) REVERT: e 120 HIS cc_start: 0.8099 (OUTLIER) cc_final: 0.7212 (m90) REVERT: f 1 MET cc_start: 0.7968 (tpt) cc_final: 0.7323 (tpt) REVERT: f 14 GLN cc_start: 0.8791 (mt0) cc_final: 0.8534 (mp10) REVERT: f 65 GLU cc_start: 0.8005 (tp30) cc_final: 0.7172 (tm-30) REVERT: g 5 VAL cc_start: 0.7734 (OUTLIER) cc_final: 0.7166 (p) REVERT: g 17 PHE cc_start: 0.7784 (p90) cc_final: 0.7553 (p90) REVERT: g 43 TYR cc_start: 0.8306 (m-80) cc_final: 0.7918 (m-80) REVERT: g 46 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8273 (tp) REVERT: g 67 ASN cc_start: 0.8368 (OUTLIER) cc_final: 0.7861 (t0) REVERT: g 77 ARG cc_start: 0.6591 (ttt180) cc_final: 0.4849 (tmm160) REVERT: g 122 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6354 (tp30) REVERT: g 128 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7412 (tm-30) REVERT: g 129 ASN cc_start: 0.8401 (p0) cc_final: 0.8058 (p0) REVERT: h 28 SER cc_start: 0.9169 (t) cc_final: 0.8802 (m) REVERT: h 42 GLU cc_start: 0.8552 (tp30) cc_final: 0.8216 (tp30) REVERT: h 59 GLU cc_start: 0.7615 (pm20) cc_final: 0.7151 (pm20) REVERT: h 117 GLN cc_start: 0.8475 (tp40) cc_final: 0.8267 (mm-40) REVERT: h 120 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7249 (pt) REVERT: i 32 ARG cc_start: 0.8680 (mmm-85) cc_final: 0.8391 (mmm-85) REVERT: i 67 LYS cc_start: 0.8946 (mtmm) cc_final: 0.8651 (mtmt) REVERT: j 24 GLU cc_start: 0.8570 (tp30) cc_final: 0.7897 (tm-30) REVERT: j 68 ARG cc_start: 0.8870 (mtt180) cc_final: 0.8624 (mtt180) REVERT: j 69 THR cc_start: 0.9142 (m) cc_final: 0.8596 (p) REVERT: k 34 THR cc_start: 0.8762 (p) cc_final: 0.8362 (t) REVERT: k 104 PHE cc_start: 0.8631 (m-80) cc_final: 0.8281 (m-80) REVERT: k 124 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7474 (pttm) REVERT: l 8 ARG cc_start: 0.8133 (tpm170) cc_final: 0.7719 (tpm170) REVERT: m 77 LYS cc_start: 0.8806 (tttm) cc_final: 0.8366 (tptt) REVERT: m 81 ASP cc_start: 0.8497 (m-30) cc_final: 0.8171 (p0) REVERT: n 25 GLU cc_start: 0.8652 (pm20) cc_final: 0.8136 (pm20) REVERT: o 39 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7891 (tt0) REVERT: o 67 ASP cc_start: 0.8439 (m-30) cc_final: 0.8151 (m-30) REVERT: o 82 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8610 (mt-10) REVERT: p 63 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7349 (tp-100) REVERT: q 4 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7507 (tp) REVERT: r 20 ILE cc_start: 0.7142 (mm) cc_final: 0.6874 (mm) REVERT: r 39 VAL cc_start: 0.9583 (t) cc_final: 0.9331 (p) REVERT: s 19 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7587 (tm-30) REVERT: s 30 LEU cc_start: 0.7656 (mp) cc_final: 0.7250 (mm) REVERT: s 62 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8243 (p) REVERT: s 79 TYR cc_start: 0.8591 (t80) cc_final: 0.7946 (t80) REVERT: t 35 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.7325 (t80) REVERT: C 33 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8852 (mp) REVERT: C 86 ARG cc_start: 0.8982 (mtt-85) cc_final: 0.8103 (ptp-110) REVERT: C 130 PRO cc_start: 0.8951 (Cg_exo) cc_final: 0.8697 (Cg_endo) REVERT: C 132 ARG cc_start: 0.9182 (ttp-110) cc_final: 0.8880 (tpp-160) REVERT: C 142 ASN cc_start: 0.9418 (t0) cc_final: 0.9131 (t0) REVERT: C 152 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8000 (mm-40) REVERT: E 116 ASP cc_start: 0.8614 (m-30) cc_final: 0.8090 (t0) REVERT: E 156 ASN cc_start: 0.8092 (t0) cc_final: 0.7591 (p0) REVERT: E 198 GLU cc_start: 0.8310 (tp30) cc_final: 0.7231 (tt0) REVERT: F 79 ARG cc_start: 0.7757 (mtm110) cc_final: 0.7031 (mmm160) REVERT: G 94 ARG cc_start: 0.8556 (mtt180) cc_final: 0.8104 (mtp180) REVERT: G 127 GLN cc_start: 0.7947 (tt0) cc_final: 0.7376 (tt0) REVERT: I 16 MET cc_start: 0.4382 (mmp) cc_final: 0.3771 (ptp) REVERT: I 116 MET cc_start: 0.3375 (mmp) cc_final: 0.1984 (tpp) REVERT: J 17 VAL cc_start: 0.9380 (OUTLIER) cc_final: 0.9162 (p) REVERT: J 96 ARG cc_start: 0.8575 (mmm160) cc_final: 0.8090 (mmm160) REVERT: J 128 ASN cc_start: 0.8433 (t0) cc_final: 0.7574 (m110) REVERT: J 131 ASN cc_start: 0.7957 (t0) cc_final: 0.7526 (t160) REVERT: K 13 ASN cc_start: 0.8412 (p0) cc_final: 0.8141 (p0) REVERT: L 63 LYS cc_start: 0.9458 (ptmt) cc_final: 0.9147 (pttt) REVERT: L 68 SER cc_start: 0.9074 (t) cc_final: 0.8803 (p) REVERT: M 30 SER cc_start: 0.8959 (m) cc_final: 0.8583 (p) REVERT: N 74 GLU cc_start: 0.9297 (tm-30) cc_final: 0.8796 (tp30) REVERT: N 78 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8357 (ttpt) REVERT: N 114 GLU cc_start: 0.8458 (pm20) cc_final: 0.7720 (pm20) REVERT: O 18 LEU cc_start: 0.9046 (mt) cc_final: 0.8838 (mt) REVERT: O 108 ASP cc_start: 0.8513 (m-30) cc_final: 0.8285 (m-30) REVERT: Q 23 TYR cc_start: 0.9128 (m-10) cc_final: 0.8825 (m-10) REVERT: Q 46 TYR cc_start: 0.9464 (t80) cc_final: 0.9229 (t80) REVERT: Q 83 LYS cc_start: 0.8554 (ttpp) cc_final: 0.7886 (mptt) REVERT: Q 90 ASP cc_start: 0.9062 (p0) cc_final: 0.8816 (p0) REVERT: R 34 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8124 (pm20) REVERT: S 3 THR cc_start: 0.8382 (m) cc_final: 0.7505 (p) REVERT: S 66 ILE cc_start: 0.8539 (mp) cc_final: 0.8059 (mp) REVERT: S 107 VAL cc_start: 0.9262 (m) cc_final: 0.8652 (m) REVERT: T 4 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8031 (tm-30) REVERT: T 52 GLU cc_start: 0.8580 (pp20) cc_final: 0.8181 (pp20) REVERT: U 25 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7934 (tttt) REVERT: V 5 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7687 (p0) REVERT: V 7 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8011 (pp20) REVERT: V 24 ASN cc_start: 0.8359 (t0) cc_final: 0.8066 (t0) REVERT: V 29 ILE cc_start: 0.9233 (tp) cc_final: 0.8947 (tp) REVERT: V 38 LEU cc_start: 0.8553 (tp) cc_final: 0.8332 (tp) REVERT: V 56 PHE cc_start: 0.9125 (t80) cc_final: 0.8794 (t80) REVERT: V 68 LYS cc_start: 0.7599 (mmtm) cc_final: 0.7339 (mppt) REVERT: W 7 ARG cc_start: 0.8031 (tpp80) cc_final: 0.7621 (mpt180) REVERT: W 66 GLU cc_start: 0.9028 (tp30) cc_final: 0.8817 (tt0) REVERT: W 72 ASN cc_start: 0.7990 (t0) cc_final: 0.7785 (t0) REVERT: X 60 LYS cc_start: 0.8376 (ttmm) cc_final: 0.7729 (ttpt) REVERT: Z 4 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8714 (pt) REVERT: Z 50 VAL cc_start: 0.9584 (m) cc_final: 0.9384 (p) REVERT: 1 9 LYS cc_start: 0.8183 (ttpt) cc_final: 0.7919 (tttt) REVERT: 1 18 HIS cc_start: 0.8380 (t-90) cc_final: 0.8075 (t-90) REVERT: 1 50 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6973 (tp30) REVERT: 4 3 VAL cc_start: 0.9288 (m) cc_final: 0.8938 (t) REVERT: 6 59 ARG cc_start: 0.8535 (ptt90) cc_final: 0.7187 (tpt90) REVERT: 6 66 ILE cc_start: 0.0939 (OUTLIER) cc_final: 0.0496 (mp) outliers start: 281 outliers final: 230 residues processed: 1736 average time/residue: 1.3172 time to fit residues: 3931.0148 Evaluate side-chains 1815 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1568 time to evaluate : 6.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 145 ASN Chi-restraints excluded: chain b residue 147 LEU Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 166 ASP Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 211 LEU Chi-restraints excluded: chain c residue 107 LYS Chi-restraints excluded: chain c residue 121 SER Chi-restraints excluded: chain c residue 125 ARG Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 194 VAL Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 44 LYS Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 82 LYS Chi-restraints excluded: chain e residue 47 PHE Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 87 SER Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 16 LYS Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 46 LEU Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 67 ASN Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 96 ASN Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 27 ILE Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 82 GLU Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 124 LYS Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 106 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 30 LEU Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 45 VAL Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 62 THR Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain t residue 8 LYS Chi-restraints excluded: chain t residue 35 TYR Chi-restraints excluded: chain t residue 56 ILE Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 114 HIS Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 52 ASP Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 17 SER Chi-restraints excluded: chain 0 residue 43 THR Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 1 residue 50 GLU Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 23 ILE Chi-restraints excluded: chain 4 residue 30 GLU Chi-restraints excluded: chain 6 residue 21 VAL Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 39 LYS Chi-restraints excluded: chain 6 residue 66 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 616 optimal weight: 50.0000 chunk 397 optimal weight: 40.0000 chunk 595 optimal weight: 9.9990 chunk 300 optimal weight: 9.9990 chunk 195 optimal weight: 2.9990 chunk 193 optimal weight: 20.0000 chunk 633 optimal weight: 20.0000 chunk 678 optimal weight: 10.0000 chunk 492 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 783 optimal weight: 20.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 38 HIS ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 175 HIS ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 GLN ** d 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 GLN f 63 ASN i 30 ASN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN l 19 ASN p 9 HIS p 18 GLN ** t 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 74 HIS D 185 ASN E 195 GLN ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 GLN L 104 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 26 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 160920 Z= 0.353 Angle : 0.730 14.095 240962 Z= 0.386 Chirality : 0.039 0.416 30724 Planarity : 0.007 0.130 12791 Dihedral : 23.465 179.961 81018 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.64 % Favored : 91.83 % Rotamer: Outliers : 6.03 % Allowed : 23.56 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.31 (0.11), residues: 5717 helix: 0.21 (0.12), residues: 1844 sheet: -1.51 (0.15), residues: 1021 loop : -1.30 (0.11), residues: 2852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP g 102 HIS 0.008 0.001 HIS 3 30 PHE 0.038 0.002 PHE c 129 TYR 0.026 0.002 TYR C 102 ARG 0.011 0.001 ARG e 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1894 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1609 time to evaluate : 6.024 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: b 81 ASP cc_start: 0.7525 (m-30) cc_final: 0.7167 (m-30) REVERT: b 90 PHE cc_start: 0.8725 (p90) cc_final: 0.8173 (p90) REVERT: b 92 ASN cc_start: 0.8745 (p0) cc_final: 0.8410 (p0) REVERT: b 168 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7219 (tp30) REVERT: b 212 TYR cc_start: 0.8373 (m-80) cc_final: 0.8015 (m-80) REVERT: c 134 LYS cc_start: 0.8737 (mttt) cc_final: 0.8497 (tmmt) REVERT: c 135 ARG cc_start: 0.8584 (ttt180) cc_final: 0.7877 (tpp-160) REVERT: c 138 GLN cc_start: 0.9133 (tt0) cc_final: 0.8673 (tt0) REVERT: c 139 ASN cc_start: 0.8862 (m-40) cc_final: 0.8549 (m-40) REVERT: c 169 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8671 (mp0) REVERT: c 205 GLU cc_start: 0.7910 (tt0) cc_final: 0.7693 (tt0) REVERT: d 9 LYS cc_start: 0.7072 (tttt) cc_final: 0.6390 (mttp) REVERT: d 13 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.7211 (tpm170) REVERT: d 43 ARG cc_start: 0.7565 (mmt180) cc_final: 0.6930 (ttt90) REVERT: d 46 ARG cc_start: 0.8296 (ttm110) cc_final: 0.7811 (mmp-170) REVERT: d 84 ASN cc_start: 0.7863 (t0) cc_final: 0.7332 (m-40) REVERT: e 110 MET cc_start: 0.9229 (mmm) cc_final: 0.8929 (mmm) REVERT: e 119 VAL cc_start: 0.8204 (t) cc_final: 0.7853 (m) REVERT: e 120 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7222 (m90) REVERT: e 134 ASN cc_start: 0.8869 (m-40) cc_final: 0.8426 (m110) REVERT: e 141 ASP cc_start: 0.8973 (m-30) cc_final: 0.8554 (t0) REVERT: f 1 MET cc_start: 0.8038 (tpt) cc_final: 0.7706 (mmm) REVERT: g 5 VAL cc_start: 0.7857 (OUTLIER) cc_final: 0.7269 (p) REVERT: g 17 PHE cc_start: 0.7712 (p90) cc_final: 0.7488 (p90) REVERT: g 43 TYR cc_start: 0.8301 (m-80) cc_final: 0.7809 (m-80) REVERT: g 67 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.7870 (t0) REVERT: g 77 ARG cc_start: 0.6635 (ttt180) cc_final: 0.4952 (tmm160) REVERT: g 122 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6401 (tp30) REVERT: g 125 ASP cc_start: 0.6984 (m-30) cc_final: 0.6579 (m-30) REVERT: g 128 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7502 (tm-30) REVERT: g 129 ASN cc_start: 0.8293 (p0) cc_final: 0.7883 (p0) REVERT: h 28 SER cc_start: 0.9145 (t) cc_final: 0.8769 (m) REVERT: h 42 GLU cc_start: 0.8528 (tp30) cc_final: 0.8223 (tp30) REVERT: h 59 GLU cc_start: 0.7532 (pm20) cc_final: 0.7077 (pm20) REVERT: h 95 MET cc_start: 0.8557 (mtt) cc_final: 0.7701 (tmm) REVERT: h 120 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7161 (pt) REVERT: i 32 ARG cc_start: 0.8651 (mmm-85) cc_final: 0.8379 (mmm-85) REVERT: j 24 GLU cc_start: 0.8560 (tp30) cc_final: 0.7890 (tm-30) REVERT: j 68 ARG cc_start: 0.8869 (mtt180) cc_final: 0.8618 (mtt180) REVERT: j 69 THR cc_start: 0.9087 (m) cc_final: 0.8576 (p) REVERT: k 34 THR cc_start: 0.8713 (p) cc_final: 0.8316 (t) REVERT: k 67 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8387 (pp20) REVERT: k 82 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8059 (mm-30) REVERT: k 104 PHE cc_start: 0.8654 (m-80) cc_final: 0.8328 (m-80) REVERT: k 124 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7490 (pttm) REVERT: l 8 ARG cc_start: 0.8051 (tpm170) cc_final: 0.7668 (tpm170) REVERT: m 77 LYS cc_start: 0.8802 (tttm) cc_final: 0.8366 (tptt) REVERT: m 81 ASP cc_start: 0.8687 (m-30) cc_final: 0.8192 (p0) REVERT: n 25 GLU cc_start: 0.8469 (pm20) cc_final: 0.8173 (pm20) REVERT: o 67 ASP cc_start: 0.8434 (m-30) cc_final: 0.8136 (m-30) REVERT: o 82 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8601 (mt-10) REVERT: p 63 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7617 (tp-100) REVERT: q 10 ARG cc_start: 0.8676 (ttp80) cc_final: 0.8369 (tmm-80) REVERT: r 20 ILE cc_start: 0.7111 (mm) cc_final: 0.6820 (mm) REVERT: s 19 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7568 (tm-30) REVERT: s 30 LEU cc_start: 0.7705 (mp) cc_final: 0.7323 (mm) REVERT: s 62 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8248 (p) REVERT: s 79 TYR cc_start: 0.8627 (t80) cc_final: 0.8032 (t80) REVERT: t 27 MET cc_start: 0.9144 (ttp) cc_final: 0.8811 (tmm) REVERT: t 35 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.7346 (t80) REVERT: C 33 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8791 (mp) REVERT: C 86 ARG cc_start: 0.8986 (mtt-85) cc_final: 0.8125 (ptp-110) REVERT: C 130 PRO cc_start: 0.8959 (Cg_exo) cc_final: 0.8657 (Cg_endo) REVERT: C 142 ASN cc_start: 0.9416 (t0) cc_final: 0.9153 (t0) REVERT: C 152 GLN cc_start: 0.9068 (mm-40) cc_final: 0.7970 (mm-40) REVERT: D 28 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8689 (tm-30) REVERT: D 167 ASN cc_start: 0.9154 (t0) cc_final: 0.8941 (t0) REVERT: E 116 ASP cc_start: 0.8603 (m-30) cc_final: 0.8031 (t0) REVERT: E 198 GLU cc_start: 0.8317 (tp30) cc_final: 0.7236 (tt0) REVERT: F 79 ARG cc_start: 0.7656 (mtm110) cc_final: 0.6984 (mmm160) REVERT: F 121 PHE cc_start: 0.7558 (m-80) cc_final: 0.7177 (m-80) REVERT: F 144 LYS cc_start: 0.8157 (tppt) cc_final: 0.7949 (tppp) REVERT: G 26 LYS cc_start: 0.7705 (mtpt) cc_final: 0.7490 (mmtp) REVERT: G 94 ARG cc_start: 0.8578 (mtt180) cc_final: 0.8115 (mtp180) REVERT: G 127 GLN cc_start: 0.7923 (tt0) cc_final: 0.7371 (tt0) REVERT: I 16 MET cc_start: 0.4553 (mmp) cc_final: 0.3948 (ptp) REVERT: I 116 MET cc_start: 0.3271 (mmp) cc_final: 0.1991 (mtp) REVERT: J 17 VAL cc_start: 0.9366 (OUTLIER) cc_final: 0.9142 (p) REVERT: J 96 ARG cc_start: 0.8550 (mmm160) cc_final: 0.8028 (mmm160) REVERT: J 99 ARG cc_start: 0.8958 (mmm-85) cc_final: 0.8363 (mmm-85) REVERT: J 128 ASN cc_start: 0.8488 (t0) cc_final: 0.7750 (m-40) REVERT: J 131 ASN cc_start: 0.7892 (t0) cc_final: 0.7458 (t0) REVERT: K 1 MET cc_start: 0.8391 (mtp) cc_final: 0.8152 (mtp) REVERT: K 13 ASN cc_start: 0.8436 (p0) cc_final: 0.8232 (p0) REVERT: L 63 LYS cc_start: 0.9475 (ptmt) cc_final: 0.9166 (pttt) REVERT: L 68 SER cc_start: 0.9046 (t) cc_final: 0.8781 (p) REVERT: M 30 SER cc_start: 0.8974 (m) cc_final: 0.8600 (p) REVERT: N 74 GLU cc_start: 0.9288 (tm-30) cc_final: 0.8738 (tm-30) REVERT: N 114 GLU cc_start: 0.8461 (pm20) cc_final: 0.7694 (pm20) REVERT: O 18 LEU cc_start: 0.9049 (mt) cc_final: 0.8832 (mt) REVERT: O 108 ASP cc_start: 0.8512 (m-30) cc_final: 0.8277 (m-30) REVERT: P 20 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7736 (mtp85) REVERT: P 81 ASP cc_start: 0.8554 (t0) cc_final: 0.8290 (t0) REVERT: P 87 ARG cc_start: 0.8125 (mtp-110) cc_final: 0.7737 (mtp180) REVERT: Q 83 LYS cc_start: 0.8579 (ttpp) cc_final: 0.7878 (mptt) REVERT: Q 90 ASP cc_start: 0.9059 (p0) cc_final: 0.8778 (p0) REVERT: R 34 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8127 (pm20) REVERT: S 3 THR cc_start: 0.8402 (m) cc_final: 0.7602 (p) REVERT: S 65 ASP cc_start: 0.8258 (t0) cc_final: 0.7789 (t0) REVERT: S 107 VAL cc_start: 0.9229 (OUTLIER) cc_final: 0.8671 (t) REVERT: T 4 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7908 (tm-30) REVERT: T 52 GLU cc_start: 0.8519 (pp20) cc_final: 0.8215 (pp20) REVERT: U 25 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7916 (tttt) REVERT: V 5 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7738 (p0) REVERT: V 7 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8014 (pp20) REVERT: V 24 ASN cc_start: 0.8421 (t0) cc_final: 0.8173 (t0) REVERT: V 29 ILE cc_start: 0.9244 (tp) cc_final: 0.8964 (tp) REVERT: V 38 LEU cc_start: 0.8539 (tp) cc_final: 0.8305 (tp) REVERT: V 68 LYS cc_start: 0.7604 (mmtm) cc_final: 0.7342 (mppt) REVERT: W 7 ARG cc_start: 0.8130 (tpp80) cc_final: 0.7729 (mpp-170) REVERT: W 66 GLU cc_start: 0.9045 (tp30) cc_final: 0.8735 (tt0) REVERT: W 72 ASN cc_start: 0.7992 (t0) cc_final: 0.7778 (t0) REVERT: X 75 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8557 (mm-30) REVERT: 0 14 MET cc_start: 0.8638 (mtm) cc_final: 0.8339 (mtp) REVERT: 1 9 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7969 (tttt) REVERT: 1 18 HIS cc_start: 0.8422 (t-90) cc_final: 0.8180 (t-90) REVERT: 1 50 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7077 (tp30) REVERT: 4 3 VAL cc_start: 0.9291 (m) cc_final: 0.8943 (t) REVERT: 6 22 MET cc_start: 0.7333 (mtp) cc_final: 0.6948 (ppp) REVERT: 6 59 ARG cc_start: 0.8514 (ptt90) cc_final: 0.7130 (tpt90) REVERT: 6 66 ILE cc_start: 0.0952 (OUTLIER) cc_final: 0.0538 (mp) outliers start: 285 outliers final: 235 residues processed: 1727 average time/residue: 1.3874 time to fit residues: 4144.5958 Evaluate side-chains 1812 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1561 time to evaluate : 6.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 145 ASN Chi-restraints excluded: chain b residue 147 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 166 ASP Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 211 LEU Chi-restraints excluded: chain c residue 107 LYS Chi-restraints excluded: chain c residue 125 ARG Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 165 GLU Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 194 VAL Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 44 LYS Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 82 LYS Chi-restraints excluded: chain e residue 47 PHE Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 87 SER Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 16 LYS Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 67 ASN Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 96 ASN Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 8 THR Chi-restraints excluded: chain i residue 27 ILE Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 82 GLU Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 124 LYS Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 106 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 30 LEU Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 45 VAL Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 62 THR Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain t residue 8 LYS Chi-restraints excluded: chain t residue 35 TYR Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 19 ASN Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 56 LYS Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 59 ASN Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 52 ASP Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 17 SER Chi-restraints excluded: chain 0 residue 43 THR Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 1 residue 50 GLU Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 25 LYS Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 3 residue 56 LEU Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 4 residue 23 ILE Chi-restraints excluded: chain 4 residue 30 GLU Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 21 VAL Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 39 LYS Chi-restraints excluded: chain 6 residue 66 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 906 optimal weight: 0.0670 chunk 954 optimal weight: 6.9990 chunk 871 optimal weight: 9.9990 chunk 928 optimal weight: 0.9990 chunk 558 optimal weight: 10.0000 chunk 404 optimal weight: 10.0000 chunk 729 optimal weight: 0.8980 chunk 285 optimal weight: 3.9990 chunk 839 optimal weight: 4.9990 chunk 878 optimal weight: 7.9990 chunk 925 optimal weight: 0.9980 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 175 HIS ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 53 GLN ** d 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN d 163 GLN ** f 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 30 ASN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 118 ASN l 19 ASN p 18 GLN ** q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 47 GLN t 74 HIS E 195 GLN F 26 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN L 35 HIS L 54 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN S 15 GLN 0 3 GLN 1 18 HIS ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.144 160920 Z= 0.141 Angle : 0.630 14.027 240962 Z= 0.340 Chirality : 0.033 0.699 30724 Planarity : 0.006 0.123 12791 Dihedral : 23.427 179.227 81018 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.84 % Favored : 92.74 % Rotamer: Outliers : 3.79 % Allowed : 26.29 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.11), residues: 5717 helix: 0.54 (0.12), residues: 1843 sheet: -1.38 (0.16), residues: 998 loop : -1.08 (0.12), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP g 102 HIS 0.016 0.001 HIS C 52 PHE 0.038 0.002 PHE c 129 TYR 0.035 0.002 TYR Q 46 ARG 0.014 0.001 ARG J 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1845 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1666 time to evaluate : 6.185 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: b 90 PHE cc_start: 0.8667 (p90) cc_final: 0.8100 (p90) REVERT: b 92 ASN cc_start: 0.8756 (p0) cc_final: 0.8485 (p0) REVERT: b 168 GLU cc_start: 0.7790 (mt-10) cc_final: 0.6916 (tp30) REVERT: b 178 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.5586 (pp) REVERT: b 212 TYR cc_start: 0.8386 (m-80) cc_final: 0.7984 (m-80) REVERT: c 134 LYS cc_start: 0.8764 (mttt) cc_final: 0.8510 (tmmt) REVERT: c 135 ARG cc_start: 0.8557 (ttt180) cc_final: 0.7861 (tpp-160) REVERT: c 138 GLN cc_start: 0.9087 (tt0) cc_final: 0.8643 (tt0) REVERT: c 139 ASN cc_start: 0.8799 (m-40) cc_final: 0.8538 (m-40) REVERT: c 174 LEU cc_start: 0.9116 (mt) cc_final: 0.8876 (mp) REVERT: d 9 LYS cc_start: 0.7019 (tttt) cc_final: 0.6362 (mttp) REVERT: d 43 ARG cc_start: 0.7511 (mmt180) cc_final: 0.6932 (ttt90) REVERT: d 46 ARG cc_start: 0.8227 (ttm110) cc_final: 0.7818 (mmp-170) REVERT: d 53 GLN cc_start: 0.8387 (mp-120) cc_final: 0.8139 (mp10) REVERT: d 56 GLU cc_start: 0.7724 (tp30) cc_final: 0.7409 (tm-30) REVERT: d 84 ASN cc_start: 0.7837 (t0) cc_final: 0.7322 (m-40) REVERT: e 110 MET cc_start: 0.9147 (mmm) cc_final: 0.8866 (mmm) REVERT: e 119 VAL cc_start: 0.8076 (t) cc_final: 0.7627 (m) REVERT: e 120 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7097 (m90) REVERT: f 1 MET cc_start: 0.7786 (tpt) cc_final: 0.6754 (mmp) REVERT: f 65 GLU cc_start: 0.8004 (tp30) cc_final: 0.6910 (tm-30) REVERT: g 5 VAL cc_start: 0.7823 (OUTLIER) cc_final: 0.7282 (p) REVERT: g 67 ASN cc_start: 0.8316 (m-40) cc_final: 0.7984 (t0) REVERT: g 77 ARG cc_start: 0.6619 (ttt180) cc_final: 0.4960 (tmm160) REVERT: g 122 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6315 (tp30) REVERT: g 125 ASP cc_start: 0.7106 (m-30) cc_final: 0.6823 (m-30) REVERT: g 129 ASN cc_start: 0.8279 (p0) cc_final: 0.7992 (t0) REVERT: h 42 GLU cc_start: 0.8496 (tp30) cc_final: 0.8247 (tp30) REVERT: h 49 LYS cc_start: 0.7417 (mmmm) cc_final: 0.6861 (mmtm) REVERT: h 120 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7105 (pt) REVERT: i 32 ARG cc_start: 0.8658 (mmm-85) cc_final: 0.8365 (mmm-85) REVERT: i 87 MET cc_start: 0.7637 (ppp) cc_final: 0.7226 (ppp) REVERT: j 24 GLU cc_start: 0.8570 (tp30) cc_final: 0.7877 (tm-30) REVERT: j 35 GLN cc_start: 0.7351 (tp40) cc_final: 0.6909 (pp30) REVERT: j 65 TYR cc_start: 0.8773 (m-80) cc_final: 0.8369 (m-80) REVERT: j 68 ARG cc_start: 0.8859 (mtt180) cc_final: 0.8622 (mtt180) REVERT: j 69 THR cc_start: 0.9056 (m) cc_final: 0.8413 (p) REVERT: k 34 THR cc_start: 0.8746 (p) cc_final: 0.8352 (t) REVERT: k 35 ASP cc_start: 0.8581 (p0) cc_final: 0.8327 (p0) REVERT: k 51 PHE cc_start: 0.7474 (m-80) cc_final: 0.7203 (m-80) REVERT: k 52 ARG cc_start: 0.8129 (tpp-160) cc_final: 0.7760 (tpp-160) REVERT: k 67 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8365 (pp20) REVERT: k 82 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: k 104 PHE cc_start: 0.8607 (m-80) cc_final: 0.8359 (m-80) REVERT: k 105 ARG cc_start: 0.6846 (ttp-170) cc_final: 0.6616 (tmm160) REVERT: k 124 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7123 (pttm) REVERT: l 111 GLN cc_start: 0.7398 (mt0) cc_final: 0.7134 (mt0) REVERT: m 77 LYS cc_start: 0.8751 (tttm) cc_final: 0.8306 (tptt) REVERT: m 81 ASP cc_start: 0.8547 (m-30) cc_final: 0.8097 (p0) REVERT: m 106 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7539 (mmp-170) REVERT: n 25 GLU cc_start: 0.8435 (pm20) cc_final: 0.7983 (pm20) REVERT: n 61 ASN cc_start: 0.8805 (t0) cc_final: 0.8557 (t0) REVERT: o 67 ASP cc_start: 0.8434 (m-30) cc_final: 0.8137 (m-30) REVERT: o 82 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8622 (mt-10) REVERT: p 35 ARG cc_start: 0.8760 (tmm160) cc_final: 0.8411 (tmm-80) REVERT: p 63 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7510 (tp-100) REVERT: q 10 ARG cc_start: 0.8689 (ttp80) cc_final: 0.8400 (tmm-80) REVERT: r 20 ILE cc_start: 0.7100 (mm) cc_final: 0.6821 (mm) REVERT: s 19 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7632 (tm-30) REVERT: s 23 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6874 (mt-10) REVERT: s 30 LEU cc_start: 0.7644 (mp) cc_final: 0.7289 (mm) REVERT: s 62 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8276 (p) REVERT: s 79 TYR cc_start: 0.8484 (t80) cc_final: 0.7841 (t80) REVERT: t 26 MET cc_start: 0.9248 (ptm) cc_final: 0.8974 (ppp) REVERT: t 27 MET cc_start: 0.9105 (ttp) cc_final: 0.8737 (tmm) REVERT: t 35 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.7341 (t80) REVERT: t 43 LYS cc_start: 0.8292 (pttt) cc_final: 0.8069 (tttt) REVERT: C 33 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8503 (mp) REVERT: C 86 ARG cc_start: 0.8923 (mtt-85) cc_final: 0.8208 (ptp-110) REVERT: C 130 PRO cc_start: 0.8965 (Cg_exo) cc_final: 0.8713 (Cg_endo) REVERT: C 131 MET cc_start: 0.8755 (mpp) cc_final: 0.7898 (mpp) REVERT: C 142 ASN cc_start: 0.9374 (t0) cc_final: 0.9058 (t0) REVERT: C 152 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8056 (mm-40) REVERT: D 1 MET cc_start: 0.6089 (ptp) cc_final: 0.5747 (ptm) REVERT: D 28 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8684 (tm-30) REVERT: D 167 ASN cc_start: 0.9218 (t0) cc_final: 0.8946 (t0) REVERT: E 116 ASP cc_start: 0.8521 (m-30) cc_final: 0.7989 (t0) REVERT: E 127 GLU cc_start: 0.7828 (pm20) cc_final: 0.7459 (pm20) REVERT: E 156 ASN cc_start: 0.8145 (t0) cc_final: 0.7637 (p0) REVERT: E 198 GLU cc_start: 0.8279 (tp30) cc_final: 0.7566 (pt0) REVERT: F 79 ARG cc_start: 0.7691 (mtm110) cc_final: 0.7037 (mmm160) REVERT: F 144 LYS cc_start: 0.8099 (tppt) cc_final: 0.7860 (tppp) REVERT: G 94 ARG cc_start: 0.8558 (mtt180) cc_final: 0.8112 (mtp180) REVERT: G 127 GLN cc_start: 0.7810 (tt0) cc_final: 0.7230 (tt0) REVERT: I 16 MET cc_start: 0.4381 (mmp) cc_final: 0.3757 (ptp) REVERT: I 116 MET cc_start: 0.3358 (mmp) cc_final: 0.2612 (mmm) REVERT: J 99 ARG cc_start: 0.8773 (mmm-85) cc_final: 0.8374 (mmm-85) REVERT: J 128 ASN cc_start: 0.8415 (t0) cc_final: 0.7619 (m110) REVERT: L 60 ARG cc_start: 0.8964 (mtm110) cc_final: 0.8516 (ptt-90) REVERT: L 63 LYS cc_start: 0.9449 (ptmt) cc_final: 0.9145 (pttt) REVERT: M 30 SER cc_start: 0.8918 (m) cc_final: 0.8535 (p) REVERT: M 58 LYS cc_start: 0.7721 (mppt) cc_final: 0.7336 (mmtt) REVERT: N 4 ARG cc_start: 0.9156 (mmm-85) cc_final: 0.8925 (mtm-85) REVERT: N 74 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8738 (tp30) REVERT: N 114 GLU cc_start: 0.8326 (pm20) cc_final: 0.7647 (pm20) REVERT: O 15 ARG cc_start: 0.8821 (tpp80) cc_final: 0.8352 (ttm-80) REVERT: O 108 ASP cc_start: 0.8515 (m-30) cc_final: 0.8299 (m-30) REVERT: P 87 ARG cc_start: 0.8056 (mtp-110) cc_final: 0.7386 (ttt180) REVERT: Q 83 LYS cc_start: 0.8455 (ttpp) cc_final: 0.7840 (mptt) REVERT: R 34 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7931 (pm20) REVERT: R 86 GLN cc_start: 0.9073 (tt0) cc_final: 0.8861 (tt0) REVERT: S 3 THR cc_start: 0.8444 (m) cc_final: 0.7731 (p) REVERT: S 48 LYS cc_start: 0.8741 (tttt) cc_final: 0.8524 (ttpt) REVERT: S 107 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.8708 (t) REVERT: T 1 MET cc_start: 0.5295 (ptm) cc_final: 0.4374 (ttp) REVERT: T 4 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7829 (tm-30) REVERT: T 52 GLU cc_start: 0.8510 (pp20) cc_final: 0.8094 (mt-10) REVERT: T 92 ASN cc_start: 0.7829 (p0) cc_final: 0.7581 (p0) REVERT: U 25 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7736 (tttt) REVERT: V 24 ASN cc_start: 0.8425 (t0) cc_final: 0.8213 (t0) REVERT: V 29 ILE cc_start: 0.9088 (tp) cc_final: 0.8748 (tp) REVERT: V 38 LEU cc_start: 0.8527 (tp) cc_final: 0.8183 (tp) REVERT: V 68 LYS cc_start: 0.7615 (mmtm) cc_final: 0.7387 (mppt) REVERT: W 7 ARG cc_start: 0.8162 (tpp80) cc_final: 0.7698 (mtm-85) REVERT: W 46 ASN cc_start: 0.9068 (m-40) cc_final: 0.8828 (m110) REVERT: X 60 LYS cc_start: 0.8332 (ttmm) cc_final: 0.7825 (tttp) REVERT: X 75 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8537 (tt0) REVERT: Y 28 LEU cc_start: 0.8087 (mp) cc_final: 0.7832 (tt) REVERT: 0 14 MET cc_start: 0.8440 (mtm) cc_final: 0.8136 (mtm) REVERT: 0 16 ARG cc_start: 0.8996 (mtt-85) cc_final: 0.8595 (mtt-85) REVERT: 1 50 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6839 (tp30) REVERT: 4 30 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: 6 22 MET cc_start: 0.7385 (mtp) cc_final: 0.7066 (ppp) REVERT: 6 59 ARG cc_start: 0.8327 (ptt90) cc_final: 0.6967 (tpt90) REVERT: 6 66 ILE cc_start: 0.1988 (OUTLIER) cc_final: 0.1420 (mt) outliers start: 179 outliers final: 133 residues processed: 1733 average time/residue: 1.3259 time to fit residues: 3940.3207 Evaluate side-chains 1753 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1605 time to evaluate : 5.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 145 ASN Chi-restraints excluded: chain b residue 147 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain c residue 107 LYS Chi-restraints excluded: chain c residue 125 ARG Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 82 LYS Chi-restraints excluded: chain e residue 21 SER Chi-restraints excluded: chain e residue 47 PHE Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 17 GLN Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 16 LYS Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 40 SER Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 96 ASN Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 8 THR Chi-restraints excluded: chain i residue 27 ILE Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 30 ASN Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 82 GLU Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 124 LYS Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 106 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 13 SER Chi-restraints excluded: chain q residue 45 VAL Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain s residue 62 THR Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain t residue 8 LYS Chi-restraints excluded: chain t residue 35 TYR Chi-restraints excluded: chain t residue 56 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain W residue 52 ASP Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 37 LYS Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 1 residue 50 GLU Chi-restraints excluded: chain 2 residue 25 LYS Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 4 residue 23 ILE Chi-restraints excluded: chain 4 residue 30 GLU Chi-restraints excluded: chain 6 residue 21 VAL Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 39 LYS Chi-restraints excluded: chain 6 residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 609 optimal weight: 10.0000 chunk 982 optimal weight: 10.0000 chunk 599 optimal weight: 10.0000 chunk 465 optimal weight: 10.0000 chunk 682 optimal weight: 20.0000 chunk 1030 optimal weight: 1.9990 chunk 948 optimal weight: 9.9990 chunk 820 optimal weight: 0.0050 chunk 85 optimal weight: 20.0000 chunk 633 optimal weight: 20.0000 chunk 502 optimal weight: 10.0000 overall best weight: 6.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 38 HIS ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 175 HIS ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 GLN ** f 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 30 ASN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 19 ASN t 74 HIS D 185 ASN E 195 GLN ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 160920 Z= 0.279 Angle : 0.680 14.132 240962 Z= 0.362 Chirality : 0.036 0.327 30724 Planarity : 0.007 0.128 12791 Dihedral : 23.359 179.140 81018 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.66 % Favored : 91.90 % Rotamer: Outliers : 3.53 % Allowed : 27.24 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % 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: -1.01 (0.11), residues: 5717 helix: 0.51 (0.12), residues: 1840 sheet: -1.36 (0.16), residues: 998 loop : -1.16 (0.12), residues: 2879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP g 102 HIS 0.006 0.001 HIS f 11 PHE 0.034 0.002 PHE u 36 TYR 0.039 0.002 TYR d 75 ARG 0.013 0.001 ARG G 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11434 Ramachandran restraints generated. 5717 Oldfield, 0 Emsley, 5717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1737 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1570 time to evaluate : 6.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 90 PHE cc_start: 0.8699 (p90) cc_final: 0.8123 (p90) REVERT: b 92 ASN cc_start: 0.8682 (p0) cc_final: 0.8398 (p0) REVERT: b 168 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7178 (tp30) REVERT: b 178 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.5757 (pp) REVERT: b 212 TYR cc_start: 0.8386 (m-80) cc_final: 0.7987 (m-80) REVERT: c 35 ASP cc_start: 0.8840 (t0) cc_final: 0.8569 (t0) REVERT: c 134 LYS cc_start: 0.8780 (mttt) cc_final: 0.8514 (tmmt) REVERT: c 135 ARG cc_start: 0.8527 (ttt180) cc_final: 0.7773 (tpp-160) REVERT: c 138 GLN cc_start: 0.9093 (tt0) cc_final: 0.8639 (tt0) REVERT: c 139 ASN cc_start: 0.8863 (m-40) cc_final: 0.8521 (m-40) REVERT: d 9 LYS cc_start: 0.7107 (tttt) cc_final: 0.6427 (mttp) REVERT: d 43 ARG cc_start: 0.7562 (mmt180) cc_final: 0.6950 (ttt90) REVERT: d 46 ARG cc_start: 0.8348 (ttm110) cc_final: 0.7907 (mmp-170) REVERT: d 53 GLN cc_start: 0.8404 (mp-120) cc_final: 0.8119 (mp10) REVERT: d 56 GLU cc_start: 0.7751 (tp30) cc_final: 0.7367 (tm-30) REVERT: d 84 ASN cc_start: 0.7899 (t0) cc_final: 0.7371 (m-40) REVERT: e 110 MET cc_start: 0.9200 (mmm) cc_final: 0.8918 (mmm) REVERT: e 119 VAL cc_start: 0.8155 (t) cc_final: 0.7786 (m) REVERT: e 120 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7118 (m90) REVERT: e 141 ASP cc_start: 0.8893 (m-30) cc_final: 0.8599 (t0) REVERT: f 36 ILE cc_start: 0.8325 (mm) cc_final: 0.8085 (tp) REVERT: g 5 VAL cc_start: 0.7990 (OUTLIER) cc_final: 0.7427 (p) REVERT: g 35 LYS cc_start: 0.8405 (tptt) cc_final: 0.8179 (tptt) REVERT: g 43 TYR cc_start: 0.8091 (m-80) cc_final: 0.7522 (m-80) REVERT: g 67 ASN cc_start: 0.8372 (m-40) cc_final: 0.8031 (t0) REVERT: g 77 ARG cc_start: 0.6665 (ttt180) cc_final: 0.4978 (tmm160) REVERT: g 122 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6210 (tp30) REVERT: g 125 ASP cc_start: 0.7093 (m-30) cc_final: 0.6830 (m-30) REVERT: g 129 ASN cc_start: 0.8249 (p0) cc_final: 0.7964 (t0) REVERT: h 2 MET cc_start: 0.8519 (tpt) cc_final: 0.7779 (ptm) REVERT: h 17 GLN cc_start: 0.8716 (mm110) cc_final: 0.8304 (mm110) REVERT: h 42 GLU cc_start: 0.8508 (tp30) cc_final: 0.8228 (tp30) REVERT: h 59 GLU cc_start: 0.7712 (pm20) cc_final: 0.7201 (pm20) REVERT: h 120 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7138 (pt) REVERT: i 32 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8359 (mmm-85) REVERT: j 24 GLU cc_start: 0.8574 (tp30) cc_final: 0.7899 (tm-30) REVERT: j 68 ARG cc_start: 0.8876 (mtt180) cc_final: 0.8624 (mtt180) REVERT: j 69 THR cc_start: 0.9057 (m) cc_final: 0.8442 (p) REVERT: k 34 THR cc_start: 0.8762 (p) cc_final: 0.8382 (t) REVERT: k 35 ASP cc_start: 0.8878 (p0) cc_final: 0.8668 (p0) REVERT: k 51 PHE cc_start: 0.7786 (m-80) cc_final: 0.7562 (m-80) REVERT: k 82 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8051 (mm-30) REVERT: k 104 PHE cc_start: 0.8631 (m-80) cc_final: 0.8343 (m-80) REVERT: k 124 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7425 (pttm) REVERT: l 8 ARG cc_start: 0.8017 (tpm170) cc_final: 0.7627 (tpm170) REVERT: m 77 LYS cc_start: 0.8787 (tttm) cc_final: 0.8341 (tptt) REVERT: m 81 ASP cc_start: 0.8622 (m-30) cc_final: 0.8138 (p0) REVERT: m 99 GLN cc_start: 0.8811 (mp10) cc_final: 0.8441 (mt0) REVERT: m 106 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7517 (mmp-170) REVERT: m 109 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8472 (mtmt) REVERT: n 25 GLU cc_start: 0.8425 (pm20) cc_final: 0.8089 (pm20) REVERT: o 67 ASP cc_start: 0.8424 (m-30) cc_final: 0.8129 (m-30) REVERT: o 82 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8634 (mt-10) REVERT: p 63 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7721 (tp40) REVERT: q 10 ARG cc_start: 0.8752 (ttp80) cc_final: 0.8490 (tmm-80) REVERT: r 20 ILE cc_start: 0.7127 (mm) cc_final: 0.6849 (mm) REVERT: s 19 GLU cc_start: 0.8514 (mm-30) cc_final: 0.7664 (tm-30) REVERT: s 30 LEU cc_start: 0.7678 (mp) cc_final: 0.7311 (mm) REVERT: s 62 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8152 (p) REVERT: s 79 TYR cc_start: 0.8647 (t80) cc_final: 0.8046 (t80) REVERT: t 27 MET cc_start: 0.9121 (ttp) cc_final: 0.8803 (tmm) REVERT: t 35 TYR cc_start: 0.7645 (OUTLIER) cc_final: 0.7312 (t80) REVERT: C 33 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8688 (mp) REVERT: C 130 PRO cc_start: 0.9026 (Cg_exo) cc_final: 0.8732 (Cg_endo) REVERT: C 131 MET cc_start: 0.8870 (mpp) cc_final: 0.8035 (mpp) REVERT: C 142 ASN cc_start: 0.9423 (t0) cc_final: 0.9121 (t0) REVERT: C 152 GLN cc_start: 0.9071 (mm-40) cc_final: 0.7971 (mm-40) REVERT: D 1 MET cc_start: 0.5894 (ptp) cc_final: 0.5462 (ptm) REVERT: D 28 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8701 (tm-30) REVERT: D 167 ASN cc_start: 0.9177 (t0) cc_final: 0.8936 (t0) REVERT: E 116 ASP cc_start: 0.8605 (m-30) cc_final: 0.8090 (t0) REVERT: E 198 GLU cc_start: 0.8204 (tp30) cc_final: 0.7195 (tt0) REVERT: F 79 ARG cc_start: 0.7615 (mtm110) cc_final: 0.6927 (mmm160) REVERT: F 144 LYS cc_start: 0.8062 (tppt) cc_final: 0.7561 (mmtm) REVERT: G 94 ARG cc_start: 0.8487 (mtt180) cc_final: 0.8097 (mtp180) REVERT: G 127 GLN cc_start: 0.7897 (tt0) cc_final: 0.7378 (tt0) REVERT: I 16 MET cc_start: 0.4602 (mmp) cc_final: 0.4004 (ptp) REVERT: I 116 MET cc_start: 0.3489 (mmp) cc_final: 0.2540 (mmm) REVERT: J 99 ARG cc_start: 0.8911 (mmm-85) cc_final: 0.8587 (mmm-85) REVERT: J 128 ASN cc_start: 0.8447 (t0) cc_final: 0.7745 (m-40) REVERT: K 13 ASN cc_start: 0.8386 (p0) cc_final: 0.8176 (p0) REVERT: L 63 LYS cc_start: 0.9487 (ptmt) cc_final: 0.9167 (pttt) REVERT: L 68 SER cc_start: 0.9049 (t) cc_final: 0.8790 (p) REVERT: M 30 SER cc_start: 0.8948 (m) cc_final: 0.8578 (p) REVERT: N 74 GLU cc_start: 0.9254 (tm-30) cc_final: 0.8771 (tm-30) REVERT: N 114 GLU cc_start: 0.8398 (pm20) cc_final: 0.7637 (pm20) REVERT: O 108 ASP cc_start: 0.8497 (m-30) cc_final: 0.8261 (m-30) REVERT: P 20 ARG cc_start: 0.7961 (mtp85) cc_final: 0.7694 (mtp85) REVERT: P 81 ASP cc_start: 0.8542 (t0) cc_final: 0.8257 (t0) REVERT: P 87 ARG cc_start: 0.8132 (mtp-110) cc_final: 0.7487 (ttt180) REVERT: Q 83 LYS cc_start: 0.8506 (ttpp) cc_final: 0.7854 (mptt) REVERT: R 34 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7976 (pm20) REVERT: S 3 THR cc_start: 0.8433 (m) cc_final: 0.7614 (p) REVERT: S 48 LYS cc_start: 0.8753 (tttt) cc_final: 0.8320 (ttpt) REVERT: S 52 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8835 (mm-30) REVERT: S 107 VAL cc_start: 0.9241 (OUTLIER) cc_final: 0.8732 (m) REVERT: T 1 MET cc_start: 0.6079 (ptm) cc_final: 0.5033 (ttp) REVERT: T 4 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7860 (tm-30) REVERT: T 52 GLU cc_start: 0.8489 (pp20) cc_final: 0.8226 (pp20) REVERT: U 25 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7823 (tttt) REVERT: V 24 ASN cc_start: 0.8465 (t0) cc_final: 0.8251 (t0) REVERT: V 29 ILE cc_start: 0.9200 (tp) cc_final: 0.8905 (tp) REVERT: V 38 LEU cc_start: 0.8546 (tp) cc_final: 0.8305 (tp) REVERT: V 56 PHE cc_start: 0.9074 (t80) cc_final: 0.8744 (t80) REVERT: V 68 LYS cc_start: 0.7620 (mmtm) cc_final: 0.7386 (mppt) REVERT: W 46 ASN cc_start: 0.9129 (m-40) cc_final: 0.8887 (m110) REVERT: W 66 GLU cc_start: 0.8908 (tt0) cc_final: 0.8623 (tt0) REVERT: W 72 ASN cc_start: 0.8021 (t0) cc_final: 0.7778 (t0) REVERT: X 75 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8515 (mm-30) REVERT: 0 3 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8906 (pm20) REVERT: 0 14 MET cc_start: 0.8595 (mtm) cc_final: 0.8324 (mtp) REVERT: 0 51 ARG cc_start: 0.8683 (ptm160) cc_final: 0.8313 (ptm-80) REVERT: 1 50 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6676 (tp30) REVERT: 6 22 MET cc_start: 0.7511 (mtp) cc_final: 0.7026 (ppp) REVERT: 6 59 ARG cc_start: 0.8399 (ptt90) cc_final: 0.7007 (tpt90) REVERT: 6 66 ILE cc_start: 0.1002 (OUTLIER) cc_final: 0.0453 (mt) outliers start: 167 outliers final: 143 residues processed: 1643 average time/residue: 1.2964 time to fit residues: 3674.8041 Evaluate side-chains 1707 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1549 time to evaluate : 5.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 145 ASN Chi-restraints excluded: chain b residue 147 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain c residue 40 GLN Chi-restraints excluded: chain c residue 107 LYS Chi-restraints excluded: chain c residue 125 ARG Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 165 GLU Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 194 VAL Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 82 LYS Chi-restraints excluded: chain e residue 21 SER Chi-restraints excluded: chain e residue 47 PHE Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 17 GLN Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 16 LYS Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 96 ASN Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 8 THR Chi-restraints excluded: chain i residue 27 ILE Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 82 GLU Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 124 LYS Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 106 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 45 VAL Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 62 THR Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain t residue 8 LYS Chi-restraints excluded: chain t residue 35 TYR Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 114 HIS Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain W residue 52 ASP Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 37 LYS Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 1 residue 50 GLU Chi-restraints excluded: chain 2 residue 25 LYS Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 23 ILE Chi-restraints excluded: chain 6 residue 21 VAL Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 39 LYS Chi-restraints excluded: chain 6 residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 651 optimal weight: 9.9990 chunk 873 optimal weight: 6.9990 chunk 251 optimal weight: 8.9990 chunk 756 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 chunk 227 optimal weight: 8.9990 chunk 821 optimal weight: 10.0000 chunk 343 optimal weight: 4.9990 chunk 843 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 175 HIS ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 GLN e 121 ASN ** f 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 27 ASN i 30 ASN ** i 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 19 ASN r 30 ASN ** t 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 74 HIS D 185 ASN E 195 GLN ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.124701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.097547 restraints weight = 301432.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100041 restraints weight = 110803.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.100371 restraints weight = 65619.690| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.396 160920 Z= 0.305 Angle : 0.697 65.897 240962 Z= 0.375 Chirality : 0.036 0.412 30724 Planarity : 0.007 0.202 12791 Dihedral : 23.359 179.153 81018 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.73 % Favored : 91.83 % Rotamer: Outliers : 3.85 % Allowed : 26.92 % Favored : 69.23 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.52 % 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: -1.01 (0.11), residues: 5717 helix: 0.51 (0.12), residues: 1841 sheet: -1.35 (0.16), residues: 998 loop : -1.16 (0.12), residues: 2878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP M 92 HIS 0.006 0.001 HIS f 11 PHE 0.033 0.002 PHE u 36 TYR 0.035 0.002 TYR d 75 ARG 0.012 0.001 ARG G 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51208.25 seconds wall clock time: 888 minutes 37.01 seconds (53317.01 seconds total)