Starting phenix.real_space_refine on Mon Feb 19 18:44:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az1_7024/02_2024/6az1_7024_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az1_7024/02_2024/6az1_7024.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az1_7024/02_2024/6az1_7024_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az1_7024/02_2024/6az1_7024_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az1_7024/02_2024/6az1_7024_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az1_7024/02_2024/6az1_7024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az1_7024/02_2024/6az1_7024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az1_7024/02_2024/6az1_7024_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6az1_7024/02_2024/6az1_7024_neut_updated.pdb" } resolution = 2.7 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= 0.015 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 1997 5.49 5 Mg 24 5.21 5 S 198 5.16 5 C 42824 2.51 5 N 14894 2.21 5 O 20657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 62": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ARG 145": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "E ARG 8": "NH1" <-> "NH2" Residue "E ARG 27": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 145": "NH1" <-> "NH2" Residue "E ARG 218": "NH1" <-> "NH2" Residue "E ARG 250": "NH1" <-> "NH2" Residue "E ARG 253": "NH1" <-> "NH2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F ARG 186": "NH1" <-> "NH2" Residue "F ARG 213": "NH1" <-> "NH2" Residue "G ARG 9": "NH1" <-> "NH2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G ARG 89": "NH1" <-> "NH2" Residue "G ARG 101": "NH1" <-> "NH2" Residue "G ARG 135": "NH1" <-> "NH2" Residue "G ARG 186": "NH1" <-> "NH2" Residue "G ARG 191": "NH1" <-> "NH2" Residue "H ARG 41": "NH1" <-> "NH2" Residue "H ARG 41": "NH1" <-> "NH2" Residue "H ARG 46": "NH1" <-> "NH2" Residue "H ARG 122": "NH1" <-> "NH2" Residue "I ARG 38": "NH1" <-> "NH2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I ARG 69": "NH1" <-> "NH2" Residue "I ARG 117": "NH1" <-> "NH2" Residue "I ARG 146": "NH1" <-> "NH2" Residue "J ARG 12": "NH1" <-> "NH2" Residue "J ARG 28": "NH1" <-> "NH2" Residue "K ARG 5": "NH1" <-> "NH2" Residue "K ARG 11": "NH1" <-> "NH2" Residue "K ARG 22": "NH1" <-> "NH2" Residue "K ARG 42": "NH1" <-> "NH2" Residue "K ARG 59": "NH1" <-> "NH2" Residue "K ARG 75": "NH1" <-> "NH2" Residue "K ARG 77": "NH1" <-> "NH2" Residue "K ARG 160": "NH1" <-> "NH2" Residue "K ARG 180": "NH1" <-> "NH2" Residue "K ARG 183": "NH1" <-> "NH2" Residue "L ARG 143": "NH1" <-> "NH2" Residue "L ARG 149": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 56": "NH1" <-> "NH2" Residue "M ARG 84": "NH1" <-> "NH2" Residue "N ARG 41": "NH1" <-> "NH2" Residue "N ARG 100": "NH1" <-> "NH2" Residue "O ARG 59": "NH1" <-> "NH2" Residue "O ARG 110": "NH1" <-> "NH2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 121": "NH1" <-> "NH2" Residue "O ARG 134": "NH1" <-> "NH2" Residue "O ARG 139": "NH1" <-> "NH2" Residue "O ARG 140": "NH1" <-> "NH2" Residue "P ARG 17": "NH1" <-> "NH2" Residue "P ARG 18": "NH1" <-> "NH2" Residue "P ARG 29": "NH1" <-> "NH2" Residue "P ARG 71": "NH1" <-> "NH2" Residue "P ARG 135": "NH1" <-> "NH2" Residue "P ARG 142": "NH1" <-> "NH2" Residue "Q ARG 124": "NH1" <-> "NH2" Residue "R ARG 32": "NH1" <-> "NH2" Residue "R ARG 40": "NH1" <-> "NH2" Residue "R ARG 56": "NH1" <-> "NH2" Residue "R ARG 114": "NH1" <-> "NH2" Residue "R ARG 125": "NH1" <-> "NH2" Residue "S ARG 20": "NH1" <-> "NH2" Residue "S ARG 41": "NH1" <-> "NH2" Residue "T ARG 20": "NH1" <-> "NH2" Residue "T ARG 124": "NH1" <-> "NH2" Residue "U ARG 35": "NH1" <-> "NH2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 103": "NH1" <-> "NH2" Residue "U ARG 151": "NH1" <-> "NH2" Residue "V ARG 5": "NH1" <-> "NH2" Residue "V ARG 104": "NH1" <-> "NH2" Residue "V ARG 119": "NH1" <-> "NH2" Residue "V ARG 119": "NH1" <-> "NH2" Residue "V ARG 122": "NH1" <-> "NH2" Residue "W ARG 25": "NH1" <-> "NH2" Residue "W ARG 54": "NH1" <-> "NH2" Residue "W ARG 68": "NH1" <-> "NH2" Residue "X ARG 75": "NH1" <-> "NH2" Residue "X ARG 77": "NH1" <-> "NH2" Residue "X ARG 99": "NH1" <-> "NH2" Residue "X ARG 110": "NH1" <-> "NH2" Residue "X ARG 173": "NH1" <-> "NH2" Residue "Z ARG 107": "NH1" <-> "NH2" Residue "Z ARG 118": "NH1" <-> "NH2" Residue "a ARG 90": "NH1" <-> "NH2" Residue "a ARG 103": "NH1" <-> "NH2" Residue "b ARG 6": "NH1" <-> "NH2" Residue "b ARG 19": "NH1" <-> "NH2" Residue "c ARG 14": "NH1" <-> "NH2" Residue "c ARG 81": "NH1" <-> "NH2" Residue "d ARG 45": "NH1" <-> "NH2" Residue "e ARG 31": "NH1" <-> "NH2" Residue "e ARG 43": "NH1" <-> "NH2" Residue "f TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 47": "NH1" <-> "NH2" Residue "g ARG 304": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 80594 Number of models: 1 Model: "" Number of chains: 66 Chain: "A" Number of atoms: 1829 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1805 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 218} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 225, 1805 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 218} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 1803 Chain: "B" Number of atoms: 1676 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 211, 1659 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 211, 1659 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 1674 Chain: "C" Number of atoms: 1668 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 212, 1628 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 205} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 212, 1628 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 205} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 1605 Chain: "D" Number of atoms: 1504 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 182, 1493 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 173} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 182, 1493 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 173} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 1510 Chain: "E" Number of atoms: 2029 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 260, 2015 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 245} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 32 Conformer: "B" Number of residues, atoms: 260, 2015 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 245} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 32 bond proxies already assigned to first conformer: 2038 Chain: "F" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1656 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 13, 'TRANS': 206} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "G" Number of atoms: 1796 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 238, 1790 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 8, 'TRANS': 229} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 63 Conformer: "B" Number of residues, atoms: 238, 1790 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 8, 'TRANS': 229} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 63 bond proxies already assigned to first conformer: 1807 Chain: "H" Number of atoms: 1438 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 184, 1427 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 184, 1427 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 1437 Chain: "I" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1613 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 190} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "J" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1014 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1403 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 57 Chain: "L" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1127 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 138} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 809 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 102, 798 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 102, 798 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 796 Chain: "N" Number of atoms: 728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 91, 720 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 86} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 91, 720 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 86} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 733 Chain: "O" Number of atoms: 1032 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 137, 1012 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 130} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 137, 1012 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 130} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1005 Chain: "P" Number of atoms: 1134 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 142, 1110 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 142, 1110 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1103 Chain: "Q" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 746 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'CIS': 5, 'TRANS': 109} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 92 Chain: "R" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1080 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 136} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "S" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 441 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "T" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1153 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1241 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 150} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "V" Number of atoms: 935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 924 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 47 Conformer: "B" Number of residues, atoms: 122, 924 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 47 bond proxies already assigned to first conformer: 922 Chain: "W" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 822 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "X" Number of atoms: 1202 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 152, 1196 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 144} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 152, 1196 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 144} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 1220 Chain: "Y" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 664 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain: "Z" Number of atoms: 1032 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 127, 1025 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 127, 1025 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 1036 Chain: "a" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 544 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "b" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 95} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "c" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 656 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "d" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 466 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "e" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 449 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 53} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "f" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 385 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'CIS': 3, 'PTRANS': 3, 'TRANS': 53} Chain breaks: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 76 Chain: "g" Number of atoms: 2240 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 300, 2231 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain breaks: 2 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Conformer: "B" Number of residues, atoms: 300, 2231 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain breaks: 2 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 bond proxies already assigned to first conformer: 2275 Chain: "1" Number of atoms: 37613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1760, 37613 Classifications: {'RNA': 1760} Modifications used: {'5*END': 1, 'rna2p': 3, 'rna2p_pur': 160, 'rna2p_pyr': 147, 'rna3p': 27, 'rna3p_pur': 783, 'rna3p_pyr': 633} Link IDs: {'rna2p': 309, 'rna3p': 1450} Chain breaks: 30 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' C%rna3p_pyr:plan2': 1, ' C%rna3p_pyr:plan': 1, ' G%rna2p_pur:plan2': 1, ' G%rna2p_pur:plan': 1, ' U%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "2" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1626 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p': 1, 'rna3p_pur': 34, 'rna3p_pyr': 35} Link IDs: {'rna2p': 5, 'rna3p': 70} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "3" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1639 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 32, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 65} Chain: "4" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1619 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 32, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 66} Chain: "5" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 251 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 10} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 272 Unusual residues: {' MG': 20, 'PAR': 6} Classifications: {'undetermined': 26} Link IDs: {None: 25} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "X" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "c" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "1" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 217 Classifications: {'water': 217} Link IDs: {None: 216} Chain: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N AARG A 177 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 177 " occ=0.50 residue: pdb=" N AGLU B 199 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU B 199 " occ=0.50 residue: pdb=" N AARG C 66 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 66 " occ=0.50 residue: pdb=" N APHE C 106 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 106 " occ=0.50 residue: pdb=" N AARG C 145 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 145 " occ=0.50 residue: pdb=" N AARG D 16 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 16 " occ=0.50 residue: pdb=" N AARG H 41 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG H 41 " occ=0.50 residue: pdb=" N AARG M 18 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG M 18 " occ=0.50 residue: pdb=" N AARG O 59 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG O 59 " occ=0.50 residue: pdb=" N ALYS O 136 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS O 136 " occ=0.50 residue: pdb=" N AARG V 119 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG V 119 " occ=0.50 residue: pdb=" N ALYS g 299 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS g 299 " occ=0.50 Time building chain proxies: 37.92, per 1000 atoms: 0.47 Number of scatterers: 80594 At special positions: 0 Unit cell: (233.58, 225.42, 207.06, 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 198 16.00 P 1997 15.00 Mg 24 11.99 O 20657 8.00 N 14894 7.00 C 42824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 25 " distance=2.06 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 40 " distance=2.02 Simple disulfide: pdb=" SG CYS S 25 " - pdb=" SG CYS S 40 " distance=2.02 Simple disulfide: pdb=" SG CYS S 25 " - pdb=" SG CYS S 43 " distance=2.08 Simple disulfide: pdb=" SG CYS S 40 " - pdb=" SG CYS S 43 " distance=1.98 Simple disulfide: pdb=" SG CYS b 25 " - pdb=" SG CYS b 28 " distance=2.02 Simple disulfide: pdb=" SG CYS b 28 " - pdb=" SG CYS b 78 " distance=2.05 Simple disulfide: pdb=" SG CYS b 28 " - pdb=" SG CYS b 81 " distance=2.00 Simple disulfide: pdb=" SG CYS b 78 " - pdb=" SG CYS b 81 " distance=2.06 Simple disulfide: pdb=" SG CYS c 38 " - pdb=" SG CYS c 41 " distance=2.03 Simple disulfide: pdb=" SG CYS c 38 " - pdb=" SG CYS c 60 " distance=2.04 Simple disulfide: pdb=" SG CYS c 41 " - pdb=" SG CYS c 60 " distance=2.00 Simple disulfide: pdb=" SG CYS c 57 " - pdb=" SG CYS c 60 " distance=2.02 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 29.71 Conformation dependent library (CDL) restraints added in 8.1 seconds 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9018 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 153 helices and 50 sheets defined 28.1% alpha, 14.7% beta 456 base pairs and 1093 stacking pairs defined. Time for finding SS restraints: 31.09 Creating SS restraints... Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.692A pdb=" N ARG A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLY A 63 " --> pdb=" O ASP A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 115 removed outlier: 3.573A pdb=" N ALA A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 177 Processing helix chain 'A' and resid 183 through 203 removed outlier: 4.542A pdb=" N ARG A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N SER A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 removed outlier: 3.543A pdb=" N ALA A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 23 Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 84 through 97 removed outlier: 4.744A pdb=" N ARG B 88 " --> pdb=" O TYR B 85 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 90 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B 93 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS B 96 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL B 97 " --> pdb=" O SER B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 173 through 189 removed outlier: 5.901A pdb=" N TYR B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 205 Processing helix chain 'C' and resid 6 through 29 removed outlier: 3.668A pdb=" N ILE C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA C 29 " --> pdb=" O LYS C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 57 No H-bonds generated for 'chain 'C' and resid 54 through 57' Processing helix chain 'C' and resid 63 through 76 removed outlier: 3.741A pdb=" N ILE C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 109 removed outlier: 3.765A pdb=" N GLU C 102 " --> pdb=" O MET C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 162 through 166 removed outlier: 3.674A pdb=" N PHE C 166 " --> pdb=" O HIS C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 32 Processing helix chain 'D' and resid 38 through 60 removed outlier: 3.751A pdb=" N VAL D 44 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR D 60 " --> pdb=" O ARG D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 69 No H-bonds generated for 'chain 'D' and resid 66 through 69' Processing helix chain 'D' and resid 75 through 82 Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'D' and resid 100 through 106 removed outlier: 4.464A pdb=" N ARG D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 115 removed outlier: 3.588A pdb=" N PHE D 113 " --> pdb=" O GLN D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 129 removed outlier: 3.829A pdb=" N VAL D 126 " --> pdb=" O HIS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 181 removed outlier: 3.683A pdb=" N LYS D 180 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 15 No H-bonds generated for 'chain 'E' and resid 13 through 15' Processing helix chain 'E' and resid 41 through 46 Processing helix chain 'E' and resid 55 through 62 removed outlier: 3.581A pdb=" N MET E 60 " --> pdb=" O ARG E 56 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 259 removed outlier: 3.661A pdb=" N ARG E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 56 Processing helix chain 'F' and resid 63 through 67 removed outlier: 3.693A pdb=" N PHE F 67 " --> pdb=" O GLU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 82 Processing helix chain 'F' and resid 133 through 146 removed outlier: 3.567A pdb=" N LYS F 145 " --> pdb=" O MET F 141 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU F 146 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 202 removed outlier: 3.537A pdb=" N LYS F 198 " --> pdb=" O PRO F 194 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE F 199 " --> pdb=" O VAL F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 234 removed outlier: 3.748A pdb=" N MET F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR F 233 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TYR F 234 " --> pdb=" O LEU F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 254 No H-bonds generated for 'chain 'F' and resid 251 through 254' Processing helix chain 'F' and resid 256 through 262 removed outlier: 3.696A pdb=" N GLU F 261 " --> pdb=" O GLU F 257 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 23 No H-bonds generated for 'chain 'G' and resid 20 through 23' Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 143 through 147 removed outlier: 3.642A pdb=" N LEU G 147 " --> pdb=" O LYS G 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 143 through 147' Processing helix chain 'G' and resid 185 through 235 removed outlier: 3.801A pdb=" N LYS G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA G 195 " --> pdb=" O ARG G 191 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS G 196 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS G 201 " --> pdb=" O ASP G 197 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG G 214 " --> pdb=" O ARG G 210 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN G 219 " --> pdb=" O LEU G 215 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU G 223 " --> pdb=" O ASN G 219 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP G 227 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER G 229 " --> pdb=" O GLN G 225 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS G 232 " --> pdb=" O HIS G 228 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN G 234 " --> pdb=" O LYS G 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 24 No H-bonds generated for 'chain 'H' and resid 22 through 24' Processing helix chain 'H' and resid 48 through 50 No H-bonds generated for 'chain 'H' and resid 48 through 50' Processing helix chain 'H' and resid 54 through 62 removed outlier: 3.599A pdb=" N ALA H 59 " --> pdb=" O VAL H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 90 removed outlier: 3.537A pdb=" N THR H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU H 84 " --> pdb=" O LYS H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 103 Processing helix chain 'H' and resid 129 through 149 removed outlier: 4.688A pdb=" N GLY H 143 " --> pdb=" O GLN H 139 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA H 144 " --> pdb=" O MET H 140 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLU H 146 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA H 148 " --> pdb=" O ALA H 144 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE H 149 " --> pdb=" O ARG H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 167 removed outlier: 3.624A pdb=" N ALA H 160 " --> pdb=" O PRO H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 188 Processing helix chain 'I' and resid 3 through 6 removed outlier: 3.595A pdb=" N ARG I 6 " --> pdb=" O PRO I 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 3 through 6' Processing helix chain 'I' and resid 10 through 12 No H-bonds generated for 'chain 'I' and resid 10 through 12' Processing helix chain 'I' and resid 18 through 29 Processing helix chain 'I' and resid 36 through 38 No H-bonds generated for 'chain 'I' and resid 36 through 38' Processing helix chain 'I' and resid 68 through 75 removed outlier: 3.553A pdb=" N LEU I 71 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N MET I 72 " --> pdb=" O ARG I 69 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG I 75 " --> pdb=" O MET I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 88 Processing helix chain 'I' and resid 109 through 113 removed outlier: 3.635A pdb=" N GLN I 113 " --> pdb=" O VAL I 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 109 through 113' Processing helix chain 'I' and resid 121 through 132 Processing helix chain 'I' and resid 159 through 161 No H-bonds generated for 'chain 'I' and resid 159 through 161' Processing helix chain 'I' and resid 168 through 180 removed outlier: 3.503A pdb=" N TYR I 174 " --> pdb=" O ARG I 170 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS I 177 " --> pdb=" O ALA I 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 19 Processing helix chain 'J' and resid 32 through 43 removed outlier: 3.640A pdb=" N VAL J 40 " --> pdb=" O LYS J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 93 removed outlier: 3.725A pdb=" N TYR J 86 " --> pdb=" O THR J 83 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU J 87 " --> pdb=" O THR J 84 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS J 88 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET J 90 " --> pdb=" O GLU J 87 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS J 91 " --> pdb=" O LYS J 88 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN J 92 " --> pdb=" O TRP J 89 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE J 93 " --> pdb=" O MET J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'K' and resid 26 through 28 No H-bonds generated for 'chain 'K' and resid 26 through 28' Processing helix chain 'K' and resid 49 through 51 No H-bonds generated for 'chain 'K' and resid 49 through 51' Processing helix chain 'K' and resid 89 through 92 No H-bonds generated for 'chain 'K' and resid 89 through 92' Processing helix chain 'K' and resid 107 through 115 Processing helix chain 'K' and resid 173 through 181 removed outlier: 3.658A pdb=" N GLN K 178 " --> pdb=" O ALA K 174 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 195 No H-bonds generated for 'chain 'K' and resid 192 through 195' Processing helix chain 'K' and resid 205 through 215 removed outlier: 3.822A pdb=" N LYS K 213 " --> pdb=" O GLN K 209 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG K 214 " --> pdb=" O PHE K 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 59 removed outlier: 3.527A pdb=" N ILE L 54 " --> pdb=" O LEU L 50 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA L 57 " --> pdb=" O LYS L 53 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE L 58 " --> pdb=" O ILE L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 100 removed outlier: 3.840A pdb=" N ALA L 84 " --> pdb=" O GLN L 80 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE L 96 " --> pdb=" O ALA L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 118 removed outlier: 3.548A pdb=" N PHE L 115 " --> pdb=" O LEU L 111 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR L 118 " --> pdb=" O LYS L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 122 No H-bonds generated for 'chain 'L' and resid 120 through 122' Processing helix chain 'M' and resid 26 through 39 removed outlier: 3.711A pdb=" N GLU M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN M 35 " --> pdb=" O SER M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 99 Processing helix chain 'N' and resid 38 through 50 removed outlier: 3.530A pdb=" N ASP N 42 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 89 Processing helix chain 'N' and resid 108 through 118 removed outlier: 3.517A pdb=" N ALA N 112 " --> pdb=" O ASP N 108 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER N 116 " --> pdb=" O ALA N 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 53 No H-bonds generated for 'chain 'O' and resid 51 through 53' Processing helix chain 'O' and resid 58 through 60 No H-bonds generated for 'chain 'O' and resid 58 through 60' Processing helix chain 'O' and resid 64 through 81 removed outlier: 3.531A pdb=" N ARG O 77 " --> pdb=" O ASP O 73 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU O 80 " --> pdb=" O ALA O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 114 Processing helix chain 'P' and resid 10 through 20 Processing helix chain 'P' and resid 25 through 29 removed outlier: 3.536A pdb=" N ARG P 29 " --> pdb=" O LYS P 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 25 through 29' Processing helix chain 'P' and resid 34 through 37 No H-bonds generated for 'chain 'P' and resid 34 through 37' Processing helix chain 'P' and resid 130 through 134 Processing helix chain 'Q' and resid 29 through 39 removed outlier: 3.694A pdb=" N VAL Q 33 " --> pdb=" O ALA Q 29 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE Q 34 " --> pdb=" O VAL Q 30 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN Q 35 " --> pdb=" O ARG Q 31 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU Q 39 " --> pdb=" O GLN Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 55 removed outlier: 3.660A pdb=" N ASP Q 55 " --> pdb=" O ALA Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 72 No H-bonds generated for 'chain 'Q' and resid 70 through 72' Processing helix chain 'Q' and resid 76 through 83 removed outlier: 4.006A pdb=" N LYS Q 82 " --> pdb=" O THR Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 135 No H-bonds generated for 'chain 'Q' and resid 133 through 135' Processing helix chain 'R' and resid 27 through 31 Processing helix chain 'R' and resid 38 through 48 removed outlier: 4.379A pdb=" N LEU R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 59 No H-bonds generated for 'chain 'R' and resid 57 through 59' Processing helix chain 'R' and resid 62 through 73 removed outlier: 3.588A pdb=" N LYS R 67 " --> pdb=" O GLU R 63 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU R 70 " --> pdb=" O GLU R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 78 Processing helix chain 'R' and resid 82 through 84 No H-bonds generated for 'chain 'R' and resid 82 through 84' Processing helix chain 'R' and resid 101 through 117 removed outlier: 4.359A pdb=" N ASP R 105 " --> pdb=" O SER R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 127 removed outlier: 3.953A pdb=" N HIS R 126 " --> pdb=" O ARG R 122 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 12 No H-bonds generated for 'chain 'S' and resid 9 through 12' Processing helix chain 'S' and resid 41 through 45 removed outlier: 3.815A pdb=" N ARG S 45 " --> pdb=" O ARG S 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 41 through 45' Processing helix chain 'S' and resid 48 through 51 No H-bonds generated for 'chain 'S' and resid 48 through 51' Processing helix chain 'T' and resid 30 through 42 removed outlier: 3.568A pdb=" N VAL T 34 " --> pdb=" O SER T 30 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG T 42 " --> pdb=" O CYS T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 47 through 56 removed outlier: 3.585A pdb=" N GLY T 51 " --> pdb=" O PRO T 47 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET T 52 " --> pdb=" O SER T 48 " (cutoff:3.500A) Processing helix chain 'T' and resid 63 through 66 No H-bonds generated for 'chain 'T' and resid 63 through 66' Processing helix chain 'T' and resid 71 through 78 Processing helix chain 'T' and resid 86 through 104 removed outlier: 3.552A pdb=" N GLN T 97 " --> pdb=" O LYS T 93 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG T 104 " --> pdb=" O LYS T 100 " (cutoff:3.500A) Processing helix chain 'T' and resid 109 through 131 removed outlier: 3.508A pdb=" N TYR T 113 " --> pdb=" O ARG T 109 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG T 127 " --> pdb=" O HIS T 123 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR T 128 " --> pdb=" O ARG T 124 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 19 Processing helix chain 'V' and resid 21 through 23 No H-bonds generated for 'chain 'V' and resid 21 through 23' Processing helix chain 'V' and resid 28 through 38 removed outlier: 4.005A pdb=" N ARG V 33 " --> pdb=" O TYR V 29 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP V 37 " --> pdb=" O ARG V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 63 removed outlier: 3.593A pdb=" N THR V 55 " --> pdb=" O ALA V 51 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU V 61 " --> pdb=" O ILE V 57 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG V 63 " --> pdb=" O LYS V 59 " (cutoff:3.500A) Processing helix chain 'V' and resid 74 through 82 removed outlier: 3.678A pdb=" N ARG V 80 " --> pdb=" O GLU V 76 " (cutoff:3.500A) Processing helix chain 'V' and resid 92 through 95 No H-bonds generated for 'chain 'V' and resid 92 through 95' Processing helix chain 'V' and resid 103 through 111 removed outlier: 4.430A pdb=" N ARG V 111 " --> pdb=" O GLN V 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 29 through 34 removed outlier: 3.635A pdb=" N ALA W 34 " --> pdb=" O ASP W 30 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 41 Processing helix chain 'W' and resid 46 through 55 Processing helix chain 'W' and resid 62 through 68 removed outlier: 3.842A pdb=" N ARG W 68 " --> pdb=" O LEU W 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 94 through 96 No H-bonds generated for 'chain 'W' and resid 94 through 96' Processing helix chain 'W' and resid 116 through 118 No H-bonds generated for 'chain 'W' and resid 116 through 118' Processing helix chain 'W' and resid 123 through 125 No H-bonds generated for 'chain 'W' and resid 123 through 125' Processing helix chain 'X' and resid 43 through 57 removed outlier: 3.605A pdb=" N LYS X 55 " --> pdb=" O ALA X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 68 removed outlier: 3.690A pdb=" N GLU X 67 " --> pdb=" O ASN X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 87 No H-bonds generated for 'chain 'X' and resid 84 through 87' Processing helix chain 'X' and resid 91 through 97 Processing helix chain 'X' and resid 104 through 110 removed outlier: 3.648A pdb=" N ARG X 110 " --> pdb=" O GLY X 106 " (cutoff:3.500A) Processing helix chain 'X' and resid 129 through 142 Processing helix chain 'X' and resid 157 through 171 removed outlier: 3.667A pdb=" N GLN X 171 " --> pdb=" O ALA X 167 " (cutoff:3.500A) Processing helix chain 'Y' and resid 61 through 66 Processing helix chain 'Y' and resid 69 through 80 Processing helix chain 'Z' and resid 22 through 24 No H-bonds generated for 'chain 'Z' and resid 22 through 24' Processing helix chain 'Z' and resid 43 through 54 removed outlier: 3.538A pdb=" N LYS Z 48 " --> pdb=" O GLN Z 44 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS Z 49 " --> pdb=" O LEU Z 45 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR Z 54 " --> pdb=" O LEU Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 59 through 61 No H-bonds generated for 'chain 'Z' and resid 59 through 61' Processing helix chain 'Z' and resid 86 through 92 Processing helix chain 'Z' and resid 95 through 101 Processing helix chain 'Z' and resid 111 through 120 Processing helix chain 'a' and resid 44 through 52 removed outlier: 3.558A pdb=" N ASP a 48 " --> pdb=" O LYS a 44 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER a 52 " --> pdb=" O ASP a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 54 through 56 No H-bonds generated for 'chain 'a' and resid 54 through 56' Processing helix chain 'a' and resid 64 through 68 Processing helix chain 'a' and resid 73 through 85 removed outlier: 3.851A pdb=" N ALA a 78 " --> pdb=" O SER a 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN a 82 " --> pdb=" O ALA a 78 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU a 83 " --> pdb=" O GLY a 79 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG a 85 " --> pdb=" O LYS a 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 57 removed outlier: 3.643A pdb=" N ASP b 54 " --> pdb=" O ALA b 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 79 through 84 Processing helix chain 'b' and resid 93 through 95 No H-bonds generated for 'chain 'b' and resid 93 through 95' Processing helix chain 'c' and resid 13 through 18 removed outlier: 3.829A pdb=" N MET c 18 " --> pdb=" O ARG c 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 8 through 10 No H-bonds generated for 'chain 'e' and resid 8 through 10' Processing helix chain 'e' and resid 13 through 17 Processing helix chain 'e' and resid 32 through 43 removed outlier: 3.576A pdb=" N LYS e 36 " --> pdb=" O ARG e 33 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR e 40 " --> pdb=" O ARG e 37 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR e 41 " --> pdb=" O LEU e 38 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG e 43 " --> pdb=" O TYR e 40 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 31 through 33 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 69 removed outlier: 5.397A pdb=" N THR A 89 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N PHE A 102 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 12.379A pdb=" N GLN A 101 " --> pdb=" O ARG A 221 " (cutoff:3.500A) removed outlier: 11.900A pdb=" N ARG A 221 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N HIS A 103 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR A 136 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 122 through 125 removed outlier: 3.541A pdb=" N GLU A 211 " --> pdb=" O PHE A 144 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 103 removed outlier: 6.354A pdb=" N VAL B 124 " --> pdb=" O CYS B 78 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N CYS B 80 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL B 126 " --> pdb=" O CYS B 80 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL B 127 " --> pdb=" O PRO B 146 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE B 148 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE B 162 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N CYS B 151 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE B 164 " --> pdb=" O CYS B 151 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.745A pdb=" N ILE B 51 " --> pdb=" O TYR B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 35 through 41 removed outlier: 3.826A pdb=" N GLY C 35 " --> pdb=" O LYS C 50 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG C 44 " --> pdb=" O THR C 41 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 147 through 154 removed outlier: 4.027A pdb=" N GLY C 132 " --> pdb=" O MET C 188 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 86 through 89 Processing sheet with id= I, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.645A pdb=" N ASP E 168 " --> pdb=" O VAL E 158 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 222 through 226 removed outlier: 6.902A pdb=" N ALA E 177 " --> pdb=" O ILE E 225 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N HIS E 206 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL E 195 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE E 204 " --> pdb=" O VAL E 195 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 123 through 129 removed outlier: 6.519A pdb=" N VAL E 137 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU E 126 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL E 135 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR E 128 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL E 133 " --> pdb=" O THR E 128 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 124 through 130 removed outlier: 3.690A pdb=" N GLY F 105 " --> pdb=" O THR F 102 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS F 94 " --> pdb=" O PHE F 113 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL F 115 " --> pdb=" O MET F 92 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N MET F 92 " --> pdb=" O VAL F 115 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLY F 117 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASP F 90 " --> pdb=" O GLY F 117 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 170 through 174 Processing sheet with id= N, first strand: chain 'G' and resid 2 through 6 removed outlier: 3.909A pdb=" N LEU G 111 " --> pdb=" O SER G 57 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 36 through 38 removed outlier: 3.658A pdb=" N LYS G 118 " --> pdb=" O ILE G 50 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG G 52 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE G 116 " --> pdb=" O ARG G 52 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 73 through 78 Processing sheet with id= Q, first strand: chain 'H' and resid 109 through 113 Processing sheet with id= R, first strand: chain 'I' and resid 92 through 99 removed outlier: 6.382A pdb=" N THR I 60 " --> pdb=" O LEU I 93 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N MET I 95 " --> pdb=" O THR I 60 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU I 62 " --> pdb=" O MET I 95 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL I 97 " --> pdb=" O LEU I 62 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL I 64 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN I 99 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR I 66 " --> pdb=" O GLN I 99 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL I 46 " --> pdb=" O PRO I 67 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 184 through 189 removed outlier: 8.724A pdb=" N SER I 185 " --> pdb=" O LYS I 151 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET I 153 " --> pdb=" O SER I 185 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N GLY I 187 " --> pdb=" O MET I 153 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL I 155 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N MET I 189 " --> pdb=" O VAL I 155 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU I 157 " --> pdb=" O MET I 189 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER I 150 " --> pdb=" O ARG I 146 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP I 158 " --> pdb=" O VAL I 138 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N VAL I 138 " --> pdb=" O ASP I 158 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 24 through 27 Processing sheet with id= U, first strand: chain 'J' and resid 71 through 74 removed outlier: 6.789A pdb=" N VAL J 103 " --> pdb=" O LEU J 126 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE J 128 " --> pdb=" O PHE J 101 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE J 101 " --> pdb=" O PHE J 128 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 42 through 47 Processing sheet with id= W, first strand: chain 'K' and resid 62 through 67 removed outlier: 3.578A pdb=" N ILE K 72 " --> pdb=" O TRP K 67 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 200 through 202 removed outlier: 6.658A pdb=" N ALA K 103 " --> pdb=" O VAL K 81 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL K 81 " --> pdb=" O ALA K 103 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 11 through 17 removed outlier: 6.100A pdb=" N ASN L 34 " --> pdb=" O ILE L 71 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL L 73 " --> pdb=" O ASN L 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS L 36 " --> pdb=" O VAL L 73 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL L 75 " --> pdb=" O LYS L 36 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 107 through 113 removed outlier: 4.633A pdb=" N LYS M 83 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 60 through 63 Processing sheet with id= AB, first strand: chain 'N' and resid 53 through 57 Processing sheet with id= AC, first strand: chain 'O' and resid 21 through 27 removed outlier: 6.767A pdb=" N ALA O 85 " --> pdb=" O GLY O 22 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL O 24 " --> pdb=" O ALA O 85 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS O 87 " --> pdb=" O VAL O 24 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE O 26 " --> pdb=" O HIS O 87 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LYS O 89 " --> pdb=" O ILE O 26 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'O' and resid 34 through 38 removed outlier: 3.533A pdb=" N VAL O 47 " --> pdb=" O VAL O 37 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'P' and resid 80 through 84 removed outlier: 3.590A pdb=" N GLU P 53 " --> pdb=" O ARG P 71 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN P 73 " --> pdb=" O VAL P 51 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL P 51 " --> pdb=" O GLN P 73 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SER P 103 " --> pdb=" O ILE P 122 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ILE P 122 " --> pdb=" O SER P 103 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Q' and resid 87 through 91 Processing sheet with id= AG, first strand: chain 'R' and resid 13 through 15 Processing sheet with id= AH, first strand: chain 'U' and resid 117 through 125 removed outlier: 3.551A pdb=" N SER U 92 " --> pdb=" O VAL U 100 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ARG U 102 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL U 90 " --> pdb=" O ARG U 102 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ASN U 104 " --> pdb=" O GLY U 88 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N GLY U 88 " --> pdb=" O ASN U 104 " (cutoff:3.500A) removed outlier: 15.670A pdb=" N LEU U 106 " --> pdb=" O LEU U 86 " (cutoff:3.500A) removed outlier: 17.013A pdb=" N LEU U 86 " --> pdb=" O LEU U 106 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY U 141 " --> pdb=" O VAL U 154 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL U 154 " --> pdb=" O GLY U 141 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'W' and resid 83 through 85 removed outlier: 3.615A pdb=" N VAL W 83 " --> pdb=" O VAL W 100 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'X' and resid 113 through 115 removed outlier: 3.737A pdb=" N HIS X 123 " --> pdb=" O LYS X 115 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'Y' and resid 37 through 42 Processing sheet with id= AL, first strand: chain 'Z' and resid 11 through 14 Processing sheet with id= AM, first strand: chain 'Z' and resid 18 through 20 Processing sheet with id= AN, first strand: chain 'a' and resid 89 through 94 removed outlier: 6.762A pdb=" N VAL a 100 " --> pdb=" O VAL a 92 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'b' and resid 22 through 24 Processing sheet with id= AP, first strand: chain 'b' and resid 38 through 40 removed outlier: 3.579A pdb=" N VAL b 38 " --> pdb=" O PHE b 77 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'c' and resid 44 through 48 removed outlier: 3.626A pdb=" N ARG c 81 " --> pdb=" O ASP c 35 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY c 79 " --> pdb=" O SER c 37 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'd' and resid 72 through 75 removed outlier: 6.694A pdb=" N ARG d 43 " --> pdb=" O ILE d 27 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N VAL d 29 " --> pdb=" O GLN d 41 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N GLN d 41 " --> pdb=" O VAL d 29 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'g' and resid 2 through 4 removed outlier: 3.504A pdb=" N GLU g 4 " --> pdb=" O VAL g 305 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL g 305 " --> pdb=" O GLU g 4 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER g 284 " --> pdb=" O GLY g 297 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'g' and resid 30 through 32 removed outlier: 5.140A pdb=" N LYS g 42 " --> pdb=" O PRO g 57 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'g' and resid 68 through 73 removed outlier: 6.668A pdb=" N ALA g 83 " --> pdb=" O SER g 69 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL g 71 " --> pdb=" O LEU g 81 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU g 81 " --> pdb=" O VAL g 71 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU g 73 " --> pdb=" O TYR g 79 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TYR g 79 " --> pdb=" O LEU g 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG g 101 " --> pdb=" O MET g 91 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP g 93 " --> pdb=" O SER g 99 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER g 99 " --> pdb=" O ASP g 93 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'g' and resid 110 through 115 removed outlier: 6.765A pdb=" N ALA g 125 " --> pdb=" O LEU g 111 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL g 113 " --> pdb=" O VAL g 123 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL g 123 " --> pdb=" O VAL g 113 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N PHE g 115 " --> pdb=" O LEU g 121 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU g 121 " --> pdb=" O PHE g 115 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL g 131 " --> pdb=" O PHE g 144 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN g 135 " --> pdb=" O CYS g 140 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N CYS g 140 " --> pdb=" O ASN g 135 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'g' and resid 238 through 243 removed outlier: 6.333A pdb=" N ALA g 253 " --> pdb=" O ASN g 239 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE g 241 " --> pdb=" O CYS g 251 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N CYS g 251 " --> pdb=" O ILE g 241 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N PHE g 243 " --> pdb=" O TRP g 249 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TRP g 249 " --> pdb=" O PHE g 243 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER g 259 " --> pdb=" O VAL g 252 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU g 258 " --> pdb=" O LEU g 272 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP g 262 " --> pdb=" O VAL g 268 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL g 268 " --> pdb=" O ASP g 262 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'g' and resid 197 through 202 removed outlier: 6.673A pdb=" N GLY g 212 " --> pdb=" O SER g 198 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL g 200 " --> pdb=" O ALA g 210 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA g 210 " --> pdb=" O VAL g 200 " (cutoff:3.500A) 1013 hydrogen bonds defined for protein. 2866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1105 hydrogen bonds 1768 hydrogen bond angles 0 basepair planarities 456 basepair parallelities 1093 stacking parallelities Total time for adding SS restraints: 66.26 Time building geometry restraints manager: 32.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 14484 1.33 - 1.48: 41601 1.48 - 1.63: 29659 1.63 - 1.78: 134 1.78 - 1.94: 188 Bond restraints: 86066 Sorted by residual: bond pdb=" C2' A2M 12021 " pdb=" C1' A2M 12021 " ideal model delta sigma weight residual 1.277 1.547 -0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C2' A2M 1 668 " pdb=" C1' A2M 1 668 " ideal model delta sigma weight residual 1.277 1.547 -0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C4' A2M 1 912 " pdb=" C3' A2M 1 912 " ideal model delta sigma weight residual 1.276 1.515 -0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C2' A2M 1 479 " pdb=" C1' A2M 1 479 " ideal model delta sigma weight residual 1.277 1.516 -0.239 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C13 PAR 12302 " pdb=" O43 PAR 12302 " ideal model delta sigma weight residual 1.402 1.636 -0.234 2.00e-02 2.50e+03 1.37e+02 ... (remaining 86061 not shown) Histogram of bond angle deviations from ideal: 95.81 - 104.25: 8374 104.25 - 112.69: 50164 112.69 - 121.14: 44056 121.14 - 129.58: 21973 129.58 - 138.02: 1491 Bond angle restraints: 126058 Sorted by residual: angle pdb=" CA CYS b 78 " pdb=" CB CYS b 78 " pdb=" SG CYS b 78 " ideal model delta sigma weight residual 114.40 138.02 -23.62 2.30e+00 1.89e-01 1.05e+02 angle pdb=" C LEU Q 47 " pdb=" N SER Q 48 " pdb=" CA SER Q 48 " ideal model delta sigma weight residual 121.70 137.64 -15.94 1.80e+00 3.09e-01 7.85e+01 angle pdb=" C4' A 12165 " pdb=" C3' A 12165 " pdb=" O3' A 12165 " ideal model delta sigma weight residual 113.00 126.18 -13.18 1.50e+00 4.44e-01 7.72e+01 angle pdb=" C GLU a 53 " pdb=" N VAL a 54 " pdb=" CA VAL a 54 " ideal model delta sigma weight residual 120.24 125.12 -4.88 6.30e-01 2.52e+00 6.00e+01 angle pdb=" O3' G 1 913 " pdb=" C3' G 1 913 " pdb=" C2' G 1 913 " ideal model delta sigma weight residual 109.50 98.19 11.31 1.50e+00 4.44e-01 5.69e+01 ... (remaining 126053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 48819 35.95 - 71.89: 5113 71.89 - 107.84: 619 107.84 - 143.78: 26 143.78 - 179.73: 80 Dihedral angle restraints: 54657 sinusoidal: 40683 harmonic: 13974 Sorted by residual: dihedral pdb=" CA HIS f 122 " pdb=" C HIS f 122 " pdb=" N PRO f 123 " pdb=" CA PRO f 123 " ideal model delta harmonic sigma weight residual 180.00 105.28 74.72 0 5.00e+00 4.00e-02 2.23e+02 dihedral pdb=" CD BARG V 119 " pdb=" NE BARG V 119 " pdb=" CZ BARG V 119 " pdb=" NH1BARG V 119 " ideal model delta sinusoidal sigma weight residual 0.00 -179.59 179.59 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA ASP g 300 " pdb=" C ASP g 300 " pdb=" N ASN g 301 " pdb=" CA ASN g 301 " ideal model delta harmonic sigma weight residual -180.00 -127.45 -52.55 0 5.00e+00 4.00e-02 1.10e+02 ... (remaining 54654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 15074 0.131 - 0.262: 583 0.262 - 0.393: 46 0.393 - 0.524: 14 0.524 - 0.655: 4 Chirality restraints: 15721 Sorted by residual: chirality pdb=" C3' G 1 510 " pdb=" C4' G 1 510 " pdb=" O3' G 1 510 " pdb=" C2' G 1 510 " both_signs ideal model delta sigma weight residual False -2.48 -1.82 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CB VAL H 35 " pdb=" CA VAL H 35 " pdb=" CG1 VAL H 35 " pdb=" CG2 VAL H 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.03 -0.60 2.00e-01 2.50e+01 9.05e+00 chirality pdb=" C33 PAR 12305 " pdb=" C23 PAR 12305 " pdb=" C43 PAR 12305 " pdb=" O33 PAR 12305 " both_signs ideal model delta sigma weight residual False -2.68 -2.10 -0.57 2.00e-01 2.50e+01 8.24e+00 ... (remaining 15718 not shown) Planarity restraints: 8568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMU 1 33 " -0.108 2.00e-02 2.50e+03 6.17e-01 8.57e+03 pdb=" C4' OMU 1 33 " -0.434 2.00e-02 2.50e+03 pdb=" O4' OMU 1 33 " -0.562 2.00e-02 2.50e+03 pdb=" C3' OMU 1 33 " 0.607 2.00e-02 2.50e+03 pdb=" O3' OMU 1 33 " 0.719 2.00e-02 2.50e+03 pdb=" C2' OMU 1 33 " 0.139 2.00e-02 2.50e+03 pdb=" O2' OMU 1 33 " -1.055 2.00e-02 2.50e+03 pdb=" C1' OMU 1 33 " -0.224 2.00e-02 2.50e+03 pdb=" N1 OMU 1 33 " 0.918 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 11866 " 0.101 2.00e-02 2.50e+03 6.16e-01 8.54e+03 pdb=" C4' OMC 11866 " 0.451 2.00e-02 2.50e+03 pdb=" O4' OMC 11866 " 0.594 2.00e-02 2.50e+03 pdb=" C3' OMC 11866 " -0.599 2.00e-02 2.50e+03 pdb=" O3' OMC 11866 " -0.712 2.00e-02 2.50e+03 pdb=" C2' OMC 11866 " -0.158 2.00e-02 2.50e+03 pdb=" O2' OMC 11866 " 1.033 2.00e-02 2.50e+03 pdb=" C1' OMC 11866 " 0.209 2.00e-02 2.50e+03 pdb=" N1 OMC 11866 " -0.920 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMU 12048 " 0.084 2.00e-02 2.50e+03 6.12e-01 8.42e+03 pdb=" C4' OMU 12048 " 0.429 2.00e-02 2.50e+03 pdb=" O4' OMU 12048 " 0.597 2.00e-02 2.50e+03 pdb=" C3' OMU 12048 " -0.611 2.00e-02 2.50e+03 pdb=" O3' OMU 12048 " -0.688 2.00e-02 2.50e+03 pdb=" C2' OMU 12048 " -0.151 2.00e-02 2.50e+03 pdb=" O2' OMU 12048 " 1.032 2.00e-02 2.50e+03 pdb=" C1' OMU 12048 " 0.222 2.00e-02 2.50e+03 pdb=" N1 OMU 12048 " -0.914 2.00e-02 2.50e+03 ... (remaining 8565 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 3 1.90 - 2.65: 3254 2.65 - 3.40: 95673 3.40 - 4.15: 249658 4.15 - 4.90: 373689 Nonbonded interactions: 722277 Sorted by model distance: nonbonded pdb=" N GLN f 124 " pdb=" CG2 THR f 146 " model vdw 1.149 3.540 nonbonded pdb=" C PRO f 123 " pdb=" CG2 THR f 146 " model vdw 1.249 3.690 nonbonded pdb=" O PRO f 123 " pdb=" CG2 THR f 146 " model vdw 1.565 3.460 nonbonded pdb=" O2' A 1 576 " pdb=" C5' U 1 577 " model vdw 2.003 3.440 nonbonded pdb=" O PRO f 123 " pdb=" CB THR f 146 " model vdw 2.013 3.470 ... (remaining 722272 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '2' and (resid 1 through 36 or resid 38 through 76)) selection = (chain '4' and (resid 1 through 36 or resid 38 through 76)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 14.880 Check model and map are aligned: 0.900 Set scattering table: 0.550 Process input model: 226.270 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.280 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: 0.010 Load rotamer database and sin/cos tables:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 261.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.270 86066 Z= 0.767 Angle : 1.241 23.624 126058 Z= 0.618 Chirality : 0.063 0.655 15721 Planarity : 0.038 0.617 8568 Dihedral : 23.605 179.727 45600 Min Nonbonded Distance : 1.149 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.03 % Favored : 93.87 % Rotamer: Outliers : 1.36 % Allowed : 4.43 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.13 % Twisted Proline : 0.53 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.10), residues: 4779 helix: -4.21 (0.07), residues: 1464 sheet: -1.05 (0.16), residues: 836 loop : -2.04 (0.11), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.006 TRP K 67 HIS 0.018 0.004 HIS E 5 PHE 0.100 0.005 PHE P 105 TYR 0.072 0.004 TYR Z 83 ARG 0.032 0.002 ARG E 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 954 time to evaluate : 4.313 Fit side-chains REVERT: A 40 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7711 (ptmt) REVERT: A 197 ASP cc_start: 0.7966 (m-30) cc_final: 0.7643 (m-30) REVERT: B 32 ASN cc_start: 0.8589 (m110) cc_final: 0.8137 (m-40) REVERT: C 22 GLU cc_start: 0.7660 (tp30) cc_final: 0.7297 (tp30) REVERT: C 124 TYR cc_start: 0.8466 (t80) cc_final: 0.8264 (t80) REVERT: C 168 ASP cc_start: 0.7667 (t0) cc_final: 0.7278 (t0) REVERT: D 51 MET cc_start: 0.7902 (mtm) cc_final: 0.7701 (mtp) REVERT: E 194 LYS cc_start: 0.8139 (tmtt) cc_final: 0.7462 (tppt) REVERT: E 249 GLU cc_start: 0.8250 (tm-30) cc_final: 0.8026 (tm-30) REVERT: F 198 LYS cc_start: 0.8198 (tppp) cc_final: 0.7913 (ttmm) REVERT: G 64 MET cc_start: 0.8679 (mtp) cc_final: 0.8276 (mtp) REVERT: G 201 LYS cc_start: 0.7883 (ptmm) cc_final: 0.7682 (ptmm) REVERT: G 211 GLU cc_start: 0.7551 (pp20) cc_final: 0.7190 (tm-30) REVERT: H 167 SER cc_start: 0.8390 (t) cc_final: 0.8160 (p) REVERT: I 68 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8586 (tp) REVERT: K 37 ARG cc_start: 0.7421 (mtt90) cc_final: 0.6883 (mtp180) REVERT: K 92 ARG cc_start: 0.6026 (tpt170) cc_final: 0.4681 (tmt170) REVERT: L 64 LYS cc_start: 0.8249 (ptpt) cc_final: 0.7875 (ptmt) REVERT: O 69 MET cc_start: 0.7423 (mtm) cc_final: 0.7195 (mmp) REVERT: O 79 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7924 (pptt) REVERT: P 131 TYR cc_start: 0.8563 (t80) cc_final: 0.8360 (t80) REVERT: R 4 THR cc_start: 0.7469 (p) cc_final: 0.7227 (m) REVERT: U 39 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7941 (ttpt) REVERT: V 106 MET cc_start: 0.9058 (tpp) cc_final: 0.8762 (mmm) REVERT: W 41 ARG cc_start: 0.6965 (ttp-110) cc_final: 0.6723 (ttp-110) REVERT: X 161 LYS cc_start: 0.8269 (mtpm) cc_final: 0.8033 (mtpp) REVERT: Z 112 LYS cc_start: 0.8193 (ttmm) cc_final: 0.7724 (tptp) REVERT: Z 119 ASN cc_start: 0.8643 (m110) cc_final: 0.8156 (m110) REVERT: a 95 SER cc_start: 0.8772 (t) cc_final: 0.8572 (m) REVERT: b 73 MET cc_start: 0.7353 (ptp) cc_final: 0.7144 (ptp) REVERT: c 71 LYS cc_start: 0.8763 (mttt) cc_final: 0.8491 (mttt) REVERT: g 11 ARG cc_start: 0.7681 (mtp85) cc_final: 0.7385 (mtm110) REVERT: g 90 ARG cc_start: 0.7546 (mtt-85) cc_final: 0.7301 (mtt-85) REVERT: g 304 ARG cc_start: 0.7457 (mpt180) cc_final: 0.7022 (mpt180) outliers start: 28 outliers final: 13 residues processed: 977 average time/residue: 1.7569 time to fit residues: 2237.7427 Evaluate side-chains 755 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 740 time to evaluate : 4.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain U residue 39 LYS Chi-restraints excluded: chain b residue 28 CYS Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain f residue 100 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 564 optimal weight: 4.9990 chunk 506 optimal weight: 0.7980 chunk 280 optimal weight: 0.9980 chunk 172 optimal weight: 0.1980 chunk 341 optimal weight: 1.9990 chunk 270 optimal weight: 6.9990 chunk 523 optimal weight: 5.9990 chunk 202 optimal weight: 0.9980 chunk 318 optimal weight: 0.9980 chunk 389 optimal weight: 3.9990 chunk 606 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 ASN A 101 GLN A 228 GLN B 33 GLN B 73 ASN B 102 HIS B 167 ASN D 65 HIS D 132 HIS D 138 GLN E 5 HIS E 54 ASN E 72 HIS E 185 ASN ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 ASN G 219 ASN H 74 GLN H 151 ASN I 89 HIS I 113 GLN I 191 ASN I 196 GLN J 64 ASN J 70 ASN K 64 ASN K 194 GLN L 11 GLN ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN L 76 HIS O 31 ASN P 20 ASN P 63 ASN ** Q 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 ASN S 27 ASN S 47 ASN T 49 GLN T 62 GLN T 65 ASN T 97 GLN T 134 GLN U 24 GLN U 107 HIS U 116 GLN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 110 ASN X 160 HIS Y 8 ASN Y 13 ASN Y 23 HIS Y 26 ASN Y 51 ASN Y 71 HIS Z 16 GLN Z 61 GLN a 82 GLN c 20 HIS c 43 GLN c 50 HIS d 41 GLN ** e 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 10 HIS g 44 ASN g 59 HIS g 75 HIS g 129 ASN g 301 ASN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 86066 Z= 0.168 Angle : 0.953 27.364 126058 Z= 0.504 Chirality : 0.040 0.318 15721 Planarity : 0.009 0.127 8568 Dihedral : 25.181 179.999 36767 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.07 % Favored : 94.88 % Rotamer: Outliers : 3.70 % Allowed : 13.01 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.17 % Twisted Proline : 0.53 % Twisted General : 0.11 % 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: -2.60 (0.11), residues: 4779 helix: -2.39 (0.11), residues: 1476 sheet: -0.73 (0.17), residues: 847 loop : -1.59 (0.11), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP g 134 HIS 0.009 0.001 HIS L 76 PHE 0.026 0.001 PHE P 105 TYR 0.019 0.001 TYR I 4 ARG 0.009 0.001 ARG a 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 864 time to evaluate : 4.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8055 (ttpt) cc_final: 0.7848 (ptmt) REVERT: A 197 ASP cc_start: 0.7986 (m-30) cc_final: 0.7720 (m-30) REVERT: B 32 ASN cc_start: 0.8542 (m110) cc_final: 0.8089 (m-40) REVERT: B 167 ASN cc_start: 0.8125 (t0) cc_final: 0.7786 (t0) REVERT: B 169 ARG cc_start: 0.7841 (mtm110) cc_final: 0.7461 (mtp180) REVERT: C 22 GLU cc_start: 0.7518 (tp30) cc_final: 0.7299 (tp30) REVERT: C 86 TYR cc_start: 0.7408 (m-80) cc_final: 0.7033 (m-80) REVERT: E 57 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6764 (mm-30) REVERT: E 171 LYS cc_start: 0.8787 (mmmm) cc_final: 0.8528 (mmmt) REVERT: E 199 PRO cc_start: 0.8695 (Cg_endo) cc_final: 0.8446 (Cg_exo) REVERT: E 251 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: F 198 LYS cc_start: 0.7859 (tppp) cc_final: 0.7639 (ttmm) REVERT: G 52 ARG cc_start: 0.7849 (tpp80) cc_final: 0.7645 (tpp80) REVERT: G 64 MET cc_start: 0.8667 (mtp) cc_final: 0.8334 (mtp) REVERT: G 69 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7679 (tm) REVERT: G 145 ARG cc_start: 0.6890 (ttt90) cc_final: 0.6088 (ttm-80) REVERT: G 201 LYS cc_start: 0.7773 (ptmm) cc_final: 0.7537 (ptmm) REVERT: H 167 SER cc_start: 0.8197 (t) cc_final: 0.7961 (p) REVERT: I 29 GLU cc_start: 0.7370 (tp30) cc_final: 0.7158 (tp30) REVERT: K 37 ARG cc_start: 0.7359 (mtt90) cc_final: 0.6952 (mtp180) REVERT: K 92 ARG cc_start: 0.6099 (tpt170) cc_final: 0.4621 (tmt170) REVERT: L 55 MET cc_start: 0.8217 (mmm) cc_final: 0.8001 (mmm) REVERT: L 64 LYS cc_start: 0.8317 (ptpt) cc_final: 0.8052 (pttt) REVERT: L 65 TYR cc_start: 0.8095 (m-80) cc_final: 0.7643 (m-80) REVERT: L 114 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8068 (mtmt) REVERT: L 146 LYS cc_start: 0.8330 (ttmm) cc_final: 0.7983 (ttmt) REVERT: O 89 LYS cc_start: 0.9106 (mtpp) cc_final: 0.8682 (mttt) REVERT: O 117 MET cc_start: 0.8344 (tpt) cc_final: 0.8118 (mmt) REVERT: P 66 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8137 (mt) REVERT: P 131 TYR cc_start: 0.8535 (t80) cc_final: 0.8312 (t80) REVERT: R 4 THR cc_start: 0.7362 (p) cc_final: 0.7160 (m) REVERT: R 67 LYS cc_start: 0.8022 (tptt) cc_final: 0.7182 (tttt) REVERT: T 87 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: U 39 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7966 (ttpt) REVERT: V 36 MET cc_start: 0.7824 (mtm) cc_final: 0.7610 (mpp) REVERT: X 57 GLU cc_start: 0.7373 (tt0) cc_final: 0.6911 (pt0) REVERT: X 150 GLN cc_start: 0.7960 (pm20) cc_final: 0.7752 (pm20) REVERT: Y 78 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8067 (mp) REVERT: Z 112 LYS cc_start: 0.7651 (ttmm) cc_final: 0.7314 (tptp) REVERT: a 80 LEU cc_start: 0.8538 (mt) cc_final: 0.8296 (mp) REVERT: a 90 ARG cc_start: 0.8184 (ttm170) cc_final: 0.7900 (ttm170) REVERT: c 14 ARG cc_start: 0.8127 (ttt-90) cc_final: 0.7582 (ttt90) REVERT: e 39 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7540 (mttp) REVERT: g 231 LYS cc_start: 0.7319 (ptmm) cc_final: 0.7070 (pttt) REVERT: g 302 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7315 (pp) REVERT: g 304 ARG cc_start: 0.7140 (mpt180) cc_final: 0.6639 (mpt180) outliers start: 116 outliers final: 45 residues processed: 921 average time/residue: 1.6739 time to fit residues: 2037.3433 Evaluate side-chains 802 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 749 time to evaluate : 4.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 163 LYS Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain T residue 87 ASP Chi-restraints excluded: chain T residue 132 VAL Chi-restraints excluded: chain U residue 39 LYS Chi-restraints excluded: chain V residue 43 SER Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain X residue 40 ASP Chi-restraints excluded: chain Y residue 12 GLU Chi-restraints excluded: chain Y residue 78 ILE Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain b residue 28 CYS Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 43 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 95 ASN Chi-restraints excluded: chain c residue 9 SER Chi-restraints excluded: chain c residue 43 GLN Chi-restraints excluded: chain c residue 60 CYS Chi-restraints excluded: chain c residue 68 THR Chi-restraints excluded: chain d residue 35 SER Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 39 LYS Chi-restraints excluded: chain f residue 100 TYR Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 179 TRP Chi-restraints excluded: chain g residue 248 PHE Chi-restraints excluded: chain g residue 283 ILE Chi-restraints excluded: chain g residue 302 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 337 optimal weight: 0.0980 chunk 188 optimal weight: 5.9990 chunk 504 optimal weight: 9.9990 chunk 413 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 607 optimal weight: 10.0000 chunk 656 optimal weight: 10.0000 chunk 541 optimal weight: 10.0000 chunk 602 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 487 optimal weight: 10.0000 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN A 91 GLN A 228 GLN B 73 ASN B 96 HIS D 122 HIS E 54 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN F 114 ASN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 GLN ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 GLN J 42 GLN J 64 ASN ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 ASN M 89 HIS P 110 HIS T 97 GLN T 134 GLN U 91 HIS U 116 GLN X 160 HIS Y 43 ASN Y 51 ASN Z 61 GLN a 82 GLN b 8 HIS b 24 HIS b 84 HIS c 43 GLN ** e 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 193 HIS g 301 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 86066 Z= 0.421 Angle : 0.987 25.267 126058 Z= 0.518 Chirality : 0.047 0.337 15721 Planarity : 0.010 0.140 8568 Dihedral : 25.007 179.896 36762 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.17 % Favored : 93.81 % Rotamer: Outliers : 5.82 % Allowed : 14.30 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.17 % Twisted Proline : 0.53 % Twisted General : 0.11 % 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: -2.10 (0.11), residues: 4779 helix: -1.64 (0.12), residues: 1471 sheet: -0.67 (0.17), residues: 839 loop : -1.43 (0.12), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 165 HIS 0.010 0.002 HIS K 116 PHE 0.052 0.003 PHE P 105 TYR 0.034 0.002 TYR Z 83 ARG 0.012 0.001 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 769 time to evaluate : 4.167 Fit side-chains revert: symmetry clash REVERT: A 70 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8414 (tp) REVERT: A 197 ASP cc_start: 0.8118 (m-30) cc_final: 0.7843 (m-30) REVERT: B 32 ASN cc_start: 0.8486 (m110) cc_final: 0.8133 (m-40) REVERT: C 22 GLU cc_start: 0.7633 (tp30) cc_final: 0.7335 (tp30) REVERT: C 63 ARG cc_start: 0.7592 (ttt180) cc_final: 0.5757 (tpp-160) REVERT: C 134 GLU cc_start: 0.7537 (tt0) cc_final: 0.7067 (mt-10) REVERT: E 16 MET cc_start: 0.8562 (mtm) cc_final: 0.8332 (mtt) REVERT: E 191 GLU cc_start: 0.7170 (tp30) cc_final: 0.6555 (tp30) REVERT: E 194 LYS cc_start: 0.7975 (tmtt) cc_final: 0.7391 (tppt) REVERT: E 199 PRO cc_start: 0.8719 (Cg_endo) cc_final: 0.8488 (Cg_exo) REVERT: E 243 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6723 (ttp-170) REVERT: E 244 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.6456 (mpm) REVERT: E 245 ASN cc_start: 0.8005 (OUTLIER) cc_final: 0.7524 (m110) REVERT: E 251 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: F 65 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: F 198 LYS cc_start: 0.8058 (tppp) cc_final: 0.7784 (ttmm) REVERT: G 52 ARG cc_start: 0.7953 (tpp80) cc_final: 0.7753 (tpp80) REVERT: G 64 MET cc_start: 0.8711 (mtp) cc_final: 0.8442 (mtp) REVERT: H 167 SER cc_start: 0.8288 (t) cc_final: 0.8006 (p) REVERT: I 29 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7242 (tp30) REVERT: I 53 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.6832 (tmtm) REVERT: I 93 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7649 (tt) REVERT: I 144 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7082 (mtm180) REVERT: J 87 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7785 (mm-30) REVERT: K 37 ARG cc_start: 0.7534 (mtt90) cc_final: 0.7045 (mtp85) REVERT: K 92 ARG cc_start: 0.5916 (tpt170) cc_final: 0.4581 (tmt170) REVERT: L 65 TYR cc_start: 0.8310 (m-80) cc_final: 0.7194 (m-80) REVERT: O 40 THR cc_start: 0.8472 (p) cc_final: 0.8148 (p) REVERT: P 131 TYR cc_start: 0.8599 (t80) cc_final: 0.8339 (t80) REVERT: R 52 ASP cc_start: 0.7875 (t0) cc_final: 0.7562 (t0) REVERT: R 67 LYS cc_start: 0.7976 (tptt) cc_final: 0.7187 (tttt) REVERT: R 97 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: U 39 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8043 (ttpt) REVERT: U 114 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.6822 (mtt90) REVERT: V 36 MET cc_start: 0.7871 (mtm) cc_final: 0.7602 (mpp) REVERT: W 131 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7102 (mtm180) REVERT: X 57 GLU cc_start: 0.7440 (tt0) cc_final: 0.6956 (pt0) REVERT: Y 78 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.7987 (mp) REVERT: Y 79 ASP cc_start: 0.7882 (m-30) cc_final: 0.7672 (m-30) REVERT: Z 112 LYS cc_start: 0.7765 (ttmm) cc_final: 0.7380 (tptp) REVERT: a 49 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7612 (mtpp) REVERT: a 57 TYR cc_start: 0.7725 (m-10) cc_final: 0.7370 (m-10) REVERT: a 80 LEU cc_start: 0.8754 (mt) cc_final: 0.8457 (mp) REVERT: b 51 SER cc_start: 0.8574 (t) cc_final: 0.8060 (m) REVERT: e 39 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7657 (mttp) REVERT: g 90 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6926 (mtt-85) REVERT: g 214 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7845 (tttp) REVERT: g 304 ARG cc_start: 0.7131 (mpt180) cc_final: 0.6718 (mpt180) outliers start: 195 outliers final: 95 residues processed: 878 average time/residue: 1.6714 time to fit residues: 1947.6743 Evaluate side-chains 843 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 729 time to evaluate : 4.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain E residue 240 GLN Chi-restraints excluded: chain E residue 243 ARG Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain E residue 245 ASN Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 163 LYS Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 40 CYS Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 87 ASP Chi-restraints excluded: chain T residue 132 VAL Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 39 LYS Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain V residue 43 SER Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 131 ARG Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 40 ASP Chi-restraints excluded: chain X residue 132 LEU Chi-restraints excluded: chain Y residue 12 GLU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Y residue 78 ILE Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 21 LYS Chi-restraints excluded: chain b residue 25 CYS Chi-restraints excluded: chain b residue 28 CYS Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 95 ASN Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain c residue 9 SER Chi-restraints excluded: chain c residue 60 CYS Chi-restraints excluded: chain d residue 35 SER Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 59 ILE Chi-restraints excluded: chain e residue 39 LYS Chi-restraints excluded: chain f residue 100 TYR Chi-restraints excluded: chain f residue 116 THR Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 33 SER Chi-restraints excluded: chain g residue 90 ARG Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 179 TRP Chi-restraints excluded: chain g residue 214 LYS Chi-restraints excluded: chain g residue 232 ILE Chi-restraints excluded: chain g residue 234 VAL Chi-restraints excluded: chain g residue 283 ILE Chi-restraints excluded: chain g residue 300 ASP Chi-restraints excluded: chain g residue 302 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 600 optimal weight: 8.9990 chunk 456 optimal weight: 10.0000 chunk 315 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 290 optimal weight: 4.9990 chunk 408 optimal weight: 0.9980 chunk 609 optimal weight: 10.0000 chunk 645 optimal weight: 5.9990 chunk 318 optimal weight: 4.9990 chunk 578 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 GLN A 228 GLN B 73 ASN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN F 122 HIS H 48 HIS ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 127 ASN J 64 ASN ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN M 72 ASN U 46 HIS U 113 GLN Y 43 ASN Y 51 ASN Z 61 GLN ** c 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 GLN g 301 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 86066 Z= 0.368 Angle : 0.944 24.399 126058 Z= 0.502 Chirality : 0.044 0.328 15721 Planarity : 0.010 0.137 8568 Dihedral : 24.868 179.851 36761 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.28 % Favored : 93.70 % Rotamer: Outliers : 5.75 % Allowed : 16.63 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.17 % Twisted Proline : 0.53 % Twisted General : 0.11 % 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: -1.79 (0.11), residues: 4779 helix: -1.20 (0.13), residues: 1464 sheet: -0.60 (0.17), residues: 817 loop : -1.32 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP g 179 HIS 0.009 0.001 HIS K 116 PHE 0.048 0.002 PHE P 105 TYR 0.028 0.002 TYR A 30 ARG 0.014 0.001 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 753 time to evaluate : 4.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6619 (mp0) REVERT: A 45 LYS cc_start: 0.8228 (ttmm) cc_final: 0.7795 (mtmm) REVERT: A 213 ARG cc_start: 0.7906 (ttm170) cc_final: 0.7421 (ttm170) REVERT: B 32 ASN cc_start: 0.8492 (m110) cc_final: 0.8158 (m-40) REVERT: C 22 GLU cc_start: 0.7663 (tp30) cc_final: 0.7276 (tp30) REVERT: C 44 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7540 (ttt-90) REVERT: E 171 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8629 (mmpt) REVERT: E 174 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7088 (tt0) REVERT: E 191 GLU cc_start: 0.7163 (tp30) cc_final: 0.6532 (tp30) REVERT: E 194 LYS cc_start: 0.8161 (tmtt) cc_final: 0.7496 (tppt) REVERT: E 243 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6741 (ttp-170) REVERT: E 251 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: F 65 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: F 128 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7319 (mpt180) REVERT: F 198 LYS cc_start: 0.8106 (tppp) cc_final: 0.7846 (ttmm) REVERT: G 52 ARG cc_start: 0.7979 (tpp80) cc_final: 0.7722 (tpp80) REVERT: G 64 MET cc_start: 0.8743 (mtp) cc_final: 0.8541 (mtp) REVERT: H 167 SER cc_start: 0.8271 (t) cc_final: 0.7982 (p) REVERT: I 53 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.6819 (tmtm) REVERT: I 93 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7673 (tt) REVERT: I 99 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: I 132 MET cc_start: 0.8204 (mtt) cc_final: 0.7935 (mtt) REVERT: I 144 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.6691 (mtm180) REVERT: I 146 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7128 (mtm-85) REVERT: J 43 LYS cc_start: 0.8428 (ttpp) cc_final: 0.7964 (ttpp) REVERT: K 37 ARG cc_start: 0.7542 (mtt90) cc_final: 0.7129 (mtp180) REVERT: K 92 ARG cc_start: 0.5723 (tpt170) cc_final: 0.4474 (tmt170) REVERT: L 55 MET cc_start: 0.8287 (mmm) cc_final: 0.8063 (mmm) REVERT: L 64 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7739 (ptpp) REVERT: L 65 TYR cc_start: 0.8331 (m-80) cc_final: 0.6925 (m-80) REVERT: M 89 HIS cc_start: 0.6678 (m-70) cc_final: 0.6476 (m90) REVERT: O 40 THR cc_start: 0.8397 (p) cc_final: 0.8130 (p) REVERT: O 89 LYS cc_start: 0.9049 (mtpp) cc_final: 0.8648 (mtpt) REVERT: P 25 LYS cc_start: 0.8475 (mtpt) cc_final: 0.8040 (mmtt) REVERT: P 66 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8248 (pp) REVERT: P 131 TYR cc_start: 0.8587 (t80) cc_final: 0.8348 (t80) REVERT: R 32 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8079 (ptm160) REVERT: R 52 ASP cc_start: 0.7828 (t0) cc_final: 0.7525 (t0) REVERT: R 67 LYS cc_start: 0.8005 (tptt) cc_final: 0.7233 (tttt) REVERT: R 97 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7432 (mt-10) REVERT: R 122 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7462 (ttm170) REVERT: U 39 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8023 (ttmt) REVERT: U 114 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.6695 (mtt90) REVERT: V 36 MET cc_start: 0.7764 (mtm) cc_final: 0.7505 (mpp) REVERT: V 63 ARG cc_start: 0.7071 (mtt-85) cc_final: 0.6810 (mtm110) REVERT: X 57 GLU cc_start: 0.7433 (tt0) cc_final: 0.7085 (pt0) REVERT: X 59 LYS cc_start: 0.7958 (mmmm) cc_final: 0.7297 (ptmt) REVERT: X 89 CYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8012 (p) REVERT: X 150 GLN cc_start: 0.8166 (pm20) cc_final: 0.7826 (pm20) REVERT: Y 30 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: Y 78 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8122 (mp) REVERT: Z 112 LYS cc_start: 0.7805 (ttmm) cc_final: 0.7361 (tptp) REVERT: a 48 ASP cc_start: 0.6744 (m-30) cc_final: 0.6495 (m-30) REVERT: a 49 LYS cc_start: 0.7985 (mtpp) cc_final: 0.7650 (mtpp) REVERT: a 57 TYR cc_start: 0.7882 (m-10) cc_final: 0.7232 (m-10) REVERT: a 80 LEU cc_start: 0.8756 (mt) cc_final: 0.8451 (mp) REVERT: b 51 SER cc_start: 0.8583 (t) cc_final: 0.8079 (m) REVERT: e 39 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7659 (mttp) REVERT: g 98 GLN cc_start: 0.7845 (mm110) cc_final: 0.7554 (mm-40) REVERT: g 100 GLN cc_start: 0.7876 (mp10) cc_final: 0.5704 (mp10) REVERT: g 304 ARG cc_start: 0.7127 (mpt180) cc_final: 0.6675 (mpt180) outliers start: 192 outliers final: 104 residues processed: 866 average time/residue: 1.6342 time to fit residues: 1888.7116 Evaluate side-chains 845 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 719 time to evaluate : 4.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 243 ARG Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain I residue 146 ARG Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 163 LYS Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 32 ARG Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 86 ASN Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 122 ARG Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 31 ARG Chi-restraints excluded: chain T residue 87 ASP Chi-restraints excluded: chain T residue 132 VAL Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain V residue 43 SER Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 40 ASP Chi-restraints excluded: chain X residue 89 CYS Chi-restraints excluded: chain X residue 132 LEU Chi-restraints excluded: chain Y residue 12 GLU Chi-restraints excluded: chain Y residue 30 GLU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Y residue 78 ILE Chi-restraints excluded: chain a residue 59 LEU Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 21 LYS Chi-restraints excluded: chain b residue 25 CYS Chi-restraints excluded: chain b residue 28 CYS Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 95 ASN Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain c residue 9 SER Chi-restraints excluded: chain c residue 34 MET Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 60 CYS Chi-restraints excluded: chain d residue 35 SER Chi-restraints excluded: chain d residue 38 ASN Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 59 ILE Chi-restraints excluded: chain e residue 39 LYS Chi-restraints excluded: chain f residue 100 TYR Chi-restraints excluded: chain f residue 116 THR Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 33 SER Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 179 TRP Chi-restraints excluded: chain g residue 301 ASN Chi-restraints excluded: chain g residue 302 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 537 optimal weight: 10.0000 chunk 366 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 480 optimal weight: 8.9990 chunk 266 optimal weight: 1.9990 chunk 550 optimal weight: 10.0000 chunk 446 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 329 optimal weight: 2.9990 chunk 579 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 GLN A 228 GLN B 73 ASN B 167 ASN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN G 219 ASN ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 ASN Y 43 ASN Y 51 ASN Z 61 GLN a 82 GLN ** c 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 301 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 86066 Z= 0.314 Angle : 0.914 23.717 126058 Z= 0.489 Chirality : 0.042 0.312 15721 Planarity : 0.009 0.136 8568 Dihedral : 24.781 179.824 36757 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.30 % Favored : 93.68 % Rotamer: Outliers : 5.35 % Allowed : 18.39 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.17 % Twisted Proline : 0.53 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.12), residues: 4779 helix: -0.86 (0.13), residues: 1460 sheet: -0.64 (0.17), residues: 834 loop : -1.26 (0.12), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP g 179 HIS 0.008 0.001 HIS K 116 PHE 0.040 0.002 PHE P 105 TYR 0.023 0.002 TYR A 30 ARG 0.009 0.001 ARG a 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 742 time to evaluate : 4.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8002 (ttpt) cc_final: 0.7684 (ptmt) REVERT: A 45 LYS cc_start: 0.8307 (ttmm) cc_final: 0.7814 (mtmm) REVERT: A 213 ARG cc_start: 0.7884 (ttm170) cc_final: 0.7652 (ttm170) REVERT: B 32 ASN cc_start: 0.8482 (m110) cc_final: 0.8179 (m-40) REVERT: B 169 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.6794 (mtp85) REVERT: C 22 GLU cc_start: 0.7749 (tp30) cc_final: 0.7325 (tp30) REVERT: E 171 LYS cc_start: 0.8851 (mmmm) cc_final: 0.8576 (mmpt) REVERT: E 174 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7403 (tp-100) REVERT: E 191 GLU cc_start: 0.7081 (tp30) cc_final: 0.6430 (tp30) REVERT: E 243 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6733 (ttp-170) REVERT: E 244 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.6425 (mpm) REVERT: E 251 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: F 198 LYS cc_start: 0.8062 (tppp) cc_final: 0.7803 (ttmm) REVERT: F 249 ARG cc_start: 0.8186 (mtp-110) cc_final: 0.7939 (mtp-110) REVERT: G 52 ARG cc_start: 0.7977 (tpp80) cc_final: 0.7726 (tpp80) REVERT: G 64 MET cc_start: 0.8759 (mtp) cc_final: 0.8510 (mtp) REVERT: H 45 ARG cc_start: 0.7352 (mtm110) cc_final: 0.7070 (mtm110) REVERT: H 84 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7668 (mm-30) REVERT: H 167 SER cc_start: 0.8262 (t) cc_final: 0.7983 (p) REVERT: I 53 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.6846 (tmtm) REVERT: I 93 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7647 (tt) REVERT: I 99 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: I 132 MET cc_start: 0.8151 (mtt) cc_final: 0.7897 (mtt) REVERT: I 144 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.6651 (mtm180) REVERT: J 43 LYS cc_start: 0.8421 (ttpp) cc_final: 0.7925 (ttpp) REVERT: K 37 ARG cc_start: 0.7660 (mtt90) cc_final: 0.7254 (mtp180) REVERT: L 65 TYR cc_start: 0.8347 (m-80) cc_final: 0.6925 (m-80) REVERT: O 40 THR cc_start: 0.8354 (p) cc_final: 0.8141 (p) REVERT: P 18 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7628 (ttp80) REVERT: P 66 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8207 (pp) REVERT: P 131 TYR cc_start: 0.8602 (t80) cc_final: 0.8327 (t80) REVERT: R 52 ASP cc_start: 0.7857 (t0) cc_final: 0.7564 (t0) REVERT: R 97 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: R 122 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7486 (ttm170) REVERT: S 17 LYS cc_start: 0.8082 (ttmm) cc_final: 0.7850 (ttmt) REVERT: U 39 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7992 (ttpp) REVERT: V 36 MET cc_start: 0.7748 (mtm) cc_final: 0.7543 (mpp) REVERT: V 63 ARG cc_start: 0.7160 (mtt-85) cc_final: 0.6954 (mtm110) REVERT: W 35 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7902 (mp) REVERT: X 33 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7688 (mtp85) REVERT: X 57 GLU cc_start: 0.7433 (tt0) cc_final: 0.7095 (pt0) REVERT: X 59 LYS cc_start: 0.7962 (mmmm) cc_final: 0.7291 (ptmt) REVERT: X 89 CYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7962 (p) REVERT: X 150 GLN cc_start: 0.8246 (pm20) cc_final: 0.7861 (pm20) REVERT: Y 30 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: Y 78 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8090 (mp) REVERT: Y 80 ARG cc_start: 0.8192 (mmt90) cc_final: 0.7974 (mmt-90) REVERT: Z 31 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7228 (pm20) REVERT: Z 112 LYS cc_start: 0.7765 (ttmm) cc_final: 0.7324 (tptp) REVERT: a 48 ASP cc_start: 0.6631 (m-30) cc_final: 0.6418 (m-30) REVERT: a 49 LYS cc_start: 0.8001 (mtpp) cc_final: 0.7560 (mtpp) REVERT: a 57 TYR cc_start: 0.7818 (m-10) cc_final: 0.7320 (m-10) REVERT: a 80 LEU cc_start: 0.8764 (mt) cc_final: 0.8464 (mp) REVERT: b 51 SER cc_start: 0.8577 (t) cc_final: 0.8072 (m) REVERT: e 39 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7683 (mttp) REVERT: g 28 LYS cc_start: 0.7949 (mmmt) cc_final: 0.7580 (mmmt) REVERT: g 109 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8581 (m-30) REVERT: g 304 ARG cc_start: 0.7094 (mpt180) cc_final: 0.6619 (mpt180) outliers start: 177 outliers final: 111 residues processed: 840 average time/residue: 1.6756 time to fit residues: 1879.5299 Evaluate side-chains 848 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 715 time to evaluate : 4.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 243 ARG Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 163 LYS Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain P residue 18 ARG Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 122 ARG Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 31 ARG Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 87 ASP Chi-restraints excluded: chain T residue 132 VAL Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 39 LYS Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain V residue 43 SER Chi-restraints excluded: chain W residue 35 LEU Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 128 MET Chi-restraints excluded: chain X residue 33 ARG Chi-restraints excluded: chain X residue 40 ASP Chi-restraints excluded: chain X residue 89 CYS Chi-restraints excluded: chain X residue 132 LEU Chi-restraints excluded: chain Y residue 12 GLU Chi-restraints excluded: chain Y residue 30 GLU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 78 ILE Chi-restraints excluded: chain Z residue 31 GLU Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain a residue 59 LEU Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain b residue 21 LYS Chi-restraints excluded: chain b residue 28 CYS Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 95 ASN Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain c residue 9 SER Chi-restraints excluded: chain c residue 34 MET Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 60 CYS Chi-restraints excluded: chain d residue 35 SER Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 59 ILE Chi-restraints excluded: chain e residue 39 LYS Chi-restraints excluded: chain f residue 100 TYR Chi-restraints excluded: chain f residue 116 THR Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 33 SER Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 179 TRP Chi-restraints excluded: chain g residue 189 THR Chi-restraints excluded: chain g residue 240 GLN Chi-restraints excluded: chain g residue 283 ILE Chi-restraints excluded: chain g residue 302 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 217 optimal weight: 9.9990 chunk 581 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 379 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 646 optimal weight: 50.0000 chunk 536 optimal weight: 10.0000 chunk 299 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 chunk 339 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN A 91 GLN A 228 GLN B 27 HIS B 73 ASN B 116 GLN B 167 ASN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN M 72 ASN M 89 HIS U 116 GLN Y 43 ASN Y 51 ASN Z 61 GLN a 82 GLN ** c 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 17 GLN ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 86066 Z= 0.171 Angle : 0.854 22.770 126058 Z= 0.463 Chirality : 0.037 0.284 15721 Planarity : 0.008 0.130 8568 Dihedral : 24.624 179.893 36757 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.37 % Favored : 94.61 % Rotamer: Outliers : 4.77 % Allowed : 19.75 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.17 % Twisted Proline : 0.53 % Twisted General : 0.09 % 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 (0.12), residues: 4779 helix: -0.34 (0.13), residues: 1458 sheet: -0.51 (0.18), residues: 827 loop : -1.14 (0.12), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP g 179 HIS 0.005 0.001 HIS H 27 PHE 0.028 0.001 PHE I 28 TYR 0.024 0.001 TYR I 4 ARG 0.009 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 776 time to evaluate : 4.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7754 (ptmt) REVERT: A 45 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7592 (mtmm) REVERT: A 192 ARG cc_start: 0.8382 (mmt90) cc_final: 0.8018 (mtt-85) REVERT: B 32 ASN cc_start: 0.8472 (m110) cc_final: 0.8207 (m-40) REVERT: C 22 GLU cc_start: 0.7645 (tp30) cc_final: 0.7302 (tp30) REVERT: C 84 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7409 (tm130) REVERT: C 86 TYR cc_start: 0.7269 (m-80) cc_final: 0.6861 (m-10) REVERT: C 159 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.8279 (t) REVERT: D 27 MET cc_start: 0.8397 (tpp) cc_final: 0.8181 (tpp) REVERT: E 171 LYS cc_start: 0.8874 (mmmm) cc_final: 0.8475 (mmpt) REVERT: E 174 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7226 (tp-100) REVERT: E 191 GLU cc_start: 0.6999 (tp30) cc_final: 0.6331 (tp30) REVERT: E 194 LYS cc_start: 0.8079 (tttt) cc_final: 0.7391 (tppt) REVERT: E 244 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.6461 (mpm) REVERT: F 128 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7268 (mpt180) REVERT: F 198 LYS cc_start: 0.7991 (tppp) cc_final: 0.7704 (ttmm) REVERT: G 52 ARG cc_start: 0.7916 (tpp80) cc_final: 0.7712 (tpp80) REVERT: G 64 MET cc_start: 0.8768 (mtp) cc_final: 0.8541 (mtp) REVERT: H 167 SER cc_start: 0.8249 (t) cc_final: 0.8031 (p) REVERT: I 56 ARG cc_start: 0.5500 (mmt180) cc_final: 0.5286 (mmp80) REVERT: I 93 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7543 (tt) REVERT: I 99 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: I 144 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6636 (mtm180) REVERT: J 43 LYS cc_start: 0.8349 (ttpp) cc_final: 0.7918 (ttpp) REVERT: J 114 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7226 (mt-10) REVERT: K 37 ARG cc_start: 0.7668 (mtt90) cc_final: 0.7228 (mtp85) REVERT: K 94 LYS cc_start: 0.8345 (mtmm) cc_final: 0.8117 (mtmt) REVERT: L 55 MET cc_start: 0.8361 (mmm) cc_final: 0.8030 (mmm) REVERT: L 64 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7738 (ptpp) REVERT: L 65 TYR cc_start: 0.8357 (m-80) cc_final: 0.7057 (m-80) REVERT: M 51 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8739 (t) REVERT: O 40 THR cc_start: 0.8176 (p) cc_final: 0.7943 (p) REVERT: O 89 LYS cc_start: 0.8948 (mtpp) cc_final: 0.8490 (mtpt) REVERT: P 1 MET cc_start: 0.5527 (ptp) cc_final: 0.5223 (ptp) REVERT: P 66 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8185 (pp) REVERT: P 131 TYR cc_start: 0.8589 (t80) cc_final: 0.8303 (t80) REVERT: R 67 LYS cc_start: 0.8011 (tptt) cc_final: 0.7256 (tttt) REVERT: R 133 ARG cc_start: 0.7913 (mtt180) cc_final: 0.7461 (mtt90) REVERT: T 87 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7614 (m-30) REVERT: U 39 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7924 (ttpt) REVERT: V 63 ARG cc_start: 0.7088 (mtt-85) cc_final: 0.6862 (mtm110) REVERT: V 67 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7485 (ttm170) REVERT: X 57 GLU cc_start: 0.7332 (tt0) cc_final: 0.7056 (pt0) REVERT: X 59 LYS cc_start: 0.7838 (mmmm) cc_final: 0.7395 (ptmt) REVERT: X 85 TYR cc_start: 0.8367 (t80) cc_final: 0.7946 (t80) REVERT: X 89 CYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7921 (p) REVERT: X 150 GLN cc_start: 0.8173 (pm20) cc_final: 0.7824 (pm20) REVERT: Y 30 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: Y 78 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.7997 (mp) REVERT: Y 80 ARG cc_start: 0.8156 (mmt90) cc_final: 0.7933 (mmt-90) REVERT: Z 112 LYS cc_start: 0.7646 (ttmm) cc_final: 0.7271 (tptp) REVERT: a 57 TYR cc_start: 0.7741 (m-10) cc_final: 0.7308 (m-10) REVERT: a 80 LEU cc_start: 0.8778 (mt) cc_final: 0.8473 (mp) REVERT: b 51 SER cc_start: 0.8627 (t) cc_final: 0.8128 (m) REVERT: e 39 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7659 (mttp) REVERT: g 28 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7796 (mmmt) REVERT: g 100 GLN cc_start: 0.7915 (mp10) cc_final: 0.7508 (mm110) REVERT: g 269 ILE cc_start: 0.8376 (pt) cc_final: 0.8157 (pt) REVERT: g 304 ARG cc_start: 0.7093 (mpt180) cc_final: 0.6708 (mpt180) outliers start: 155 outliers final: 74 residues processed: 868 average time/residue: 1.6448 time to fit residues: 1898.0322 Evaluate side-chains 828 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 737 time to evaluate : 4.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 163 LYS Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 87 ASP Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 39 LYS Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain V residue 43 SER Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain X residue 40 ASP Chi-restraints excluded: chain X residue 89 CYS Chi-restraints excluded: chain Y residue 30 GLU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 78 ILE Chi-restraints excluded: chain a residue 92 VAL Chi-restraints excluded: chain b residue 28 CYS Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 95 ASN Chi-restraints excluded: chain c residue 9 SER Chi-restraints excluded: chain c residue 34 MET Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 60 CYS Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 59 ILE Chi-restraints excluded: chain e residue 39 LYS Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 100 TYR Chi-restraints excluded: chain f residue 116 THR Chi-restraints excluded: chain g residue 33 SER Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 179 TRP Chi-restraints excluded: chain g residue 281 GLU Chi-restraints excluded: chain g residue 300 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 623 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 368 optimal weight: 7.9990 chunk 471 optimal weight: 7.9990 chunk 365 optimal weight: 0.8980 chunk 544 optimal weight: 10.0000 chunk 360 optimal weight: 8.9990 chunk 643 optimal weight: 7.9990 chunk 402 optimal weight: 7.9990 chunk 392 optimal weight: 8.9990 chunk 297 optimal weight: 9.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 ASN A 91 GLN A 228 GLN B 73 ASN B 116 GLN D 32 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN F 219 HIS ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 GLN J 64 ASN L 13 GLN M 72 ASN ** M 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 ASN U 113 GLN U 116 GLN Y 13 ASN Y 34 HIS Y 51 ASN Z 61 GLN a 82 GLN ** c 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 86066 Z= 0.496 Angle : 0.989 24.113 126058 Z= 0.519 Chirality : 0.048 0.351 15721 Planarity : 0.010 0.143 8568 Dihedral : 24.756 179.791 36757 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.79 % Favored : 93.19 % Rotamer: Outliers : 5.61 % Allowed : 19.70 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.17 % Twisted Proline : 0.53 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.12), residues: 4779 helix: -0.70 (0.13), residues: 1472 sheet: -0.61 (0.18), residues: 817 loop : -1.21 (0.12), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP g 179 HIS 0.011 0.002 HIS K 116 PHE 0.051 0.003 PHE P 105 TYR 0.028 0.003 TYR A 30 ARG 0.011 0.001 ARG V 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 720 time to evaluate : 4.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8426 (ttmm) cc_final: 0.7930 (mtmm) REVERT: A 197 ASP cc_start: 0.8229 (m-30) cc_final: 0.7918 (m-30) REVERT: A 218 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7792 (ttp-110) REVERT: B 25 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7716 (mtp85) REVERT: B 32 ASN cc_start: 0.8513 (m110) cc_final: 0.8216 (m-40) REVERT: C 22 GLU cc_start: 0.7769 (tp30) cc_final: 0.7371 (tp30) REVERT: E 171 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8591 (mmpt) REVERT: E 191 GLU cc_start: 0.7216 (tp30) cc_final: 0.6562 (tp30) REVERT: E 194 LYS cc_start: 0.8218 (tttt) cc_final: 0.7508 (tppt) REVERT: E 243 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6726 (ttp-170) REVERT: E 244 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6507 (mpm) REVERT: F 128 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7488 (mpt180) REVERT: F 198 LYS cc_start: 0.8168 (tppp) cc_final: 0.7817 (ttmm) REVERT: G 52 ARG cc_start: 0.8017 (tpp80) cc_final: 0.7733 (tpp80) REVERT: G 64 MET cc_start: 0.8784 (mtp) cc_final: 0.8578 (mtp) REVERT: H 167 SER cc_start: 0.8294 (t) cc_final: 0.7991 (p) REVERT: I 99 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: I 144 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7087 (mtm180) REVERT: J 3 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.7968 (ttp) REVERT: K 94 LYS cc_start: 0.8394 (mtmm) cc_final: 0.8166 (mtmt) REVERT: L 55 MET cc_start: 0.8312 (mmm) cc_final: 0.8062 (mmm) REVERT: L 64 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7701 (ptpp) REVERT: L 65 TYR cc_start: 0.8374 (m-80) cc_final: 0.6855 (m-80) REVERT: M 51 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8759 (m) REVERT: O 128 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8374 (mp) REVERT: P 66 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8268 (pp) REVERT: P 131 TYR cc_start: 0.8620 (t80) cc_final: 0.8370 (t80) REVERT: U 39 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8040 (ttpp) REVERT: V 63 ARG cc_start: 0.7142 (mtt-85) cc_final: 0.6895 (mtm110) REVERT: V 103 LYS cc_start: 0.7803 (tptm) cc_final: 0.7094 (ttmm) REVERT: W 35 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7891 (mp) REVERT: W 131 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7203 (mtm110) REVERT: X 57 GLU cc_start: 0.7454 (tt0) cc_final: 0.7079 (pt0) REVERT: X 59 LYS cc_start: 0.7982 (mmmm) cc_final: 0.7333 (ptmt) REVERT: X 89 CYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8048 (p) REVERT: X 150 GLN cc_start: 0.8317 (pm20) cc_final: 0.7920 (pm20) REVERT: Y 30 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: Y 78 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8088 (mp) REVERT: Z 112 LYS cc_start: 0.7782 (ttmm) cc_final: 0.7324 (tptp) REVERT: a 57 TYR cc_start: 0.7850 (m-10) cc_final: 0.7360 (m-10) REVERT: b 51 SER cc_start: 0.8597 (t) cc_final: 0.8069 (m) REVERT: b 100 TYR cc_start: 0.8670 (m-80) cc_final: 0.8448 (m-80) REVERT: e 39 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7663 (mttp) REVERT: e 64 LYS cc_start: 0.8526 (mtpt) cc_final: 0.8114 (mtmt) REVERT: g 28 LYS cc_start: 0.8062 (mmmt) cc_final: 0.7781 (mmmt) REVERT: g 100 GLN cc_start: 0.7894 (mp10) cc_final: 0.7475 (mm110) REVERT: g 109 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8597 (m-30) REVERT: g 269 ILE cc_start: 0.8437 (pt) cc_final: 0.8204 (pt) REVERT: g 304 ARG cc_start: 0.7144 (mpt180) cc_final: 0.6696 (mpt180) outliers start: 187 outliers final: 112 residues processed: 825 average time/residue: 1.6197 time to fit residues: 1783.2228 Evaluate side-chains 838 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 706 time to evaluate : 4.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 243 ARG Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 163 LYS Chi-restraints excluded: chain J residue 3 MET Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 86 ASN Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 87 ASP Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 39 LYS Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 87 ARG Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain U residue 159 SER Chi-restraints excluded: chain V residue 43 SER Chi-restraints excluded: chain W residue 35 LEU Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 128 MET Chi-restraints excluded: chain W residue 131 ARG Chi-restraints excluded: chain X residue 40 ASP Chi-restraints excluded: chain X residue 89 CYS Chi-restraints excluded: chain X residue 132 LEU Chi-restraints excluded: chain Y residue 30 GLU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 78 ILE Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 92 VAL Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 25 CYS Chi-restraints excluded: chain b residue 28 CYS Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 95 ASN Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain c residue 9 SER Chi-restraints excluded: chain c residue 34 MET Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 60 CYS Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 59 ILE Chi-restraints excluded: chain e residue 39 LYS Chi-restraints excluded: chain f residue 100 TYR Chi-restraints excluded: chain f residue 116 THR Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 33 SER Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain g residue 121 LEU Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 179 TRP Chi-restraints excluded: chain g residue 281 GLU Chi-restraints excluded: chain g residue 300 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 398 optimal weight: 1.9990 chunk 257 optimal weight: 7.9990 chunk 384 optimal weight: 5.9990 chunk 193 optimal weight: 0.2980 chunk 126 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 409 optimal weight: 1.9990 chunk 438 optimal weight: 3.9990 chunk 318 optimal weight: 0.3980 chunk 60 optimal weight: 10.0000 chunk 506 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 GLN A 228 GLN B 73 ASN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN L 13 GLN M 72 ASN ** M 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 116 GLN V 107 GLN Y 51 ASN Z 61 GLN a 82 GLN ** c 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 86066 Z= 0.160 Angle : 0.857 22.717 126058 Z= 0.464 Chirality : 0.037 0.289 15721 Planarity : 0.008 0.129 8568 Dihedral : 24.563 179.455 36757 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.31 % Favored : 94.67 % Rotamer: Outliers : 3.91 % Allowed : 21.88 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.17 % Twisted Proline : 0.53 % Twisted General : 0.09 % 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: -1.10 (0.12), residues: 4779 helix: -0.19 (0.14), residues: 1466 sheet: -0.51 (0.18), residues: 824 loop : -1.08 (0.12), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP g 179 HIS 0.005 0.001 HIS E 33 PHE 0.032 0.001 PHE I 28 TYR 0.019 0.001 TYR N 102 ARG 0.009 0.000 ARG a 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 748 time to evaluate : 4.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLU cc_start: 0.7346 (mp0) cc_final: 0.7140 (mt-10) REVERT: A 40 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7652 (ptmt) REVERT: A 45 LYS cc_start: 0.8223 (ttmm) cc_final: 0.7691 (mtmm) REVERT: A 192 ARG cc_start: 0.8389 (mmt90) cc_final: 0.8020 (mtt-85) REVERT: A 213 ARG cc_start: 0.7628 (ttm170) cc_final: 0.7314 (ttm170) REVERT: B 32 ASN cc_start: 0.8449 (m110) cc_final: 0.8188 (m-40) REVERT: C 22 GLU cc_start: 0.7650 (tp30) cc_final: 0.7323 (tp30) REVERT: C 86 TYR cc_start: 0.7263 (m-80) cc_final: 0.6888 (m-10) REVERT: D 27 MET cc_start: 0.8403 (tpp) cc_final: 0.8083 (tpp) REVERT: E 171 LYS cc_start: 0.8870 (mmmm) cc_final: 0.8630 (mmpt) REVERT: E 174 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7298 (tp-100) REVERT: E 191 GLU cc_start: 0.7029 (tp30) cc_final: 0.6303 (tp30) REVERT: E 194 LYS cc_start: 0.8096 (tttt) cc_final: 0.7448 (tppt) REVERT: E 243 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6703 (ttp-170) REVERT: E 244 MET cc_start: 0.6691 (OUTLIER) cc_final: 0.6445 (mpm) REVERT: F 128 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7266 (mpt180) REVERT: F 198 LYS cc_start: 0.8015 (tppp) cc_final: 0.7685 (ttmm) REVERT: G 52 ARG cc_start: 0.7956 (tpp80) cc_final: 0.7732 (tpp80) REVERT: G 64 MET cc_start: 0.8772 (mtp) cc_final: 0.8512 (mtp) REVERT: H 167 SER cc_start: 0.8254 (t) cc_final: 0.8029 (p) REVERT: I 99 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: I 144 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6596 (mtm180) REVERT: J 43 LYS cc_start: 0.8364 (ttpp) cc_final: 0.7887 (ttpp) REVERT: K 37 ARG cc_start: 0.7509 (mtt180) cc_final: 0.7046 (mtp85) REVERT: L 55 MET cc_start: 0.8242 (mmm) cc_final: 0.7946 (mmm) REVERT: L 65 TYR cc_start: 0.8376 (m-80) cc_final: 0.7039 (m-80) REVERT: O 89 LYS cc_start: 0.8935 (mtpp) cc_final: 0.8493 (mtpt) REVERT: P 66 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8195 (mt) REVERT: P 131 TYR cc_start: 0.8552 (t80) cc_final: 0.8308 (t80) REVERT: R 67 LYS cc_start: 0.7952 (tptt) cc_final: 0.7235 (tttt) REVERT: R 133 ARG cc_start: 0.7855 (mtt180) cc_final: 0.7428 (mtt90) REVERT: T 3 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7279 (tpm-80) REVERT: T 87 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7583 (m-30) REVERT: T 109 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7132 (ptm160) REVERT: U 39 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7945 (ttpt) REVERT: V 63 ARG cc_start: 0.7038 (mtt-85) cc_final: 0.6793 (mtm110) REVERT: V 103 LYS cc_start: 0.7812 (tptm) cc_final: 0.7021 (ttmm) REVERT: W 35 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7931 (mp) REVERT: X 57 GLU cc_start: 0.7351 (tt0) cc_final: 0.7075 (pt0) REVERT: X 59 LYS cc_start: 0.7785 (mmmm) cc_final: 0.7417 (ptmt) REVERT: X 85 TYR cc_start: 0.8351 (t80) cc_final: 0.7940 (t80) REVERT: X 89 CYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8017 (p) REVERT: X 150 GLN cc_start: 0.8254 (pm20) cc_final: 0.7785 (pm20) REVERT: Y 78 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8021 (mp) REVERT: Z 112 LYS cc_start: 0.7692 (ttmm) cc_final: 0.7306 (tptp) REVERT: a 50 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.7989 (tp) REVERT: a 57 TYR cc_start: 0.7638 (m-10) cc_final: 0.7282 (m-10) REVERT: b 51 SER cc_start: 0.8626 (t) cc_final: 0.8126 (m) REVERT: d 47 MET cc_start: 0.7083 (ttm) cc_final: 0.6881 (ttt) REVERT: e 39 LYS cc_start: 0.8064 (mptt) cc_final: 0.7672 (mttp) REVERT: g 28 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7819 (mmmt) REVERT: g 100 GLN cc_start: 0.7860 (mp10) cc_final: 0.7546 (mm110) REVERT: g 231 LYS cc_start: 0.7482 (ptmm) cc_final: 0.7189 (tmmt) REVERT: g 269 ILE cc_start: 0.8351 (pt) cc_final: 0.8118 (pt) REVERT: g 304 ARG cc_start: 0.7083 (mpt180) cc_final: 0.6660 (mpt180) outliers start: 122 outliers final: 75 residues processed: 825 average time/residue: 1.6358 time to fit residues: 1809.9696 Evaluate side-chains 809 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 719 time to evaluate : 4.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 243 ARG Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 163 LYS Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 86 ASN Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 87 ASP Chi-restraints excluded: chain T residue 109 ARG Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 39 LYS Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 87 ARG Chi-restraints excluded: chain V residue 43 SER Chi-restraints excluded: chain W residue 35 LEU Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain X residue 40 ASP Chi-restraints excluded: chain X residue 89 CYS Chi-restraints excluded: chain Y residue 44 VAL Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 78 ILE Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain a residue 92 VAL Chi-restraints excluded: chain b residue 28 CYS Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 9 SER Chi-restraints excluded: chain c residue 34 MET Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 60 CYS Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 59 ILE Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 100 TYR Chi-restraints excluded: chain f residue 116 THR Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 33 SER Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 179 TRP Chi-restraints excluded: chain g residue 302 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 585 optimal weight: 9.9990 chunk 616 optimal weight: 10.0000 chunk 562 optimal weight: 8.9990 chunk 599 optimal weight: 9.9990 chunk 361 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 471 optimal weight: 7.9990 chunk 184 optimal weight: 0.5980 chunk 542 optimal weight: 10.0000 chunk 567 optimal weight: 8.9990 chunk 597 optimal weight: 7.9990 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN A 91 GLN A 228 GLN B 73 ASN C 84 GLN D 129 GLN ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 GLN J 64 ASN L 13 GLN M 72 ASN ** M 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN U 113 GLN U 116 GLN ** Y 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 ASN Z 61 GLN a 82 GLN ** c 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 86066 Z= 0.485 Angle : 0.983 23.866 126058 Z= 0.517 Chirality : 0.048 0.349 15721 Planarity : 0.010 0.142 8568 Dihedral : 24.697 179.740 36756 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.98 % Favored : 92.98 % Rotamer: Outliers : 4.56 % Allowed : 21.14 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.17 % Twisted Proline : 0.53 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.12), residues: 4779 helix: -0.59 (0.13), residues: 1476 sheet: -0.62 (0.18), residues: 818 loop : -1.18 (0.12), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP g 179 HIS 0.011 0.002 HIS K 116 PHE 0.049 0.003 PHE P 105 TYR 0.028 0.003 TYR A 30 ARG 0.010 0.001 ARG a 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 720 time to evaluate : 4.742 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8389 (ttmm) cc_final: 0.7866 (mtmm) REVERT: A 85 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8426 (pmtt) REVERT: A 197 ASP cc_start: 0.8230 (m-30) cc_final: 0.7917 (m-30) REVERT: B 32 ASN cc_start: 0.8637 (m110) cc_final: 0.8359 (m-40) REVERT: C 22 GLU cc_start: 0.7781 (tp30) cc_final: 0.7387 (tp30) REVERT: C 84 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7463 (tm130) REVERT: C 86 TYR cc_start: 0.7357 (m-80) cc_final: 0.7060 (m-10) REVERT: E 171 LYS cc_start: 0.8864 (mmmm) cc_final: 0.8605 (mmpt) REVERT: E 191 GLU cc_start: 0.7176 (tp30) cc_final: 0.6519 (tp30) REVERT: E 194 LYS cc_start: 0.8220 (tttt) cc_final: 0.7516 (tppt) REVERT: E 243 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6732 (ttp-170) REVERT: E 244 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6503 (mpm) REVERT: F 128 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7407 (mpt180) REVERT: F 198 LYS cc_start: 0.8174 (tppp) cc_final: 0.7793 (ttmm) REVERT: G 14 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7601 (mmmt) REVERT: G 52 ARG cc_start: 0.8019 (tpp80) cc_final: 0.7730 (tpp80) REVERT: H 167 SER cc_start: 0.8296 (t) cc_final: 0.7994 (p) REVERT: I 99 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: I 144 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7082 (mtm180) REVERT: J 43 LYS cc_start: 0.8386 (ttpp) cc_final: 0.7706 (ttpp) REVERT: K 37 ARG cc_start: 0.7610 (mtt180) cc_final: 0.7111 (mtp180) REVERT: L 55 MET cc_start: 0.8287 (mmm) cc_final: 0.8022 (mmm) REVERT: L 64 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7689 (ptpp) REVERT: L 65 TYR cc_start: 0.8382 (m-80) cc_final: 0.6899 (m-80) REVERT: O 89 LYS cc_start: 0.9043 (mtpp) cc_final: 0.8612 (mtpt) REVERT: P 66 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8271 (pp) REVERT: P 131 TYR cc_start: 0.8609 (t80) cc_final: 0.8405 (t80) REVERT: S 39 VAL cc_start: 0.8724 (t) cc_final: 0.8499 (p) REVERT: T 3 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7501 (tpm-80) REVERT: U 39 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7965 (ttpp) REVERT: V 103 LYS cc_start: 0.7922 (tptm) cc_final: 0.7101 (ttmm) REVERT: W 35 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7919 (mp) REVERT: X 57 GLU cc_start: 0.7447 (tt0) cc_final: 0.7076 (pt0) REVERT: X 59 LYS cc_start: 0.7982 (mmmm) cc_final: 0.7347 (ptmt) REVERT: X 89 CYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8015 (p) REVERT: X 150 GLN cc_start: 0.8353 (pm20) cc_final: 0.7937 (pm20) REVERT: Y 30 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: Y 78 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8044 (mp) REVERT: Z 112 LYS cc_start: 0.7782 (ttmm) cc_final: 0.7326 (tptp) REVERT: a 49 LYS cc_start: 0.7797 (mtpp) cc_final: 0.7529 (mtpp) REVERT: a 57 TYR cc_start: 0.7904 (m-10) cc_final: 0.7446 (m-10) REVERT: b 51 SER cc_start: 0.8592 (t) cc_final: 0.8064 (m) REVERT: b 100 TYR cc_start: 0.8707 (m-80) cc_final: 0.8504 (m-80) REVERT: e 39 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7681 (mttp) REVERT: e 64 LYS cc_start: 0.8507 (mtpt) cc_final: 0.8082 (mtmt) REVERT: g 28 LYS cc_start: 0.8101 (mmmt) cc_final: 0.7834 (mmmt) REVERT: g 100 GLN cc_start: 0.7860 (mp10) cc_final: 0.7499 (mm110) REVERT: g 269 ILE cc_start: 0.8429 (pt) cc_final: 0.8164 (pt) outliers start: 147 outliers final: 105 residues processed: 801 average time/residue: 1.6551 time to fit residues: 1767.4489 Evaluate side-chains 826 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 705 time to evaluate : 4.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 243 ARG Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 163 LYS Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 86 ASN Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 87 ASP Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 39 LYS Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain U residue 122 LEU Chi-restraints excluded: chain U residue 159 SER Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 43 SER Chi-restraints excluded: chain W residue 35 LEU Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain X residue 40 ASP Chi-restraints excluded: chain X residue 89 CYS Chi-restraints excluded: chain X residue 132 LEU Chi-restraints excluded: chain Y residue 30 GLU Chi-restraints excluded: chain Y residue 44 VAL Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 78 ILE Chi-restraints excluded: chain a residue 92 VAL Chi-restraints excluded: chain a residue 99 ARG Chi-restraints excluded: chain b residue 25 CYS Chi-restraints excluded: chain b residue 28 CYS Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain c residue 9 SER Chi-restraints excluded: chain c residue 34 MET Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 60 CYS Chi-restraints excluded: chain d residue 35 SER Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 59 ILE Chi-restraints excluded: chain e residue 39 LYS Chi-restraints excluded: chain f residue 100 TYR Chi-restraints excluded: chain f residue 116 THR Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 33 SER Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 179 TRP Chi-restraints excluded: chain g residue 232 ILE Chi-restraints excluded: chain g residue 240 GLN Chi-restraints excluded: chain g residue 281 GLU Chi-restraints excluded: chain g residue 302 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 393 optimal weight: 3.9990 chunk 634 optimal weight: 7.9990 chunk 387 optimal weight: 2.9990 chunk 300 optimal weight: 8.9990 chunk 441 optimal weight: 8.9990 chunk 665 optimal weight: 40.0000 chunk 612 optimal weight: 10.0000 chunk 529 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 409 optimal weight: 5.9990 chunk 324 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN A 91 GLN A 228 GLN ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN L 13 GLN M 72 ASN ** M 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 ASN Z 61 GLN a 82 GLN ** c 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 86066 Z= 0.261 Angle : 0.892 23.176 126058 Z= 0.479 Chirality : 0.040 0.307 15721 Planarity : 0.009 0.134 8568 Dihedral : 24.641 179.909 36756 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.05 % Favored : 93.93 % Rotamer: Outliers : 3.99 % Allowed : 22.01 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.17 % Twisted Proline : 0.53 % Twisted General : 0.11 % 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: -1.25 (0.12), residues: 4779 helix: -0.37 (0.13), residues: 1470 sheet: -0.62 (0.18), residues: 830 loop : -1.13 (0.12), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP g 179 HIS 0.005 0.001 HIS K 116 PHE 0.033 0.002 PHE I 28 TYR 0.019 0.002 TYR N 102 ARG 0.010 0.001 ARG a 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 720 time to evaluate : 4.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLU cc_start: 0.7651 (mp0) cc_final: 0.7424 (mt-10) REVERT: A 45 LYS cc_start: 0.8279 (ttmm) cc_final: 0.7746 (mtmm) REVERT: A 85 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8353 (pmtt) REVERT: A 192 ARG cc_start: 0.8416 (mmt90) cc_final: 0.8027 (mtt-85) REVERT: B 32 ASN cc_start: 0.8600 (m110) cc_final: 0.8319 (m-40) REVERT: C 22 GLU cc_start: 0.7731 (tp30) cc_final: 0.7320 (tp30) REVERT: C 84 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7405 (tm130) REVERT: C 86 TYR cc_start: 0.7329 (m-80) cc_final: 0.6890 (m-10) REVERT: E 171 LYS cc_start: 0.8884 (mmmm) cc_final: 0.8641 (mmpt) REVERT: E 191 GLU cc_start: 0.7091 (tp30) cc_final: 0.6383 (tp30) REVERT: E 194 LYS cc_start: 0.8167 (tttt) cc_final: 0.7489 (tppt) REVERT: E 243 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6712 (ttp-170) REVERT: E 244 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.6444 (mpm) REVERT: E 251 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: F 128 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7331 (mpt180) REVERT: F 198 LYS cc_start: 0.8103 (tppp) cc_final: 0.7735 (ttmm) REVERT: G 14 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7939 (mptp) REVERT: G 52 ARG cc_start: 0.7973 (tpp80) cc_final: 0.7692 (tpp80) REVERT: H 167 SER cc_start: 0.8264 (t) cc_final: 0.7984 (p) REVERT: I 99 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: I 132 MET cc_start: 0.8102 (mtt) cc_final: 0.7886 (mtt) REVERT: I 144 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.6635 (mtm180) REVERT: J 43 LYS cc_start: 0.8343 (ttpp) cc_final: 0.7967 (ttpp) REVERT: K 37 ARG cc_start: 0.7518 (mtt180) cc_final: 0.7030 (mtp180) REVERT: L 64 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7703 (ptpp) REVERT: L 65 TYR cc_start: 0.8382 (m-80) cc_final: 0.7000 (m-80) REVERT: O 89 LYS cc_start: 0.9027 (mtpp) cc_final: 0.8583 (mtpt) REVERT: P 66 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8228 (pp) REVERT: P 131 TYR cc_start: 0.8562 (t80) cc_final: 0.8302 (t80) REVERT: T 3 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7316 (tpm-80) REVERT: U 39 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7955 (ttpp) REVERT: V 103 LYS cc_start: 0.7964 (tptm) cc_final: 0.7186 (ttmm) REVERT: W 35 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7919 (mp) REVERT: X 57 GLU cc_start: 0.7405 (tt0) cc_final: 0.7070 (pt0) REVERT: X 59 LYS cc_start: 0.7916 (mmmm) cc_final: 0.7340 (ptmt) REVERT: X 85 TYR cc_start: 0.8393 (t80) cc_final: 0.7987 (t80) REVERT: X 89 CYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7973 (p) REVERT: X 150 GLN cc_start: 0.8249 (pm20) cc_final: 0.7778 (pm20) REVERT: Y 30 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: Y 78 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8004 (mp) REVERT: Z 112 LYS cc_start: 0.7698 (ttmm) cc_final: 0.7301 (tptp) REVERT: a 49 LYS cc_start: 0.7889 (mtpp) cc_final: 0.7627 (mtpp) REVERT: a 57 TYR cc_start: 0.7758 (m-10) cc_final: 0.7344 (m-10) REVERT: b 51 SER cc_start: 0.8568 (t) cc_final: 0.8064 (m) REVERT: d 43 ARG cc_start: 0.8089 (tpp80) cc_final: 0.7885 (tpp80) REVERT: e 39 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7701 (mttp) REVERT: e 64 LYS cc_start: 0.8499 (mtpt) cc_final: 0.8098 (mtmt) REVERT: g 28 LYS cc_start: 0.8067 (mmmt) cc_final: 0.7791 (mmmt) REVERT: g 100 GLN cc_start: 0.7853 (mp10) cc_final: 0.7516 (mm110) REVERT: g 269 ILE cc_start: 0.8373 (pt) cc_final: 0.8166 (pt) outliers start: 125 outliers final: 97 residues processed: 792 average time/residue: 1.6394 time to fit residues: 1728.2042 Evaluate side-chains 825 residues out of total 4078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 711 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 243 ARG Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 163 LYS Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 86 ASN Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 69 ARG Chi-restraints excluded: chain T residue 87 ASP Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 39 LYS Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 43 SER Chi-restraints excluded: chain W residue 35 LEU Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain X residue 40 ASP Chi-restraints excluded: chain X residue 89 CYS Chi-restraints excluded: chain X residue 132 LEU Chi-restraints excluded: chain Y residue 30 GLU Chi-restraints excluded: chain Y residue 44 VAL Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 78 ILE Chi-restraints excluded: chain a residue 92 VAL Chi-restraints excluded: chain a residue 99 ARG Chi-restraints excluded: chain b residue 28 CYS Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 95 ASN Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain c residue 9 SER Chi-restraints excluded: chain c residue 34 MET Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 60 CYS Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 59 ILE Chi-restraints excluded: chain e residue 39 LYS Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 100 TYR Chi-restraints excluded: chain f residue 116 THR Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 33 SER Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 179 TRP Chi-restraints excluded: chain g residue 240 GLN Chi-restraints excluded: chain g residue 281 GLU Chi-restraints excluded: chain g residue 302 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 420 optimal weight: 0.0470 chunk 564 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 488 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 530 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 545 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 GLN A 228 GLN B 73 ASN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN E 240 GLN ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN L 13 GLN M 72 ASN ** M 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 107 GLN Y 51 ASN Z 61 GLN a 82 GLN ** c 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.118290 restraints weight = 227425.300| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.89 r_work: 0.3182 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 86066 Z= 0.276 Angle : 0.891 23.289 126058 Z= 0.478 Chirality : 0.040 0.306 15721 Planarity : 0.009 0.134 8568 Dihedral : 24.588 179.468 36756 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.64 % Favored : 93.34 % Rotamer: Outliers : 4.20 % Allowed : 21.96 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.17 % Twisted Proline : 0.53 % Twisted General : 0.11 % 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 (0.12), residues: 4779 helix: -0.32 (0.13), residues: 1476 sheet: -0.63 (0.17), residues: 837 loop : -1.11 (0.12), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP g 179 HIS 0.006 0.001 HIS K 116 PHE 0.036 0.002 PHE I 28 TYR 0.020 0.002 TYR C 124 ARG 0.010 0.001 ARG a 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27707.46 seconds wall clock time: 482 minutes 30.63 seconds (28950.63 seconds total)