Starting phenix.real_space_refine on Fri Mar 22 11:45:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0z_10077/03_2024/6s0z_10077_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0z_10077/03_2024/6s0z_10077.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0z_10077/03_2024/6s0z_10077_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0z_10077/03_2024/6s0z_10077_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0z_10077/03_2024/6s0z_10077_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0z_10077/03_2024/6s0z_10077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0z_10077/03_2024/6s0z_10077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0z_10077/03_2024/6s0z_10077_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0z_10077/03_2024/6s0z_10077_trim_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3018 5.49 5 S 62 5.16 5 C 43842 2.51 5 N 16375 2.21 5 O 25281 1.98 5 H 57218 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 238": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 243": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 272": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 274": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 89": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 168": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 54": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 152": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 2": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 53": "OD1" <-> "OD2" Residue "H ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 115": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 79": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 145796 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 93573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2905, 93573 Classifications: {'RNA': 2905} Modifications used: {'3*END': 1, 'rna2p_pur': 310, 'rna2p_pyr': 172, 'rna3p_pur': 1355, 'rna3p_pyr': 1068} Link IDs: {'rna2p': 482, 'rna3p': 2422} Chain breaks: 8 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' G%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 3654 Classifications: {'RNA': 114} Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 9, 'rna3p_pur': 54, 'rna3p_pyr': 46} Link IDs: {'rna2p': 14, 'rna3p': 99} Chain: "C" Number of atoms: 4291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 4291 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 17, 'TRANS': 256} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3294 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 8, 'TRANS': 206} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3191 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2653 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "G" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2454 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 7, 'TRANS': 165} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2293 Classifications: {'peptide': 145} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1899 Classifications: {'peptide': 122} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2211 Classifications: {'peptide': 146} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2216 Classifications: {'peptide': 137} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 129} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1915 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "M" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1796 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "N" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1826 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "O" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1957 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "P" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1620 Classifications: {'peptide': 102} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1734 Classifications: {'peptide': 110} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1463 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "S" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1579 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "T" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1488 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "U" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1187 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 779 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1104 Classifications: {'peptide': 67} Link IDs: {'TRANS': 66} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 940 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Y" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 613 Classifications: {'peptide': 59} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 55} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "Z" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 718 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 17 Chain: "1" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 773 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 782 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "3" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1107 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "4" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 635 Classifications: {'peptide': 37} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ERY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 47.00, per 1000 atoms: 0.32 Number of scatterers: 145796 At special positions: 0 Unit cell: (218.735, 232.606, 195.261, 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) S 62 16.00 P 3018 15.00 O 25281 8.00 N 16375 7.00 C 43842 6.00 H 57218 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 1 12 " - pdb=" SG CYS 1 36 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 14 " - pdb=" SG CYS 4 27 " distance=2.03 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: 94.67 Conformation dependent library (CDL) restraints added in 4.3 seconds 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5664 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: 78 helices and 45 sheets defined 30.4% alpha, 20.3% beta 899 base pairs and 1506 stacking pairs defined. Time for finding SS restraints: 71.61 Creating SS restraints... Processing helix chain 'C' and resid 10 through 15 removed outlier: 5.769A pdb=" N ASN C 15 " --> pdb=" O ASN C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.838A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.884A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 264 through 271 removed outlier: 4.753A pdb=" N LYS C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU C 269 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 202 removed outlier: 3.990A pdb=" N GLU C 201 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 81 removed outlier: 3.550A pdb=" N LYS D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA D 80 " --> pdb=" O HIS D 76 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 removed outlier: 4.349A pdb=" N TYR D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLU D 100 " --> pdb=" O VAL D 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 100' Processing helix chain 'D' and resid 106 through 111 removed outlier: 4.836A pdb=" N PHE D 110 " --> pdb=" O SER D 106 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL D 111 " --> pdb=" O VAL D 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 111' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 129 through 135 removed outlier: 4.201A pdb=" N HIS D 134 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY D 135 " --> pdb=" O ALA D 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 129 through 135' Processing helix chain 'E' and resid 29 through 45 removed outlier: 3.605A pdb=" N LEU E 44 " --> pdb=" O GLN E 40 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 121 removed outlier: 3.880A pdb=" N ASN E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 147 removed outlier: 4.606A pdb=" N GLU E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 169 removed outlier: 4.709A pdb=" N ASN E 169 " --> pdb=" O LEU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.824A pdb=" N ALA E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASP E 190 " --> pdb=" O ILE E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'F' and resid 4 through 21 removed outlier: 4.442A pdb=" N PHE F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N THR F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET F 17 " --> pdb=" O THR F 13 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LYS F 18 " --> pdb=" O GLU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 62 removed outlier: 4.785A pdb=" N GLY F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 112 removed outlier: 3.827A pdb=" N LYS F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.783A pdb=" N ALA F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 9 removed outlier: 3.719A pdb=" N LYS G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE G 8 " --> pdb=" O VAL G 4 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE G 9 " --> pdb=" O GLY G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 81 removed outlier: 3.838A pdb=" N GLY G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.735A pdb=" N VAL G 151 " --> pdb=" O ASN G 147 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Proline residue: G 153 - end of helix Processing helix chain 'H' and resid 25 through 39 removed outlier: 4.142A pdb=" N GLU H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 97 removed outlier: 3.794A pdb=" N ASN H 97 " --> pdb=" O LEU H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 111 removed outlier: 3.521A pdb=" N ILE H 102 " --> pdb=" O PRO H 98 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) Proline residue: H 111 - end of helix Processing helix chain 'H' and resid 113 through 123 removed outlier: 3.756A pdb=" N LYS H 122 " --> pdb=" O LYS H 118 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU H 123 " --> pdb=" O GLN H 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 110 removed outlier: 4.837A pdb=" N GLU I 108 " --> pdb=" O ARG I 104 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY I 109 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN I 110 " --> pdb=" O LEU I 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 104 through 110' Processing helix chain 'I' and resid 111 through 118 Processing helix chain 'J' and resid 37 through 42 removed outlier: 4.093A pdb=" N ARG J 41 " --> pdb=" O GLY J 37 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N SER J 42 " --> pdb=" O GLN J 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 37 through 42' Processing helix chain 'J' and resid 56 through 62 Proline residue: J 62 - end of helix Processing helix chain 'J' and resid 78 through 84 removed outlier: 3.689A pdb=" N LEU J 82 " --> pdb=" O ASN J 78 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN J 83 " --> pdb=" O LEU J 79 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS J 84 " --> pdb=" O ASP J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 78 through 84' Processing helix chain 'J' and resid 92 through 100 Processing helix chain 'J' and resid 129 through 140 removed outlier: 3.811A pdb=" N LYS J 139 " --> pdb=" O ALA J 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 59 removed outlier: 6.342A pdb=" N ILE K 47 " --> pdb=" O THR K 43 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU K 48 " --> pdb=" O SER K 44 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR K 57 " --> pdb=" O ALA K 53 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET K 58 " --> pdb=" O MET K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 126 removed outlier: 3.767A pdb=" N LYS K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU K 125 " --> pdb=" O ALA K 121 " (cutoff:3.500A) Proline residue: K 126 - end of helix Processing helix chain 'L' and resid 9 through 28 Processing helix chain 'L' and resid 34 through 54 removed outlier: 4.711A pdb=" N SER L 42 " --> pdb=" O LYS L 38 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL L 43 " --> pdb=" O GLU L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 66 removed outlier: 4.128A pdb=" N THR L 65 " --> pdb=" O ASN L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 94 removed outlier: 3.876A pdb=" N ILE L 89 " --> pdb=" O LEU L 85 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ALA L 90 " --> pdb=" O PHE L 86 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU L 91 " --> pdb=" O GLY L 87 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR L 93 " --> pdb=" O ILE L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 23 removed outlier: 4.382A pdb=" N VAL M 10 " --> pdb=" O ASP M 6 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR M 20 " --> pdb=" O ALA M 16 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASN M 21 " --> pdb=" O ARG M 17 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU M 22 " --> pdb=" O VAL M 18 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER M 23 " --> pdb=" O ARG M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 88 removed outlier: 6.588A pdb=" N LEU M 72 " --> pdb=" O THR M 68 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA M 73 " --> pdb=" O LYS M 69 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP M 86 " --> pdb=" O LYS M 82 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LYS M 87 " --> pdb=" O LYS M 83 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY M 88 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 116 removed outlier: 3.786A pdb=" N GLY M 116 " --> pdb=" O ALA M 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 16 removed outlier: 5.069A pdb=" N SER N 13 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLN N 14 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU N 15 " --> pdb=" O THR N 11 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ARG N 16 " --> pdb=" O LYS N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 106 removed outlier: 4.907A pdb=" N ARG N 103 " --> pdb=" O LEU N 99 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER N 104 " --> pdb=" O TYR N 100 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU N 105 " --> pdb=" O TYR N 101 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ARG N 106 " --> pdb=" O LEU N 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 99 through 106' Processing helix chain 'N' and resid 107 through 112 removed outlier: 3.764A pdb=" N ARG N 111 " --> pdb=" O GLY N 107 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE N 112 " --> pdb=" O LYS N 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 107 through 112' Processing helix chain 'O' and resid 8 through 22 removed outlier: 3.693A pdb=" N THR O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS O 22 " --> pdb=" O ILE O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 31 removed outlier: 4.784A pdb=" N HIS O 29 " --> pdb=" O PHE O 25 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR O 30 " --> pdb=" O GLY O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 37 Processing helix chain 'O' and resid 39 through 73 removed outlier: 3.989A pdb=" N ARG O 51 " --> pdb=" O PHE O 47 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG O 55 " --> pdb=" O ARG O 51 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN O 71 " --> pdb=" O ALA O 67 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS O 72 " --> pdb=" O ALA O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 87 Processing helix chain 'O' and resid 91 through 102 Processing helix chain 'O' and resid 103 through 117 removed outlier: 3.734A pdb=" N LYS O 112 " --> pdb=" O GLN O 108 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU O 117 " --> pdb=" O ALA O 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 25 removed outlier: 3.901A pdb=" N LEU Q 19 " --> pdb=" O ARG Q 15 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU Q 23 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE Q 24 " --> pdb=" O VAL Q 20 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG Q 25 " --> pdb=" O LEU Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 40 removed outlier: 5.709A pdb=" N ASN Q 40 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 61 Processing helix chain 'R' and resid 2 through 8 removed outlier: 6.531A pdb=" N ILE R 6 " --> pdb=" O GLU R 2 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU R 7 " --> pdb=" O ALA R 3 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LYS R 8 " --> pdb=" O ARG R 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 2 through 8' Processing helix chain 'R' and resid 13 through 23 removed outlier: 3.856A pdb=" N GLU R 22 " --> pdb=" O GLU R 18 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP R 23 " --> pdb=" O ALA R 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 46 Processing helix chain 'S' and resid 64 through 69 removed outlier: 4.222A pdb=" N VAL S 68 " --> pdb=" O HIS S 64 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLN S 69 " --> pdb=" O VAL S 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 64 through 69' Processing helix chain 'T' and resid 14 through 25 removed outlier: 4.259A pdb=" N GLY T 25 " --> pdb=" O LEU T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 56 Processing helix chain 'V' and resid 50 through 57 removed outlier: 4.363A pdb=" N SER V 56 " --> pdb=" O ARG V 52 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 10 removed outlier: 4.146A pdb=" N ILE W 6 " --> pdb=" O LYS W 2 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG W 7 " --> pdb=" O ALA W 3 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP W 8 " --> pdb=" O LYS W 4 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N THR W 10 " --> pdb=" O ILE W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 35 removed outlier: 4.621A pdb=" N GLU W 15 " --> pdb=" O THR W 11 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLY W 35 " --> pdb=" O GLN W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 65 removed outlier: 4.626A pdb=" N ARG W 44 " --> pdb=" O THR W 40 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR W 45 " --> pdb=" O ALA W 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 27 removed outlier: 3.531A pdb=" N GLY X 27 " --> pdb=" O VAL X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 51 Processing helix chain 'Z' and resid 9 through 19 removed outlier: 3.708A pdb=" N THR Z 18 " --> pdb=" O ASN Z 14 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N HIS Z 19 " --> pdb=" O LYS Z 15 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 17 Processing helix chain '2' and resid 18 through 26 removed outlier: 4.100A pdb=" N THR 2 25 " --> pdb=" O LYS 2 21 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS 2 26 " --> pdb=" O ARG 2 22 " (cutoff:3.500A) Processing helix chain '2' and resid 27 through 39 removed outlier: 3.698A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 28 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 14 removed outlier: 3.585A pdb=" N ARG 3 13 " --> pdb=" O GLY 3 9 " (cutoff:3.500A) Processing helix chain '3' and resid 32 through 37 removed outlier: 5.124A pdb=" N LYS 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER 3 37 " --> pdb=" O PHE 3 33 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 32 through 37' Processing helix chain '3' and resid 38 through 46 removed outlier: 3.677A pdb=" N ARG 3 45 " --> pdb=" O LYS 3 41 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS 3 46 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 59 removed outlier: 4.027A pdb=" N ARG 3 57 " --> pdb=" O SER 3 53 " (cutoff:3.500A) Processing helix chain '4' and resid 29 through 34 removed outlier: 4.333A pdb=" N LYS 4 33 " --> pdb=" O ASN 4 29 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLN 4 34 " --> pdb=" O PRO 4 30 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 29 through 34' Processing sheet with id= 1, first strand: chain 'C' and resid 2 through 5 removed outlier: 7.000A pdb=" N ALA C 2 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 75 through 78 removed outlier: 4.646A pdb=" N GLN C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 80 through 83 removed outlier: 5.291A pdb=" N ASN C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.592A pdb=" N THR C 139 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 3 through 7 removed outlier: 6.890A pdb=" N LYS D 3 " --> pdb=" O THR D 213 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR D 213 " --> pdb=" O LYS D 3 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASN D 176 " --> pdb=" O SER D 122 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 11 through 17 removed outlier: 3.680A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU D 21 " --> pdb=" O GLY D 17 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN D 187 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 33 through 36 removed outlier: 6.731A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE D 87 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 114 through 117 removed outlier: 4.636A pdb=" N ASP D 114 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 2 through 7 removed outlier: 8.409A pdb=" N ALA E 2 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU E 18 " --> pdb=" O ALA E 2 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR E 4 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER E 16 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL E 6 " --> pdb=" O SER E 14 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 122 through 125 Processing sheet with id= 11, first strand: chain 'F' and resid 65 through 69 removed outlier: 7.009A pdb=" N ALA F 87 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL F 89 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE F 156 " --> pdb=" O TYR F 128 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR F 128 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLY F 126 " --> pdb=" O THR F 158 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'G' and resid 15 through 20 removed outlier: 3.778A pdb=" N LYS G 27 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS G 23 " --> pdb=" O ASP G 20 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ASN G 22 " --> pdb=" O THR G 36 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N THR G 36 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL G 24 " --> pdb=" O SER G 34 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER G 34 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL G 26 " --> pdb=" O GLU G 32 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLY G 28 " --> pdb=" O LYS G 30 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 41 through 46 removed outlier: 6.297A pdb=" N THR G 49 " --> pdb=" O GLU G 46 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 94 through 99 removed outlier: 3.976A pdb=" N ASP G 102 " --> pdb=" O GLN G 99 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 121 through 126 removed outlier: 6.673A pdb=" N VAL G 130 " --> pdb=" O GLU G 126 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 53 through 58 removed outlier: 5.047A pdb=" N ASP H 20 " --> pdb=" O TYR H 141 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'H' and resid 75 through 79 removed outlier: 7.237A pdb=" N GLY H 84 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'I' and resid 6 through 9 removed outlier: 4.590A pdb=" N THR I 6 " --> pdb=" O THR I 21 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'I' and resid 37 through 41 removed outlier: 4.929A pdb=" N ASP I 37 " --> pdb=" O ILE I 62 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LYS I 59 " --> pdb=" O ILE I 87 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'I' and resid 68 through 71 removed outlier: 4.039A pdb=" N SER I 75 " --> pdb=" O ARG I 71 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 74 through 77 Processing sheet with id= 22, first strand: chain 'J' and resid 121 through 124 removed outlier: 3.781A pdb=" N ALA J 142 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'K' and resid 63 through 67 removed outlier: 6.345A pdb=" N LEU K 103 " --> pdb=" O LYS K 67 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE K 104 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS K 128 " --> pdb=" O THR K 37 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'L' and resid 29 through 32 removed outlier: 4.490A pdb=" N SER L 116 " --> pdb=" O GLN L 106 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 29 through 35 removed outlier: 6.588A pdb=" N ILE M 40 " --> pdb=" O SER M 58 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA M 54 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'N' and resid 39 through 47 removed outlier: 3.825A pdb=" N ARG N 39 " --> pdb=" O GLU N 36 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'N' and resid 51 through 55 removed outlier: 3.600A pdb=" N LYS N 51 " --> pdb=" O THR N 62 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY N 55 " --> pdb=" O SER N 58 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N GLU N 59 " --> pdb=" O LEU N 78 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'P' and resid 11 through 15 removed outlier: 4.502A pdb=" N PHE P 2 " --> pdb=" O GLY P 42 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE P 40 " --> pdb=" O ILE P 4 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'P' and resid 18 through 23 removed outlier: 4.356A pdb=" N GLN P 18 " --> pdb=" O ILE P 97 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP P 31 " --> pdb=" O VAL P 62 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'P' and resid 67 through 77 No H-bonds generated for sheet with id= 30 Processing sheet with id= 31, first strand: chain 'Q' and resid 2 through 8 removed outlier: 6.788A pdb=" N VAL Q 104 " --> pdb=" O LYS Q 72 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Q' and resid 73 through 79 removed outlier: 5.095A pdb=" N THR Q 98 " --> pdb=" O GLY Q 79 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 81 through 86 removed outlier: 3.914A pdb=" N SER Q 92 " --> pdb=" O ARG Q 86 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 24 through 29 removed outlier: 4.176A pdb=" N ARG R 76 " --> pdb=" O VAL R 29 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LYS R 61 " --> pdb=" O THR R 72 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LYS R 74 " --> pdb=" O LYS R 59 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LYS R 59 " --> pdb=" O LYS R 74 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG R 76 " --> pdb=" O ASN R 57 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN R 57 " --> pdb=" O ARG R 76 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA R 78 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE R 55 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL R 80 " --> pdb=" O VAL R 53 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL R 53 " --> pdb=" O VAL R 80 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 7 through 11 removed outlier: 4.601A pdb=" N ASP S 7 " --> pdb=" O VAL S 23 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS S 19 " --> pdb=" O VAL S 11 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 39 through 45 removed outlier: 5.351A pdb=" N ASN S 39 " --> pdb=" O ALA S 61 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR S 59 " --> pdb=" O MET S 41 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLY S 55 " --> pdb=" O GLN S 45 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'T' and resid 68 through 73 removed outlier: 6.202A pdb=" N ALA T 2 " --> pdb=" O VAL T 60 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU T 4 " --> pdb=" O GLU T 62 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP T 76 " --> pdb=" O ASP T 90 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'U' and resid 53 through 56 removed outlier: 6.376A pdb=" N VAL U 89 " --> pdb=" O GLY U 56 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 58 through 62 removed outlier: 8.307A pdb=" N ASN U 58 " --> pdb=" O LYS U 70 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR U 66 " --> pdb=" O GLY U 62 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'V' and resid 13 through 19 removed outlier: 8.101A pdb=" N SER V 13 " --> pdb=" O ARG V 28 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG V 28 " --> pdb=" O SER V 13 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY V 15 " --> pdb=" O LYS V 26 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS V 26 " --> pdb=" O GLY V 15 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG V 17 " --> pdb=" O SER V 24 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER V 24 " --> pdb=" O ARG V 17 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER V 19 " --> pdb=" O LEU V 22 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'X' and resid 32 through 38 removed outlier: 4.027A pdb=" N SER X 33 " --> pdb=" O LEU X 8 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain '1' and resid 2 through 7 removed outlier: 4.830A pdb=" N TYR 1 17 " --> pdb=" O LEU 1 7 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '1' and resid 30 through 34 removed outlier: 5.807A pdb=" N ILE 1 30 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '3' and resid 22 through 25 removed outlier: 5.615A pdb=" N LEU 3 22 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG 3 48 " --> pdb=" O ARG 3 24 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '4' and resid 14 through 19 819 hydrogen bonds defined for protein. 2403 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2241 hydrogen bonds 3584 hydrogen bond angles 0 basepair planarities 899 basepair parallelities 1506 stacking parallelities Total time for adding SS restraints: 146.38 Time building geometry restraints manager: 99.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 57213 1.03 - 1.23: 732 1.23 - 1.42: 49937 1.42 - 1.62: 45856 1.62 - 1.82: 114 Bond restraints: 153852 Sorted by residual: bond pdb=" C1 ERY A3001 " pdb=" O2 ERY A3001 " ideal model delta sigma weight residual 1.459 1.586 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C12 ERY A3001 " pdb=" C13 ERY A3001 " ideal model delta sigma weight residual 1.529 1.598 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C4 ERY A3001 " pdb=" C5 ERY A3001 " ideal model delta sigma weight residual 1.526 1.586 -0.060 2.00e-02 2.50e+03 9.10e+00 bond pdb=" C6 ERY A3001 " pdb=" C7 ERY A3001 " ideal model delta sigma weight residual 1.544 1.592 -0.048 2.00e-02 2.50e+03 5.70e+00 bond pdb=" C28 ERY A3001 " pdb=" N1 ERY A3001 " ideal model delta sigma weight residual 1.450 1.496 -0.046 2.00e-02 2.50e+03 5.28e+00 ... (remaining 153847 not shown) Histogram of bond angle deviations from ideal: 79.22 - 90.19: 9 90.19 - 101.16: 635 101.16 - 112.14: 165524 112.14 - 123.11: 88522 123.11 - 134.09: 21746 Bond angle restraints: 276436 Sorted by residual: angle pdb=" C17 ERY A3001 " pdb=" C16 ERY A3001 " pdb=" O5 ERY A3001 " ideal model delta sigma weight residual 108.94 79.22 29.72 3.00e+00 1.11e-01 9.82e+01 angle pdb=" O3' G A 770 " pdb=" P G A 771 " pdb=" OP1 G A 771 " ideal model delta sigma weight residual 108.00 79.89 28.11 3.00e+00 1.11e-01 8.78e+01 angle pdb=" C7 ERY A3001 " pdb=" C6 ERY A3001 " pdb=" O10 ERY A3001 " ideal model delta sigma weight residual 109.47 83.44 26.03 3.00e+00 1.11e-01 7.53e+01 angle pdb=" C35 ERY A3001 " pdb=" C12 ERY A3001 " pdb=" O13 ERY A3001 " ideal model delta sigma weight residual 109.44 84.46 24.98 3.00e+00 1.11e-01 6.93e+01 angle pdb=" C13 ERY A3001 " pdb=" C12 ERY A3001 " pdb=" O13 ERY A3001 " ideal model delta sigma weight residual 109.49 86.93 22.56 3.00e+00 1.11e-01 5.65e+01 ... (remaining 276431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 65323 35.98 - 71.96: 9344 71.96 - 107.93: 1155 107.93 - 143.91: 22 143.91 - 179.89: 39 Dihedral angle restraints: 75883 sinusoidal: 66170 harmonic: 9713 Sorted by residual: dihedral pdb=" O4' U B 108 " pdb=" C1' U B 108 " pdb=" N1 U B 108 " pdb=" C2 U B 108 " ideal model delta sinusoidal sigma weight residual -160.00 19.89 -179.89 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A1287 " pdb=" C1' U A1287 " pdb=" N1 U A1287 " pdb=" C2 U A1287 " ideal model delta sinusoidal sigma weight residual 200.00 20.61 179.39 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A 593 " pdb=" C1' U A 593 " pdb=" N1 U A 593 " pdb=" C2 U A 593 " ideal model delta sinusoidal sigma weight residual -160.00 18.31 -178.31 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 75880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.486: 18781 0.486 - 0.972: 0 0.972 - 1.459: 0 1.459 - 1.945: 0 1.945 - 2.431: 4 Chirality restraints: 18785 Sorted by residual: chirality pdb=" C16 ERY A3001 " pdb=" C15 ERY A3001 " pdb=" C17 ERY A3001 " pdb=" C19 ERY A3001 " both_signs ideal model delta sigma weight residual False 2.68 0.25 2.43 2.00e-01 2.50e+01 1.48e+02 chirality pdb=" P G A 771 " pdb=" OP1 G A 771 " pdb=" OP2 G A 771 " pdb=" O5' G A 771 " both_signs ideal model delta sigma weight residual True 2.41 0.19 2.22 2.00e-01 2.50e+01 1.23e+02 chirality pdb=" C6 ERY A3001 " pdb=" C32 ERY A3001 " pdb=" C5 ERY A3001 " pdb=" C7 ERY A3001 " both_signs ideal model delta sigma weight residual False -2.75 -0.57 -2.19 2.00e-01 2.50e+01 1.20e+02 ... (remaining 18782 not shown) Planarity restraints: 12479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 296 " 0.046 2.00e-02 2.50e+03 1.81e-02 1.14e+01 pdb=" N9 G A 296 " -0.045 2.00e-02 2.50e+03 pdb=" C8 G A 296 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G A 296 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A 296 " -0.007 2.00e-02 2.50e+03 pdb=" C6 G A 296 " 0.006 2.00e-02 2.50e+03 pdb=" O6 G A 296 " 0.011 2.00e-02 2.50e+03 pdb=" N1 G A 296 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 296 " -0.004 2.00e-02 2.50e+03 pdb=" N2 G A 296 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G A 296 " -0.007 2.00e-02 2.50e+03 pdb=" C4 G A 296 " -0.004 2.00e-02 2.50e+03 pdb=" H8 G A 296 " -0.001 2.00e-02 2.50e+03 pdb=" H1 G A 296 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A2591 " -0.042 2.00e-02 2.50e+03 1.84e-02 1.10e+01 pdb=" N9 A A2591 " 0.049 2.00e-02 2.50e+03 pdb=" C8 A A2591 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A A2591 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A2591 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A A2591 " -0.008 2.00e-02 2.50e+03 pdb=" N6 A A2591 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A A2591 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A A2591 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A A2591 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A A2591 " 0.007 2.00e-02 2.50e+03 pdb=" H8 A A2591 " 0.000 2.00e-02 2.50e+03 pdb=" H2 A A2591 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 45 " -0.036 2.00e-02 2.50e+03 1.71e-02 1.02e+01 pdb=" N9 G A 45 " 0.051 2.00e-02 2.50e+03 pdb=" C8 G A 45 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G A 45 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A 45 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G A 45 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G A 45 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G A 45 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G A 45 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G A 45 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G A 45 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G A 45 " -0.006 2.00e-02 2.50e+03 pdb=" H8 G A 45 " 0.002 2.00e-02 2.50e+03 pdb=" H1 G A 45 " -0.003 2.00e-02 2.50e+03 ... (remaining 12476 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 2694 2.12 - 2.74: 198466 2.74 - 3.36: 363786 3.36 - 3.98: 554231 3.98 - 4.60: 813882 Nonbonded interactions: 1933059 Sorted by model distance: nonbonded pdb=" O4 U A1499 " pdb=" H42 C A2731 " model vdw 1.497 1.850 nonbonded pdb=" OP2 C A2259 " pdb="HH22 ARG V 27 " model vdw 1.649 1.850 nonbonded pdb=" HE2 HIS P 88 " pdb=" OE1 GLN P 90 " model vdw 1.656 1.850 nonbonded pdb=" O2 U A1455 " pdb=" H3 U A1457 " model vdw 1.674 1.850 nonbonded pdb="HO2' G A1490 " pdb=" O4' C A1491 " model vdw 1.674 1.850 ... (remaining 1933054 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.190 Extract box with map and model: 17.390 Check model and map are aligned: 1.540 Set scattering table: 0.980 Process input model: 487.920 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.260 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:9.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 523.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 96634 Z= 0.396 Angle : 0.803 29.722 145412 Z= 0.394 Chirality : 0.055 2.431 18785 Planarity : 0.005 0.062 7170 Dihedral : 23.764 179.891 56090 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.15 % Favored : 92.82 % Rotamer: Outliers : 6.96 % Allowed : 8.90 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.13), residues: 3050 helix: -1.10 (0.16), residues: 772 sheet: -1.67 (0.19), residues: 624 loop : -2.48 (0.13), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 65 HIS 0.009 0.001 HIS O 29 PHE 0.017 0.002 PHE T 91 TYR 0.012 0.002 TYR H 126 ARG 0.010 0.001 ARG Z 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 883 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 710 time to evaluate : 4.782 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 TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. REVERT: C 4 LYS cc_start: 0.8131 (ptpt) cc_final: 0.7546 (ptmt) REVERT: C 40 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7941 (mmmt) REVERT: C 66 ASP cc_start: 0.8318 (t70) cc_final: 0.8079 (t0) REVERT: C 117 GLU cc_start: 0.7519 (pt0) cc_final: 0.7028 (pm20) REVERT: C 133 GLN cc_start: 0.7675 (tt0) cc_final: 0.7425 (tp40) REVERT: C 168 GLU cc_start: 0.6086 (OUTLIER) cc_final: 0.5648 (mm-30) REVERT: C 174 ILE cc_start: 0.8540 (tt) cc_final: 0.8340 (mt) REVERT: C 194 GLN cc_start: 0.8309 (tt0) cc_final: 0.8085 (tt0) REVERT: C 258 LYS cc_start: 0.8116 (mttm) cc_final: 0.7881 (mttm) REVERT: D 12 MET cc_start: 0.8159 (mtp) cc_final: 0.7846 (mtp) REVERT: D 13 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8492 (t) REVERT: D 15 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8214 (m) REVERT: D 27 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8338 (p) REVERT: D 71 LYS cc_start: 0.7464 (mmmt) cc_final: 0.7262 (mtpt) REVERT: E 8 LYS cc_start: 0.7618 (mtpt) cc_final: 0.7290 (mtpp) REVERT: E 66 LYS cc_start: 0.7891 (ttmt) cc_final: 0.7557 (mmtp) REVERT: E 100 LYS cc_start: 0.8513 (mttm) cc_final: 0.8022 (mttt) REVERT: E 107 ARG cc_start: 0.7384 (mtp85) cc_final: 0.7175 (mtp85) REVERT: E 141 ASN cc_start: 0.7975 (m-40) cc_final: 0.7543 (m110) REVERT: E 150 LYS cc_start: 0.7888 (tmmt) cc_final: 0.7644 (tttm) REVERT: E 152 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8212 (p) REVERT: E 154 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7773 (t) REVERT: E 177 THR cc_start: 0.8155 (m) cc_final: 0.7599 (p) REVERT: F 17 MET cc_start: 0.5292 (mmm) cc_final: 0.4941 (tpp) REVERT: F 26 MET cc_start: 0.4806 (mmt) cc_final: 0.4498 (mmt) REVERT: F 33 LYS cc_start: 0.4906 (pttt) cc_final: 0.4588 (ttpt) REVERT: F 56 GLU cc_start: 0.5969 (mt-10) cc_final: 0.5446 (mm-30) REVERT: F 67 VAL cc_start: 0.6483 (m) cc_final: 0.6212 (p) REVERT: F 88 LYS cc_start: 0.5677 (pttp) cc_final: 0.5322 (ptpt) REVERT: F 94 GLU cc_start: 0.5681 (mp0) cc_final: 0.5415 (tp30) REVERT: F 120 LYS cc_start: 0.4284 (OUTLIER) cc_final: 0.4031 (pttt) REVERT: F 168 GLU cc_start: 0.4828 (mt-10) cc_final: 0.4348 (mt-10) REVERT: G 39 GLU cc_start: 0.5781 (pp20) cc_final: 0.5307 (pm20) REVERT: G 79 VAL cc_start: 0.4084 (OUTLIER) cc_final: 0.3820 (p) REVERT: G 98 MET cc_start: 0.3896 (mmm) cc_final: 0.3595 (mmm) REVERT: G 132 LYS cc_start: 0.4949 (mtpp) cc_final: 0.4548 (mppt) REVERT: H 49 VAL cc_start: 0.8588 (p) cc_final: 0.8331 (m) REVERT: H 50 ASP cc_start: 0.8183 (t0) cc_final: 0.7867 (t0) REVERT: H 103 GLU cc_start: 0.7322 (pt0) cc_final: 0.7121 (mt-10) REVERT: I 4 GLN cc_start: 0.8036 (tt0) cc_final: 0.7756 (tt0) REVERT: I 12 ASP cc_start: 0.7364 (p0) cc_final: 0.7157 (p0) REVERT: J 41 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8248 (mpt90) REVERT: K 20 ARG cc_start: 0.6824 (mtp85) cc_final: 0.6497 (mtm110) REVERT: L 31 GLU cc_start: 0.7214 (tt0) cc_final: 0.7012 (mt-10) REVERT: L 46 LYS cc_start: 0.7880 (mttt) cc_final: 0.7614 (mttp) REVERT: L 91 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6516 (mm-30) REVERT: L 97 GLN cc_start: 0.7689 (mt0) cc_final: 0.7216 (mp-120) REVERT: M 7 LYS cc_start: 0.6974 (mttp) cc_final: 0.6638 (mttm) REVERT: M 28 LYS cc_start: 0.7482 (mttp) cc_final: 0.7275 (tppp) REVERT: M 33 VAL cc_start: 0.7937 (t) cc_final: 0.7683 (p) REVERT: M 47 ASP cc_start: 0.6913 (m-30) cc_final: 0.6580 (m-30) REVERT: M 90 LYS cc_start: 0.6506 (mptt) cc_final: 0.6260 (mmmt) REVERT: M 102 HIS cc_start: 0.6121 (t70) cc_final: 0.5894 (t-170) REVERT: N 66 ILE cc_start: 0.8684 (mt) cc_final: 0.8468 (mm) REVERT: O 15 LYS cc_start: 0.8280 (mtpm) cc_final: 0.7928 (mtpp) REVERT: O 19 LYS cc_start: 0.8296 (tttp) cc_final: 0.7504 (mmtp) REVERT: O 51 ARG cc_start: 0.8008 (mtt180) cc_final: 0.7457 (mtt90) REVERT: O 56 ASP cc_start: 0.7453 (m-30) cc_final: 0.7148 (m-30) REVERT: O 59 LYS cc_start: 0.8123 (ttpt) cc_final: 0.7793 (ttmm) REVERT: O 75 SER cc_start: 0.7264 (OUTLIER) cc_final: 0.6992 (p) REVERT: P 12 ILE cc_start: 0.8697 (mt) cc_final: 0.8493 (mp) REVERT: P 15 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7238 (mt-10) REVERT: P 22 VAL cc_start: 0.8067 (OUTLIER) cc_final: 0.7779 (p) REVERT: P 47 LYS cc_start: 0.8498 (mttp) cc_final: 0.8278 (mttp) REVERT: P 63 ASN cc_start: 0.5847 (OUTLIER) cc_final: 0.5473 (p0) REVERT: P 69 LYS cc_start: 0.8001 (ttmt) cc_final: 0.7793 (tttp) REVERT: P 78 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6815 (ptp-170) REVERT: P 86 LYS cc_start: 0.8299 (mtpt) cc_final: 0.7749 (mttm) REVERT: P 100 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7633 (mt) REVERT: Q 11 ARG cc_start: 0.7803 (mmt90) cc_final: 0.7278 (mmm160) REVERT: Q 59 GLU cc_start: 0.7401 (tt0) cc_final: 0.7150 (tt0) REVERT: Q 65 ASN cc_start: 0.7782 (t0) cc_final: 0.7502 (t0) REVERT: Q 73 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7442 (mt-10) REVERT: Q 96 LYS cc_start: 0.8265 (mmtp) cc_final: 0.8043 (mptm) REVERT: Q 104 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8220 (p) REVERT: Q 106 SER cc_start: 0.8979 (p) cc_final: 0.8609 (t) REVERT: R 6 ILE cc_start: 0.6821 (pt) cc_final: 0.6567 (pt) REVERT: R 14 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6000 (mt-10) REVERT: R 30 ASP cc_start: 0.7555 (t70) cc_final: 0.7353 (t0) REVERT: R 62 LYS cc_start: 0.8265 (ttmp) cc_final: 0.8043 (ttpp) REVERT: R 69 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6685 (pm20) REVERT: R 75 ARG cc_start: 0.7654 (ptt90) cc_final: 0.7397 (ptt-90) REVERT: S 5 LYS cc_start: 0.7341 (tttt) cc_final: 0.7014 (tttm) REVERT: S 72 ASP cc_start: 0.7356 (t0) cc_final: 0.6558 (t0) REVERT: S 75 THR cc_start: 0.6702 (m) cc_final: 0.6404 (m) REVERT: T 26 LYS cc_start: 0.7711 (mptp) cc_final: 0.7440 (mmmm) REVERT: T 31 VAL cc_start: 0.8100 (OUTLIER) cc_final: 0.7847 (t) REVERT: T 50 LYS cc_start: 0.6640 (mttt) cc_final: 0.6367 (mmtm) REVERT: T 83 LYS cc_start: 0.7169 (ptpt) cc_final: 0.6472 (ptmt) REVERT: V 20 HIS cc_start: 0.7446 (m-70) cc_final: 0.7145 (t-90) REVERT: V 27 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7884 (ptm160) REVERT: X 57 GLU cc_start: 0.7297 (pt0) cc_final: 0.6968 (pt0) REVERT: 2 40 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.5413 (mpt90) REVERT: 3 21 GLN cc_start: 0.7474 (mm-40) cc_final: 0.7025 (mm110) REVERT: 3 48 ARG cc_start: 0.7783 (mtp85) cc_final: 0.7498 (mtt180) REVERT: 3 52 LYS cc_start: 0.7161 (ptpp) cc_final: 0.6869 (pttp) REVERT: 4 4 ARG cc_start: 0.7077 (ptp-170) cc_final: 0.6726 (pmm-80) REVERT: 4 8 LYS cc_start: 0.7380 (mtmt) cc_final: 0.7156 (mtpp) REVERT: 4 13 LYS cc_start: 0.6766 (mttt) cc_final: 0.6463 (mppt) REVERT: 4 22 LYS cc_start: 0.6950 (mttt) cc_final: 0.6523 (mttp) REVERT: 4 24 MET cc_start: 0.7078 (mtt) cc_final: 0.6866 (mpp) outliers start: 173 outliers final: 35 residues processed: 833 average time/residue: 3.3371 time to fit residues: 3617.6151 Evaluate side-chains 551 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 495 time to evaluate : 4.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 41 ARG Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 120 LYS Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 78 ARG Chi-restraints excluded: chain P residue 100 ILE Chi-restraints excluded: chain Q residue 103 ILE Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 27 ARG Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain 2 residue 40 ARG Chi-restraints excluded: chain 3 residue 31 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 504 optimal weight: 0.9980 chunk 452 optimal weight: 0.7980 chunk 251 optimal weight: 3.9990 chunk 154 optimal weight: 50.0000 chunk 305 optimal weight: 0.5980 chunk 241 optimal weight: 7.9990 chunk 467 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 348 optimal weight: 0.7980 chunk 542 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 ASN E 46 GLN E 169 ASN G 64 ASN H 11 ASN J 104 ASN L 61 ASN R 47 ASN T 84 ASN T 85 GLN ** 1 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 17 HIS 2 27 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 96634 Z= 0.146 Angle : 0.597 27.232 145412 Z= 0.299 Chirality : 0.044 2.166 18785 Planarity : 0.004 0.068 7170 Dihedral : 24.235 179.721 50245 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.74 % Allowed : 18.64 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.14), residues: 3050 helix: 0.26 (0.18), residues: 773 sheet: -1.04 (0.19), residues: 634 loop : -1.93 (0.14), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 65 HIS 0.005 0.001 HIS 2 17 PHE 0.013 0.001 PHE N 76 TYR 0.012 0.001 TYR C 103 ARG 0.006 0.000 ARG P 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 616 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 523 time to evaluate : 4.920 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 TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 4 LYS cc_start: 0.8147 (ptpt) cc_final: 0.7791 (ptmm) REVERT: C 40 LYS cc_start: 0.8485 (mmpt) cc_final: 0.7932 (mmmt) REVERT: C 66 ASP cc_start: 0.8297 (t70) cc_final: 0.7964 (t0) REVERT: C 117 GLU cc_start: 0.7659 (pt0) cc_final: 0.7023 (pm20) REVERT: C 133 GLN cc_start: 0.7805 (tt0) cc_final: 0.7565 (tp-100) REVERT: C 168 GLU cc_start: 0.6051 (OUTLIER) cc_final: 0.5650 (mm-30) REVERT: C 194 GLN cc_start: 0.8481 (tt0) cc_final: 0.8059 (tt0) REVERT: C 258 LYS cc_start: 0.8141 (mttm) cc_final: 0.7925 (mttm) REVERT: D 12 MET cc_start: 0.8176 (mtp) cc_final: 0.7829 (mtp) REVERT: D 13 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8495 (t) REVERT: D 71 LYS cc_start: 0.7407 (mmmt) cc_final: 0.7204 (mttp) REVERT: D 78 LYS cc_start: 0.7675 (ttmm) cc_final: 0.7161 (mtmm) REVERT: E 8 LYS cc_start: 0.7467 (mtpt) cc_final: 0.7178 (mtpp) REVERT: E 66 LYS cc_start: 0.7933 (ttmt) cc_final: 0.7600 (mmtp) REVERT: E 100 LYS cc_start: 0.8510 (mttm) cc_final: 0.8081 (mttt) REVERT: E 107 ARG cc_start: 0.7485 (mtp85) cc_final: 0.7274 (mtp85) REVERT: E 141 ASN cc_start: 0.7850 (m-40) cc_final: 0.7599 (m110) REVERT: E 150 LYS cc_start: 0.7816 (tmmt) cc_final: 0.7518 (tttp) REVERT: E 177 THR cc_start: 0.8234 (m) cc_final: 0.7820 (p) REVERT: F 17 MET cc_start: 0.4613 (mmm) cc_final: 0.4310 (tpp) REVERT: F 26 MET cc_start: 0.4995 (mmt) cc_final: 0.4703 (mmt) REVERT: F 33 LYS cc_start: 0.4972 (pttt) cc_final: 0.4681 (ttpt) REVERT: F 56 GLU cc_start: 0.5933 (mt-10) cc_final: 0.5368 (mm-30) REVERT: F 67 VAL cc_start: 0.6550 (m) cc_final: 0.6297 (p) REVERT: F 94 GLU cc_start: 0.5994 (mp0) cc_final: 0.5542 (tp30) REVERT: F 98 GLU cc_start: 0.3360 (tp30) cc_final: 0.2877 (tm-30) REVERT: F 120 LYS cc_start: 0.4355 (OUTLIER) cc_final: 0.3997 (pttm) REVERT: F 168 GLU cc_start: 0.4762 (mt-10) cc_final: 0.4556 (mt-10) REVERT: G 39 GLU cc_start: 0.5873 (pp20) cc_final: 0.5448 (pm20) REVERT: G 59 LYS cc_start: 0.5787 (mtpp) cc_final: 0.5401 (mmtt) REVERT: G 87 LEU cc_start: 0.4313 (OUTLIER) cc_final: 0.4097 (pt) REVERT: G 98 MET cc_start: 0.4013 (mmm) cc_final: 0.3599 (mmm) REVERT: H 49 VAL cc_start: 0.8661 (p) cc_final: 0.8373 (m) REVERT: H 50 ASP cc_start: 0.8266 (t0) cc_final: 0.8006 (t0) REVERT: H 74 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8495 (t) REVERT: H 85 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8497 (tt) REVERT: I 4 GLN cc_start: 0.7939 (tt0) cc_final: 0.7738 (tt0) REVERT: I 12 ASP cc_start: 0.7306 (p0) cc_final: 0.7055 (p0) REVERT: I 81 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.6785 (pm20) REVERT: I 98 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8679 (mt) REVERT: K 20 ARG cc_start: 0.6951 (mtp85) cc_final: 0.6629 (mtm110) REVERT: K 68 ILE cc_start: 0.8308 (mm) cc_final: 0.7826 (pt) REVERT: L 31 GLU cc_start: 0.7405 (tt0) cc_final: 0.7029 (mt-10) REVERT: L 46 LYS cc_start: 0.8022 (mttt) cc_final: 0.7785 (mttp) REVERT: L 97 GLN cc_start: 0.7714 (mt0) cc_final: 0.7121 (mm-40) REVERT: M 28 LYS cc_start: 0.7575 (mttp) cc_final: 0.7355 (tppp) REVERT: M 90 LYS cc_start: 0.6500 (mptt) cc_final: 0.6247 (mmmt) REVERT: O 15 LYS cc_start: 0.8427 (mtpm) cc_final: 0.8161 (mtpp) REVERT: O 19 LYS cc_start: 0.8222 (tttp) cc_final: 0.8003 (tttm) REVERT: O 51 ARG cc_start: 0.8203 (mtt180) cc_final: 0.7722 (mtt90) REVERT: O 56 ASP cc_start: 0.7677 (m-30) cc_final: 0.7434 (m-30) REVERT: O 59 LYS cc_start: 0.8144 (ttpt) cc_final: 0.7802 (ttmm) REVERT: O 75 SER cc_start: 0.7529 (OUTLIER) cc_final: 0.7303 (p) REVERT: O 85 LYS cc_start: 0.8245 (mttt) cc_final: 0.8000 (mtmt) REVERT: P 15 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7272 (mt-10) REVERT: P 22 VAL cc_start: 0.7861 (OUTLIER) cc_final: 0.7586 (m) REVERT: P 63 ASN cc_start: 0.5874 (OUTLIER) cc_final: 0.5438 (p0) REVERT: P 86 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7542 (mttm) REVERT: Q 11 ARG cc_start: 0.7759 (mmt90) cc_final: 0.7275 (mmm160) REVERT: Q 59 GLU cc_start: 0.7363 (tt0) cc_final: 0.7062 (tt0) REVERT: Q 82 LEU cc_start: 0.7695 (mt) cc_final: 0.7305 (mt) REVERT: R 14 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6381 (mt-10) REVERT: R 18 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7159 (mt-10) REVERT: R 69 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6662 (pm20) REVERT: R 75 ARG cc_start: 0.7702 (ptt90) cc_final: 0.7402 (ptt-90) REVERT: R 80 VAL cc_start: 0.8137 (OUTLIER) cc_final: 0.7926 (t) REVERT: S 12 ILE cc_start: 0.7277 (mt) cc_final: 0.6967 (mm) REVERT: S 72 ASP cc_start: 0.7345 (t0) cc_final: 0.6600 (t0) REVERT: S 75 THR cc_start: 0.6784 (m) cc_final: 0.6500 (m) REVERT: T 26 LYS cc_start: 0.7766 (mptp) cc_final: 0.7494 (mmmm) REVERT: T 31 VAL cc_start: 0.8165 (OUTLIER) cc_final: 0.7926 (t) REVERT: T 50 LYS cc_start: 0.6657 (mttt) cc_final: 0.6411 (mmtm) REVERT: T 83 LYS cc_start: 0.7027 (ptpt) cc_final: 0.6360 (ptmt) REVERT: U 57 GLU cc_start: 0.7423 (tt0) cc_final: 0.7175 (tt0) REVERT: V 20 HIS cc_start: 0.7511 (m-70) cc_final: 0.7197 (t-90) REVERT: V 27 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7837 (ptm160) REVERT: X 57 GLU cc_start: 0.7349 (pt0) cc_final: 0.7035 (pt0) REVERT: 3 21 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7051 (mm110) REVERT: 3 48 ARG cc_start: 0.7786 (mtp85) cc_final: 0.7496 (mtt180) REVERT: 3 52 LYS cc_start: 0.7362 (ptpp) cc_final: 0.7052 (pttp) REVERT: 4 4 ARG cc_start: 0.7013 (ptp-170) cc_final: 0.6488 (pmm-80) REVERT: 4 8 LYS cc_start: 0.7423 (mtmt) cc_final: 0.7158 (mtpp) REVERT: 4 13 LYS cc_start: 0.6772 (mttt) cc_final: 0.6532 (mppt) REVERT: 4 22 LYS cc_start: 0.6835 (mttt) cc_final: 0.6437 (mttm) REVERT: 4 24 MET cc_start: 0.7183 (mtt) cc_final: 0.6947 (mpp) outliers start: 93 outliers final: 38 residues processed: 591 average time/residue: 3.4252 time to fit residues: 2628.3958 Evaluate side-chains 535 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 481 time to evaluate : 4.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain Q residue 103 ILE Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 27 ARG Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain 1 residue 34 LYS Chi-restraints excluded: chain 3 residue 31 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 301 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 451 optimal weight: 5.9990 chunk 369 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 543 optimal weight: 7.9990 chunk 586 optimal weight: 3.9990 chunk 483 optimal weight: 0.8980 chunk 538 optimal weight: 0.6980 chunk 185 optimal weight: 6.9990 chunk 435 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 176 ASN I 72 ASN J 17 ASN J 27 ASN J 104 ASN L 61 ASN Q 61 ASN Q 65 ASN R 47 ASN T 85 GLN 2 17 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 96634 Z= 0.242 Angle : 0.690 28.610 145412 Z= 0.347 Chirality : 0.047 2.108 18785 Planarity : 0.005 0.067 7170 Dihedral : 24.212 179.876 50207 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.59 % Allowed : 19.00 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.14), residues: 3050 helix: 0.66 (0.19), residues: 765 sheet: -0.66 (0.20), residues: 649 loop : -1.61 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 250 HIS 0.006 0.001 HIS 2 13 PHE 0.016 0.002 PHE N 76 TYR 0.019 0.002 TYR H 126 ARG 0.008 0.001 ARG O 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 632 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 518 time to evaluate : 4.831 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 TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. REVERT: C 4 LYS cc_start: 0.8204 (ptpt) cc_final: 0.7767 (ptmm) REVERT: C 16 MET cc_start: 0.8792 (ttt) cc_final: 0.8567 (ttm) REVERT: C 40 LYS cc_start: 0.8600 (mmpt) cc_final: 0.8056 (mmmt) REVERT: C 66 ASP cc_start: 0.8327 (t70) cc_final: 0.8056 (t0) REVERT: C 117 GLU cc_start: 0.7621 (pt0) cc_final: 0.7011 (pm20) REVERT: C 133 GLN cc_start: 0.7793 (tt0) cc_final: 0.7554 (tp-100) REVERT: C 168 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5885 (mm-30) REVERT: D 12 MET cc_start: 0.8410 (mtp) cc_final: 0.7870 (mtp) REVERT: D 13 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8561 (t) REVERT: D 15 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8320 (m) REVERT: D 100 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: D 159 ASP cc_start: 0.6762 (OUTLIER) cc_final: 0.6299 (t70) REVERT: E 8 LYS cc_start: 0.7503 (mtpt) cc_final: 0.7212 (mtpp) REVERT: E 62 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7939 (ptp-170) REVERT: E 66 LYS cc_start: 0.7904 (ttmt) cc_final: 0.7587 (mmtp) REVERT: E 93 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8186 (p) REVERT: E 100 LYS cc_start: 0.8572 (mttm) cc_final: 0.8165 (mtmt) REVERT: E 105 MET cc_start: 0.7844 (mtp) cc_final: 0.7624 (mtp) REVERT: E 141 ASN cc_start: 0.7715 (m-40) cc_final: 0.7495 (m110) REVERT: E 150 LYS cc_start: 0.7617 (tmmt) cc_final: 0.7299 (tttm) REVERT: E 152 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8255 (t) REVERT: E 177 THR cc_start: 0.8651 (m) cc_final: 0.8430 (p) REVERT: F 17 MET cc_start: 0.4338 (mmm) cc_final: 0.4017 (mpp) REVERT: F 26 MET cc_start: 0.5083 (mmt) cc_final: 0.4804 (mmt) REVERT: F 56 GLU cc_start: 0.5855 (mt-10) cc_final: 0.5495 (tp30) REVERT: F 67 VAL cc_start: 0.6697 (m) cc_final: 0.6427 (p) REVERT: F 94 GLU cc_start: 0.5787 (mp0) cc_final: 0.5565 (tp30) REVERT: F 98 GLU cc_start: 0.3826 (tp30) cc_final: 0.3050 (tm-30) REVERT: F 120 LYS cc_start: 0.4907 (OUTLIER) cc_final: 0.4492 (pttt) REVERT: F 148 LYS cc_start: 0.1846 (tptp) cc_final: 0.1611 (mmtt) REVERT: G 39 GLU cc_start: 0.5860 (pp20) cc_final: 0.5450 (pm20) REVERT: G 43 PHE cc_start: 0.3605 (OUTLIER) cc_final: 0.3349 (m-80) REVERT: G 87 LEU cc_start: 0.4238 (OUTLIER) cc_final: 0.4013 (pt) REVERT: G 98 MET cc_start: 0.4000 (mmm) cc_final: 0.3647 (mmm) REVERT: G 132 LYS cc_start: 0.5712 (OUTLIER) cc_final: 0.5268 (mptt) REVERT: H 74 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8598 (t) REVERT: H 85 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8615 (tt) REVERT: I 4 GLN cc_start: 0.7859 (tt0) cc_final: 0.7630 (tt0) REVERT: I 9 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7672 (ttmt) REVERT: I 12 ASP cc_start: 0.7441 (p0) cc_final: 0.7166 (p0) REVERT: I 42 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8235 (t) REVERT: I 81 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.6711 (pm20) REVERT: I 98 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8668 (mt) REVERT: I 104 ARG cc_start: 0.7897 (ttm-80) cc_final: 0.7622 (ttt180) REVERT: K 20 ARG cc_start: 0.7133 (mtp85) cc_final: 0.6652 (mtm110) REVERT: K 31 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6496 (mt-10) REVERT: K 51 ARG cc_start: 0.7484 (ttp80) cc_final: 0.7205 (ttp80) REVERT: K 55 THR cc_start: 0.8106 (m) cc_final: 0.7828 (p) REVERT: K 68 ILE cc_start: 0.8439 (mm) cc_final: 0.8151 (pt) REVERT: K 76 LYS cc_start: 0.8152 (tptt) cc_final: 0.7878 (tttm) REVERT: L 31 GLU cc_start: 0.7261 (tt0) cc_final: 0.6953 (mt-10) REVERT: L 46 LYS cc_start: 0.8162 (mttt) cc_final: 0.7922 (mttp) REVERT: L 97 GLN cc_start: 0.7797 (mt0) cc_final: 0.7188 (mm110) REVERT: M 12 LEU cc_start: 0.7691 (mt) cc_final: 0.7490 (mt) REVERT: M 22 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6543 (tp) REVERT: M 90 LYS cc_start: 0.6757 (mptt) cc_final: 0.6280 (mmmt) REVERT: O 19 LYS cc_start: 0.8263 (tttp) cc_final: 0.8030 (tttm) REVERT: O 59 LYS cc_start: 0.8182 (ttpt) cc_final: 0.7847 (ttmm) REVERT: O 75 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.8094 (p) REVERT: O 85 LYS cc_start: 0.8358 (mttt) cc_final: 0.8070 (mtmt) REVERT: P 15 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7279 (mt-10) REVERT: P 36 ASP cc_start: 0.7555 (p0) cc_final: 0.7335 (p0) REVERT: P 86 LYS cc_start: 0.8093 (mtpt) cc_final: 0.7541 (mttm) REVERT: P 100 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7791 (mt) REVERT: Q 11 ARG cc_start: 0.7921 (mmt90) cc_final: 0.7510 (mmm160) REVERT: Q 59 GLU cc_start: 0.7619 (tt0) cc_final: 0.7253 (tt0) REVERT: Q 83 LYS cc_start: 0.7743 (mmtm) cc_final: 0.7514 (mmtp) REVERT: Q 96 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8183 (mptm) REVERT: R 14 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6744 (mt-10) REVERT: R 18 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7272 (mt-10) REVERT: R 69 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6765 (pm20) REVERT: R 75 ARG cc_start: 0.7789 (ptt90) cc_final: 0.7547 (ptt-90) REVERT: S 72 ASP cc_start: 0.7345 (t0) cc_final: 0.7064 (t0) REVERT: T 26 LYS cc_start: 0.7831 (mptp) cc_final: 0.7504 (mmmm) REVERT: T 50 LYS cc_start: 0.6688 (mttt) cc_final: 0.6373 (mmtm) REVERT: T 83 LYS cc_start: 0.7021 (ptpt) cc_final: 0.6320 (ptmt) REVERT: U 71 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8083 (pp) REVERT: V 20 HIS cc_start: 0.7568 (m-70) cc_final: 0.7206 (t70) REVERT: V 28 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6775 (mmt90) REVERT: W 58 ARG cc_start: 0.7523 (tpt90) cc_final: 0.7293 (tpt170) REVERT: X 57 GLU cc_start: 0.7418 (pt0) cc_final: 0.7099 (pt0) REVERT: 2 31 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8214 (t) REVERT: 3 21 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7073 (mm110) REVERT: 3 48 ARG cc_start: 0.7624 (mtp85) cc_final: 0.7356 (mtt-85) REVERT: 3 52 LYS cc_start: 0.7556 (ptpp) cc_final: 0.7255 (pttp) REVERT: 4 4 ARG cc_start: 0.7116 (ptp-170) cc_final: 0.6508 (pmm-80) REVERT: 4 8 LYS cc_start: 0.7417 (mtmt) cc_final: 0.7211 (mtpt) REVERT: 4 13 LYS cc_start: 0.6709 (mttt) cc_final: 0.6115 (pttm) REVERT: 4 22 LYS cc_start: 0.6866 (mttt) cc_final: 0.6456 (mttm) REVERT: 4 24 MET cc_start: 0.7356 (mtt) cc_final: 0.6790 (mpp) REVERT: 4 33 LYS cc_start: 0.6614 (tttm) cc_final: 0.6318 (ttpt) outliers start: 114 outliers final: 49 residues processed: 594 average time/residue: 3.5578 time to fit residues: 2751.6862 Evaluate side-chains 564 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 488 time to evaluate : 4.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain I residue 9 LYS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 100 ILE Chi-restraints excluded: chain Q residue 96 LYS Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 97 SER Chi-restraints excluded: chain T residue 23 LYS Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain V residue 27 ARG Chi-restraints excluded: chain V residue 28 ARG Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 31 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 536 optimal weight: 0.8980 chunk 408 optimal weight: 4.9990 chunk 281 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 259 optimal weight: 4.9990 chunk 364 optimal weight: 0.9980 chunk 545 optimal weight: 0.7980 chunk 577 optimal weight: 1.9990 chunk 284 optimal weight: 4.9990 chunk 516 optimal weight: 3.9990 chunk 155 optimal weight: 30.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN E 148 GLN H 11 ASN I 72 ASN Q 65 ASN R 47 ASN T 38 ASN T 85 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 96634 Z= 0.162 Angle : 0.595 28.291 145412 Z= 0.301 Chirality : 0.045 2.128 18785 Planarity : 0.004 0.065 7170 Dihedral : 24.110 179.400 50201 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.74 % Allowed : 20.25 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3050 helix: 1.05 (0.19), residues: 761 sheet: -0.58 (0.20), residues: 657 loop : -1.45 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 65 HIS 0.004 0.001 HIS C 230 PHE 0.014 0.001 PHE O 57 TYR 0.016 0.001 TYR 2 6 ARG 0.005 0.000 ARG D 162 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 592 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 499 time to evaluate : 4.808 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 TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. REVERT: C 4 LYS cc_start: 0.8214 (ptpt) cc_final: 0.7774 (ptmm) REVERT: C 40 LYS cc_start: 0.8596 (mmpt) cc_final: 0.8059 (mmmt) REVERT: C 66 ASP cc_start: 0.8353 (t70) cc_final: 0.8097 (t0) REVERT: C 100 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6594 (tt0) REVERT: C 117 GLU cc_start: 0.7638 (pt0) cc_final: 0.7037 (pm20) REVERT: C 133 GLN cc_start: 0.7859 (tt0) cc_final: 0.7613 (tp-100) REVERT: C 168 GLU cc_start: 0.6096 (OUTLIER) cc_final: 0.5811 (mm-30) REVERT: C 174 ILE cc_start: 0.8663 (mt) cc_final: 0.8419 (mm) REVERT: D 12 MET cc_start: 0.8355 (mtp) cc_final: 0.7869 (mtp) REVERT: D 100 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: E 8 LYS cc_start: 0.7521 (mtpt) cc_final: 0.7235 (mtpp) REVERT: E 66 LYS cc_start: 0.7938 (ttmt) cc_final: 0.7591 (mmtp) REVERT: E 93 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.8127 (p) REVERT: E 100 LYS cc_start: 0.8572 (mttm) cc_final: 0.8113 (mttt) REVERT: E 141 ASN cc_start: 0.7698 (m-40) cc_final: 0.7474 (m110) REVERT: E 150 LYS cc_start: 0.7548 (tmmt) cc_final: 0.7293 (tttp) REVERT: E 177 THR cc_start: 0.8540 (m) cc_final: 0.8261 (p) REVERT: F 17 MET cc_start: 0.4001 (mmm) cc_final: 0.3755 (mpp) REVERT: F 26 MET cc_start: 0.5108 (mmt) cc_final: 0.4785 (mmt) REVERT: F 56 GLU cc_start: 0.5810 (mt-10) cc_final: 0.5119 (mm-30) REVERT: F 94 GLU cc_start: 0.5989 (mp0) cc_final: 0.5544 (tp30) REVERT: F 98 GLU cc_start: 0.3816 (tp30) cc_final: 0.3206 (tm-30) REVERT: F 120 LYS cc_start: 0.5010 (OUTLIER) cc_final: 0.4465 (pttm) REVERT: F 148 LYS cc_start: 0.2011 (tptp) cc_final: 0.1697 (mmtt) REVERT: G 39 GLU cc_start: 0.5833 (pp20) cc_final: 0.5435 (pm20) REVERT: G 59 LYS cc_start: 0.5816 (mtpp) cc_final: 0.5419 (mttt) REVERT: G 87 LEU cc_start: 0.4140 (OUTLIER) cc_final: 0.3915 (pt) REVERT: G 98 MET cc_start: 0.3983 (mmm) cc_final: 0.3640 (mmm) REVERT: G 132 LYS cc_start: 0.5733 (ptmm) cc_final: 0.5246 (mptt) REVERT: H 1 MET cc_start: 0.7842 (mpm) cc_final: 0.7541 (mpm) REVERT: H 50 ASP cc_start: 0.8313 (t0) cc_final: 0.8016 (t0) REVERT: H 62 LYS cc_start: 0.8486 (mmtm) cc_final: 0.8253 (mptp) REVERT: H 85 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8563 (tt) REVERT: I 4 GLN cc_start: 0.7868 (tt0) cc_final: 0.7641 (tt0) REVERT: I 12 ASP cc_start: 0.7394 (p0) cc_final: 0.7125 (p0) REVERT: I 81 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.6618 (pm20) REVERT: I 98 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8662 (mt) REVERT: I 104 ARG cc_start: 0.7935 (ttm-80) cc_final: 0.7650 (ttt180) REVERT: J 139 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7315 (mttp) REVERT: K 20 ARG cc_start: 0.7105 (mtp85) cc_final: 0.6633 (mtm110) REVERT: K 31 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6462 (mt-10) REVERT: K 76 LYS cc_start: 0.8152 (tptt) cc_final: 0.7904 (tttm) REVERT: L 16 MET cc_start: 0.8638 (ttp) cc_final: 0.8405 (ttp) REVERT: L 31 GLU cc_start: 0.7265 (tt0) cc_final: 0.6942 (mt-10) REVERT: L 97 GLN cc_start: 0.7753 (mt0) cc_final: 0.7349 (mp10) REVERT: M 90 LYS cc_start: 0.6726 (mptt) cc_final: 0.6316 (mmmt) REVERT: O 15 LYS cc_start: 0.8471 (mtpm) cc_final: 0.8195 (mttm) REVERT: O 16 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7723 (ptpp) REVERT: O 19 LYS cc_start: 0.8255 (tttp) cc_final: 0.8025 (tttm) REVERT: O 51 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8109 (mtt-85) REVERT: O 59 LYS cc_start: 0.8281 (ttpt) cc_final: 0.7926 (ttmm) REVERT: O 80 MET cc_start: 0.8682 (mmm) cc_final: 0.8476 (mmm) REVERT: P 15 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7237 (mt-10) REVERT: P 36 ASP cc_start: 0.7646 (p0) cc_final: 0.7426 (p0) REVERT: P 86 LYS cc_start: 0.8074 (mtpt) cc_final: 0.7510 (mttm) REVERT: P 100 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7862 (mt) REVERT: Q 11 ARG cc_start: 0.7860 (mmt90) cc_final: 0.7505 (mmm160) REVERT: Q 40 ASN cc_start: 0.7869 (p0) cc_final: 0.7200 (t0) REVERT: Q 83 LYS cc_start: 0.7765 (mmtm) cc_final: 0.7478 (mmtp) REVERT: R 14 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6721 (mt-10) REVERT: R 18 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7308 (mt-10) REVERT: R 49 LYS cc_start: 0.7837 (tptm) cc_final: 0.7515 (tppt) REVERT: R 69 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6802 (pm20) REVERT: R 75 ARG cc_start: 0.7830 (ptt90) cc_final: 0.7546 (ptt-90) REVERT: S 100 GLU cc_start: 0.6039 (OUTLIER) cc_final: 0.5337 (mp0) REVERT: T 26 LYS cc_start: 0.7883 (mptp) cc_final: 0.7581 (mmmm) REVERT: T 50 LYS cc_start: 0.6644 (mttt) cc_final: 0.6367 (mmtm) REVERT: T 83 LYS cc_start: 0.7017 (ptpt) cc_final: 0.6329 (ptmt) REVERT: U 57 GLU cc_start: 0.7378 (tt0) cc_final: 0.7133 (tt0) REVERT: V 20 HIS cc_start: 0.7619 (m-70) cc_final: 0.7208 (t70) REVERT: V 27 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7840 (ptm160) REVERT: W 54 LYS cc_start: 0.7691 (mmmt) cc_final: 0.7413 (mttp) REVERT: W 55 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7878 (m) REVERT: X 57 GLU cc_start: 0.7357 (pt0) cc_final: 0.7032 (pt0) REVERT: 2 31 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8097 (t) REVERT: 3 21 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7076 (mm110) REVERT: 3 48 ARG cc_start: 0.7687 (mtp85) cc_final: 0.7413 (mtt-85) REVERT: 3 52 LYS cc_start: 0.7516 (ptpp) cc_final: 0.7220 (pttp) REVERT: 4 4 ARG cc_start: 0.6981 (ptp-170) cc_final: 0.6445 (pmm-80) REVERT: 4 8 LYS cc_start: 0.7465 (mtmt) cc_final: 0.7232 (mtpt) REVERT: 4 13 LYS cc_start: 0.6830 (mttt) cc_final: 0.6193 (pttm) REVERT: 4 22 LYS cc_start: 0.6846 (mttt) cc_final: 0.6452 (mttp) REVERT: 4 24 MET cc_start: 0.7208 (mtt) cc_final: 0.6593 (mpp) REVERT: 4 33 LYS cc_start: 0.6796 (tttm) cc_final: 0.6408 (ttpt) outliers start: 93 outliers final: 47 residues processed: 563 average time/residue: 3.5981 time to fit residues: 2606.7383 Evaluate side-chains 547 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 481 time to evaluate : 4.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 100 ILE Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain U residue 25 GLU Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain V residue 27 ARG Chi-restraints excluded: chain W residue 55 THR Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 31 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 480 optimal weight: 0.4980 chunk 327 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 429 optimal weight: 4.9990 chunk 238 optimal weight: 8.9990 chunk 492 optimal weight: 2.9990 chunk 398 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 517 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 ASN L 106 GLN O 44 GLN Q 65 ASN T 38 ASN T 85 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 96634 Z= 0.371 Angle : 0.811 29.003 145412 Z= 0.402 Chirality : 0.052 2.093 18785 Planarity : 0.006 0.091 7170 Dihedral : 24.239 179.222 50196 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.34 % Favored : 92.62 % Rotamer: Outliers : 4.71 % Allowed : 19.61 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3050 helix: 0.80 (0.19), residues: 761 sheet: -0.48 (0.20), residues: 650 loop : -1.47 (0.14), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 250 HIS 0.009 0.002 HIS 2 17 PHE 0.018 0.002 PHE O 57 TYR 0.019 0.002 TYR 2 6 ARG 0.010 0.001 ARG O 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 621 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 504 time to evaluate : 4.884 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 TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. REVERT: C 4 LYS cc_start: 0.8279 (ptpt) cc_final: 0.7870 (ptmm) REVERT: C 35 LYS cc_start: 0.8440 (mttm) cc_final: 0.8151 (mmmm) REVERT: C 40 LYS cc_start: 0.8643 (mmpt) cc_final: 0.8081 (mmmt) REVERT: C 66 ASP cc_start: 0.8353 (t70) cc_final: 0.8093 (t0) REVERT: C 100 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6720 (tt0) REVERT: C 117 GLU cc_start: 0.7631 (pt0) cc_final: 0.7005 (pm20) REVERT: C 133 GLN cc_start: 0.7911 (tt0) cc_final: 0.7668 (tp-100) REVERT: C 168 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6138 (mm-30) REVERT: C 174 ILE cc_start: 0.8746 (mt) cc_final: 0.8484 (mm) REVERT: C 263 LYS cc_start: 0.8194 (mttt) cc_final: 0.7892 (mttp) REVERT: D 12 MET cc_start: 0.8495 (mtp) cc_final: 0.7804 (mtp) REVERT: D 15 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8385 (m) REVERT: D 100 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7110 (tp30) REVERT: E 8 LYS cc_start: 0.7498 (mtpt) cc_final: 0.7165 (mtpp) REVERT: E 17 ILE cc_start: 0.8718 (tt) cc_final: 0.8194 (tp) REVERT: E 62 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7338 (ptt180) REVERT: E 66 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7603 (mmtp) REVERT: E 100 LYS cc_start: 0.8586 (mttm) cc_final: 0.8142 (mttt) REVERT: E 141 ASN cc_start: 0.7715 (m-40) cc_final: 0.7510 (m110) REVERT: E 150 LYS cc_start: 0.7628 (tmmt) cc_final: 0.7213 (tttm) REVERT: F 17 MET cc_start: 0.4220 (mmm) cc_final: 0.3865 (mpp) REVERT: F 38 MET cc_start: 0.3104 (ttp) cc_final: 0.2844 (ptm) REVERT: F 56 GLU cc_start: 0.5748 (mt-10) cc_final: 0.5091 (mm-30) REVERT: F 94 GLU cc_start: 0.6002 (mp0) cc_final: 0.5736 (tp30) REVERT: F 98 GLU cc_start: 0.3929 (tp30) cc_final: 0.3250 (tm-30) REVERT: F 120 LYS cc_start: 0.4885 (OUTLIER) cc_final: 0.4330 (pttm) REVERT: G 39 GLU cc_start: 0.5874 (pp20) cc_final: 0.5449 (pm20) REVERT: G 59 LYS cc_start: 0.5728 (mtpp) cc_final: 0.5250 (mttm) REVERT: G 87 LEU cc_start: 0.4265 (OUTLIER) cc_final: 0.4021 (pt) REVERT: G 98 MET cc_start: 0.3955 (mmm) cc_final: 0.3659 (mmm) REVERT: H 62 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8421 (mptp) REVERT: H 85 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8644 (tt) REVERT: H 137 GLN cc_start: 0.8329 (mt0) cc_final: 0.8064 (mt0) REVERT: I 9 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7726 (ttmt) REVERT: I 81 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.6782 (pm20) REVERT: I 104 ARG cc_start: 0.7947 (ttm-80) cc_final: 0.7622 (ttt180) REVERT: K 20 ARG cc_start: 0.7110 (mtp85) cc_final: 0.6583 (mtm110) REVERT: K 31 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6462 (mt-10) REVERT: K 76 LYS cc_start: 0.8210 (tttt) cc_final: 0.7932 (tttm) REVERT: L 31 GLU cc_start: 0.7390 (tt0) cc_final: 0.7050 (mt-10) REVERT: L 97 GLN cc_start: 0.7844 (mt0) cc_final: 0.7377 (mp10) REVERT: M 22 LEU cc_start: 0.7511 (mt) cc_final: 0.7310 (mt) REVERT: M 90 LYS cc_start: 0.6798 (mptt) cc_final: 0.6362 (mmmt) REVERT: O 19 LYS cc_start: 0.8272 (tttp) cc_final: 0.8029 (tttm) REVERT: O 51 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8240 (mtt-85) REVERT: O 59 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7926 (ttmm) REVERT: P 36 ASP cc_start: 0.7657 (p0) cc_final: 0.7436 (p0) REVERT: P 80 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6417 (mmtp) REVERT: P 86 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7702 (mttm) REVERT: Q 11 ARG cc_start: 0.7886 (mmt90) cc_final: 0.7405 (mmm160) REVERT: Q 83 LYS cc_start: 0.7780 (mmtm) cc_final: 0.7540 (mmtp) REVERT: R 14 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6850 (mt-10) REVERT: R 49 LYS cc_start: 0.7797 (tptm) cc_final: 0.7446 (tppt) REVERT: R 69 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.6823 (pm20) REVERT: R 75 ARG cc_start: 0.7957 (ptt90) cc_final: 0.7658 (ptt-90) REVERT: S 20 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: S 77 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7241 (mt-10) REVERT: T 26 LYS cc_start: 0.7967 (mptp) cc_final: 0.7662 (mmmm) REVERT: T 50 LYS cc_start: 0.6986 (mttt) cc_final: 0.6544 (mmtm) REVERT: T 83 LYS cc_start: 0.6883 (ptpt) cc_final: 0.6202 (ptmt) REVERT: V 20 HIS cc_start: 0.7666 (m-70) cc_final: 0.7234 (t70) REVERT: V 46 LYS cc_start: 0.8242 (tttm) cc_final: 0.7944 (mttm) REVERT: W 13 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6515 (mm-30) REVERT: W 23 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7101 (tp30) REVERT: W 54 LYS cc_start: 0.7717 (mmmt) cc_final: 0.7433 (mttp) REVERT: W 55 THR cc_start: 0.8175 (OUTLIER) cc_final: 0.7890 (m) REVERT: X 57 GLU cc_start: 0.7405 (pt0) cc_final: 0.7047 (pt0) REVERT: 3 14 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8234 (m) REVERT: 3 48 ARG cc_start: 0.7626 (mtp85) cc_final: 0.7390 (mtt-85) REVERT: 3 52 LYS cc_start: 0.7659 (ptpp) cc_final: 0.7362 (pttp) REVERT: 4 4 ARG cc_start: 0.6989 (ptp-170) cc_final: 0.6416 (pmm-80) REVERT: 4 8 LYS cc_start: 0.7413 (mtmt) cc_final: 0.7172 (mtpt) REVERT: 4 13 LYS cc_start: 0.7102 (mttt) cc_final: 0.6473 (pttm) REVERT: 4 22 LYS cc_start: 0.6869 (mttt) cc_final: 0.6495 (mttm) REVERT: 4 24 MET cc_start: 0.7338 (mtt) cc_final: 0.6685 (mpp) REVERT: 4 33 LYS cc_start: 0.6791 (tttm) cc_final: 0.6463 (ttpt) outliers start: 117 outliers final: 72 residues processed: 579 average time/residue: 3.6453 time to fit residues: 2720.5004 Evaluate side-chains 573 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 484 time to evaluate : 4.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain I residue 9 LYS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 74 MET Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 80 LYS Chi-restraints excluded: chain P residue 100 ILE Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 9 ARG Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 97 SER Chi-restraints excluded: chain T residue 23 LYS Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain W residue 55 THR Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 31 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 194 optimal weight: 7.9990 chunk 519 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 338 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 577 optimal weight: 1.9990 chunk 479 optimal weight: 6.9990 chunk 267 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 303 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 ASN I 72 ASN Q 65 ASN T 38 ASN T 85 GLN 3 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 96634 Z= 0.314 Angle : 0.734 28.800 145412 Z= 0.366 Chirality : 0.050 2.113 18785 Planarity : 0.006 0.066 7170 Dihedral : 24.188 179.622 50191 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.90 % Allowed : 21.01 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.03 % 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: -0.99 (0.14), residues: 3050 helix: 0.77 (0.19), residues: 766 sheet: -0.51 (0.20), residues: 660 loop : -1.45 (0.14), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 250 HIS 0.008 0.001 HIS 2 17 PHE 0.018 0.002 PHE O 57 TYR 0.019 0.002 TYR 2 6 ARG 0.011 0.001 ARG V 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 599 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 502 time to evaluate : 4.820 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 TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. REVERT: C 35 LYS cc_start: 0.8425 (mttm) cc_final: 0.8121 (mmmm) REVERT: C 40 LYS cc_start: 0.8574 (mmpt) cc_final: 0.8068 (mmmt) REVERT: C 66 ASP cc_start: 0.8334 (t70) cc_final: 0.8075 (t0) REVERT: C 100 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6734 (tt0) REVERT: C 117 GLU cc_start: 0.7679 (pt0) cc_final: 0.7024 (pm20) REVERT: C 133 GLN cc_start: 0.7924 (tt0) cc_final: 0.7709 (tp-100) REVERT: C 168 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5959 (mm-30) REVERT: C 174 ILE cc_start: 0.8752 (mt) cc_final: 0.8506 (mm) REVERT: C 263 LYS cc_start: 0.8184 (mttt) cc_final: 0.7878 (mttp) REVERT: D 12 MET cc_start: 0.8512 (mtp) cc_final: 0.7789 (mtp) REVERT: D 100 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: E 8 LYS cc_start: 0.7498 (mtpt) cc_final: 0.7163 (mtpp) REVERT: E 17 ILE cc_start: 0.8763 (tt) cc_final: 0.8236 (tp) REVERT: E 62 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7299 (ptt180) REVERT: E 66 LYS cc_start: 0.7908 (ttmt) cc_final: 0.7542 (mmtp) REVERT: E 93 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8129 (p) REVERT: E 100 LYS cc_start: 0.8590 (mttm) cc_final: 0.8142 (mttt) REVERT: E 141 ASN cc_start: 0.7686 (m-40) cc_final: 0.7468 (m110) REVERT: E 150 LYS cc_start: 0.7599 (tmmt) cc_final: 0.7284 (tttp) REVERT: F 17 MET cc_start: 0.4197 (mmm) cc_final: 0.3965 (tpt) REVERT: F 56 GLU cc_start: 0.5633 (mt-10) cc_final: 0.5353 (tp30) REVERT: F 94 GLU cc_start: 0.5987 (mp0) cc_final: 0.5648 (tp30) REVERT: F 98 GLU cc_start: 0.4234 (tp30) cc_final: 0.3509 (tm-30) REVERT: F 120 LYS cc_start: 0.4839 (OUTLIER) cc_final: 0.4276 (pttm) REVERT: G 39 GLU cc_start: 0.5867 (pp20) cc_final: 0.5455 (pm20) REVERT: G 59 LYS cc_start: 0.5740 (mtpp) cc_final: 0.5222 (mttm) REVERT: G 87 LEU cc_start: 0.4369 (OUTLIER) cc_final: 0.4100 (pt) REVERT: G 98 MET cc_start: 0.3892 (mmm) cc_final: 0.3633 (mmm) REVERT: H 12 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7457 (mt) REVERT: H 62 LYS cc_start: 0.8628 (mmtm) cc_final: 0.8410 (mptp) REVERT: H 85 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8614 (tt) REVERT: H 137 GLN cc_start: 0.8315 (mt0) cc_final: 0.8014 (mt0) REVERT: J 86 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6218 (pp20) REVERT: K 20 ARG cc_start: 0.7111 (mtp85) cc_final: 0.6609 (mtm110) REVERT: K 31 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6523 (mt-10) REVERT: K 76 LYS cc_start: 0.8193 (tttt) cc_final: 0.7931 (tttm) REVERT: L 16 MET cc_start: 0.8639 (ttp) cc_final: 0.8397 (ttp) REVERT: L 97 GLN cc_start: 0.7837 (mt0) cc_final: 0.7390 (mp10) REVERT: M 90 LYS cc_start: 0.6814 (mptt) cc_final: 0.6345 (mmmt) REVERT: N 85 LYS cc_start: 0.7963 (ttpt) cc_final: 0.7725 (ttpt) REVERT: O 19 LYS cc_start: 0.8283 (tttp) cc_final: 0.8036 (tttm) REVERT: O 51 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8175 (mtt-85) REVERT: O 59 LYS cc_start: 0.8217 (ttpt) cc_final: 0.7923 (ttmm) REVERT: O 101 SER cc_start: 0.8019 (m) cc_final: 0.7698 (p) REVERT: P 36 ASP cc_start: 0.7623 (p0) cc_final: 0.7403 (p0) REVERT: P 86 LYS cc_start: 0.8240 (mtpt) cc_final: 0.7688 (mttm) REVERT: Q 11 ARG cc_start: 0.7834 (mmt90) cc_final: 0.7532 (mmm160) REVERT: Q 83 LYS cc_start: 0.7718 (mmtm) cc_final: 0.7467 (mmtp) REVERT: R 14 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6732 (mt-10) REVERT: R 18 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7099 (mt-10) REVERT: R 49 LYS cc_start: 0.7806 (tptm) cc_final: 0.7440 (tppt) REVERT: R 69 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6868 (OUTLIER) REVERT: R 75 ARG cc_start: 0.7973 (ptt90) cc_final: 0.7560 (ptt-90) REVERT: S 20 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: T 26 LYS cc_start: 0.7971 (mptp) cc_final: 0.7645 (mmmm) REVERT: T 46 VAL cc_start: 0.8001 (t) cc_final: 0.7799 (p) REVERT: T 50 LYS cc_start: 0.7213 (mttt) cc_final: 0.6616 (mmtm) REVERT: T 71 LYS cc_start: 0.7898 (mttp) cc_final: 0.7670 (mttm) REVERT: T 74 VAL cc_start: 0.8020 (t) cc_final: 0.7778 (m) REVERT: T 83 LYS cc_start: 0.6860 (ptpt) cc_final: 0.6193 (ptmt) REVERT: U 78 GLU cc_start: 0.8599 (pm20) cc_final: 0.8360 (pm20) REVERT: V 20 HIS cc_start: 0.7676 (m-70) cc_final: 0.7138 (t70) REVERT: V 46 LYS cc_start: 0.8287 (tttm) cc_final: 0.8082 (mttm) REVERT: W 13 GLU cc_start: 0.6570 (mt-10) cc_final: 0.6353 (mm-30) REVERT: W 23 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7103 (tp30) REVERT: W 54 LYS cc_start: 0.7746 (mmmt) cc_final: 0.7374 (mtpp) REVERT: W 55 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7828 (m) REVERT: X 13 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7487 (pt) REVERT: X 57 GLU cc_start: 0.7418 (pt0) cc_final: 0.7078 (pt0) REVERT: 2 31 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8167 (t) REVERT: 3 48 ARG cc_start: 0.7596 (mtp85) cc_final: 0.7375 (mtt-85) REVERT: 3 52 LYS cc_start: 0.7653 (ptpp) cc_final: 0.7373 (pttp) REVERT: 4 4 ARG cc_start: 0.6911 (ptp-170) cc_final: 0.6518 (pmm-80) REVERT: 4 13 LYS cc_start: 0.7100 (mttt) cc_final: 0.6553 (pttm) REVERT: 4 22 LYS cc_start: 0.6878 (mttt) cc_final: 0.6500 (mttm) REVERT: 4 24 MET cc_start: 0.7390 (mtt) cc_final: 0.6712 (mpp) REVERT: 4 33 LYS cc_start: 0.6802 (tttm) cc_final: 0.6513 (ttpt) outliers start: 97 outliers final: 62 residues processed: 567 average time/residue: 3.5239 time to fit residues: 2587.6513 Evaluate side-chains 572 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 494 time to evaluate : 4.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 9 ARG Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 28 ASP Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain T residue 23 LYS Chi-restraints excluded: chain U residue 25 GLU Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain W residue 55 THR Chi-restraints excluded: chain W residue 62 ILE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 31 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 556 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 329 optimal weight: 5.9990 chunk 421 optimal weight: 1.9990 chunk 326 optimal weight: 5.9990 chunk 486 optimal weight: 2.9990 chunk 322 optimal weight: 1.9990 chunk 575 optimal weight: 30.0000 chunk 360 optimal weight: 4.9990 chunk 350 optimal weight: 0.9980 chunk 265 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 72 ASN Q 65 ASN T 38 ASN T 85 GLN 3 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 96634 Z= 0.241 Angle : 0.673 28.531 145412 Z= 0.339 Chirality : 0.047 2.124 18785 Planarity : 0.005 0.066 7170 Dihedral : 24.113 179.987 50190 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.54 % Allowed : 21.50 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 3050 helix: 1.03 (0.19), residues: 764 sheet: -0.37 (0.20), residues: 656 loop : -1.38 (0.14), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 65 HIS 0.006 0.001 HIS 2 17 PHE 0.017 0.002 PHE O 57 TYR 0.017 0.002 TYR 2 6 ARG 0.006 0.001 ARG 2 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 575 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 487 time to evaluate : 4.844 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 TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. REVERT: C 35 LYS cc_start: 0.8436 (mttm) cc_final: 0.8124 (mmmm) REVERT: C 40 LYS cc_start: 0.8537 (mmpt) cc_final: 0.8056 (mmmt) REVERT: C 66 ASP cc_start: 0.8382 (t70) cc_final: 0.8110 (t0) REVERT: C 100 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6758 (tt0) REVERT: C 168 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.6123 (mm-30) REVERT: C 174 ILE cc_start: 0.8767 (mt) cc_final: 0.8542 (mm) REVERT: C 263 LYS cc_start: 0.8184 (mttt) cc_final: 0.7870 (mttp) REVERT: D 12 MET cc_start: 0.8480 (mtp) cc_final: 0.7873 (mtp) REVERT: D 100 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: D 159 ASP cc_start: 0.6581 (OUTLIER) cc_final: 0.6320 (t0) REVERT: E 8 LYS cc_start: 0.7512 (mtpt) cc_final: 0.7252 (mtpp) REVERT: E 62 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7285 (ptt180) REVERT: E 66 LYS cc_start: 0.7889 (ttmt) cc_final: 0.7523 (mmtp) REVERT: E 93 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8177 (p) REVERT: E 100 LYS cc_start: 0.8553 (mttm) cc_final: 0.8115 (mttt) REVERT: E 141 ASN cc_start: 0.7701 (m-40) cc_final: 0.7483 (m110) REVERT: E 150 LYS cc_start: 0.7565 (tmmt) cc_final: 0.7266 (tttp) REVERT: F 17 MET cc_start: 0.4110 (mmm) cc_final: 0.3817 (tpt) REVERT: F 56 GLU cc_start: 0.5747 (mt-10) cc_final: 0.5354 (tp30) REVERT: F 94 GLU cc_start: 0.5886 (mp0) cc_final: 0.5559 (tp30) REVERT: F 98 GLU cc_start: 0.4397 (tp30) cc_final: 0.3661 (tm-30) REVERT: F 120 LYS cc_start: 0.4813 (OUTLIER) cc_final: 0.4378 (pttt) REVERT: G 39 GLU cc_start: 0.5828 (pp20) cc_final: 0.5436 (pm20) REVERT: G 59 LYS cc_start: 0.5718 (mtpp) cc_final: 0.5175 (mttm) REVERT: G 87 LEU cc_start: 0.4352 (OUTLIER) cc_final: 0.4075 (pt) REVERT: H 12 ILE cc_start: 0.8201 (pt) cc_final: 0.7587 (mt) REVERT: H 62 LYS cc_start: 0.8674 (mmtm) cc_final: 0.8448 (mptp) REVERT: H 85 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8611 (tt) REVERT: H 137 GLN cc_start: 0.8312 (mt0) cc_final: 0.8026 (mt0) REVERT: I 81 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.6758 (pm20) REVERT: J 86 GLU cc_start: 0.6811 (pm20) cc_final: 0.6553 (pp20) REVERT: K 20 ARG cc_start: 0.7103 (mtp85) cc_final: 0.6602 (mtm110) REVERT: K 31 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6469 (mt-10) REVERT: K 76 LYS cc_start: 0.8177 (tttt) cc_final: 0.7926 (tttm) REVERT: L 16 MET cc_start: 0.8657 (ttp) cc_final: 0.8448 (ttp) REVERT: L 97 GLN cc_start: 0.7795 (mt0) cc_final: 0.7329 (mp10) REVERT: M 90 LYS cc_start: 0.6875 (mptt) cc_final: 0.6404 (mmmt) REVERT: N 85 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7702 (ttpt) REVERT: O 19 LYS cc_start: 0.8260 (tttp) cc_final: 0.8017 (tttm) REVERT: O 51 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8430 (mtt-85) REVERT: O 59 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7928 (ttmm) REVERT: O 109 LEU cc_start: 0.8189 (pp) cc_final: 0.7761 (mt) REVERT: P 36 ASP cc_start: 0.7639 (p0) cc_final: 0.7436 (p0) REVERT: P 80 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6477 (mmtp) REVERT: P 86 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7670 (mttm) REVERT: Q 11 ARG cc_start: 0.7794 (mmt90) cc_final: 0.7448 (mmm160) REVERT: Q 83 LYS cc_start: 0.7709 (mmtm) cc_final: 0.7432 (mmtp) REVERT: R 49 LYS cc_start: 0.7857 (tptm) cc_final: 0.7485 (tppt) REVERT: R 69 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6861 (tt0) REVERT: R 75 ARG cc_start: 0.8001 (ptt90) cc_final: 0.7577 (ptt-90) REVERT: S 77 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7288 (mt-10) REVERT: T 26 LYS cc_start: 0.7984 (mptp) cc_final: 0.7652 (mmmm) REVERT: T 50 LYS cc_start: 0.7308 (mttt) cc_final: 0.6708 (mmtm) REVERT: T 74 VAL cc_start: 0.8117 (t) cc_final: 0.7879 (m) REVERT: U 78 GLU cc_start: 0.8566 (pm20) cc_final: 0.8323 (pm20) REVERT: V 20 HIS cc_start: 0.7685 (m-70) cc_final: 0.7138 (t70) REVERT: W 54 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7351 (mtpp) REVERT: W 55 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7874 (m) REVERT: X 18 THR cc_start: 0.8106 (p) cc_final: 0.7717 (t) REVERT: X 57 GLU cc_start: 0.7350 (pt0) cc_final: 0.7030 (pt0) REVERT: 2 31 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8145 (t) REVERT: 3 14 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8202 (m) REVERT: 3 48 ARG cc_start: 0.7587 (mtp85) cc_final: 0.7354 (mtt-85) REVERT: 3 52 LYS cc_start: 0.7611 (ptpp) cc_final: 0.7337 (pttp) REVERT: 4 4 ARG cc_start: 0.6880 (ptp-170) cc_final: 0.6523 (pmm-80) REVERT: 4 13 LYS cc_start: 0.7082 (mttt) cc_final: 0.6507 (pttm) REVERT: 4 22 LYS cc_start: 0.6877 (mttt) cc_final: 0.6514 (mttm) REVERT: 4 24 MET cc_start: 0.7453 (mtt) cc_final: 0.6853 (mpp) REVERT: 4 33 LYS cc_start: 0.6713 (tttm) cc_final: 0.6428 (ttpt) outliers start: 88 outliers final: 58 residues processed: 541 average time/residue: 3.5376 time to fit residues: 2471.0556 Evaluate side-chains 556 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 482 time to evaluate : 4.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 80 LYS Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 9 ARG Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 97 SER Chi-restraints excluded: chain T residue 23 LYS Chi-restraints excluded: chain U residue 25 GLU Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain W residue 55 THR Chi-restraints excluded: chain W residue 62 ILE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 31 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 355 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 343 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 113 optimal weight: 30.0000 chunk 111 optimal weight: 20.0000 chunk 365 optimal weight: 5.9990 chunk 392 optimal weight: 10.0000 chunk 284 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 452 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 72 ASN Q 65 ASN T 38 ASN T 85 GLN 3 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 96634 Z= 0.348 Angle : 0.779 28.883 145412 Z= 0.389 Chirality : 0.051 2.126 18785 Planarity : 0.006 0.066 7170 Dihedral : 24.200 179.921 50187 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.34 % Favored : 92.62 % Rotamer: Outliers : 3.99 % Allowed : 21.50 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.03 % 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: -0.94 (0.14), residues: 3050 helix: 0.80 (0.19), residues: 765 sheet: -0.41 (0.20), residues: 643 loop : -1.43 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 250 HIS 0.009 0.002 HIS 2 17 PHE 0.017 0.002 PHE O 57 TYR 0.020 0.002 TYR 2 6 ARG 0.010 0.001 ARG 2 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 592 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 493 time to evaluate : 4.830 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 TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. REVERT: C 35 LYS cc_start: 0.8420 (mttm) cc_final: 0.8094 (mmmm) REVERT: C 40 LYS cc_start: 0.8567 (mmpt) cc_final: 0.8060 (mmmt) REVERT: C 66 ASP cc_start: 0.8338 (t70) cc_final: 0.8085 (t0) REVERT: C 100 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6818 (tt0) REVERT: C 168 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.6048 (mm-30) REVERT: C 174 ILE cc_start: 0.8751 (mt) cc_final: 0.8514 (mm) REVERT: C 263 LYS cc_start: 0.8181 (mttt) cc_final: 0.7879 (mttp) REVERT: D 12 MET cc_start: 0.8522 (mtp) cc_final: 0.7922 (mtp) REVERT: D 74 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6955 (tp30) REVERT: D 100 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: D 159 ASP cc_start: 0.6767 (OUTLIER) cc_final: 0.6495 (t0) REVERT: E 8 LYS cc_start: 0.7426 (mtpt) cc_final: 0.7121 (mtpp) REVERT: E 62 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7855 (ptp-170) REVERT: E 66 LYS cc_start: 0.7900 (mtmt) cc_final: 0.7528 (mmtp) REVERT: E 100 LYS cc_start: 0.8629 (mttm) cc_final: 0.8055 (mttt) REVERT: E 141 ASN cc_start: 0.7707 (m-40) cc_final: 0.7485 (m110) REVERT: E 150 LYS cc_start: 0.7571 (tmmt) cc_final: 0.7293 (tttm) REVERT: F 17 MET cc_start: 0.4349 (mmm) cc_final: 0.3859 (tpp) REVERT: F 38 MET cc_start: 0.3143 (ttp) cc_final: 0.2914 (ptm) REVERT: F 94 GLU cc_start: 0.5907 (mp0) cc_final: 0.5618 (tp30) REVERT: F 98 GLU cc_start: 0.4229 (tp30) cc_final: 0.3438 (tm-30) REVERT: F 120 LYS cc_start: 0.4886 (OUTLIER) cc_final: 0.4490 (pttt) REVERT: G 39 GLU cc_start: 0.5918 (pp20) cc_final: 0.5464 (pm20) REVERT: G 59 LYS cc_start: 0.5764 (mtpp) cc_final: 0.5211 (mttm) REVERT: G 87 LEU cc_start: 0.4513 (OUTLIER) cc_final: 0.4209 (pt) REVERT: H 12 ILE cc_start: 0.8159 (pt) cc_final: 0.7749 (mt) REVERT: H 62 LYS cc_start: 0.8698 (mmtm) cc_final: 0.8476 (mptp) REVERT: H 85 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8629 (tt) REVERT: H 137 GLN cc_start: 0.8325 (mt0) cc_final: 0.8029 (mt0) REVERT: I 81 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.6760 (pm20) REVERT: J 86 GLU cc_start: 0.6695 (pm20) cc_final: 0.6438 (pp20) REVERT: K 20 ARG cc_start: 0.7112 (mtp85) cc_final: 0.6614 (mtm110) REVERT: K 31 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6544 (mt-10) REVERT: K 76 LYS cc_start: 0.8218 (tttt) cc_final: 0.7964 (tttm) REVERT: L 16 MET cc_start: 0.8654 (ttp) cc_final: 0.8420 (ttp) REVERT: L 97 GLN cc_start: 0.7857 (mt0) cc_final: 0.7381 (mp10) REVERT: N 85 LYS cc_start: 0.7946 (ttpt) cc_final: 0.7721 (ttpt) REVERT: O 19 LYS cc_start: 0.8288 (tttp) cc_final: 0.8032 (tttm) REVERT: O 51 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8395 (mtt-85) REVERT: O 59 LYS cc_start: 0.8226 (ttpt) cc_final: 0.7935 (ttmm) REVERT: O 101 SER cc_start: 0.7966 (m) cc_final: 0.7638 (p) REVERT: P 36 ASP cc_start: 0.7588 (p0) cc_final: 0.7387 (p0) REVERT: P 86 LYS cc_start: 0.8259 (mtpt) cc_final: 0.7706 (mttm) REVERT: Q 11 ARG cc_start: 0.7805 (mmt90) cc_final: 0.7287 (mmm160) REVERT: Q 83 LYS cc_start: 0.7726 (mmtm) cc_final: 0.7457 (mmtp) REVERT: R 14 GLU cc_start: 0.7109 (mp0) cc_final: 0.6514 (mt-10) REVERT: R 18 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7086 (mp0) REVERT: R 23 ASP cc_start: 0.5953 (m-30) cc_final: 0.5709 (m-30) REVERT: R 49 LYS cc_start: 0.7849 (tptm) cc_final: 0.7468 (tppt) REVERT: R 69 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6745 (pm20) REVERT: S 20 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: S 77 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7314 (mt-10) REVERT: T 23 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7475 (tppt) REVERT: T 26 LYS cc_start: 0.7986 (mptp) cc_final: 0.7634 (mmmm) REVERT: T 46 VAL cc_start: 0.8162 (t) cc_final: 0.7954 (p) REVERT: T 50 LYS cc_start: 0.7404 (mttt) cc_final: 0.6738 (mmtm) REVERT: T 74 VAL cc_start: 0.8101 (t) cc_final: 0.7893 (m) REVERT: U 78 GLU cc_start: 0.8586 (pm20) cc_final: 0.8320 (pm20) REVERT: V 20 HIS cc_start: 0.7684 (m-70) cc_final: 0.7143 (t70) REVERT: W 23 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7136 (tp30) REVERT: W 54 LYS cc_start: 0.7764 (mmmt) cc_final: 0.7377 (mtpp) REVERT: W 55 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7840 (m) REVERT: X 18 THR cc_start: 0.8158 (p) cc_final: 0.7821 (t) REVERT: X 57 GLU cc_start: 0.7431 (pt0) cc_final: 0.7086 (pt0) REVERT: 1 41 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6747 (ptmm) REVERT: 2 31 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8169 (t) REVERT: 3 14 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8273 (m) REVERT: 3 48 ARG cc_start: 0.7587 (mtp85) cc_final: 0.7380 (mtt-85) REVERT: 3 52 LYS cc_start: 0.7608 (ptpp) cc_final: 0.7333 (pttp) REVERT: 4 4 ARG cc_start: 0.6863 (ptp-170) cc_final: 0.6505 (pmm-80) REVERT: 4 13 LYS cc_start: 0.7092 (mttt) cc_final: 0.6512 (pttm) REVERT: 4 22 LYS cc_start: 0.6863 (mttt) cc_final: 0.6504 (mttm) REVERT: 4 24 MET cc_start: 0.7519 (mtt) cc_final: 0.6850 (mpp) REVERT: 4 33 LYS cc_start: 0.6666 (tttm) cc_final: 0.6462 (ttpt) outliers start: 99 outliers final: 66 residues processed: 553 average time/residue: 3.5436 time to fit residues: 2538.9335 Evaluate side-chains 574 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 490 time to evaluate : 4.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 74 MET Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 108 GLN Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 9 ARG Chi-restraints excluded: chain R residue 28 ASP Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 97 SER Chi-restraints excluded: chain T residue 23 LYS Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 55 THR Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain 1 residue 41 LYS Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 31 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 523 optimal weight: 4.9990 chunk 551 optimal weight: 3.9990 chunk 502 optimal weight: 0.1980 chunk 536 optimal weight: 3.9990 chunk 322 optimal weight: 1.9990 chunk 233 optimal weight: 8.9990 chunk 421 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 484 optimal weight: 2.9990 chunk 507 optimal weight: 6.9990 chunk 534 optimal weight: 0.8980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 11 ASN I 72 ASN Q 65 ASN T 85 GLN 3 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 96634 Z= 0.181 Angle : 0.622 28.410 145412 Z= 0.315 Chirality : 0.046 2.138 18785 Planarity : 0.005 0.065 7170 Dihedral : 24.079 179.797 50187 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.06 % Allowed : 22.58 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 3050 helix: 1.11 (0.19), residues: 766 sheet: -0.34 (0.20), residues: 655 loop : -1.33 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 65 HIS 0.005 0.001 HIS 2 17 PHE 0.015 0.001 PHE O 57 TYR 0.016 0.001 TYR 2 6 ARG 0.008 0.000 ARG C 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 566 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 490 time to evaluate : 4.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. REVERT: C 35 LYS cc_start: 0.8452 (mttm) cc_final: 0.8130 (mmmm) REVERT: C 40 LYS cc_start: 0.8523 (mmpt) cc_final: 0.8042 (mmmt) REVERT: C 66 ASP cc_start: 0.8384 (t70) cc_final: 0.8111 (t0) REVERT: C 100 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6743 (tt0) REVERT: C 168 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.6035 (mm-30) REVERT: C 174 ILE cc_start: 0.8796 (mt) cc_final: 0.8584 (mm) REVERT: C 263 LYS cc_start: 0.8185 (mttt) cc_final: 0.7868 (mttp) REVERT: D 12 MET cc_start: 0.8460 (mtp) cc_final: 0.7812 (mtp) REVERT: D 74 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6857 (tp30) REVERT: D 100 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: E 8 LYS cc_start: 0.7424 (mtpt) cc_final: 0.6738 (mtmt) REVERT: E 62 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7847 (ptp-170) REVERT: E 66 LYS cc_start: 0.7903 (mtmt) cc_final: 0.7544 (mmtp) REVERT: E 93 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8124 (p) REVERT: E 100 LYS cc_start: 0.8537 (mttm) cc_final: 0.8098 (mttt) REVERT: E 141 ASN cc_start: 0.7681 (m-40) cc_final: 0.7460 (m110) REVERT: E 150 LYS cc_start: 0.7572 (tmmt) cc_final: 0.7297 (tttm) REVERT: F 17 MET cc_start: 0.4164 (mmm) cc_final: 0.3694 (tpp) REVERT: F 56 GLU cc_start: 0.5822 (mt-10) cc_final: 0.5370 (tp30) REVERT: F 94 GLU cc_start: 0.5866 (mp0) cc_final: 0.5568 (tp30) REVERT: F 98 GLU cc_start: 0.4284 (tp30) cc_final: 0.3473 (tm-30) REVERT: F 120 LYS cc_start: 0.4908 (OUTLIER) cc_final: 0.4514 (pttt) REVERT: F 168 GLU cc_start: 0.5052 (mt-10) cc_final: 0.4661 (pt0) REVERT: G 59 LYS cc_start: 0.5718 (mtpp) cc_final: 0.5171 (mttm) REVERT: G 87 LEU cc_start: 0.4489 (OUTLIER) cc_final: 0.4227 (pt) REVERT: H 1 MET cc_start: 0.7976 (mpm) cc_final: 0.7484 (mpm) REVERT: H 12 ILE cc_start: 0.8174 (pt) cc_final: 0.7950 (mt) REVERT: H 62 LYS cc_start: 0.8596 (mmtm) cc_final: 0.8392 (mptp) REVERT: H 85 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8578 (tt) REVERT: H 137 GLN cc_start: 0.8311 (mt0) cc_final: 0.8034 (mt0) REVERT: J 86 GLU cc_start: 0.6733 (pm20) cc_final: 0.6476 (pp20) REVERT: K 20 ARG cc_start: 0.7059 (mtp85) cc_final: 0.6585 (mtm110) REVERT: K 31 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6460 (mt-10) REVERT: K 76 LYS cc_start: 0.8141 (tttt) cc_final: 0.7893 (tttm) REVERT: L 16 MET cc_start: 0.8652 (ttp) cc_final: 0.8443 (ttp) REVERT: L 97 GLN cc_start: 0.7763 (mt0) cc_final: 0.7311 (mp-120) REVERT: O 19 LYS cc_start: 0.8270 (tttp) cc_final: 0.8024 (tttm) REVERT: O 51 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8373 (mtt-85) REVERT: O 59 LYS cc_start: 0.8247 (ttpt) cc_final: 0.7890 (ttmm) REVERT: O 101 SER cc_start: 0.7956 (m) cc_final: 0.7653 (p) REVERT: P 36 ASP cc_start: 0.7586 (p0) cc_final: 0.7371 (p0) REVERT: P 80 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.6470 (mmtp) REVERT: P 86 LYS cc_start: 0.8223 (mtpt) cc_final: 0.7659 (mttm) REVERT: Q 11 ARG cc_start: 0.7749 (mmt90) cc_final: 0.7442 (mmm160) REVERT: Q 83 LYS cc_start: 0.7688 (mmtm) cc_final: 0.7410 (mmtp) REVERT: R 18 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7221 (mt-10) REVERT: R 49 LYS cc_start: 0.7830 (tptm) cc_final: 0.7463 (tppt) REVERT: R 69 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6759 (pm20) REVERT: S 20 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: S 77 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7345 (mt-10) REVERT: T 26 LYS cc_start: 0.7988 (mptp) cc_final: 0.7649 (mmmm) REVERT: T 50 LYS cc_start: 0.7444 (mttt) cc_final: 0.6809 (mmtm) REVERT: T 74 VAL cc_start: 0.8117 (t) cc_final: 0.7913 (m) REVERT: V 20 HIS cc_start: 0.7688 (m-70) cc_final: 0.7136 (t70) REVERT: W 54 LYS cc_start: 0.7756 (mmmt) cc_final: 0.7321 (mtpp) REVERT: W 55 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7852 (m) REVERT: X 18 THR cc_start: 0.8123 (p) cc_final: 0.7781 (t) REVERT: X 57 GLU cc_start: 0.7340 (pt0) cc_final: 0.7033 (pt0) REVERT: 2 31 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8152 (t) REVERT: 3 14 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8213 (m) REVERT: 3 31 HIS cc_start: 0.6167 (OUTLIER) cc_final: 0.5847 (t-170) REVERT: 3 52 LYS cc_start: 0.7624 (ptpp) cc_final: 0.7350 (pttp) REVERT: 4 4 ARG cc_start: 0.6857 (ptp-170) cc_final: 0.6544 (pmm-80) REVERT: 4 13 LYS cc_start: 0.7043 (mttt) cc_final: 0.6468 (pttm) REVERT: 4 22 LYS cc_start: 0.6884 (mttt) cc_final: 0.6521 (mttm) REVERT: 4 24 MET cc_start: 0.7505 (mtt) cc_final: 0.6843 (mpp) outliers start: 76 outliers final: 47 residues processed: 540 average time/residue: 3.5530 time to fit residues: 2492.0542 Evaluate side-chains 545 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 481 time to evaluate : 4.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 108 GLN Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 80 LYS Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 9 ARG Chi-restraints excluded: chain R residue 28 ASP Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 97 SER Chi-restraints excluded: chain U residue 25 GLU Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 55 THR Chi-restraints excluded: chain W residue 62 ILE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 31 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 352 optimal weight: 2.9990 chunk 567 optimal weight: 0.9980 chunk 346 optimal weight: 4.9990 chunk 268 optimal weight: 5.9990 chunk 394 optimal weight: 10.0000 chunk 594 optimal weight: 0.9990 chunk 547 optimal weight: 9.9990 chunk 473 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 365 optimal weight: 5.9990 chunk 290 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 72 ASN Q 65 ASN T 38 ASN T 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 96634 Z= 0.254 Angle : 0.684 28.602 145412 Z= 0.345 Chirality : 0.048 2.125 18785 Planarity : 0.005 0.065 7170 Dihedral : 24.104 179.619 50185 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.98 % Allowed : 22.50 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.15), residues: 3050 helix: 1.07 (0.19), residues: 765 sheet: -0.34 (0.20), residues: 646 loop : -1.32 (0.14), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 65 HIS 0.007 0.001 HIS 2 17 PHE 0.015 0.002 PHE O 57 TYR 0.019 0.002 TYR 2 6 ARG 0.007 0.001 ARG O 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Evaluate side-chains 562 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 488 time to evaluate : 4.833 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 TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. REVERT: C 35 LYS cc_start: 0.8444 (mttm) cc_final: 0.8117 (mmmm) REVERT: C 40 LYS cc_start: 0.8568 (mmpt) cc_final: 0.8051 (mmmt) REVERT: C 66 ASP cc_start: 0.8355 (t70) cc_final: 0.8096 (t0) REVERT: C 100 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6771 (tt0) REVERT: C 168 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.6008 (mm-30) REVERT: C 174 ILE cc_start: 0.8792 (mt) cc_final: 0.8575 (mm) REVERT: C 263 LYS cc_start: 0.8185 (mttt) cc_final: 0.7873 (mttp) REVERT: D 12 MET cc_start: 0.8481 (mtp) cc_final: 0.7848 (mtp) REVERT: D 74 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6864 (tp30) REVERT: D 100 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7086 (tp30) REVERT: E 8 LYS cc_start: 0.7420 (mtpt) cc_final: 0.6756 (mtmt) REVERT: E 66 LYS cc_start: 0.7890 (mtmt) cc_final: 0.7521 (mmtp) REVERT: E 93 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8124 (p) REVERT: E 100 LYS cc_start: 0.8626 (mttm) cc_final: 0.8063 (mttt) REVERT: E 141 ASN cc_start: 0.7671 (m-40) cc_final: 0.7455 (m110) REVERT: E 150 LYS cc_start: 0.7565 (tmmt) cc_final: 0.7292 (tttm) REVERT: F 17 MET cc_start: 0.4450 (mmm) cc_final: 0.3975 (tpp) REVERT: F 56 GLU cc_start: 0.5896 (mt-10) cc_final: 0.5404 (tp30) REVERT: F 98 GLU cc_start: 0.4372 (tp30) cc_final: 0.3604 (tm-30) REVERT: F 120 LYS cc_start: 0.4773 (OUTLIER) cc_final: 0.4408 (pttt) REVERT: G 59 LYS cc_start: 0.5681 (mtpp) cc_final: 0.5129 (mttm) REVERT: G 87 LEU cc_start: 0.4541 (OUTLIER) cc_final: 0.4216 (pt) REVERT: H 85 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8605 (tt) REVERT: H 137 GLN cc_start: 0.8327 (mt0) cc_final: 0.8045 (mt0) REVERT: J 86 GLU cc_start: 0.6723 (pm20) cc_final: 0.6469 (pp20) REVERT: K 20 ARG cc_start: 0.7096 (mtp85) cc_final: 0.6601 (mtm110) REVERT: K 31 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6525 (mt-10) REVERT: K 76 LYS cc_start: 0.8194 (tttt) cc_final: 0.7948 (tttm) REVERT: L 16 MET cc_start: 0.8657 (ttp) cc_final: 0.8421 (ttp) REVERT: L 97 GLN cc_start: 0.7803 (mt0) cc_final: 0.7327 (mp10) REVERT: O 19 LYS cc_start: 0.8264 (tttp) cc_final: 0.8015 (tttm) REVERT: O 51 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8435 (mtt-85) REVERT: O 59 LYS cc_start: 0.8225 (ttpt) cc_final: 0.7917 (ttmm) REVERT: O 101 SER cc_start: 0.8006 (m) cc_final: 0.7705 (p) REVERT: P 36 ASP cc_start: 0.7586 (p0) cc_final: 0.7373 (p0) REVERT: P 80 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.6501 (mmtp) REVERT: P 86 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7675 (mttm) REVERT: Q 11 ARG cc_start: 0.7771 (mmt90) cc_final: 0.7439 (mmm160) REVERT: Q 83 LYS cc_start: 0.7706 (mmtm) cc_final: 0.7432 (mmtp) REVERT: R 18 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7198 (mt-10) REVERT: R 49 LYS cc_start: 0.7845 (tptm) cc_final: 0.7473 (tppt) REVERT: R 69 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6774 (pm20) REVERT: S 20 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: S 77 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7320 (mt-10) REVERT: T 26 LYS cc_start: 0.7986 (mptp) cc_final: 0.7688 (mmmm) REVERT: T 50 LYS cc_start: 0.7535 (mttt) cc_final: 0.6933 (mmtm) REVERT: U 75 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8233 (m) REVERT: V 20 HIS cc_start: 0.7689 (m-70) cc_final: 0.7138 (t70) REVERT: W 54 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7326 (mtpp) REVERT: W 55 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7905 (m) REVERT: X 18 THR cc_start: 0.8144 (p) cc_final: 0.7802 (t) REVERT: X 57 GLU cc_start: 0.7381 (pt0) cc_final: 0.7054 (pt0) REVERT: 2 31 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8133 (t) REVERT: 3 14 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8246 (m) REVERT: 3 31 HIS cc_start: 0.6196 (OUTLIER) cc_final: 0.5865 (t-170) REVERT: 3 52 LYS cc_start: 0.7671 (ptpp) cc_final: 0.7401 (pttp) REVERT: 4 4 ARG cc_start: 0.6869 (ptp-170) cc_final: 0.6547 (pmm-80) REVERT: 4 13 LYS cc_start: 0.7049 (mttt) cc_final: 0.6484 (pttm) REVERT: 4 22 LYS cc_start: 0.6894 (mttt) cc_final: 0.6534 (mttm) REVERT: 4 24 MET cc_start: 0.7453 (mtt) cc_final: 0.6782 (mpp) outliers start: 74 outliers final: 53 residues processed: 537 average time/residue: 3.5192 time to fit residues: 2457.4457 Evaluate side-chains 548 residues out of total 2618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 478 time to evaluate : 4.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 74 MET Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 108 GLN Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 80 LYS Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 9 ARG Chi-restraints excluded: chain R residue 28 ASP Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 97 SER Chi-restraints excluded: chain U residue 25 GLU Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 55 THR Chi-restraints excluded: chain W residue 62 ILE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain Z residue 3 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 31 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 376 optimal weight: 1.9990 chunk 504 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 436 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 474 optimal weight: 0.7980 chunk 198 optimal weight: 5.9990 chunk 487 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 11 ASN I 72 ASN Q 65 ASN T 38 ASN T 85 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.182805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.117091 restraints weight = 172939.694| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 0.85 r_work: 0.3011 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 96634 Z= 0.196 Angle : 0.643 28.457 145412 Z= 0.326 Chirality : 0.046 2.128 18785 Planarity : 0.005 0.106 7170 Dihedral : 24.093 179.862 50185 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.70 % Allowed : 22.87 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 3050 helix: 1.12 (0.19), residues: 765 sheet: -0.34 (0.20), residues: 656 loop : -1.30 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 65 HIS 0.009 0.001 HIS N 4 PHE 0.014 0.002 PHE O 57 TYR 0.019 0.001 TYR 2 6 ARG 0.014 0.001 ARG T 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 54767.74 seconds wall clock time: 938 minutes 29.88 seconds (56309.88 seconds total)