Starting phenix.real_space_refine on Sun Feb 25 03:42:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r70_4738/02_2024/6r70_4738.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r70_4738/02_2024/6r70_4738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r70_4738/02_2024/6r70_4738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r70_4738/02_2024/6r70_4738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r70_4738/02_2024/6r70_4738.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r70_4738/02_2024/6r70_4738.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 301 5.16 5 C 30722 2.51 5 N 8328 2.21 5 O 9230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M ASP 73": "OD1" <-> "OD2" Residue "M ARG 100": "NH1" <-> "NH2" Residue "M GLU 119": "OE1" <-> "OE2" Residue "M TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 126": "OD1" <-> "OD2" Residue "M GLU 164": "OE1" <-> "OE2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ASP 180": "OD1" <-> "OD2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "C ASP 4": "OD1" <-> "OD2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C ASP 67": "OD1" <-> "OD2" Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C ASP 214": "OD1" <-> "OD2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D ASP 71": "OD1" <-> "OD2" Residue "D ASP 90": "OD1" <-> "OD2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ASP 127": "OD1" <-> "OD2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "E ASP 7": "OD1" <-> "OD2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ASP 139": "OD1" <-> "OD2" Residue "E ASP 204": "OD1" <-> "OD2" Residue "E ASP 228": "OD1" <-> "OD2" Residue "F ASP 8": "OD1" <-> "OD2" Residue "F ASP 17": "OD1" <-> "OD2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 177": "OE1" <-> "OE2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G GLU 108": "OE1" <-> "OE2" Residue "G ASP 188": "OD1" <-> "OD2" Residue "G GLU 223": "OE1" <-> "OE2" Residue "G ASP 236": "OD1" <-> "OD2" Residue "G GLU 244": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 140": "OD1" <-> "OD2" Residue "H ARG 143": "NH1" <-> "NH2" Residue "H ASP 166": "OD1" <-> "OD2" Residue "I ARG 25": "NH1" <-> "NH2" Residue "I ASP 37": "OD1" <-> "OD2" Residue "I ARG 69": "NH1" <-> "NH2" Residue "I ARG 79": "NH1" <-> "NH2" Residue "I ASP 134": "OD1" <-> "OD2" Residue "I GLU 154": "OE1" <-> "OE2" Residue "I ASP 192": "OD1" <-> "OD2" Residue "J GLU 2": "OE1" <-> "OE2" Residue "J ASP 33": "OD1" <-> "OD2" Residue "J TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 86": "NH1" <-> "NH2" Residue "J PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 144": "OD1" <-> "OD2" Residue "J ARG 153": "NH1" <-> "NH2" Residue "K PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 17": "OD1" <-> "OD2" Residue "K ASP 51": "OD1" <-> "OD2" Residue "K GLU 72": "OE1" <-> "OE2" Residue "K GLU 117": "OE1" <-> "OE2" Residue "K ASP 140": "OD1" <-> "OD2" Residue "K ASP 146": "OD1" <-> "OD2" Residue "K ARG 186": "NH1" <-> "NH2" Residue "K ASP 190": "OD1" <-> "OD2" Residue "L ASP 26": "OD1" <-> "OD2" Residue "L GLU 31": "OE1" <-> "OE2" Residue "L GLU 69": "OE1" <-> "OE2" Residue "L TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 99": "NH1" <-> "NH2" Residue "L ASP 125": "OD1" <-> "OD2" Residue "L GLU 162": "OE1" <-> "OE2" Residue "L ARG 173": "NH1" <-> "NH2" Residue "N ASP 32": "OD1" <-> "OD2" Residue "N GLU 145": "OE1" <-> "OE2" Residue "O TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 184": "OE1" <-> "OE2" Residue "O GLU 204": "OE1" <-> "OE2" Residue "P GLU 26": "OE1" <-> "OE2" Residue "P GLU 70": "OE1" <-> "OE2" Residue "P ASP 178": "OD1" <-> "OD2" Residue "P GLU 183": "OE1" <-> "OE2" Residue "P ASP 202": "OD1" <-> "OD2" Residue "P ARG 226": "NH1" <-> "NH2" Residue "P GLU 234": "OE1" <-> "OE2" Residue "Q ASP 13": "OD1" <-> "OD2" Residue "Q ASP 39": "OD1" <-> "OD2" Residue "Q ASP 67": "OD1" <-> "OD2" Residue "Q PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "Q PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 178": "OD1" <-> "OD2" Residue "Q ASP 185": "OD1" <-> "OD2" Residue "Q GLU 231": "OE1" <-> "OE2" Residue "Q GLU 238": "OE1" <-> "OE2" Residue "R GLU 69": "OE1" <-> "OE2" Residue "R ASP 71": "OD1" <-> "OD2" Residue "R ASP 90": "OD1" <-> "OD2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "R PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 232": "OE1" <-> "OE2" Residue "R GLU 235": "OE1" <-> "OE2" Residue "R GLU 236": "OE1" <-> "OE2" Residue "R ASP 240": "OD1" <-> "OD2" Residue "S PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 18": "NH1" <-> "NH2" Residue "S GLU 55": "OE1" <-> "OE2" Residue "S ARG 101": "NH1" <-> "NH2" Residue "S ASP 139": "OD1" <-> "OD2" Residue "S GLU 181": "OE1" <-> "OE2" Residue "S GLU 237": "OE1" <-> "OE2" Residue "S ARG 239": "NH1" <-> "NH2" Residue "T ASP 89": "OD1" <-> "OD2" Residue "T GLU 93": "OE1" <-> "OE2" Residue "T PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 144": "OD1" <-> "OD2" Residue "T ARG 169": "NH1" <-> "NH2" Residue "T GLU 218": "OE1" <-> "OE2" Residue "T ASP 230": "OD1" <-> "OD2" Residue "U ASP 58": "OD1" <-> "OD2" Residue "U GLU 74": "OE1" <-> "OE2" Residue "U GLU 214": "OE1" <-> "OE2" Residue "U GLU 223": "OE1" <-> "OE2" Residue "U GLU 232": "OE1" <-> "OE2" Residue "U ASP 236": "OD1" <-> "OD2" Residue "V TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 140": "OD1" <-> "OD2" Residue "V ASP 166": "OD1" <-> "OD2" Residue "V ARG 198": "NH1" <-> "NH2" Residue "V GLU 220": "OE1" <-> "OE2" Residue "W ASP 37": "OD1" <-> "OD2" Residue "W ARG 79": "NH1" <-> "NH2" Residue "W ASP 133": "OD1" <-> "OD2" Residue "W ASP 134": "OD1" <-> "OD2" Residue "W GLU 143": "OE1" <-> "OE2" Residue "W GLU 154": "OE1" <-> "OE2" Residue "W ASP 158": "OD1" <-> "OD2" Residue "W ASP 192": "OD1" <-> "OD2" Residue "X GLU 2": "OE1" <-> "OE2" Residue "X ASP 33": "OD1" <-> "OD2" Residue "X TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 74": "OE1" <-> "OE2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ASP 90": "OD1" <-> "OD2" Residue "X GLU 111": "OE1" <-> "OE2" Residue "X ARG 153": "NH1" <-> "NH2" Residue "X GLU 166": "OE1" <-> "OE2" Residue "Y ASP 17": "OD1" <-> "OD2" Residue "Y GLU 36": "OE1" <-> "OE2" Residue "Y ASP 51": "OD1" <-> "OD2" Residue "Y ASP 105": "OD1" <-> "OD2" Residue "Y GLU 117": "OE1" <-> "OE2" Residue "Y ASP 140": "OD1" <-> "OD2" Residue "Y ASP 146": "OD1" <-> "OD2" Residue "Y ASP 190": "OD1" <-> "OD2" Residue "Y ASP 194": "OD1" <-> "OD2" Residue "Z PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 26": "OD1" <-> "OD2" Residue "Z GLU 31": "OE1" <-> "OE2" Residue "Z GLU 69": "OE1" <-> "OE2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z ASP 125": "OD1" <-> "OD2" Residue "Z ASP 169": "OD1" <-> "OD2" Residue "Z GLU 184": "OE1" <-> "OE2" Residue "Z GLU 205": "OE1" <-> "OE2" Residue "a ASP 126": "OD1" <-> "OD2" Residue "a TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "b ARG 29": "NH1" <-> "NH2" Residue "b ASP 32": "OD1" <-> "OD2" Residue "b GLU 145": "OE1" <-> "OE2" Residue "b GLU 185": "OE1" <-> "OE2" Residue "b ASP 192": "OD1" <-> "OD2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 48581 Number of models: 1 Model: "" Number of chains: 28 Chain: "M" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1687 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 208} Chain: "A" Number of atoms: 1811 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 230, 1798 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Conformer: "B" Number of residues, atoms: 230, 1798 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} bond proxies already assigned to first conformer: 1822 Chain: "B" Number of atoms: 1958 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1953 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 5, 'TRANS': 242} Conformer: "B" Number of residues, atoms: 248, 1953 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 5, 'TRANS': 242} bond proxies already assigned to first conformer: 1977 Chain: "C" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1864 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Chain: "D" Number of atoms: 1791 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 233, 1777 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 8, 'TRANS': 224} Conformer: "B" Number of residues, atoms: 233, 1777 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 8, 'TRANS': 224} bond proxies already assigned to first conformer: 1788 Chain: "E" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1831 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "F" Number of atoms: 1894 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 239, 1874 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Conformer: "B" Number of residues, atoms: 239, 1874 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} bond proxies already assigned to first conformer: 1885 Chain: "G" Number of atoms: 1892 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 241, 1885 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 241, 1885 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain breaks: 3 bond proxies already assigned to first conformer: 1907 Chain: "H" Number of atoms: 1672 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1659 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Conformer: "B" Number of residues, atoms: 220, 1659 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} bond proxies already assigned to first conformer: 1671 Chain: "I" Number of atoms: 1633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Conformer: "B" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} bond proxies already assigned to first conformer: 1574 Chain: "J" Number of atoms: 1580 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 195, 1565 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 195, 1565 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 1 bond proxies already assigned to first conformer: 1578 Chain: "K" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1559 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "L" Number of atoms: 1660 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 1654 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 206} Conformer: "B" Number of residues, atoms: 213, 1654 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 206} bond proxies already assigned to first conformer: 1676 Chain: "N" Number of atoms: 1519 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 202, 1514 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Conformer: "B" Number of residues, atoms: 202, 1514 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} bond proxies already assigned to first conformer: 1534 Chain: "O" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1798 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "P" Number of atoms: 1950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1942 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 5, 'TRANS': 241} Conformer: "B" Number of residues, atoms: 247, 1942 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 5, 'TRANS': 241} bond proxies already assigned to first conformer: 1962 Chain: "Q" Number of atoms: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1832 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 223} Chain breaks: 2 Chain: "R" Number of atoms: 1783 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 233, 1778 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 224} Conformer: "B" Number of residues, atoms: 233, 1778 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 224} bond proxies already assigned to first conformer: 1799 Chain: "S" Number of atoms: 1888 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 237, 1873 Classifications: {'peptide': 237} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 237, 1873 Classifications: {'peptide': 237} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 bond proxies already assigned to first conformer: 1888 Chain: "T" Number of atoms: 1884 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 240, 1881 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Conformer: "B" Number of residues, atoms: 240, 1881 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} bond proxies already assigned to first conformer: 1912 Chain: "U" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 8, 'TRANS': 223} Chain breaks: 4 Chain: "V" Number of atoms: 1669 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1659 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Conformer: "B" Number of residues, atoms: 220, 1659 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} bond proxies already assigned to first conformer: 1674 Chain: "W" Number of atoms: 1608 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Conformer: "B" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} bond proxies already assigned to first conformer: 1601 Chain: "X" Number of atoms: 1575 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 195, 1565 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 195, 1565 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 1 bond proxies already assigned to first conformer: 1583 Chain: "Y" Number of atoms: 1570 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 199, 1549 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 2, 'TRANS': 196} Conformer: "B" Number of residues, atoms: 199, 1549 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 2, 'TRANS': 196} bond proxies already assigned to first conformer: 1556 Chain: "Z" Number of atoms: 1657 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 1654 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 206} Conformer: "B" Number of residues, atoms: 213, 1654 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 206} bond proxies already assigned to first conformer: 1680 Chain: "a" Number of atoms: 1692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 1687 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 208} Conformer: "B" Number of residues, atoms: 216, 1687 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 208} bond proxies already assigned to first conformer: 1714 Chain: "b" Number of atoms: 1526 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 1521 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Conformer: "B" Number of residues, atoms: 203, 1521 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} bond proxies already assigned to first conformer: 1542 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N AALA D 120 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA D 120 " occ=0.50 residue: pdb=" N AGLU D 175 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU D 175 " occ=0.50 residue: pdb=" N ALYS I 16 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS I 16 " occ=0.50 residue: pdb=" N AASN I 17 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN I 17 " occ=0.50 residue: pdb=" N AGLU I 77 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU I 77 " occ=0.50 residue: pdb=" N AGLY I 78 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY I 78 " occ=0.50 residue: pdb=" N AHIS J 99 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS J 99 " occ=0.50 residue: pdb=" N AALA R 120 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA R 120 " occ=0.50 residue: pdb=" N ALYS W 16 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS W 16 " occ=0.50 Time building chain proxies: 39.36, per 1000 atoms: 0.81 Number of scatterers: 48581 At special positions: 0 Unit cell: (178.64, 200.97, 141.085, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 301 16.00 O 9230 8.00 N 8328 7.00 C 30722 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.50 Conformation dependent library (CDL) restraints added in 14.9 seconds 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11528 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 73 sheets defined 38.9% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.17 Creating SS restraints... Processing helix chain 'M' and resid 57 through 76 Processing helix chain 'M' and resid 84 through 102 removed outlier: 3.835A pdb=" N LYS M 102 " --> pdb=" O SER M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 144 Processing helix chain 'M' and resid 145 through 157 removed outlier: 4.328A pdb=" N LEU M 149 " --> pdb=" O LEU M 145 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS M 156 " --> pdb=" O GLU M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 180 removed outlier: 3.533A pdb=" N VAL M 175 " --> pdb=" O ARG M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 209 through 214 Processing helix chain 'A' and resid 18 through 30 removed outlier: 3.881A pdb=" N ALA A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 101 removed outlier: 3.740A pdb=" N VAL A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 120 removed outlier: 3.966A pdb=" N ARG A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.614A pdb=" N HIS A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 221 through 231 removed outlier: 4.101A pdb=" N ALA A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 79 through 102 Processing helix chain 'B' and resid 106 through 124 removed outlier: 3.878A pdb=" N LEU B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 111 " --> pdb=" O CYS B 107 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 185 through 201 removed outlier: 3.706A pdb=" N LYS B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 246 Processing helix chain 'C' and resid 11 through 15 removed outlier: 4.031A pdb=" N HIS C 15 " --> pdb=" O PRO C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 28 Processing helix chain 'C' and resid 56 through 60 removed outlier: 3.513A pdb=" N VAL C 59 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG C 60 " --> pdb=" O ARG C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 60' Processing helix chain 'C' and resid 76 through 99 removed outlier: 3.761A pdb=" N VAL C 89 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 118 removed outlier: 3.940A pdb=" N ILE C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 176 Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 221 through 233 removed outlier: 3.714A pdb=" N ILE C 225 " --> pdb=" O ASN C 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 32 removed outlier: 4.190A pdb=" N LYS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 104 removed outlier: 3.658A pdb=" N ALA D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 119 removed outlier: 3.855A pdb=" N LEU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 185 removed outlier: 3.848A pdb=" N ALA D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER D 179 " --> pdb=" O AGLU D 175 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 206 Processing helix chain 'D' and resid 230 through 239 removed outlier: 3.603A pdb=" N LYS D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 24 Processing helix chain 'E' and resid 26 through 32 removed outlier: 4.043A pdb=" N GLY E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 100 Processing helix chain 'E' and resid 104 through 118 removed outlier: 3.641A pdb=" N SER E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 165 through 176 Processing helix chain 'E' and resid 183 through 199 removed outlier: 3.683A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS E 189 " --> pdb=" O ASN E 185 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 199 " --> pdb=" O LEU E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'F' and resid 20 through 31 removed outlier: 3.779A pdb=" N LYS F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU F 31 " --> pdb=" O MET F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 103 removed outlier: 3.663A pdb=" N SER F 86 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 121 removed outlier: 3.807A pdb=" N MET F 117 " --> pdb=" O ASP F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 178 removed outlier: 3.505A pdb=" N LYS F 178 " --> pdb=" O THR F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 184 removed outlier: 3.654A pdb=" N GLU F 183 " --> pdb=" O GLN F 180 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET F 184 " --> pdb=" O MET F 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 180 through 184' Processing helix chain 'F' and resid 185 through 201 removed outlier: 4.008A pdb=" N LYS F 191 " --> pdb=" O ARG F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 228 through 244 removed outlier: 3.627A pdb=" N LYS F 244 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 Processing helix chain 'G' and resid 29 through 34 removed outlier: 3.686A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.902A pdb=" N ARG G 117 " --> pdb=" O MET G 113 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 186 removed outlier: 4.160A pdb=" N LYS G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 190 Processing helix chain 'G' and resid 193 through 207 removed outlier: 3.710A pdb=" N ALA G 198 " --> pdb=" O THR G 194 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE G 199 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL G 205 " --> pdb=" O CYS G 201 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 244 Processing helix chain 'H' and resid 48 through 71 removed outlier: 4.113A pdb=" N SER H 60 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU H 68 " --> pdb=" O GLU H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.969A pdb=" N ALA H 79 " --> pdb=" O ARG H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 removed outlier: 3.638A pdb=" N ALA H 134 " --> pdb=" O GLY H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 165 Processing helix chain 'I' and resid 55 through 78 removed outlier: 3.641A pdb=" N GLN I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU I 72 " --> pdb=" O PHE I 68 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N BGLY I 78 " --> pdb=" O GLU I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 97 removed outlier: 4.013A pdb=" N LYS I 97 " --> pdb=" O LEU I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 153 removed outlier: 3.920A pdb=" N SER I 151 " --> pdb=" O GLY I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 175 removed outlier: 3.706A pdb=" N ASP I 175 " --> pdb=" O LEU I 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 72 removed outlier: 3.621A pdb=" N ASN J 63 " --> pdb=" O TYR J 59 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS J 68 " --> pdb=" O VAL J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 90 Processing helix chain 'J' and resid 92 through 94 No H-bonds generated for 'chain 'J' and resid 92 through 94' Processing helix chain 'J' and resid 134 through 147 removed outlier: 3.849A pdb=" N LEU J 138 " --> pdb=" O TYR J 134 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N SER J 141 " --> pdb=" O PHE J 137 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE J 142 " --> pdb=" O LEU J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 170 Processing helix chain 'K' and resid 48 through 70 removed outlier: 3.765A pdb=" N CYS K 52 " --> pdb=" O GLY K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 89 removed outlier: 3.666A pdb=" N LYS K 81 " --> pdb=" O ALA K 77 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN K 89 " --> pdb=" O ASN K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 141 removed outlier: 3.564A pdb=" N ALA K 135 " --> pdb=" O GLY K 131 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY K 137 " --> pdb=" O VAL K 133 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL K 138 " --> pdb=" O TYR K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 167 Processing helix chain 'K' and resid 192 through 200 removed outlier: 3.545A pdb=" N GLU K 197 " --> pdb=" O ALA K 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 80 removed outlier: 3.786A pdb=" N THR L 65 " --> pdb=" O CYS L 61 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS L 73 " --> pdb=" O GLU L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 99 removed outlier: 3.548A pdb=" N THR L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG L 99 " --> pdb=" O ILE L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 153 removed outlier: 3.583A pdb=" N LEU L 145 " --> pdb=" O ALA L 141 " (cutoff:3.500A) Proline residue: L 147 - end of helix Processing helix chain 'L' and resid 167 through 186 removed outlier: 3.601A pdb=" N ARG L 185 " --> pdb=" O SER L 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 71 removed outlier: 4.017A pdb=" N ALA N 56 " --> pdb=" O THR N 52 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP N 57 " --> pdb=" O GLN N 53 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA N 58 " --> pdb=" O ALA N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 90 removed outlier: 3.650A pdb=" N PHE N 83 " --> pdb=" O ALA N 79 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET N 86 " --> pdb=" O LEU N 82 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR N 88 " --> pdb=" O LYS N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 134 Processing helix chain 'N' and resid 135 through 143 removed outlier: 3.562A pdb=" N VAL N 139 " --> pdb=" O ILE N 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 167 removed outlier: 3.513A pdb=" N ALA N 163 " --> pdb=" O ALA N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 194 removed outlier: 3.665A pdb=" N ILE N 194 " --> pdb=" O GLY N 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 30 removed outlier: 3.782A pdb=" N ALA O 26 " --> pdb=" O GLU O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 61 removed outlier: 3.953A pdb=" N VAL O 61 " --> pdb=" O GLU O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 101 Processing helix chain 'O' and resid 105 through 120 removed outlier: 3.861A pdb=" N SER O 115 " --> pdb=" O GLN O 111 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR O 120 " --> pdb=" O VAL O 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 177 removed outlier: 3.586A pdb=" N TYR O 177 " --> pdb=" O LEU O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 195 removed outlier: 3.570A pdb=" N LEU O 192 " --> pdb=" O HIS O 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 196 through 198 No H-bonds generated for 'chain 'O' and resid 196 through 198' Processing helix chain 'O' and resid 221 through 230 Processing helix chain 'P' and resid 18 through 29 Processing helix chain 'P' and resid 79 through 102 removed outlier: 3.844A pdb=" N ARG P 91 " --> pdb=" O THR P 87 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU P 92 " --> pdb=" O ASN P 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 124 removed outlier: 3.878A pdb=" N LEU P 110 " --> pdb=" O PRO P 106 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL P 111 " --> pdb=" O CYS P 107 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR P 121 " --> pdb=" O ILE P 117 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR P 122 " --> pdb=" O LYS P 118 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN P 123 " --> pdb=" O GLN P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 179 removed outlier: 4.168A pdb=" N GLN P 177 " --> pdb=" O SER P 173 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP P 178 " --> pdb=" O MET P 174 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR P 179 " --> pdb=" O LEU P 175 " (cutoff:3.500A) Processing helix chain 'P' and resid 185 through 201 removed outlier: 3.750A pdb=" N LYS P 199 " --> pdb=" O LYS P 195 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET P 201 " --> pdb=" O LEU P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 229 through 246 removed outlier: 3.511A pdb=" N HIS P 240 " --> pdb=" O LEU P 236 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLU P 243 " --> pdb=" O LYS P 239 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 28 Processing helix chain 'Q' and resid 76 through 99 removed outlier: 3.739A pdb=" N VAL Q 89 " --> pdb=" O ASN Q 85 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU Q 99 " --> pdb=" O ARG Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 118 removed outlier: 3.850A pdb=" N ILE Q 107 " --> pdb=" O THR Q 103 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR Q 118 " --> pdb=" O LEU Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 176 Processing helix chain 'Q' and resid 183 through 196 Processing helix chain 'Q' and resid 221 through 238 removed outlier: 3.551A pdb=" N ILE Q 225 " --> pdb=" O ASN Q 221 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU Q 235 " --> pdb=" O GLU Q 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 32 removed outlier: 3.679A pdb=" N LYS R 32 " --> pdb=" O ILE R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'R' and resid 81 through 104 removed outlier: 3.706A pdb=" N ALA R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 118 Processing helix chain 'R' and resid 173 through 185 removed outlier: 3.839A pdb=" N ALA R 177 " --> pdb=" O ALA R 173 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER R 179 " --> pdb=" O GLU R 175 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 206 Processing helix chain 'R' and resid 230 through 239 removed outlier: 3.569A pdb=" N VAL R 237 " --> pdb=" O GLU R 233 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 32 removed outlier: 3.515A pdb=" N ALA S 25 " --> pdb=" O GLN S 21 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU S 27 " --> pdb=" O GLU S 23 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA S 28 " --> pdb=" O TYR S 24 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL S 29 " --> pdb=" O ALA S 25 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY S 32 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 100 Processing helix chain 'S' and resid 104 through 118 removed outlier: 3.625A pdb=" N SER S 110 " --> pdb=" O SER S 106 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE S 118 " --> pdb=" O SER S 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 121 No H-bonds generated for 'chain 'S' and resid 119 through 121' Processing helix chain 'S' and resid 165 through 176 Processing helix chain 'S' and resid 183 through 199 removed outlier: 3.623A pdb=" N VAL S 188 " --> pdb=" O LEU S 184 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR S 198 " --> pdb=" O ALA S 194 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU S 199 " --> pdb=" O LEU S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 229 through 234 Processing helix chain 'T' and resid 20 through 31 removed outlier: 3.681A pdb=" N LYS T 28 " --> pdb=" O GLU T 24 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU T 31 " --> pdb=" O MET T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 103 removed outlier: 3.547A pdb=" N ALA T 84 " --> pdb=" O LEU T 80 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER T 86 " --> pdb=" O ALA T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 107 through 121 removed outlier: 3.765A pdb=" N MET T 117 " --> pdb=" O ASP T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 178 removed outlier: 3.504A pdb=" N LYS T 178 " --> pdb=" O THR T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 180 through 184 removed outlier: 3.961A pdb=" N GLU T 183 " --> pdb=" O GLN T 180 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET T 184 " --> pdb=" O MET T 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 180 through 184' Processing helix chain 'T' and resid 185 through 188 Processing helix chain 'T' and resid 189 through 201 Processing helix chain 'T' and resid 219 through 221 No H-bonds generated for 'chain 'T' and resid 219 through 221' Processing helix chain 'T' and resid 228 through 244 Processing helix chain 'U' and resid 22 through 28 Processing helix chain 'U' and resid 29 through 34 removed outlier: 3.645A pdb=" N ASN U 33 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 106 Processing helix chain 'U' and resid 111 through 123 removed outlier: 3.745A pdb=" N ARG U 117 " --> pdb=" O MET U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 127 Processing helix chain 'U' and resid 171 through 184 removed outlier: 3.848A pdb=" N LYS U 184 " --> pdb=" O GLU U 180 " (cutoff:3.500A) Processing helix chain 'U' and resid 195 through 207 removed outlier: 3.723A pdb=" N VAL U 205 " --> pdb=" O CYS U 201 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU U 206 " --> pdb=" O LEU U 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 231 through 244 Processing helix chain 'V' and resid 48 through 71 removed outlier: 3.989A pdb=" N SER V 60 " --> pdb=" O THR V 56 " (cutoff:3.500A) Processing helix chain 'V' and resid 75 through 90 removed outlier: 3.931A pdb=" N ALA V 79 " --> pdb=" O ARG V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 142 removed outlier: 3.678A pdb=" N ALA V 134 " --> pdb=" O GLY V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 165 Processing helix chain 'W' and resid 55 through 78 removed outlier: 3.566A pdb=" N LEU W 72 " --> pdb=" O PHE W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 97 removed outlier: 4.011A pdb=" N LYS W 97 " --> pdb=" O LEU W 93 " (cutoff:3.500A) Processing helix chain 'W' and resid 141 through 153 removed outlier: 3.523A pdb=" N MET W 148 " --> pdb=" O GLN W 144 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER W 151 " --> pdb=" O GLY W 147 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP W 153 " --> pdb=" O CYS W 149 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 175 removed outlier: 3.766A pdb=" N ALA W 173 " --> pdb=" O ALA W 169 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 72 Processing helix chain 'X' and resid 76 through 90 Processing helix chain 'X' and resid 92 through 94 No H-bonds generated for 'chain 'X' and resid 92 through 94' Processing helix chain 'X' and resid 135 through 147 removed outlier: 5.083A pdb=" N SER X 141 " --> pdb=" O PHE X 137 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE X 142 " --> pdb=" O LEU X 138 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 170 Processing helix chain 'Y' and resid 48 through 71 removed outlier: 3.792A pdb=" N TRP Y 55 " --> pdb=" O ASP Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 75 through 89 removed outlier: 3.600A pdb=" N LYS Y 81 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN Y 89 " --> pdb=" O ASN Y 85 " (cutoff:3.500A) Processing helix chain 'Y' and resid 131 through 141 removed outlier: 3.546A pdb=" N ALA Y 135 " --> pdb=" O GLY Y 131 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY Y 137 " --> pdb=" O VAL Y 133 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL Y 138 " --> pdb=" O TYR Y 134 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG Y 141 " --> pdb=" O GLY Y 137 " (cutoff:3.500A) Processing helix chain 'Y' and resid 148 through 167 Processing helix chain 'Y' and resid 192 through 199 removed outlier: 3.540A pdb=" N GLU Y 197 " --> pdb=" O ALA Y 193 " (cutoff:3.500A) Processing helix chain 'Z' and resid 57 through 80 removed outlier: 3.742A pdb=" N THR Z 65 " --> pdb=" O CYS Z 61 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA Z 70 " --> pdb=" O LYS Z 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 84 through 99 removed outlier: 3.574A pdb=" N THR Z 94 " --> pdb=" O ALA Z 90 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG Z 99 " --> pdb=" O ILE Z 95 " (cutoff:3.500A) Processing helix chain 'Z' and resid 141 through 153 removed outlier: 3.509A pdb=" N LEU Z 145 " --> pdb=" O ALA Z 141 " (cutoff:3.500A) Proline residue: Z 147 - end of helix Processing helix chain 'Z' and resid 167 through 186 removed outlier: 3.747A pdb=" N ARG Z 173 " --> pdb=" O ASP Z 169 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG Z 185 " --> pdb=" O SER Z 181 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 76 Processing helix chain 'a' and resid 84 through 102 removed outlier: 3.633A pdb=" N LYS a 102 " --> pdb=" O SER a 98 " (cutoff:3.500A) Processing helix chain 'a' and resid 141 through 146 Processing helix chain 'a' and resid 146 through 157 removed outlier: 3.932A pdb=" N LYS a 156 " --> pdb=" O GLU a 152 " (cutoff:3.500A) Processing helix chain 'a' and resid 161 through 180 removed outlier: 3.574A pdb=" N VAL a 175 " --> pdb=" O ARG a 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 209 through 214 Processing helix chain 'b' and resid 50 through 71 removed outlier: 4.123A pdb=" N ALA b 56 " --> pdb=" O THR b 52 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA b 58 " --> pdb=" O ALA b 54 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE b 65 " --> pdb=" O TYR b 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 90 removed outlier: 3.660A pdb=" N PHE b 83 " --> pdb=" O ALA b 79 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET b 86 " --> pdb=" O LEU b 82 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR b 88 " --> pdb=" O LYS b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 134 Processing helix chain 'b' and resid 135 through 143 removed outlier: 3.567A pdb=" N VAL b 139 " --> pdb=" O ILE b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 148 through 167 removed outlier: 3.505A pdb=" N ALA b 163 " --> pdb=" O ALA b 159 " (cutoff:3.500A) Processing helix chain 'b' and resid 190 through 194 removed outlier: 3.642A pdb=" N ILE b 194 " --> pdb=" O GLY b 191 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 33 through 36 removed outlier: 5.824A pdb=" N ALA M 34 " --> pdb=" O TYR M 30 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR M 30 " --> pdb=" O ALA M 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR M 49 " --> pdb=" O VAL M 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 33 through 36 removed outlier: 5.824A pdb=" N ALA M 34 " --> pdb=" O TYR M 30 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR M 30 " --> pdb=" O ALA M 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 136 through 138 removed outlier: 6.011A pdb=" N PHE M 187 " --> pdb=" O PRO M 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 159 through 162 Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA6, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 67 removed outlier: 4.028A pdb=" N GLY B 138 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU B 147 " --> pdb=" O TRP B 159 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 157 " --> pdb=" O GLN B 149 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY B 158 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 158 through 161 removed outlier: 3.767A pdb=" N VAL C 42 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL C 45 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU C 207 " --> pdb=" O VAL C 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 161 removed outlier: 3.767A pdb=" N VAL C 42 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 43 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA C 209 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 69 through 75 removed outlier: 3.728A pdb=" N GLY C 135 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 143 " --> pdb=" O GLY C 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 167 through 170 Processing sheet with id=AB3, first strand: chain 'D' and resid 67 through 69 removed outlier: 3.563A pdb=" N CYS D 76 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA D 140 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 153 " --> pdb=" O CYS D 165 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AB5, first strand: chain 'E' and resid 63 through 65 removed outlier: 3.522A pdb=" N LEU E 64 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE E 72 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 75 " --> pdb=" O GLY E 131 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY E 131 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE E 144 " --> pdb=" O CYS E 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 162 through 165 Processing sheet with id=AB7, first strand: chain 'F' and resid 66 through 68 Processing sheet with id=AB8, first strand: chain 'G' and resid 165 through 169 removed outlier: 6.775A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 69 through 71 removed outlier: 3.606A pdb=" N GLY G 142 " --> pdb=" O GLN G 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 124 through 128 Processing sheet with id=AC2, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.776A pdb=" N ALA H 20 " --> pdb=" O ALA H 27 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 34 through 36 Processing sheet with id=AC4, first strand: chain 'H' and resid 211 through 218 removed outlier: 6.554A pdb=" N THR I 198 " --> pdb=" O LEU H 212 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU H 214 " --> pdb=" O THR I 196 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR I 196 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE H 216 " --> pdb=" O ILE I 194 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE I 194 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL I 184 " --> pdb=" O LEU I 199 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA I 9 " --> pdb=" O ASP I 24 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 27 through 29 removed outlier: 7.351A pdb=" N PHE I 27 " --> pdb=" O VAL I 34 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 41 through 43 removed outlier: 4.101A pdb=" N ALA I 53 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU I 105 " --> pdb=" O ALA I 53 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 129 through 132 removed outlier: 3.659A pdb=" N LEU J 4 " --> pdb=" O HIS J 132 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL J 13 " --> pdb=" O ILE J 183 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 129 through 132 removed outlier: 3.659A pdb=" N LEU J 4 " --> pdb=" O HIS J 132 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL J 13 " --> pdb=" O ILE J 183 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 21 through 23 removed outlier: 6.648A pdb=" N ALA J 21 " --> pdb=" O MET J 28 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 35 through 39 removed outlier: 6.806A pdb=" N ILE J 42 " --> pdb=" O MET J 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 125 through 129 removed outlier: 3.542A pdb=" N GLY K 11 " --> pdb=" O PHE K 8 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER K 188 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N HIS K 178 " --> pdb=" O ARG K 186 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ARG K 186 " --> pdb=" O HIS K 178 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG K 180 " --> pdb=" O TRP K 184 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TRP K 184 " --> pdb=" O ARG K 180 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 20 through 22 removed outlier: 7.015A pdb=" N ALA K 20 " --> pdb=" O ALA K 27 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.529A pdb=" N LEU K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR K 44 " --> pdb=" O MET K 100 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N MET K 100 " --> pdb=" O THR K 44 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 135 through 139 Processing sheet with id=AD6, first strand: chain 'L' and resid 29 through 31 removed outlier: 6.795A pdb=" N LEU L 29 " --> pdb=" O HIS L 36 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU L 31 " --> pdb=" O SER L 34 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 43 through 47 removed outlier: 6.788A pdb=" N THR L 50 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER L 55 " --> pdb=" O TYR L 107 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN L 108 " --> pdb=" O PHE L 124 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL L 121 " --> pdb=" O ASP L 133 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN L 131 " --> pdb=" O SER L 123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 125 through 129 Processing sheet with id=AD9, first strand: chain 'N' and resid 20 through 22 removed outlier: 6.365A pdb=" N THR N 22 " --> pdb=" O ILE N 26 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE N 26 " --> pdb=" O THR N 22 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 34 through 36 removed outlier: 3.671A pdb=" N ILE N 99 " --> pdb=" O CYS N 44 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER N 46 " --> pdb=" O GLY N 97 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY N 97 " --> pdb=" O SER N 46 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 159 through 162 Processing sheet with id=AE3, first strand: chain 'O' and resid 65 through 66 removed outlier: 3.523A pdb=" N CYS O 136 " --> pdb=" O GLY O 72 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 161 through 164 Processing sheet with id=AE5, first strand: chain 'P' and resid 66 through 67 removed outlier: 3.557A pdb=" N LEU P 134 " --> pdb=" O SER P 150 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY P 138 " --> pdb=" O GLN P 146 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU P 147 " --> pdb=" O TRP P 159 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN P 149 " --> pdb=" O GLY P 157 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY P 157 " --> pdb=" O GLN P 149 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY P 158 " --> pdb=" O ASP Q 55 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 158 through 161 removed outlier: 3.729A pdb=" N ASN Q 159 " --> pdb=" O GLY Q 34 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY Q 34 " --> pdb=" O ASN Q 159 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET Q 211 " --> pdb=" O VAL Q 41 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA Q 209 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 69 through 75 removed outlier: 3.506A pdb=" N ALA Q 74 " --> pdb=" O SER Q 130 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY Q 135 " --> pdb=" O ARG Q 143 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU Q 144 " --> pdb=" O TRP Q 156 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA Q 155 " --> pdb=" O GLU R 60 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 167 through 170 Processing sheet with id=AE9, first strand: chain 'R' and resid 67 through 71 removed outlier: 6.515A pdb=" N ILE R 74 " --> pdb=" O ILE R 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA R 140 " --> pdb=" O SER R 79 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU R 153 " --> pdb=" O CYS R 165 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 158 through 161 Processing sheet with id=AF2, first strand: chain 'S' and resid 63 through 65 removed outlier: 3.622A pdb=" N LEU S 133 " --> pdb=" O SER S 73 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU S 132 " --> pdb=" O THR S 147 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE S 144 " --> pdb=" O CYS S 156 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 162 through 165 Processing sheet with id=AF4, first strand: chain 'T' and resid 66 through 70 removed outlier: 6.397A pdb=" N VAL T 73 " --> pdb=" O VAL T 69 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 165 through 169 removed outlier: 6.844A pdb=" N THR U 38 " --> pdb=" O GLN U 53 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN U 53 " --> pdb=" O THR U 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 69 through 71 removed outlier: 3.503A pdb=" N GLY U 142 " --> pdb=" O GLN U 150 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 124 through 128 removed outlier: 3.905A pdb=" N SER V 179 " --> pdb=" O LYS V 182 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS V 182 " --> pdb=" O SER V 179 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.822A pdb=" N ALA V 20 " --> pdb=" O ALA V 27 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 34 through 36 Processing sheet with id=AG1, first strand: chain 'V' and resid 211 through 218 removed outlier: 6.575A pdb=" N THR W 198 " --> pdb=" O LEU V 212 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU V 214 " --> pdb=" O THR W 196 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR W 196 " --> pdb=" O GLU V 214 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE V 216 " --> pdb=" O ILE W 194 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE W 194 " --> pdb=" O ILE V 216 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL W 184 " --> pdb=" O LEU W 199 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ALA W 9 " --> pdb=" O ASP W 24 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL W 136 " --> pdb=" O ALA W 12 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 27 through 29 removed outlier: 7.319A pdb=" N PHE W 27 " --> pdb=" O VAL W 34 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 41 through 43 removed outlier: 4.037A pdb=" N ALA W 53 " --> pdb=" O GLU W 105 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 129 through 132 removed outlier: 3.708A pdb=" N LEU X 4 " --> pdb=" O HIS X 132 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 129 through 132 removed outlier: 3.708A pdb=" N LEU X 4 " --> pdb=" O HIS X 132 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 21 through 23 removed outlier: 6.408A pdb=" N ALA X 21 " --> pdb=" O MET X 28 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'X' and resid 35 through 39 removed outlier: 3.568A pdb=" N PHE X 36 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE X 42 " --> pdb=" O MET X 38 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 125 through 129 removed outlier: 3.565A pdb=" N SER Y 188 " --> pdb=" O LEU Y 176 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N HIS Y 178 " --> pdb=" O ARG Y 186 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ARG Y 186 " --> pdb=" O HIS Y 178 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG Y 180 " --> pdb=" O TRP Y 184 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N TRP Y 184 " --> pdb=" O ARG Y 180 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 20 through 22 removed outlier: 7.000A pdb=" N ALA Y 20 " --> pdb=" O ALA Y 27 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 34 through 38 removed outlier: 6.550A pdb=" N LEU Y 41 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR Y 44 " --> pdb=" O MET Y 100 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N MET Y 100 " --> pdb=" O THR Y 44 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 135 through 139 removed outlier: 3.510A pdb=" N ILE Z 12 " --> pdb=" O GLY Z 138 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG Z 204 " --> pdb=" O ILE Z 197 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 29 through 31 removed outlier: 6.785A pdb=" N LEU Z 29 " --> pdb=" O HIS Z 36 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Z' and resid 43 through 47 removed outlier: 6.804A pdb=" N THR Z 50 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL Z 121 " --> pdb=" O ASP Z 133 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN Z 131 " --> pdb=" O SER Z 123 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'a' and resid 33 through 36 removed outlier: 5.823A pdb=" N ALA a 34 " --> pdb=" O TYR a 30 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR a 30 " --> pdb=" O ALA a 34 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR a 49 " --> pdb=" O VAL a 45 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'a' and resid 33 through 36 removed outlier: 5.823A pdb=" N ALA a 34 " --> pdb=" O TYR a 30 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR a 30 " --> pdb=" O ALA a 34 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'a' and resid 136 through 138 removed outlier: 6.032A pdb=" N PHE a 187 " --> pdb=" O PRO a 202 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'b' and resid 125 through 129 Processing sheet with id=AH9, first strand: chain 'b' and resid 20 through 22 removed outlier: 6.374A pdb=" N THR b 22 " --> pdb=" O ILE b 26 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE b 26 " --> pdb=" O THR b 22 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'b' and resid 34 through 36 removed outlier: 3.707A pdb=" N ILE b 99 " --> pdb=" O CYS b 44 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER b 46 " --> pdb=" O GLY b 97 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY b 97 " --> pdb=" O SER b 46 " (cutoff:3.500A) 2592 hydrogen bonds defined for protein. 7364 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.26 Time building geometry restraints manager: 19.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 8187 1.31 - 1.44: 12762 1.44 - 1.56: 28002 1.56 - 1.69: 23 1.69 - 1.81: 501 Bond restraints: 49475 Sorted by residual: bond pdb=" CG LYS P 239 " pdb=" CD LYS P 239 " ideal model delta sigma weight residual 1.520 1.753 -0.233 3.00e-02 1.11e+03 6.05e+01 bond pdb=" CB LYS P 239 " pdb=" CG LYS P 239 " ideal model delta sigma weight residual 1.520 1.720 -0.200 3.00e-02 1.11e+03 4.43e+01 bond pdb=" N HIS P 240 " pdb=" CA HIS P 240 " ideal model delta sigma weight residual 1.457 1.535 -0.078 1.29e-02 6.01e+03 3.65e+01 bond pdb=" CB GLN P 235 " pdb=" CG GLN P 235 " ideal model delta sigma weight residual 1.520 1.347 0.173 3.00e-02 1.11e+03 3.31e+01 bond pdb=" CD LYS P 239 " pdb=" CE LYS P 239 " ideal model delta sigma weight residual 1.520 1.679 -0.159 3.00e-02 1.11e+03 2.82e+01 ... (remaining 49470 not shown) Histogram of bond angle deviations from ideal: 92.95 - 105.06: 800 105.06 - 117.17: 34138 117.17 - 129.28: 31679 129.28 - 141.39: 246 141.39 - 153.50: 1 Bond angle restraints: 66864 Sorted by residual: angle pdb=" C LYS P 239 " pdb=" N HIS P 240 " pdb=" CA HIS P 240 " ideal model delta sigma weight residual 121.54 153.50 -31.96 1.91e+00 2.74e-01 2.80e+02 angle pdb=" N HIS P 240 " pdb=" CA HIS P 240 " pdb=" C HIS P 240 " ideal model delta sigma weight residual 110.80 129.00 -18.20 2.13e+00 2.20e-01 7.30e+01 angle pdb=" C BLYS W 16 " pdb=" N ASN W 17 " pdb=" CA ASN W 17 " ideal model delta sigma weight residual 121.08 134.97 -13.89 1.64e+00 3.72e-01 7.18e+01 angle pdb=" N LYS C 204 " pdb=" CA LYS C 204 " pdb=" C LYS C 204 " ideal model delta sigma weight residual 110.80 127.37 -16.57 2.13e+00 2.20e-01 6.05e+01 angle pdb=" N LYS P 54 " pdb=" CA LYS P 54 " pdb=" C LYS P 54 " ideal model delta sigma weight residual 108.49 99.61 8.88 1.15e+00 7.56e-01 5.97e+01 ... (remaining 66859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.01: 28336 21.01 - 42.02: 1401 42.02 - 63.03: 161 63.03 - 84.04: 40 84.04 - 105.05: 12 Dihedral angle restraints: 29950 sinusoidal: 11873 harmonic: 18077 Sorted by residual: dihedral pdb=" CA GLY C 203 " pdb=" C GLY C 203 " pdb=" N LYS C 204 " pdb=" CA LYS C 204 " ideal model delta harmonic sigma weight residual 180.00 74.95 105.05 0 5.00e+00 4.00e-02 4.41e+02 dihedral pdb=" CA GLU B 209 " pdb=" C GLU B 209 " pdb=" N LYS B 210 " pdb=" CA LYS B 210 " ideal model delta harmonic sigma weight residual 180.00 85.53 94.47 0 5.00e+00 4.00e-02 3.57e+02 dihedral pdb=" CA GLU C 233 " pdb=" C GLU C 233 " pdb=" N LYS C 234 " pdb=" CA LYS C 234 " ideal model delta harmonic sigma weight residual 180.00 117.91 62.09 0 5.00e+00 4.00e-02 1.54e+02 ... (remaining 29947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 6889 0.107 - 0.214: 594 0.214 - 0.321: 18 0.321 - 0.429: 4 0.429 - 0.536: 1 Chirality restraints: 7506 Sorted by residual: chirality pdb=" CA LYS C 204 " pdb=" N LYS C 204 " pdb=" C LYS C 204 " pdb=" CB LYS C 204 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.17e+00 chirality pdb=" CG LEU V 65 " pdb=" CB LEU V 65 " pdb=" CD1 LEU V 65 " pdb=" CD2 LEU V 65 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CB ILE X 25 " pdb=" CA ILE X 25 " pdb=" CG1 ILE X 25 " pdb=" CG2 ILE X 25 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 7503 not shown) Planarity restraints: 8619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU P 236 " -0.037 2.00e-02 2.50e+03 7.44e-02 5.54e+01 pdb=" C LEU P 236 " 0.129 2.00e-02 2.50e+03 pdb=" O LEU P 236 " -0.048 2.00e-02 2.50e+03 pdb=" N ILE P 237 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS P 238 " -0.035 2.00e-02 2.50e+03 6.97e-02 4.86e+01 pdb=" C LYS P 238 " 0.121 2.00e-02 2.50e+03 pdb=" O LYS P 238 " -0.044 2.00e-02 2.50e+03 pdb=" N LYS P 239 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN P 235 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLN P 235 " -0.073 2.00e-02 2.50e+03 pdb=" O GLN P 235 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU P 236 " 0.025 2.00e-02 2.50e+03 ... (remaining 8616 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 1291 2.69 - 3.24: 43946 3.24 - 3.79: 77871 3.79 - 4.35: 101369 4.35 - 4.90: 172229 Nonbonded interactions: 396706 Sorted by model distance: nonbonded pdb=" O LEU P 236 " pdb=" O LYS P 239 " model vdw 2.135 3.040 nonbonded pdb=" OE2 GLU R 105 " pdb=" OH TYR Z 75 " model vdw 2.257 2.440 nonbonded pdb=" O THR C 183 " pdb=" OG1 THR C 187 " model vdw 2.266 2.440 nonbonded pdb=" OG1 THR D 42 " pdb=" O GLY D 45 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR C 31 " pdb=" O ARG C 163 " model vdw 2.290 2.440 ... (remaining 396701 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 'A' and (resid 3 through 87 or resid 89 through 148 or resid 150 through \ 232)) selection = (chain 'O' and (resid 3 through 87 or resid 89 through 148 or resid 150 through \ 232)) } ncs_group { reference = (chain 'B' and (resid 2 through 6 or resid 8 through 24 or resid 26 through 248) \ ) selection = (chain 'P' and (resid 2 through 6 or resid 8 through 24 or resid 26 through 248) \ ) } ncs_group { reference = (chain 'C' and (resid 2 through 199 or resid 205 through 238)) selection = chain 'Q' } ncs_group { reference = (chain 'D' and (resid 9 through 119 or resid 121 through 174 or resid 176 throug \ h 241)) selection = (chain 'R' and (resid 9 through 119 or resid 121 through 174 or resid 176 throug \ h 240 or (resid 241 and (name N or name CA or name C or name O or name CB or nam \ e CG1 or name CG2 or name CD1)))) } ncs_group { reference = (chain 'E' and (resid 4 through 64 or resid 66 through 72 or resid 74 through 15 \ 1 or resid 153 through 237)) selection = (chain 'S' and (resid 4 through 64 or resid 66 through 72 or resid 74 through 15 \ 1 or resid 153 through 237)) } ncs_group { reference = (chain 'F' and (resid 6 through 132 or resid 134 through 138 or resid 140 throug \ h 217 or resid 219 through 231 or resid 233 through 244)) selection = (chain 'T' and (resid 6 through 132 or resid 134 through 138 or resid 140 throug \ h 217 or resid 219 through 231 or resid 233 through 244)) } ncs_group { reference = (chain 'G' and (resid 2 through 48 or resid 50 through 88 or resid 90 through 18 \ 4 or resid 194 through 245)) selection = (chain 'U' and (resid 2 through 48 or resid 50 through 88 or resid 90 through 24 \ 5)) } ncs_group { reference = (chain 'H' and (resid 1 through 103 or resid 105 through 126 or resid 128 throug \ h 186 or resid 188 through 220)) selection = (chain 'V' and (resid 1 through 103 or resid 105 through 126 or resid 128 throug \ h 186 or resid 188 through 220)) } ncs_group { reference = (chain 'I' and (resid 1 through 9 or resid 11 through 15 or resid 18 through 24 \ or resid 26 through 76 or resid 79 through 204)) selection = (chain 'W' and (resid 1 through 9 or resid 11 through 15 or resid 18 through 24 \ or resid 26 through 76 or resid 79 through 204)) } ncs_group { reference = (chain 'J' and (resid 1 through 27 or resid 29 through 45 or resid 47 through 98 \ or resid 100 through 196)) selection = (chain 'X' and (resid 1 through 27 or resid 29 through 45 or resid 47 through 98 \ or resid 100 through 196)) } ncs_group { reference = (chain 'K' and (resid 1 through 96 or resid 98 through 140 or resid 142 through \ 185 or resid 187 through 199)) selection = (chain 'Y' and (resid 1 through 96 or resid 98 through 140 or resid 142 through \ 185 or resid 187 through 199)) } ncs_group { reference = (chain 'L' and (resid 1 through 2 or resid 4 through 42 or resid 44 through 213) \ ) selection = (chain 'Z' and (resid 1 through 2 or resid 4 through 42 or resid 44 through 213) \ ) } ncs_group { reference = (chain 'M' and (resid 1 through 166 or resid 168 through 216)) selection = (chain 'a' and (resid 1 through 166 or resid 168 through 216)) } ncs_group { reference = (chain 'N' and (resid 1 through 85 or resid 87 through 146 or resid 148 through \ 202)) selection = (chain 'b' and (resid 1 through 85 or resid 87 through 146 or resid 148 through \ 202)) } 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 14.270 Check model and map are aligned: 0.720 Set scattering table: 0.450 Process input model: 143.390 Find NCS groups from input model: 5.170 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.233 49475 Z= 0.537 Angle : 1.068 31.964 66864 Z= 0.586 Chirality : 0.061 0.536 7506 Planarity : 0.007 0.088 8619 Dihedral : 12.890 105.051 18422 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.67 % Favored : 96.07 % Rotamer: Outliers : 0.52 % Allowed : 6.37 % Favored : 93.11 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.03 % Twisted Proline : 1.02 % Twisted General : 0.40 % 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: -2.76 (0.09), residues: 6184 helix: -2.28 (0.08), residues: 2213 sheet: -0.81 (0.13), residues: 1393 loop : -1.81 (0.10), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP T 215 HIS 0.014 0.002 HIS L 77 PHE 0.046 0.004 PHE R 154 TYR 0.043 0.003 TYR T 149 ARG 0.017 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1158 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1143 time to evaluate : 5.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 5 MET cc_start: 0.6085 (mmt) cc_final: 0.5133 (mmm) REVERT: M 50 MET cc_start: 0.8671 (ptt) cc_final: 0.8468 (ptp) REVERT: M 127 MET cc_start: 0.8507 (ptt) cc_final: 0.8229 (ptp) REVERT: M 185 ASN cc_start: 0.8643 (t0) cc_final: 0.8332 (t0) REVERT: A 139 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7224 (p0) REVERT: A 172 PHE cc_start: 0.8433 (t80) cc_final: 0.8149 (t80) REVERT: B 72 MET cc_start: 0.7137 (mtp) cc_final: 0.6914 (mtp) REVERT: B 156 TYR cc_start: 0.7842 (p90) cc_final: 0.6819 (p90) REVERT: B 178 ASP cc_start: 0.8050 (t0) cc_final: 0.7673 (t0) REVERT: C 71 MET cc_start: 0.7317 (ptm) cc_final: 0.7109 (ptm) REVERT: C 117 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.7451 (mtm180) REVERT: C 204 LYS cc_start: 0.7450 (mtmt) cc_final: 0.7203 (ptpp) REVERT: C 211 MET cc_start: -0.0915 (ttm) cc_final: -0.2352 (ttt) REVERT: D 82 ILE cc_start: 0.7099 (mm) cc_final: 0.6849 (mm) REVERT: D 168 ARG cc_start: 0.4754 (tpt-90) cc_final: 0.4232 (tpt-90) REVERT: E 140 MET cc_start: 0.6602 (mmm) cc_final: 0.6289 (mpp) REVERT: E 192 LEU cc_start: 0.8348 (mt) cc_final: 0.8037 (mt) REVERT: F 81 LEU cc_start: 0.9089 (tp) cc_final: 0.8659 (mm) REVERT: F 221 ASN cc_start: 0.8757 (t0) cc_final: 0.8367 (p0) REVERT: G 74 GLU cc_start: 0.6901 (tp30) cc_final: 0.6619 (tp30) REVERT: G 75 ASN cc_start: 0.8173 (m-40) cc_final: 0.7595 (t0) REVERT: G 171 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8608 (mmmt) REVERT: H 80 ASN cc_start: 0.9013 (t0) cc_final: 0.8774 (t0) REVERT: H 116 HIS cc_start: 0.7860 (m-70) cc_final: 0.7618 (m-70) REVERT: I 13 MET cc_start: 0.7804 (ttm) cc_final: 0.7471 (mtp) REVERT: I 87 MET cc_start: 0.7771 (ttp) cc_final: 0.7458 (ttp) REVERT: I 102 TYR cc_start: 0.8781 (m-80) cc_final: 0.8478 (m-80) REVERT: I 120 ILE cc_start: 0.8855 (pt) cc_final: 0.8433 (mm) REVERT: I 121 CYS cc_start: 0.8148 (p) cc_final: 0.7265 (p) REVERT: I 145 MET cc_start: 0.7633 (mtt) cc_final: 0.7187 (mtt) REVERT: I 182 MET cc_start: 0.6298 (mmm) cc_final: 0.5642 (mmm) REVERT: J 38 MET cc_start: 0.8362 (mmp) cc_final: 0.7982 (mmp) REVERT: J 61 GLN cc_start: 0.7006 (tt0) cc_final: 0.6536 (tt0) REVERT: K 81 LYS cc_start: 0.7873 (tptp) cc_final: 0.7339 (tptp) REVERT: K 97 MET cc_start: 0.2341 (ttp) cc_final: 0.1773 (ttt) REVERT: K 151 GLN cc_start: 0.8924 (tt0) cc_final: 0.8607 (mp10) REVERT: L 4 PRO cc_start: 0.8133 (Cg_endo) cc_final: 0.7892 (Cg_exo) REVERT: L 101 PHE cc_start: 0.7029 (m-80) cc_final: 0.6753 (m-80) REVERT: L 205 GLU cc_start: 0.7909 (pm20) cc_final: 0.7501 (pm20) REVERT: N 110 GLN cc_start: 0.8302 (mt0) cc_final: 0.7740 (mt0) REVERT: N 116 MET cc_start: 0.4996 (mtt) cc_final: 0.4381 (ttp) REVERT: O 165 ASN cc_start: 0.7571 (t0) cc_final: 0.7230 (t0) REVERT: O 172 PHE cc_start: 0.8630 (t80) cc_final: 0.8191 (t80) REVERT: O 192 LEU cc_start: 0.8655 (mt) cc_final: 0.8442 (tp) REVERT: P 140 ASP cc_start: 0.7873 (p0) cc_final: 0.7642 (p0) REVERT: P 156 TYR cc_start: 0.7882 (p90) cc_final: 0.7528 (p90) REVERT: Q 71 MET cc_start: 0.7718 (ptm) cc_final: 0.7482 (ptm) REVERT: R 133 MET cc_start: 0.6680 (mmt) cc_final: 0.6442 (mmp) REVERT: R 200 ILE cc_start: 0.5714 (mt) cc_final: 0.5489 (mt) REVERT: R 228 MET cc_start: 0.6670 (tpp) cc_final: 0.6376 (tpp) REVERT: S 114 SER cc_start: 0.8828 (t) cc_final: 0.8492 (m) REVERT: S 176 MET cc_start: 0.7676 (ptt) cc_final: 0.7366 (ptm) REVERT: S 180 MET cc_start: 0.7717 (mpp) cc_final: 0.7508 (mpp) REVERT: T 63 ASN cc_start: 0.7475 (m-40) cc_final: 0.7133 (m-40) REVERT: T 175 GLU cc_start: 0.8254 (tp30) cc_final: 0.8021 (tp30) REVERT: T 177 GLU cc_start: 0.7471 (tp30) cc_final: 0.7202 (tp30) REVERT: T 232 ARG cc_start: 0.8062 (ttp80) cc_final: 0.7589 (ttm110) REVERT: U 34 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7656 (mm-40) REVERT: U 75 ASN cc_start: 0.8149 (m-40) cc_final: 0.7509 (t0) REVERT: U 83 MET cc_start: 0.8462 (mtp) cc_final: 0.8154 (mtp) REVERT: V 24 MET cc_start: 0.8106 (mmt) cc_final: 0.7749 (mmt) REVERT: V 94 ILE cc_start: 0.5647 (mt) cc_final: 0.4429 (mt) REVERT: W 17 ASN cc_start: 0.8958 (t0) cc_final: 0.8751 (t0) REVERT: W 74 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7909 (mt-10) REVERT: W 87 MET cc_start: 0.8019 (ttp) cc_final: 0.7712 (ttp) REVERT: W 102 TYR cc_start: 0.8657 (m-80) cc_final: 0.8069 (m-80) REVERT: W 203 MET cc_start: 0.4504 (mmt) cc_final: 0.2945 (mmt) REVERT: X 1 MET cc_start: 0.4420 (tpt) cc_final: 0.3903 (tpt) REVERT: X 38 MET cc_start: 0.8035 (mmm) cc_final: 0.7483 (mmm) REVERT: X 74 GLU cc_start: 0.7219 (mp0) cc_final: 0.6993 (mp0) REVERT: X 111 GLU cc_start: 0.7563 (mp0) cc_final: 0.7270 (mp0) REVERT: X 162 LYS cc_start: 0.7422 (mttt) cc_final: 0.6890 (mtpt) REVERT: Y 7 LYS cc_start: 0.6752 (mtmt) cc_final: 0.5598 (ttmm) REVERT: Y 54 PHE cc_start: 0.7453 (t80) cc_final: 0.7125 (t80) REVERT: Y 81 LYS cc_start: 0.8225 (ttmt) cc_final: 0.7925 (ttpt) REVERT: Y 86 MET cc_start: 0.7567 (mtt) cc_final: 0.7349 (mtp) REVERT: Y 104 TRP cc_start: 0.4408 (t-100) cc_final: 0.4008 (t-100) REVERT: Y 111 LEU cc_start: 0.7400 (tp) cc_final: 0.6692 (mt) REVERT: Y 126 PHE cc_start: 0.7996 (m-80) cc_final: 0.7620 (m-10) REVERT: Z 97 TYR cc_start: 0.7592 (t80) cc_final: 0.7388 (t80) REVERT: Z 101 PHE cc_start: 0.7073 (m-80) cc_final: 0.6868 (m-80) REVERT: Z 129 SER cc_start: 0.8238 (t) cc_final: 0.7726 (p) REVERT: Z 213 ASP cc_start: 0.4164 (p0) cc_final: 0.3551 (p0) REVERT: a 103 MET cc_start: 0.8305 (tpp) cc_final: 0.7982 (mmt) REVERT: a 104 ASN cc_start: 0.7347 (t0) cc_final: 0.7051 (t0) REVERT: a 127 MET cc_start: 0.8582 (ptt) cc_final: 0.8273 (ptp) REVERT: a 154 LEU cc_start: 0.8318 (mm) cc_final: 0.8084 (mm) REVERT: a 185 ASN cc_start: 0.8615 (t0) cc_final: 0.8258 (t0) REVERT: b 116 MET cc_start: 0.5034 (mtt) cc_final: 0.4468 (ttp) outliers start: 15 outliers final: 8 residues processed: 1156 average time/residue: 0.6409 time to fit residues: 1208.7504 Evaluate side-chains 738 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 729 time to evaluate : 5.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain O residue 43 VAL Chi-restraints excluded: chain U residue 195 VAL Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain Z residue 199 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 515 optimal weight: 5.9990 chunk 463 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 312 optimal weight: 0.9980 chunk 247 optimal weight: 1.9990 chunk 478 optimal weight: 0.2980 chunk 185 optimal weight: 0.8980 chunk 291 optimal weight: 0.8980 chunk 356 optimal weight: 2.9990 chunk 554 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 38 ASN M 47 ASN M 61 GLN A 122 GLN B 40 ASN B 84 ASN B 109 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 230 GLN C 94 HIS ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN E 16 GLN F 63 ASN F 72 HIS ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN H 35 HIS H 172 ASN I 64 GLN J 8 GLN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 GLN J 189 HIS K 70 ASN K 89 GLN K 162 GLN K 175 ASN L 8 ASN L 80 ASN L 108 ASN L 157 ASN N 66 HIS ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN O 165 ASN P 40 ASN ** P 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 18 GLN Q 94 HIS Q 175 ASN Q 221 ASN ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 186 HIS S 53 GLN S 65 HIS A S 190 HIS T 72 HIS ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 35 HIS V 109 HIS ** V 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 92 ASN W 156 ASN ** X 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 ASN Z 80 ASN Z 108 ASN a 2 GLN a 38 ASN a 61 GLN b 53 GLN b 66 HIS b 110 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 49475 Z= 0.219 Angle : 0.676 13.781 66864 Z= 0.365 Chirality : 0.046 0.277 7506 Planarity : 0.005 0.086 8619 Dihedral : 6.007 50.167 6918 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.13 % Favored : 96.75 % Rotamer: Outliers : 1.90 % Allowed : 13.12 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.03 % Twisted Proline : 0.51 % Twisted General : 0.20 % 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: -1.08 (0.10), residues: 6184 helix: -0.11 (0.10), residues: 2244 sheet: -0.39 (0.13), residues: 1394 loop : -1.35 (0.11), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP T 215 HIS 0.009 0.001 HIS T 201 PHE 0.029 0.002 PHE X 171 TYR 0.025 0.002 TYR X 134 ARG 0.010 0.001 ARG S 196 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 829 time to evaluate : 5.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 96 MET cc_start: 0.8131 (mmm) cc_final: 0.7786 (mtp) REVERT: M 107 TRP cc_start: 0.7900 (m100) cc_final: 0.7564 (m100) REVERT: M 127 MET cc_start: 0.8499 (ptt) cc_final: 0.8107 (ptp) REVERT: A 69 LYS cc_start: 0.8116 (ptpt) cc_final: 0.7878 (ptpt) REVERT: A 139 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7380 (p0) REVERT: A 172 PHE cc_start: 0.8464 (t80) cc_final: 0.8194 (t80) REVERT: B 156 TYR cc_start: 0.7966 (p90) cc_final: 0.7116 (p90) REVERT: B 178 ASP cc_start: 0.8013 (t0) cc_final: 0.7573 (t0) REVERT: C 117 ARG cc_start: 0.7664 (mtm-85) cc_final: 0.7444 (mtm180) REVERT: C 204 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6778 (pttp) REVERT: D 240 ASP cc_start: 0.6809 (t0) cc_final: 0.6479 (p0) REVERT: E 114 SER cc_start: 0.8898 (t) cc_final: 0.8589 (m) REVERT: E 192 LEU cc_start: 0.8336 (mt) cc_final: 0.8003 (mt) REVERT: F 81 LEU cc_start: 0.9007 (tp) cc_final: 0.8659 (mp) REVERT: F 221 ASN cc_start: 0.8707 (t0) cc_final: 0.8326 (p0) REVERT: G 75 ASN cc_start: 0.7998 (m-40) cc_final: 0.7594 (t0) REVERT: I 74 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7838 (mt-10) REVERT: I 87 MET cc_start: 0.7905 (ttp) cc_final: 0.7365 (ttp) REVERT: I 121 CYS cc_start: 0.7794 (p) cc_final: 0.6092 (p) REVERT: I 137 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8444 (p) REVERT: I 145 MET cc_start: 0.7673 (mtt) cc_final: 0.7215 (mtt) REVERT: I 153 TRP cc_start: 0.6757 (t60) cc_final: 0.6406 (t60) REVERT: I 154 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7016 (mm-30) REVERT: I 182 MET cc_start: 0.6235 (mmm) cc_final: 0.5927 (mmm) REVERT: J 38 MET cc_start: 0.8282 (mmp) cc_final: 0.7632 (mmp) REVERT: K 81 LYS cc_start: 0.7895 (tptp) cc_final: 0.7309 (tptp) REVERT: K 85 ASN cc_start: 0.7882 (m-40) cc_final: 0.7617 (m-40) REVERT: K 97 MET cc_start: 0.1907 (ttp) cc_final: 0.1339 (ttt) REVERT: K 151 GLN cc_start: 0.8874 (tt0) cc_final: 0.8555 (mp10) REVERT: L 4 PRO cc_start: 0.8219 (Cg_endo) cc_final: 0.7990 (Cg_exo) REVERT: L 131 GLN cc_start: 0.8085 (pm20) cc_final: 0.7847 (pm20) REVERT: L 205 GLU cc_start: 0.7894 (pm20) cc_final: 0.7489 (pm20) REVERT: N 95 MET cc_start: 0.6933 (mmp) cc_final: 0.5957 (mmp) REVERT: N 116 MET cc_start: 0.4786 (mtt) cc_final: 0.4209 (ttp) REVERT: O 165 ASN cc_start: 0.7479 (t0) cc_final: 0.7190 (t0) REVERT: O 178 ASN cc_start: 0.7825 (OUTLIER) cc_final: 0.7599 (p0) REVERT: P 140 ASP cc_start: 0.7913 (p0) cc_final: 0.7696 (p0) REVERT: P 156 TYR cc_start: 0.7912 (p90) cc_final: 0.6969 (p90) REVERT: P 184 MET cc_start: 0.7896 (mmm) cc_final: 0.7687 (mmm) REVERT: Q 211 MET cc_start: 0.0176 (ttm) cc_final: -0.0066 (ttt) REVERT: R 200 ILE cc_start: 0.5836 (mt) cc_final: 0.5604 (mt) REVERT: S 36 VAL cc_start: 0.8495 (t) cc_final: 0.8281 (p) REVERT: S 114 SER cc_start: 0.8920 (t) cc_final: 0.8623 (m) REVERT: S 176 MET cc_start: 0.7593 (ptt) cc_final: 0.7376 (ptm) REVERT: T 63 ASN cc_start: 0.7344 (m-40) cc_final: 0.7061 (m-40) REVERT: T 232 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7556 (ttm110) REVERT: U 34 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7716 (mm-40) REVERT: U 75 ASN cc_start: 0.8003 (m-40) cc_final: 0.7474 (t0) REVERT: U 130 GLU cc_start: 0.8523 (pm20) cc_final: 0.7905 (pm20) REVERT: V 54 MET cc_start: 0.7510 (tmm) cc_final: 0.7214 (mmp) REVERT: V 57 GLN cc_start: 0.7302 (mt0) cc_final: 0.6671 (mt0) REVERT: V 116 HIS cc_start: 0.7839 (m-70) cc_final: 0.7612 (m-70) REVERT: V 172 ASN cc_start: 0.8159 (m-40) cc_final: 0.7948 (m110) REVERT: W 87 MET cc_start: 0.8177 (ttp) cc_final: 0.7673 (ttp) REVERT: W 102 TYR cc_start: 0.8589 (m-80) cc_final: 0.8127 (m-80) REVERT: W 121 CYS cc_start: 0.7763 (p) cc_final: 0.6187 (p) REVERT: W 153 TRP cc_start: 0.7191 (t60) cc_final: 0.6825 (t60) REVERT: W 154 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7134 (mm-30) REVERT: W 203 MET cc_start: 0.4241 (mmt) cc_final: 0.2660 (mmt) REVERT: X 74 GLU cc_start: 0.7100 (mp0) cc_final: 0.6810 (mp0) REVERT: X 82 ASN cc_start: 0.8549 (m110) cc_final: 0.8323 (m110) REVERT: X 111 GLU cc_start: 0.7406 (mp0) cc_final: 0.7126 (mp0) REVERT: X 118 MET cc_start: 0.7607 (mtp) cc_final: 0.7123 (mpp) REVERT: Y 44 THR cc_start: 0.6417 (m) cc_final: 0.5850 (m) REVERT: Y 54 PHE cc_start: 0.7455 (t80) cc_final: 0.7193 (t80) REVERT: Y 86 MET cc_start: 0.7587 (mtt) cc_final: 0.7373 (mtp) REVERT: Z 184 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7034 (tt0) REVERT: a 104 ASN cc_start: 0.7163 (t0) cc_final: 0.6698 (t0) REVERT: a 110 MET cc_start: 0.8281 (mtm) cc_final: 0.7811 (mpp) REVERT: a 127 MET cc_start: 0.8476 (ptt) cc_final: 0.8056 (ptp) REVERT: a 185 ASN cc_start: 0.8609 (t0) cc_final: 0.8346 (t0) REVERT: b 91 ARG cc_start: 0.6758 (ptt-90) cc_final: 0.6535 (pmt170) REVERT: b 92 GLU cc_start: 0.6804 (mp0) cc_final: 0.6547 (pm20) REVERT: b 95 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6145 (mmp) REVERT: b 116 MET cc_start: 0.4908 (mtt) cc_final: 0.4171 (ttp) outliers start: 88 outliers final: 48 residues processed: 870 average time/residue: 0.5625 time to fit residues: 835.3683 Evaluate side-chains 758 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 706 time to evaluate : 6.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 38 ASN Chi-restraints excluded: chain M residue 47 ASN Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain H residue 193 ASN Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 70 ASN Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 144 MET Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 178 ASN Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain R residue 157 ASP Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 139 ASP Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 195 VAL Chi-restraints excluded: chain V residue 193 ASN Chi-restraints excluded: chain W residue 92 ASN Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain Y residue 10 HIS Chi-restraints excluded: chain Y residue 58 LEU Chi-restraints excluded: chain Y residue 65 ILE Chi-restraints excluded: chain Y residue 105 ASP Chi-restraints excluded: chain Z residue 127 VAL Chi-restraints excluded: chain Z residue 199 THR Chi-restraints excluded: chain Z residue 205 GLU Chi-restraints excluded: chain a residue 38 ASN Chi-restraints excluded: chain b residue 90 TYR Chi-restraints excluded: chain b residue 95 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 308 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 461 optimal weight: 3.9990 chunk 377 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 555 optimal weight: 3.9990 chunk 600 optimal weight: 4.9990 chunk 495 optimal weight: 2.9990 chunk 551 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 445 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 38 ASN M 61 GLN A 94 GLN ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN C 92 GLN C 122 ASN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN G 238 HIS H 80 ASN H 109 HIS ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 HIS B J 193 ASN K 162 GLN L 108 ASN ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 GLN P 40 ASN P 53 HIS ** P 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 149 GLN ** Q 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 GLN W 92 ASN W 172 ASN X 8 GLN ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 99 HIS A X 110 HIS ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 70 ASN b 53 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 49475 Z= 0.538 Angle : 0.821 13.578 66864 Z= 0.434 Chirality : 0.051 0.359 7506 Planarity : 0.006 0.065 8619 Dihedral : 6.105 44.087 6917 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.60 % Favored : 95.33 % Rotamer: Outliers : 3.37 % Allowed : 15.20 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.03 % Twisted Proline : 0.51 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.10), residues: 6184 helix: 0.24 (0.10), residues: 2240 sheet: -0.46 (0.13), residues: 1387 loop : -1.51 (0.11), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP P 159 HIS 0.009 0.002 HIS L 36 PHE 0.038 0.003 PHE b 65 TYR 0.035 0.003 TYR F 149 ARG 0.010 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 707 time to evaluate : 5.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 107 TRP cc_start: 0.8087 (m100) cc_final: 0.7530 (m100) REVERT: M 127 MET cc_start: 0.8621 (ptt) cc_final: 0.8398 (ptt) REVERT: A 172 PHE cc_start: 0.8608 (t80) cc_final: 0.8361 (t80) REVERT: A 205 ASP cc_start: 0.8065 (m-30) cc_final: 0.7700 (t0) REVERT: B 178 ASP cc_start: 0.8348 (t0) cc_final: 0.8029 (t0) REVERT: B 192 LEU cc_start: 0.8804 (tp) cc_final: 0.8308 (tp) REVERT: B 238 LYS cc_start: 0.9123 (mmtt) cc_final: 0.8865 (ptmm) REVERT: C 8 THR cc_start: 0.8255 (m) cc_final: 0.7995 (p) REVERT: C 17 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7856 (m-10) REVERT: C 226 GLU cc_start: 0.6263 (tp30) cc_final: 0.5635 (mm-30) REVERT: D 228 MET cc_start: 0.7192 (tpp) cc_final: 0.6742 (tpp) REVERT: D 240 ASP cc_start: 0.6537 (t0) cc_final: 0.6227 (p0) REVERT: E 123 TYR cc_start: 0.8636 (t80) cc_final: 0.8435 (t80) REVERT: F 81 LEU cc_start: 0.9155 (tp) cc_final: 0.8645 (mm) REVERT: F 221 ASN cc_start: 0.8584 (t0) cc_final: 0.8262 (t0) REVERT: G 3 ARG cc_start: 0.6676 (tpm170) cc_final: 0.5746 (mmm160) REVERT: G 75 ASN cc_start: 0.8073 (m-40) cc_final: 0.7533 (t0) REVERT: H 109 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.6927 (m-70) REVERT: H 166 ASP cc_start: 0.7640 (t0) cc_final: 0.7268 (t0) REVERT: I 74 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: I 87 MET cc_start: 0.8037 (ttp) cc_final: 0.7426 (ttp) REVERT: I 121 CYS cc_start: 0.7816 (p) cc_final: 0.6124 (p) REVERT: I 145 MET cc_start: 0.7706 (mtt) cc_final: 0.7250 (mtt) REVERT: I 153 TRP cc_start: 0.6978 (t60) cc_final: 0.6218 (t60) REVERT: I 154 GLU cc_start: 0.7557 (mm-30) cc_final: 0.6811 (mm-30) REVERT: J 38 MET cc_start: 0.7825 (mmp) cc_final: 0.7459 (mmp) REVERT: K 81 LYS cc_start: 0.7972 (tptp) cc_final: 0.7531 (tptp) REVERT: K 85 ASN cc_start: 0.7881 (m-40) cc_final: 0.7654 (m-40) REVERT: K 97 MET cc_start: 0.1807 (ttp) cc_final: 0.1112 (ttt) REVERT: K 139 MET cc_start: 0.5822 (ttm) cc_final: 0.5516 (mtp) REVERT: L 4 PRO cc_start: 0.8305 (Cg_endo) cc_final: 0.8010 (Cg_exo) REVERT: L 131 GLN cc_start: 0.8279 (pm20) cc_final: 0.8053 (pm20) REVERT: L 205 GLU cc_start: 0.8018 (pm20) cc_final: 0.7817 (pm20) REVERT: N 185 GLU cc_start: 0.7131 (mp0) cc_final: 0.6858 (mp0) REVERT: O 165 ASN cc_start: 0.7452 (t0) cc_final: 0.7234 (t0) REVERT: Q 106 TYR cc_start: 0.7351 (t80) cc_final: 0.7024 (t80) REVERT: Q 211 MET cc_start: -0.0185 (ttm) cc_final: -0.0560 (ttt) REVERT: Q 217 LEU cc_start: 0.0543 (OUTLIER) cc_final: 0.0260 (tp) REVERT: R 78 MET cc_start: 0.8497 (ptp) cc_final: 0.8181 (ptp) REVERT: S 140 MET cc_start: 0.6915 (mmm) cc_final: 0.6430 (mpp) REVERT: T 232 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7530 (ttm110) REVERT: U 3 ARG cc_start: 0.7282 (tpp-160) cc_final: 0.6708 (mmt-90) REVERT: U 34 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8023 (mm-40) REVERT: U 75 ASN cc_start: 0.8114 (m-40) cc_final: 0.7450 (t0) REVERT: V 54 MET cc_start: 0.7671 (tmm) cc_final: 0.7204 (mmp) REVERT: V 57 GLN cc_start: 0.7704 (mt0) cc_final: 0.7058 (mt0) REVERT: V 166 ASP cc_start: 0.7753 (t0) cc_final: 0.7399 (t70) REVERT: V 172 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.8382 (m-40) REVERT: W 3 MET cc_start: 0.4138 (mmt) cc_final: 0.3857 (mmt) REVERT: W 77 GLU cc_start: 0.8696 (tp30) cc_final: 0.8368 (mm-30) REVERT: W 87 MET cc_start: 0.8323 (ttp) cc_final: 0.7603 (ttp) REVERT: W 153 TRP cc_start: 0.7086 (t60) cc_final: 0.6774 (t60) REVERT: W 154 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7257 (mm-30) REVERT: W 182 MET cc_start: 0.6010 (mmm) cc_final: 0.5665 (mmm) REVERT: W 203 MET cc_start: 0.3808 (mmt) cc_final: 0.3045 (mmm) REVERT: X 8 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: X 38 MET cc_start: 0.8208 (mmm) cc_final: 0.7300 (mmm) REVERT: X 62 LYS cc_start: 0.9042 (tmtt) cc_final: 0.8607 (tptp) REVERT: X 74 GLU cc_start: 0.7268 (mp0) cc_final: 0.7019 (mp0) REVERT: X 111 GLU cc_start: 0.7545 (mp0) cc_final: 0.7238 (mp0) REVERT: X 118 MET cc_start: 0.7742 (mtp) cc_final: 0.7079 (mpp) REVERT: Y 86 MET cc_start: 0.7589 (mtt) cc_final: 0.7368 (mtp) REVERT: Y 190 ASP cc_start: 0.5959 (m-30) cc_final: 0.5565 (m-30) REVERT: a 107 TRP cc_start: 0.8095 (m100) cc_final: 0.7543 (m100) REVERT: a 127 MET cc_start: 0.8638 (ptt) cc_final: 0.8427 (ptp) REVERT: a 185 ASN cc_start: 0.8668 (t0) cc_final: 0.8345 (t0) REVERT: b 93 ASP cc_start: 0.5378 (p0) cc_final: 0.5166 (p0) outliers start: 162 outliers final: 112 residues processed: 815 average time/residue: 0.5499 time to fit residues: 780.1928 Evaluate side-chains 756 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 638 time to evaluate : 5.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 215 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain H residue 109 HIS Chi-restraints excluded: chain H residue 193 ASN Chi-restraints excluded: chain I residue 74 GLU Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 30 ASP Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 186 ASN Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 121 ILE Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain N residue 43 CYS Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 43 VAL Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 150 SER Chi-restraints excluded: chain P residue 155 ASN Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 48 LYS Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 217 LEU Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 211 ASN Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 139 ASP Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain T residue 136 MET Chi-restraints excluded: chain T residue 178 LYS Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 195 VAL Chi-restraints excluded: chain U residue 242 LEU Chi-restraints excluded: chain V residue 172 ASN Chi-restraints excluded: chain V residue 193 ASN Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 138 SER Chi-restraints excluded: chain W residue 161 HIS Chi-restraints excluded: chain X residue 8 GLN Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 30 ASP Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain Y residue 58 LEU Chi-restraints excluded: chain Y residue 76 VAL Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Z residue 127 VAL Chi-restraints excluded: chain Z residue 199 THR Chi-restraints excluded: chain Z residue 205 GLU Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 154 LEU Chi-restraints excluded: chain a residue 189 ILE Chi-restraints excluded: chain b residue 43 CYS Chi-restraints excluded: chain b residue 90 TYR Chi-restraints excluded: chain b residue 121 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 549 optimal weight: 0.9990 chunk 417 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 373 optimal weight: 3.9990 chunk 557 optimal weight: 7.9990 chunk 590 optimal weight: 0.7980 chunk 291 optimal weight: 1.9990 chunk 528 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 108 ASN A 94 GLN B 40 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 HIS D 227 HIS ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN H 109 HIS ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 ASN K 162 GLN ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 ASN ** Q 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 227 HIS S 21 GLN ** S 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 92 ASN X 8 GLN ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 55 GLN X 186 ASN ** Z 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 157 ASN a 38 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 49475 Z= 0.272 Angle : 0.655 13.632 66864 Z= 0.348 Chirality : 0.045 0.335 7506 Planarity : 0.004 0.063 8619 Dihedral : 5.655 47.652 6917 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.59 % Favored : 96.36 % Rotamer: Outliers : 2.79 % Allowed : 17.28 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.03 % Twisted Proline : 0.51 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.10), residues: 6184 helix: 0.78 (0.11), residues: 2242 sheet: -0.35 (0.13), residues: 1373 loop : -1.39 (0.11), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP a 91 HIS 0.021 0.001 HIS H 109 PHE 0.029 0.002 PHE J 171 TYR 0.021 0.002 TYR E 137 ARG 0.004 0.000 ARG D 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 708 time to evaluate : 5.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 74 GLU cc_start: 0.7124 (tt0) cc_final: 0.6739 (tt0) REVERT: M 107 TRP cc_start: 0.8057 (m100) cc_final: 0.7508 (m100) REVERT: M 110 MET cc_start: 0.8135 (mtm) cc_final: 0.7715 (mpp) REVERT: M 127 MET cc_start: 0.8559 (ptt) cc_final: 0.8274 (ptt) REVERT: A 172 PHE cc_start: 0.8545 (t80) cc_final: 0.8309 (t80) REVERT: B 238 LYS cc_start: 0.9099 (mmtt) cc_final: 0.8857 (ptmm) REVERT: C 226 GLU cc_start: 0.6370 (tp30) cc_final: 0.5669 (mm-30) REVERT: D 240 ASP cc_start: 0.6455 (t0) cc_final: 0.6182 (p0) REVERT: E 220 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7729 (pp20) REVERT: F 81 LEU cc_start: 0.8999 (tp) cc_final: 0.8571 (mm) REVERT: F 221 ASN cc_start: 0.8619 (t0) cc_final: 0.8250 (t0) REVERT: G 75 ASN cc_start: 0.8062 (m-40) cc_final: 0.7570 (t0) REVERT: G 130 GLU cc_start: 0.8677 (pm20) cc_final: 0.7931 (pm20) REVERT: H 135 MET cc_start: 0.7794 (tpp) cc_final: 0.7254 (tpp) REVERT: H 166 ASP cc_start: 0.7604 (t0) cc_final: 0.7327 (t0) REVERT: H 172 ASN cc_start: 0.8415 (m-40) cc_final: 0.8172 (m-40) REVERT: I 87 MET cc_start: 0.7987 (ttp) cc_final: 0.7365 (ttp) REVERT: I 121 CYS cc_start: 0.7730 (p) cc_final: 0.5938 (p) REVERT: I 145 MET cc_start: 0.7475 (mtt) cc_final: 0.6998 (mtt) REVERT: I 153 TRP cc_start: 0.6971 (t60) cc_final: 0.6177 (t60) REVERT: I 154 GLU cc_start: 0.7518 (mm-30) cc_final: 0.6845 (mm-30) REVERT: I 182 MET cc_start: 0.6683 (mmm) cc_final: 0.6408 (mmm) REVERT: J 38 MET cc_start: 0.7849 (mmp) cc_final: 0.7454 (mmp) REVERT: J 61 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7724 (tm-30) REVERT: J 118 MET cc_start: 0.7411 (mtp) cc_final: 0.6579 (mpp) REVERT: K 81 LYS cc_start: 0.7915 (tptp) cc_final: 0.7326 (tptp) REVERT: K 85 ASN cc_start: 0.7875 (m-40) cc_final: 0.7521 (m-40) REVERT: K 97 MET cc_start: 0.2331 (ttp) cc_final: 0.1648 (ttt) REVERT: K 139 MET cc_start: 0.5731 (ttm) cc_final: 0.5524 (mtp) REVERT: L 4 PRO cc_start: 0.8274 (Cg_endo) cc_final: 0.7998 (Cg_exo) REVERT: L 131 GLN cc_start: 0.8238 (pm20) cc_final: 0.7990 (pm20) REVERT: L 211 ARG cc_start: 0.5762 (mtm110) cc_final: 0.5424 (mtm110) REVERT: O 165 ASN cc_start: 0.7368 (t0) cc_final: 0.7151 (t0) REVERT: P 238 LYS cc_start: 0.9416 (mttm) cc_final: 0.9203 (pttp) REVERT: Q 106 TYR cc_start: 0.7301 (t80) cc_final: 0.6977 (t80) REVERT: Q 211 MET cc_start: -0.0365 (ttm) cc_final: -0.0737 (ttt) REVERT: Q 217 LEU cc_start: 0.0527 (OUTLIER) cc_final: 0.0281 (tp) REVERT: S 114 SER cc_start: 0.8791 (t) cc_final: 0.8465 (m) REVERT: S 140 MET cc_start: 0.6594 (mmm) cc_final: 0.6150 (mpp) REVERT: T 108 LEU cc_start: 0.9436 (tp) cc_final: 0.9188 (tp) REVERT: T 184 MET cc_start: 0.7794 (ttm) cc_final: 0.7256 (ttp) REVERT: T 232 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7569 (ttm110) REVERT: U 3 ARG cc_start: 0.7257 (tpp-160) cc_final: 0.6598 (mmt-90) REVERT: U 34 GLN cc_start: 0.8325 (mm-40) cc_final: 0.8015 (mm-40) REVERT: U 75 ASN cc_start: 0.8087 (m-40) cc_final: 0.7514 (t0) REVERT: V 54 MET cc_start: 0.7636 (tmm) cc_final: 0.7195 (tmm) REVERT: V 166 ASP cc_start: 0.7692 (t0) cc_final: 0.7388 (t70) REVERT: V 172 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8193 (m-40) REVERT: W 77 GLU cc_start: 0.8642 (tp30) cc_final: 0.8374 (mm-30) REVERT: W 87 MET cc_start: 0.8244 (ttp) cc_final: 0.7582 (ttp) REVERT: W 153 TRP cc_start: 0.7177 (t60) cc_final: 0.6829 (t60) REVERT: W 154 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7180 (mm-30) REVERT: W 182 MET cc_start: 0.5941 (mmm) cc_final: 0.5294 (mmm) REVERT: W 203 MET cc_start: 0.3743 (mmt) cc_final: 0.2449 (mmt) REVERT: X 8 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6730 (tm-30) REVERT: X 62 LYS cc_start: 0.9053 (tmtt) cc_final: 0.8660 (tptp) REVERT: X 74 GLU cc_start: 0.7275 (mp0) cc_final: 0.6942 (mp0) REVERT: X 111 GLU cc_start: 0.7715 (mp0) cc_final: 0.7471 (mp0) REVERT: X 118 MET cc_start: 0.7755 (mtp) cc_final: 0.7141 (mpp) REVERT: Y 86 MET cc_start: 0.7602 (mtt) cc_final: 0.7165 (mtt) REVERT: Y 126 PHE cc_start: 0.7852 (m-80) cc_final: 0.7236 (m-10) REVERT: Y 190 ASP cc_start: 0.5853 (m-30) cc_final: 0.5534 (m-30) REVERT: Z 205 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7619 (pm20) REVERT: a 107 TRP cc_start: 0.8051 (m100) cc_final: 0.7468 (m100) REVERT: a 127 MET cc_start: 0.8632 (ptt) cc_final: 0.8218 (ptm) REVERT: a 183 SER cc_start: 0.9287 (t) cc_final: 0.9018 (p) REVERT: a 185 ASN cc_start: 0.8576 (t0) cc_final: 0.8288 (t0) REVERT: b 116 MET cc_start: 0.5072 (mtt) cc_final: 0.4843 (ttp) outliers start: 133 outliers final: 91 residues processed: 786 average time/residue: 0.5475 time to fit residues: 750.9432 Evaluate side-chains 745 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 649 time to evaluate : 5.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 215 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 193 ASN Chi-restraints excluded: chain I residue 74 GLU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 121 ILE Chi-restraints excluded: chain K residue 136 TYR Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 179 PHE Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 43 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 150 SER Chi-restraints excluded: chain P residue 155 ASN Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 48 LYS Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 217 LEU Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 157 ASP Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain T residue 136 MET Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 84 THR Chi-restraints excluded: chain U residue 195 VAL Chi-restraints excluded: chain U residue 242 LEU Chi-restraints excluded: chain V residue 172 ASN Chi-restraints excluded: chain V residue 193 ASN Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 121 CYS Chi-restraints excluded: chain W residue 138 SER Chi-restraints excluded: chain W residue 161 HIS Chi-restraints excluded: chain X residue 8 GLN Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain Y residue 56 GLU Chi-restraints excluded: chain Y residue 58 LEU Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Z residue 127 VAL Chi-restraints excluded: chain Z residue 199 THR Chi-restraints excluded: chain Z residue 205 GLU Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 154 LEU Chi-restraints excluded: chain a residue 189 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 491 optimal weight: 10.0000 chunk 335 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 439 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 chunk 503 optimal weight: 7.9990 chunk 408 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 301 optimal weight: 0.9990 chunk 530 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 108 ASN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS E 21 GLN ** F 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 ASN O 165 ASN O 168 ASN ** Q 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 227 HIS ** S 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 8 GLN ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 ASN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 186 ASN ** Y 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 162 GLN ** Z 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 81 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 49475 Z= 0.343 Angle : 0.678 13.431 66864 Z= 0.358 Chirality : 0.046 0.316 7506 Planarity : 0.005 0.051 8619 Dihedral : 5.610 65.323 6917 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.68 % Favored : 95.27 % Rotamer: Outliers : 3.79 % Allowed : 17.30 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.03 % Twisted Proline : 0.51 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.10), residues: 6184 helix: 0.85 (0.11), residues: 2248 sheet: -0.34 (0.13), residues: 1407 loop : -1.41 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Y 184 HIS 0.010 0.001 HIS R 227 PHE 0.026 0.002 PHE Y 8 TYR 0.023 0.002 TYR F 149 ARG 0.006 0.001 ARG T 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 677 time to evaluate : 5.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 107 TRP cc_start: 0.7991 (m100) cc_final: 0.7353 (m100) REVERT: M 110 MET cc_start: 0.8035 (mtm) cc_final: 0.7743 (mpp) REVERT: M 127 MET cc_start: 0.8543 (ptt) cc_final: 0.8144 (ptm) REVERT: A 51 GLN cc_start: 0.7351 (mm-40) cc_final: 0.7039 (mm-40) REVERT: A 172 PHE cc_start: 0.8616 (t80) cc_final: 0.8360 (t80) REVERT: B 181 GLU cc_start: 0.8630 (tt0) cc_final: 0.8300 (tm-30) REVERT: B 238 LYS cc_start: 0.9164 (mmtt) cc_final: 0.8916 (ptmm) REVERT: D 107 MET cc_start: 0.8031 (tpp) cc_final: 0.6782 (tpp) REVERT: D 240 ASP cc_start: 0.6547 (t0) cc_final: 0.6330 (p0) REVERT: E 53 GLN cc_start: 0.6494 (OUTLIER) cc_final: 0.4251 (pp30) REVERT: E 55 GLU cc_start: 0.1245 (OUTLIER) cc_final: 0.0833 (pm20) REVERT: E 101 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.6754 (pmt-80) REVERT: E 196 ARG cc_start: 0.7191 (ttp-170) cc_final: 0.6250 (tpt-90) REVERT: F 81 LEU cc_start: 0.9039 (tp) cc_final: 0.8558 (mm) REVERT: F 221 ASN cc_start: 0.8609 (t0) cc_final: 0.8187 (t0) REVERT: G 3 ARG cc_start: 0.6611 (tpm170) cc_final: 0.5652 (mmm160) REVERT: G 75 ASN cc_start: 0.8026 (m-40) cc_final: 0.7571 (t0) REVERT: H 166 ASP cc_start: 0.7522 (t0) cc_final: 0.7217 (t0) REVERT: H 172 ASN cc_start: 0.8481 (m-40) cc_final: 0.8275 (m-40) REVERT: I 87 MET cc_start: 0.8004 (ttp) cc_final: 0.7400 (ttp) REVERT: I 121 CYS cc_start: 0.7784 (p) cc_final: 0.6060 (p) REVERT: I 145 MET cc_start: 0.7357 (mtt) cc_final: 0.6934 (mtt) REVERT: I 153 TRP cc_start: 0.6967 (t60) cc_final: 0.6238 (t60) REVERT: I 154 GLU cc_start: 0.7527 (mm-30) cc_final: 0.6840 (mm-30) REVERT: J 38 MET cc_start: 0.7987 (mmp) cc_final: 0.7596 (mmp) REVERT: K 81 LYS cc_start: 0.7938 (tptp) cc_final: 0.7381 (tptp) REVERT: K 82 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6124 (mm) REVERT: K 85 ASN cc_start: 0.7825 (m-40) cc_final: 0.7482 (m-40) REVERT: K 151 GLN cc_start: 0.8913 (mp10) cc_final: 0.8620 (mp10) REVERT: L 4 PRO cc_start: 0.8220 (Cg_endo) cc_final: 0.7867 (Cg_exo) REVERT: L 131 GLN cc_start: 0.8254 (pm20) cc_final: 0.7990 (pm20) REVERT: L 211 ARG cc_start: 0.5809 (mtm110) cc_final: 0.5539 (mtm110) REVERT: O 94 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8624 (tm-30) REVERT: O 165 ASN cc_start: 0.7368 (t0) cc_final: 0.7145 (t0) REVERT: P 137 ILE cc_start: 0.8170 (pt) cc_final: 0.7781 (pt) REVERT: P 174 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7727 (tpp) REVERT: Q 217 LEU cc_start: 0.1066 (OUTLIER) cc_final: 0.0709 (tp) REVERT: R 78 MET cc_start: 0.8662 (ptp) cc_final: 0.8375 (ptp) REVERT: S 2 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.6136 (m-80) REVERT: S 140 MET cc_start: 0.6747 (mmm) cc_final: 0.6312 (mpp) REVERT: S 224 TYR cc_start: 0.8132 (m-10) cc_final: 0.7740 (m-10) REVERT: T 108 LEU cc_start: 0.9454 (tp) cc_final: 0.9202 (tp) REVERT: T 179 LEU cc_start: 0.8109 (mp) cc_final: 0.7896 (mp) REVERT: T 184 MET cc_start: 0.7775 (ttm) cc_final: 0.7242 (ttp) REVERT: T 232 ARG cc_start: 0.8029 (ttp80) cc_final: 0.7555 (ttm110) REVERT: U 3 ARG cc_start: 0.7235 (tpp-160) cc_final: 0.6601 (mmt-90) REVERT: U 75 ASN cc_start: 0.8064 (m-40) cc_final: 0.7483 (t0) REVERT: U 228 ARG cc_start: 0.8031 (ptm-80) cc_final: 0.7522 (ptm-80) REVERT: V 166 ASP cc_start: 0.7746 (t0) cc_final: 0.7371 (t0) REVERT: V 172 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8331 (m-40) REVERT: W 77 GLU cc_start: 0.8665 (tp30) cc_final: 0.8415 (mm-30) REVERT: W 87 MET cc_start: 0.8313 (ttp) cc_final: 0.7708 (ttp) REVERT: W 145 MET cc_start: 0.7797 (mmt) cc_final: 0.7506 (mmt) REVERT: W 153 TRP cc_start: 0.7285 (t60) cc_final: 0.7021 (t60) REVERT: W 203 MET cc_start: 0.3751 (mmt) cc_final: 0.2551 (mmt) REVERT: X 62 LYS cc_start: 0.9077 (tmtt) cc_final: 0.8841 (tptp) REVERT: X 65 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8061 (mm-40) REVERT: X 82 ASN cc_start: 0.8636 (m-40) cc_final: 0.8188 (m110) REVERT: X 118 MET cc_start: 0.7853 (mtp) cc_final: 0.7221 (mpp) REVERT: Y 81 LYS cc_start: 0.8525 (tttp) cc_final: 0.8317 (tttm) REVERT: Y 86 MET cc_start: 0.7682 (mtt) cc_final: 0.7228 (mtt) REVERT: Y 93 MET cc_start: 0.2165 (ttp) cc_final: -0.0242 (ttp) REVERT: Y 100 MET cc_start: 0.8159 (mmt) cc_final: 0.7718 (tpp) REVERT: Y 111 LEU cc_start: 0.7950 (tp) cc_final: 0.6524 (tp) REVERT: Y 126 PHE cc_start: 0.8200 (m-80) cc_final: 0.6831 (m-10) REVERT: Y 184 TRP cc_start: 0.6859 (p-90) cc_final: 0.6548 (p-90) REVERT: Y 190 ASP cc_start: 0.5938 (m-30) cc_final: 0.5634 (m-30) REVERT: a 107 TRP cc_start: 0.8086 (m100) cc_final: 0.7451 (m100) REVERT: a 127 MET cc_start: 0.8591 (ptt) cc_final: 0.8190 (ptm) REVERT: a 183 SER cc_start: 0.9288 (t) cc_final: 0.9007 (p) outliers start: 185 outliers final: 145 residues processed: 802 average time/residue: 0.5466 time to fit residues: 763.1244 Evaluate side-chains 795 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 641 time to evaluate : 6.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 215 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 101 ARG Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain H residue 193 ASN Chi-restraints excluded: chain I residue 74 GLU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 172 ASN Chi-restraints excluded: chain J residue 30 ASP Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 70 ASN Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 121 ILE Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 179 PHE Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 43 VAL Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 94 GLN Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 178 ASN Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 150 SER Chi-restraints excluded: chain P residue 155 ASN Chi-restraints excluded: chain P residue 174 MET Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain Q residue 48 LYS Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 154 HIS Chi-restraints excluded: chain Q residue 187 THR Chi-restraints excluded: chain Q residue 206 ILE Chi-restraints excluded: chain Q residue 217 LEU Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 157 ASP Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 227 HIS Chi-restraints excluded: chain S residue 2 PHE Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 139 ASP Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain T residue 136 MET Chi-restraints excluded: chain T residue 144 ASP Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 84 THR Chi-restraints excluded: chain U residue 140 LEU Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 146 GLU Chi-restraints excluded: chain U residue 195 VAL Chi-restraints excluded: chain V residue 172 ASN Chi-restraints excluded: chain V residue 193 ASN Chi-restraints excluded: chain W residue 11 MET Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 121 CYS Chi-restraints excluded: chain W residue 138 SER Chi-restraints excluded: chain W residue 161 HIS Chi-restraints excluded: chain X residue 8 GLN Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 30 ASP Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain X residue 186 ASN Chi-restraints excluded: chain Y residue 56 GLU Chi-restraints excluded: chain Y residue 58 LEU Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Y residue 147 LEU Chi-restraints excluded: chain Z residue 127 VAL Chi-restraints excluded: chain Z residue 199 THR Chi-restraints excluded: chain Z residue 205 GLU Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 70 MET Chi-restraints excluded: chain a residue 75 GLU Chi-restraints excluded: chain a residue 154 LEU Chi-restraints excluded: chain a residue 189 ILE Chi-restraints excluded: chain b residue 121 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 198 optimal weight: 2.9990 chunk 531 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 346 optimal weight: 6.9990 chunk 145 optimal weight: 0.7980 chunk 591 optimal weight: 0.6980 chunk 490 optimal weight: 10.0000 chunk 273 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 310 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN F 180 GLN G 53 GLN ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 HIS ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 ASN O 165 ASN O 168 ASN ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 186 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 49475 Z= 0.244 Angle : 0.631 13.257 66864 Z= 0.333 Chirality : 0.045 0.332 7506 Planarity : 0.004 0.060 8619 Dihedral : 5.448 78.249 6917 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.77 % Favored : 96.20 % Rotamer: Outliers : 3.31 % Allowed : 18.14 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.03 % Twisted Proline : 0.51 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.10), residues: 6184 helix: 1.13 (0.11), residues: 2232 sheet: -0.19 (0.13), residues: 1381 loop : -1.32 (0.12), residues: 2571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Y 104 HIS 0.025 0.001 HIS R 227 PHE 0.029 0.002 PHE X 83 TYR 0.021 0.001 TYR E 137 ARG 0.004 0.000 ARG U 228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 681 time to evaluate : 5.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 74 GLU cc_start: 0.7246 (tt0) cc_final: 0.7034 (tt0) REVERT: M 107 TRP cc_start: 0.7992 (m100) cc_final: 0.7144 (m100) REVERT: M 110 MET cc_start: 0.7968 (mtm) cc_final: 0.7729 (mpp) REVERT: M 127 MET cc_start: 0.8536 (ptt) cc_final: 0.8199 (ptp) REVERT: A 51 GLN cc_start: 0.7159 (mm-40) cc_final: 0.6862 (mm-40) REVERT: B 156 TYR cc_start: 0.7993 (p90) cc_final: 0.7621 (p90) REVERT: B 181 GLU cc_start: 0.8587 (tt0) cc_final: 0.8330 (tm-30) REVERT: B 238 LYS cc_start: 0.9179 (mmtt) cc_final: 0.8940 (ptmm) REVERT: D 107 MET cc_start: 0.7885 (tpp) cc_final: 0.7227 (tpp) REVERT: E 53 GLN cc_start: 0.6374 (OUTLIER) cc_final: 0.4360 (pp30) REVERT: E 55 GLU cc_start: 0.0562 (OUTLIER) cc_final: -0.0061 (pm20) REVERT: E 196 ARG cc_start: 0.7267 (ttp-170) cc_final: 0.6453 (tpt170) REVERT: F 81 LEU cc_start: 0.8996 (tp) cc_final: 0.8563 (mm) REVERT: F 221 ASN cc_start: 0.8506 (t0) cc_final: 0.8130 (t0) REVERT: G 3 ARG cc_start: 0.6649 (tpm170) cc_final: 0.5679 (mmm160) REVERT: G 75 ASN cc_start: 0.8014 (m-40) cc_final: 0.7593 (t0) REVERT: G 130 GLU cc_start: 0.8641 (pm20) cc_final: 0.7866 (pm20) REVERT: H 166 ASP cc_start: 0.7521 (t0) cc_final: 0.7236 (t0) REVERT: H 172 ASN cc_start: 0.8419 (m-40) cc_final: 0.8189 (m-40) REVERT: I 87 MET cc_start: 0.7986 (ttp) cc_final: 0.7352 (ttp) REVERT: I 121 CYS cc_start: 0.7676 (p) cc_final: 0.5871 (p) REVERT: I 145 MET cc_start: 0.7444 (mtt) cc_final: 0.6993 (mtt) REVERT: I 153 TRP cc_start: 0.6992 (t60) cc_final: 0.6284 (t60) REVERT: I 154 GLU cc_start: 0.7484 (mm-30) cc_final: 0.6858 (mm-30) REVERT: K 81 LYS cc_start: 0.7841 (tptp) cc_final: 0.7223 (tptp) REVERT: K 82 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.6084 (mm) REVERT: K 85 ASN cc_start: 0.7893 (m-40) cc_final: 0.7565 (m-40) REVERT: K 104 TRP cc_start: 0.3856 (t-100) cc_final: 0.2845 (t-100) REVERT: L 4 PRO cc_start: 0.8202 (Cg_endo) cc_final: 0.7946 (Cg_exo) REVERT: L 131 GLN cc_start: 0.8214 (pm20) cc_final: 0.7947 (pm20) REVERT: L 206 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7462 (tm-30) REVERT: L 211 ARG cc_start: 0.5659 (mtm110) cc_final: 0.5380 (mtm110) REVERT: N 116 MET cc_start: 0.5049 (mtt) cc_final: 0.4848 (mtt) REVERT: O 3 ARG cc_start: 0.4579 (OUTLIER) cc_final: 0.3675 (tpp-160) REVERT: O 165 ASN cc_start: 0.7342 (t0) cc_final: 0.7134 (t0) REVERT: Q 217 LEU cc_start: 0.0996 (OUTLIER) cc_final: 0.0545 (tp) REVERT: R 78 MET cc_start: 0.8687 (ptp) cc_final: 0.8346 (ptp) REVERT: S 2 PHE cc_start: 0.6507 (OUTLIER) cc_final: 0.5996 (m-80) REVERT: S 114 SER cc_start: 0.8772 (t) cc_final: 0.8454 (m) REVERT: S 140 MET cc_start: 0.6714 (mmm) cc_final: 0.6254 (mpp) REVERT: S 224 TYR cc_start: 0.8109 (m-10) cc_final: 0.7737 (m-10) REVERT: T 27 MET cc_start: 0.8314 (mmm) cc_final: 0.8022 (mmm) REVERT: T 108 LEU cc_start: 0.9418 (tp) cc_final: 0.9177 (tp) REVERT: T 175 GLU cc_start: 0.8731 (tp30) cc_final: 0.8322 (tp30) REVERT: T 179 LEU cc_start: 0.8076 (mp) cc_final: 0.7521 (mp) REVERT: T 184 MET cc_start: 0.7652 (ttm) cc_final: 0.7124 (ttp) REVERT: T 232 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7526 (ttm110) REVERT: U 3 ARG cc_start: 0.7195 (tpp-160) cc_final: 0.6643 (mmt-90) REVERT: U 75 ASN cc_start: 0.8051 (m-40) cc_final: 0.7494 (t0) REVERT: U 228 ARG cc_start: 0.8095 (ptm-80) cc_final: 0.7518 (ptm-80) REVERT: V 166 ASP cc_start: 0.7684 (t0) cc_final: 0.7354 (t0) REVERT: V 172 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.8233 (m-40) REVERT: W 87 MET cc_start: 0.8277 (ttp) cc_final: 0.7591 (ttp) REVERT: W 120 ILE cc_start: 0.8855 (mm) cc_final: 0.8432 (pt) REVERT: W 145 MET cc_start: 0.7796 (mmt) cc_final: 0.7555 (mmp) REVERT: W 153 TRP cc_start: 0.7193 (t60) cc_final: 0.6919 (t60) REVERT: W 182 MET cc_start: 0.5957 (mmm) cc_final: 0.5422 (mmm) REVERT: W 203 MET cc_start: 0.3759 (mmt) cc_final: 0.2421 (mmt) REVERT: X 2 GLU cc_start: 0.6538 (mm-30) cc_final: 0.5787 (mm-30) REVERT: X 38 MET cc_start: 0.8174 (mmm) cc_final: 0.7756 (mmm) REVERT: X 62 LYS cc_start: 0.9080 (tmtt) cc_final: 0.8600 (tptp) REVERT: X 82 ASN cc_start: 0.8551 (m-40) cc_final: 0.8082 (m110) REVERT: X 118 MET cc_start: 0.7793 (mtp) cc_final: 0.7163 (mpp) REVERT: Y 86 MET cc_start: 0.7703 (mtt) cc_final: 0.7249 (mtt) REVERT: Y 100 MET cc_start: 0.8040 (mmt) cc_final: 0.7645 (mtt) REVERT: Y 184 TRP cc_start: 0.6934 (p-90) cc_final: 0.6634 (p-90) REVERT: Y 190 ASP cc_start: 0.6094 (m-30) cc_final: 0.5807 (m-30) REVERT: Z 205 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7675 (pm20) REVERT: a 107 TRP cc_start: 0.8062 (m100) cc_final: 0.7487 (m100) REVERT: a 127 MET cc_start: 0.8546 (ptt) cc_final: 0.8139 (ptm) REVERT: a 183 SER cc_start: 0.9282 (t) cc_final: 0.9004 (p) outliers start: 160 outliers final: 121 residues processed: 787 average time/residue: 0.5568 time to fit residues: 758.8724 Evaluate side-chains 774 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 645 time to evaluate : 5.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 215 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain H residue 193 ASN Chi-restraints excluded: chain I residue 74 GLU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 172 ASN Chi-restraints excluded: chain J residue 30 ASP Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 MET Chi-restraints excluded: chain K residue 70 ASN Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain O residue 3 ARG Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 43 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 178 ASN Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 150 SER Chi-restraints excluded: chain P residue 155 ASN Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 48 LYS Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 206 ILE Chi-restraints excluded: chain Q residue 217 LEU Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 157 ASP Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain S residue 2 PHE Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 215 VAL Chi-restraints excluded: chain T residue 136 MET Chi-restraints excluded: chain T residue 144 ASP Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 140 LEU Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 146 GLU Chi-restraints excluded: chain U residue 195 VAL Chi-restraints excluded: chain V residue 172 ASN Chi-restraints excluded: chain V residue 193 ASN Chi-restraints excluded: chain W residue 11 MET Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 121 CYS Chi-restraints excluded: chain W residue 138 SER Chi-restraints excluded: chain W residue 161 HIS Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain Y residue 56 GLU Chi-restraints excluded: chain Y residue 58 LEU Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Y residue 147 LEU Chi-restraints excluded: chain Z residue 127 VAL Chi-restraints excluded: chain Z residue 199 THR Chi-restraints excluded: chain Z residue 205 GLU Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 70 MET Chi-restraints excluded: chain a residue 154 LEU Chi-restraints excluded: chain a residue 189 ILE Chi-restraints excluded: chain b residue 121 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 569 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 336 optimal weight: 6.9990 chunk 431 optimal weight: 2.9990 chunk 334 optimal weight: 0.3980 chunk 497 optimal weight: 0.8980 chunk 330 optimal weight: 0.0980 chunk 588 optimal weight: 4.9990 chunk 368 optimal weight: 9.9990 chunk 359 optimal weight: 10.0000 chunk 271 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 165 ASN O 168 ASN ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 8 GLN ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 189 HIS ** Y 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 53 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 49475 Z= 0.201 Angle : 0.611 13.685 66864 Z= 0.322 Chirality : 0.044 0.355 7506 Planarity : 0.004 0.052 8619 Dihedral : 5.309 87.631 6917 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.07 % Rotamer: Outliers : 3.12 % Allowed : 18.74 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.11), residues: 6184 helix: 1.33 (0.11), residues: 2229 sheet: -0.12 (0.13), residues: 1394 loop : -1.25 (0.12), residues: 2561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 104 HIS 0.005 0.001 HIS R 227 PHE 0.027 0.001 PHE Y 8 TYR 0.019 0.001 TYR P 156 ARG 0.008 0.000 ARG J 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 699 time to evaluate : 6.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 74 GLU cc_start: 0.7263 (tt0) cc_final: 0.7059 (tt0) REVERT: M 107 TRP cc_start: 0.7976 (m100) cc_final: 0.7229 (m100) REVERT: M 127 MET cc_start: 0.8471 (ptt) cc_final: 0.8172 (ptm) REVERT: A 94 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8161 (tt0) REVERT: A 172 PHE cc_start: 0.8616 (t80) cc_final: 0.8268 (t80) REVERT: B 156 TYR cc_start: 0.7934 (p90) cc_final: 0.7629 (p90) REVERT: B 181 GLU cc_start: 0.8580 (tt0) cc_final: 0.8363 (tm-30) REVERT: B 238 LYS cc_start: 0.9153 (mmtt) cc_final: 0.8934 (ptmm) REVERT: D 107 MET cc_start: 0.7792 (tpp) cc_final: 0.7202 (tpp) REVERT: E 101 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.6777 (pmt-80) REVERT: E 196 ARG cc_start: 0.7337 (ttp-170) cc_final: 0.6361 (tpt-90) REVERT: F 81 LEU cc_start: 0.8966 (tp) cc_final: 0.8531 (mm) REVERT: F 221 ASN cc_start: 0.8486 (t0) cc_final: 0.8115 (t0) REVERT: G 3 ARG cc_start: 0.6572 (tpm170) cc_final: 0.5623 (mmm160) REVERT: G 75 ASN cc_start: 0.7990 (m-40) cc_final: 0.7614 (t0) REVERT: G 130 GLU cc_start: 0.8582 (pm20) cc_final: 0.7818 (pm20) REVERT: H 166 ASP cc_start: 0.7495 (t0) cc_final: 0.7241 (t0) REVERT: H 172 ASN cc_start: 0.8377 (m-40) cc_final: 0.8169 (m-40) REVERT: I 87 MET cc_start: 0.7959 (ttp) cc_final: 0.7340 (ttp) REVERT: I 121 CYS cc_start: 0.7688 (p) cc_final: 0.5816 (p) REVERT: I 145 MET cc_start: 0.7254 (mtt) cc_final: 0.6848 (mtt) REVERT: I 153 TRP cc_start: 0.6979 (t60) cc_final: 0.6291 (t60) REVERT: I 154 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6892 (mm-30) REVERT: I 182 MET cc_start: 0.7805 (mtp) cc_final: 0.6621 (mmm) REVERT: K 81 LYS cc_start: 0.7789 (tptp) cc_final: 0.7180 (tptp) REVERT: K 82 LEU cc_start: 0.6328 (OUTLIER) cc_final: 0.6052 (mm) REVERT: K 85 ASN cc_start: 0.7938 (m-40) cc_final: 0.7667 (m-40) REVERT: K 151 GLN cc_start: 0.8928 (mp10) cc_final: 0.8645 (mp10) REVERT: L 2 PHE cc_start: 0.6589 (t80) cc_final: 0.6291 (t80) REVERT: L 4 PRO cc_start: 0.8200 (Cg_endo) cc_final: 0.7829 (Cg_exo) REVERT: L 131 GLN cc_start: 0.8140 (pm20) cc_final: 0.7876 (pm20) REVERT: L 150 ASP cc_start: 0.7715 (t0) cc_final: 0.7384 (t0) REVERT: O 3 ARG cc_start: 0.4683 (OUTLIER) cc_final: 0.3781 (tpp-160) REVERT: O 94 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8256 (tt0) REVERT: Q 106 TYR cc_start: 0.7498 (t80) cc_final: 0.7182 (t80) REVERT: Q 217 LEU cc_start: 0.1359 (OUTLIER) cc_final: 0.0889 (tp) REVERT: R 78 MET cc_start: 0.8677 (ptp) cc_final: 0.8451 (ptp) REVERT: R 107 MET cc_start: 0.7711 (tpp) cc_final: 0.7240 (tpp) REVERT: R 129 ASP cc_start: 0.4643 (OUTLIER) cc_final: 0.4327 (p0) REVERT: R 168 ARG cc_start: 0.5500 (tpp80) cc_final: 0.5053 (tpp80) REVERT: S 2 PHE cc_start: 0.6458 (OUTLIER) cc_final: 0.6139 (m-80) REVERT: S 114 SER cc_start: 0.8763 (t) cc_final: 0.8470 (m) REVERT: S 140 MET cc_start: 0.6680 (mmm) cc_final: 0.6295 (mpp) REVERT: S 159 MET cc_start: 0.8459 (tpp) cc_final: 0.8178 (tpt) REVERT: S 224 TYR cc_start: 0.8115 (m-10) cc_final: 0.7787 (m-10) REVERT: T 175 GLU cc_start: 0.8664 (tp30) cc_final: 0.8299 (tp30) REVERT: T 179 LEU cc_start: 0.8150 (mp) cc_final: 0.7631 (mp) REVERT: T 232 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7522 (ttm110) REVERT: U 3 ARG cc_start: 0.7243 (tpp-160) cc_final: 0.6718 (mmt-90) REVERT: U 75 ASN cc_start: 0.8004 (m-40) cc_final: 0.7503 (t0) REVERT: U 228 ARG cc_start: 0.8078 (ptm-80) cc_final: 0.7518 (ptm-80) REVERT: V 37 ILE cc_start: 0.8627 (mm) cc_final: 0.8355 (mt) REVERT: V 166 ASP cc_start: 0.7630 (t0) cc_final: 0.7307 (t0) REVERT: V 172 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8150 (m-40) REVERT: W 87 MET cc_start: 0.8252 (ttp) cc_final: 0.7688 (ttp) REVERT: W 120 ILE cc_start: 0.8841 (mm) cc_final: 0.8415 (pt) REVERT: W 153 TRP cc_start: 0.7206 (t60) cc_final: 0.6917 (t60) REVERT: W 154 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7393 (mm-30) REVERT: W 182 MET cc_start: 0.5961 (mmm) cc_final: 0.5441 (mmm) REVERT: W 203 MET cc_start: 0.3670 (mmt) cc_final: 0.2305 (mmt) REVERT: X 38 MET cc_start: 0.8352 (mmm) cc_final: 0.7243 (mmm) REVERT: X 62 LYS cc_start: 0.9057 (tmtt) cc_final: 0.8514 (tptp) REVERT: X 65 GLN cc_start: 0.8298 (mm-40) cc_final: 0.8040 (mm-40) REVERT: X 102 LEU cc_start: 0.8783 (mt) cc_final: 0.8408 (mm) REVERT: X 118 MET cc_start: 0.7771 (mtp) cc_final: 0.7189 (mpp) REVERT: Y 86 MET cc_start: 0.7711 (mtt) cc_final: 0.7237 (mtt) REVERT: Y 100 MET cc_start: 0.7980 (mmt) cc_final: 0.7680 (mtt) REVERT: Y 184 TRP cc_start: 0.7054 (p-90) cc_final: 0.6841 (p-90) REVERT: Y 190 ASP cc_start: 0.6143 (m-30) cc_final: 0.5848 (m-30) REVERT: Z 108 ASN cc_start: 0.8593 (m-40) cc_final: 0.8284 (t0) REVERT: Z 205 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7680 (pm20) REVERT: a 107 TRP cc_start: 0.8035 (m100) cc_final: 0.7375 (m100) REVERT: a 127 MET cc_start: 0.8466 (ptt) cc_final: 0.8264 (ptp) REVERT: a 183 SER cc_start: 0.9267 (t) cc_final: 0.8971 (p) outliers start: 150 outliers final: 113 residues processed: 799 average time/residue: 0.5671 time to fit residues: 787.3499 Evaluate side-chains 779 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 658 time to evaluate : 6.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 215 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 101 ARG Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 193 ASN Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 172 ASN Chi-restraints excluded: chain J residue 30 ASP Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 MET Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 179 PHE Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain O residue 3 ARG Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 43 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 178 ASN Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 150 SER Chi-restraints excluded: chain P residue 155 ASN Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 48 LYS Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 206 ILE Chi-restraints excluded: chain Q residue 217 LEU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 157 ASP Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain S residue 2 PHE Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 139 ASP Chi-restraints excluded: chain S residue 215 VAL Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 136 MET Chi-restraints excluded: chain T residue 144 ASP Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 84 THR Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 146 GLU Chi-restraints excluded: chain U residue 195 VAL Chi-restraints excluded: chain V residue 172 ASN Chi-restraints excluded: chain V residue 193 ASN Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 121 CYS Chi-restraints excluded: chain W residue 138 SER Chi-restraints excluded: chain W residue 161 HIS Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain Y residue 56 GLU Chi-restraints excluded: chain Y residue 58 LEU Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Y residue 147 LEU Chi-restraints excluded: chain Z residue 127 VAL Chi-restraints excluded: chain Z residue 199 THR Chi-restraints excluded: chain Z residue 205 GLU Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 70 MET Chi-restraints excluded: chain a residue 154 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 364 optimal weight: 0.4980 chunk 235 optimal weight: 3.9990 chunk 351 optimal weight: 0.0670 chunk 177 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 374 optimal weight: 8.9990 chunk 401 optimal weight: 3.9990 chunk 291 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 462 optimal weight: 8.9990 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 GLN O 168 ASN P 84 ASN ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 8 GLN ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 49475 Z= 0.208 Angle : 0.617 14.124 66864 Z= 0.324 Chirality : 0.044 0.346 7506 Planarity : 0.004 0.050 8619 Dihedral : 5.199 85.238 6916 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.69 % Favored : 96.26 % Rotamer: Outliers : 2.90 % Allowed : 18.81 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.11), residues: 6184 helix: 1.41 (0.11), residues: 2232 sheet: -0.04 (0.14), residues: 1381 loop : -1.22 (0.12), residues: 2571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 91 HIS 0.006 0.001 HIS N 66 PHE 0.030 0.002 PHE X 83 TYR 0.018 0.001 TYR P 156 ARG 0.011 0.000 ARG R 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 695 time to evaluate : 6.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 74 GLU cc_start: 0.7226 (tt0) cc_final: 0.7010 (tt0) REVERT: M 107 TRP cc_start: 0.7922 (m100) cc_final: 0.7272 (m100) REVERT: M 127 MET cc_start: 0.8473 (ptt) cc_final: 0.8124 (ptt) REVERT: A 172 PHE cc_start: 0.8627 (t80) cc_final: 0.8275 (t80) REVERT: B 156 TYR cc_start: 0.7938 (p90) cc_final: 0.7656 (p90) REVERT: B 174 MET cc_start: 0.7996 (mpp) cc_final: 0.7760 (tpt) REVERT: B 238 LYS cc_start: 0.9136 (mmtt) cc_final: 0.8927 (ptmm) REVERT: D 107 MET cc_start: 0.7774 (tpp) cc_final: 0.7146 (tpp) REVERT: E 101 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.6739 (pmt-80) REVERT: E 114 SER cc_start: 0.8803 (t) cc_final: 0.8535 (m) REVERT: E 196 ARG cc_start: 0.7434 (ttp-170) cc_final: 0.6436 (tpt-90) REVERT: F 81 LEU cc_start: 0.8961 (tp) cc_final: 0.8517 (mm) REVERT: G 3 ARG cc_start: 0.6560 (tpm170) cc_final: 0.5571 (mmm160) REVERT: G 75 ASN cc_start: 0.7978 (m-40) cc_final: 0.7608 (t0) REVERT: G 130 GLU cc_start: 0.8576 (pm20) cc_final: 0.7836 (pm20) REVERT: H 166 ASP cc_start: 0.7536 (t0) cc_final: 0.7252 (t0) REVERT: H 172 ASN cc_start: 0.8347 (m-40) cc_final: 0.8133 (m-40) REVERT: I 87 MET cc_start: 0.7943 (ttp) cc_final: 0.7331 (ttp) REVERT: I 121 CYS cc_start: 0.7610 (p) cc_final: 0.5703 (p) REVERT: I 145 MET cc_start: 0.7244 (mtt) cc_final: 0.6844 (mtt) REVERT: I 153 TRP cc_start: 0.6993 (t60) cc_final: 0.6297 (t60) REVERT: I 154 GLU cc_start: 0.7553 (mm-30) cc_final: 0.6927 (mm-30) REVERT: I 182 MET cc_start: 0.7897 (mtp) cc_final: 0.6652 (mtp) REVERT: J 38 MET cc_start: 0.8070 (mmp) cc_final: 0.7604 (mmp) REVERT: J 61 GLN cc_start: 0.8305 (tm-30) cc_final: 0.7925 (tm-30) REVERT: K 81 LYS cc_start: 0.7798 (tptp) cc_final: 0.7217 (tptp) REVERT: K 82 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.6001 (mm) REVERT: K 85 ASN cc_start: 0.7966 (m-40) cc_final: 0.7684 (m-40) REVERT: K 100 MET cc_start: 0.7808 (ttm) cc_final: 0.7233 (mtt) REVERT: K 151 GLN cc_start: 0.8912 (mp10) cc_final: 0.8611 (mp10) REVERT: K 184 TRP cc_start: 0.6845 (p-90) cc_final: 0.6473 (p-90) REVERT: K 190 ASP cc_start: 0.5838 (m-30) cc_final: 0.5470 (m-30) REVERT: L 4 PRO cc_start: 0.8219 (Cg_endo) cc_final: 0.7868 (Cg_exo) REVERT: L 131 GLN cc_start: 0.8156 (pm20) cc_final: 0.7872 (pm20) REVERT: L 150 ASP cc_start: 0.7665 (t0) cc_final: 0.7308 (t0) REVERT: O 3 ARG cc_start: 0.4753 (OUTLIER) cc_final: 0.3842 (tpp-160) REVERT: O 94 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8187 (tt0) REVERT: Q 85 ASN cc_start: 0.8620 (m-40) cc_final: 0.8314 (t0) REVERT: Q 217 LEU cc_start: 0.1277 (OUTLIER) cc_final: 0.0781 (tp) REVERT: R 54 ILE cc_start: 0.5339 (mm) cc_final: 0.5135 (tt) REVERT: R 59 MET cc_start: 0.4330 (ppp) cc_final: 0.3774 (ppp) REVERT: R 78 MET cc_start: 0.8679 (ptp) cc_final: 0.8449 (ptp) REVERT: R 107 MET cc_start: 0.7736 (tpp) cc_final: 0.7266 (tpp) REVERT: R 110 GLU cc_start: 0.8155 (tp30) cc_final: 0.7175 (tp30) REVERT: R 168 ARG cc_start: 0.5810 (tpp80) cc_final: 0.5596 (tpp80) REVERT: S 2 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.6239 (m-80) REVERT: S 114 SER cc_start: 0.8780 (t) cc_final: 0.8496 (m) REVERT: S 140 MET cc_start: 0.6680 (mmm) cc_final: 0.6287 (mpp) REVERT: S 160 SER cc_start: 0.8891 (m) cc_final: 0.8508 (p) REVERT: S 224 TYR cc_start: 0.8145 (m-10) cc_final: 0.7827 (m-10) REVERT: T 108 LEU cc_start: 0.9353 (tp) cc_final: 0.9150 (tp) REVERT: T 175 GLU cc_start: 0.8666 (tp30) cc_final: 0.8308 (tp30) REVERT: T 179 LEU cc_start: 0.8154 (mp) cc_final: 0.7645 (mp) REVERT: T 232 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7523 (ttm110) REVERT: U 3 ARG cc_start: 0.7244 (tpp-160) cc_final: 0.6746 (mmt-90) REVERT: U 75 ASN cc_start: 0.8003 (m-40) cc_final: 0.7509 (t0) REVERT: U 228 ARG cc_start: 0.7974 (ptm-80) cc_final: 0.7403 (ptm-80) REVERT: V 166 ASP cc_start: 0.7680 (t0) cc_final: 0.7363 (t0) REVERT: V 172 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8125 (m-40) REVERT: W 87 MET cc_start: 0.8265 (ttp) cc_final: 0.7677 (ttp) REVERT: W 120 ILE cc_start: 0.8837 (mm) cc_final: 0.8417 (pt) REVERT: W 153 TRP cc_start: 0.7240 (t60) cc_final: 0.6960 (t60) REVERT: W 154 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7317 (mm-30) REVERT: W 182 MET cc_start: 0.5916 (mmm) cc_final: 0.5401 (mmm) REVERT: W 203 MET cc_start: 0.3648 (mmt) cc_final: 0.2327 (mmt) REVERT: X 2 GLU cc_start: 0.6241 (mm-30) cc_final: 0.5597 (mm-30) REVERT: X 38 MET cc_start: 0.8365 (mmm) cc_final: 0.7366 (mmm) REVERT: X 62 LYS cc_start: 0.9048 (tmtt) cc_final: 0.8502 (tptp) REVERT: X 102 LEU cc_start: 0.8711 (mt) cc_final: 0.8325 (mm) REVERT: X 118 MET cc_start: 0.7716 (mtp) cc_final: 0.7153 (mpp) REVERT: Y 86 MET cc_start: 0.7730 (mtt) cc_final: 0.7270 (mtt) REVERT: Y 184 TRP cc_start: 0.7201 (p-90) cc_final: 0.6995 (p-90) REVERT: Y 190 ASP cc_start: 0.6240 (m-30) cc_final: 0.5989 (m-30) REVERT: Z 12 ILE cc_start: 0.8720 (mm) cc_final: 0.8214 (mt) REVERT: Z 108 ASN cc_start: 0.8579 (m-40) cc_final: 0.8304 (t0) REVERT: Z 184 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7086 (mt-10) REVERT: Z 205 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7658 (pm20) REVERT: a 5 MET cc_start: 0.6724 (tpt) cc_final: 0.6463 (tpt) REVERT: a 107 TRP cc_start: 0.8052 (m100) cc_final: 0.7345 (m100) REVERT: a 127 MET cc_start: 0.8437 (ptt) cc_final: 0.8201 (ptp) REVERT: a 183 SER cc_start: 0.9258 (t) cc_final: 0.8981 (p) REVERT: b 116 MET cc_start: 0.5953 (ttp) cc_final: 0.5604 (ttp) outliers start: 139 outliers final: 120 residues processed: 789 average time/residue: 0.5891 time to fit residues: 811.1500 Evaluate side-chains 793 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 666 time to evaluate : 6.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 215 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 101 ARG Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain H residue 193 ASN Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 172 ASN Chi-restraints excluded: chain J residue 30 ASP Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain O residue 3 ARG Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 43 VAL Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 178 ASN Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 150 SER Chi-restraints excluded: chain P residue 155 ASN Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain Q residue 48 LYS Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 187 THR Chi-restraints excluded: chain Q residue 206 ILE Chi-restraints excluded: chain Q residue 217 LEU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 157 ASP Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain S residue 2 PHE Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 139 ASP Chi-restraints excluded: chain S residue 215 VAL Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 136 MET Chi-restraints excluded: chain T residue 144 ASP Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 84 THR Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 126 THR Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 146 GLU Chi-restraints excluded: chain U residue 195 VAL Chi-restraints excluded: chain V residue 172 ASN Chi-restraints excluded: chain V residue 193 ASN Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 121 CYS Chi-restraints excluded: chain W residue 138 SER Chi-restraints excluded: chain W residue 161 HIS Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain Y residue 56 GLU Chi-restraints excluded: chain Y residue 58 LEU Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Y residue 147 LEU Chi-restraints excluded: chain Z residue 127 VAL Chi-restraints excluded: chain Z residue 199 THR Chi-restraints excluded: chain Z residue 205 GLU Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 70 MET Chi-restraints excluded: chain a residue 154 LEU Chi-restraints excluded: chain b residue 121 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 535 optimal weight: 6.9990 chunk 564 optimal weight: 8.9990 chunk 514 optimal weight: 8.9990 chunk 548 optimal weight: 2.9990 chunk 330 optimal weight: 0.3980 chunk 239 optimal weight: 10.0000 chunk 430 optimal weight: 0.5980 chunk 168 optimal weight: 0.7980 chunk 495 optimal weight: 5.9990 chunk 519 optimal weight: 3.9990 chunk 546 optimal weight: 20.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 HIS K 70 ASN ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 147 GLN b 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 49475 Z= 0.274 Angle : 0.654 14.428 66864 Z= 0.342 Chirality : 0.045 0.366 7506 Planarity : 0.004 0.051 8619 Dihedral : 5.252 76.013 6916 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.33 % Favored : 95.63 % Rotamer: Outliers : 3.19 % Allowed : 18.97 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.11), residues: 6184 helix: 1.34 (0.11), residues: 2226 sheet: -0.06 (0.14), residues: 1403 loop : -1.20 (0.12), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Q 156 HIS 0.006 0.001 HIS N 66 PHE 0.027 0.002 PHE Y 8 TYR 0.019 0.002 TYR E 137 ARG 0.010 0.000 ARG R 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 675 time to evaluate : 5.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 107 TRP cc_start: 0.7993 (m100) cc_final: 0.7320 (m100) REVERT: M 127 MET cc_start: 0.8433 (ptt) cc_final: 0.8086 (ptm) REVERT: A 172 PHE cc_start: 0.8668 (t80) cc_final: 0.8385 (t80) REVERT: B 156 TYR cc_start: 0.7856 (p90) cc_final: 0.7524 (p90) REVERT: B 174 MET cc_start: 0.8047 (mpp) cc_final: 0.7587 (tpt) REVERT: B 178 ASP cc_start: 0.8512 (t0) cc_final: 0.7636 (p0) REVERT: B 238 LYS cc_start: 0.9136 (mmtt) cc_final: 0.8913 (ptmm) REVERT: D 107 MET cc_start: 0.7787 (tpp) cc_final: 0.7160 (tpp) REVERT: E 101 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.6728 (pmt-80) REVERT: E 196 ARG cc_start: 0.7501 (ttp-170) cc_final: 0.6485 (tpt-90) REVERT: F 81 LEU cc_start: 0.9010 (tp) cc_final: 0.8565 (mm) REVERT: G 3 ARG cc_start: 0.6716 (tpm170) cc_final: 0.5699 (mmm160) REVERT: G 75 ASN cc_start: 0.7991 (m-40) cc_final: 0.7606 (t0) REVERT: H 166 ASP cc_start: 0.7592 (t0) cc_final: 0.7292 (t0) REVERT: I 87 MET cc_start: 0.7965 (ttp) cc_final: 0.7363 (ttp) REVERT: I 105 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: I 121 CYS cc_start: 0.7621 (p) cc_final: 0.5646 (p) REVERT: I 145 MET cc_start: 0.7122 (mtt) cc_final: 0.6784 (mtt) REVERT: I 153 TRP cc_start: 0.7035 (t60) cc_final: 0.6402 (t60) REVERT: I 154 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6933 (mm-30) REVERT: I 182 MET cc_start: 0.7928 (mtp) cc_final: 0.6477 (mtp) REVERT: J 38 MET cc_start: 0.7974 (mmp) cc_final: 0.7514 (mmp) REVERT: K 70 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7731 (t0) REVERT: K 81 LYS cc_start: 0.7776 (tptp) cc_final: 0.7195 (tptp) REVERT: K 82 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.6004 (mm) REVERT: K 85 ASN cc_start: 0.7962 (m-40) cc_final: 0.7685 (m-40) REVERT: K 100 MET cc_start: 0.7838 (ttm) cc_final: 0.7252 (mtt) REVERT: K 151 GLN cc_start: 0.8883 (mp10) cc_final: 0.8604 (mp10) REVERT: K 184 TRP cc_start: 0.6872 (p-90) cc_final: 0.6507 (p-90) REVERT: K 190 ASP cc_start: 0.5806 (m-30) cc_final: 0.5464 (m-30) REVERT: L 4 PRO cc_start: 0.8208 (Cg_endo) cc_final: 0.7826 (Cg_exo) REVERT: L 131 GLN cc_start: 0.8185 (pm20) cc_final: 0.7911 (pm20) REVERT: L 150 ASP cc_start: 0.7732 (t0) cc_final: 0.7371 (t0) REVERT: L 211 ARG cc_start: 0.5762 (mtm110) cc_final: 0.5502 (mtm110) REVERT: O 3 ARG cc_start: 0.4727 (OUTLIER) cc_final: 0.3779 (tpp-160) REVERT: O 94 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8246 (tt0) REVERT: Q 85 ASN cc_start: 0.8718 (m-40) cc_final: 0.8377 (t0) REVERT: Q 115 LYS cc_start: 0.7931 (mttp) cc_final: 0.7725 (ttmm) REVERT: Q 217 LEU cc_start: 0.1378 (OUTLIER) cc_final: 0.0895 (tp) REVERT: Q 234 LYS cc_start: 0.8915 (mmtm) cc_final: 0.7795 (tppt) REVERT: R 59 MET cc_start: 0.4515 (ppp) cc_final: 0.4052 (ppp) REVERT: R 78 MET cc_start: 0.8738 (ptp) cc_final: 0.8437 (ptp) REVERT: R 107 MET cc_start: 0.7779 (tpp) cc_final: 0.7285 (tpp) REVERT: R 110 GLU cc_start: 0.8127 (tp30) cc_final: 0.7233 (tp30) REVERT: S 2 PHE cc_start: 0.6635 (OUTLIER) cc_final: 0.6225 (m-80) REVERT: S 140 MET cc_start: 0.6811 (mmm) cc_final: 0.6340 (mpp) REVERT: S 160 SER cc_start: 0.8882 (m) cc_final: 0.8360 (p) REVERT: S 224 TYR cc_start: 0.8217 (m-10) cc_final: 0.7953 (m-10) REVERT: T 108 LEU cc_start: 0.9387 (tp) cc_final: 0.9185 (tp) REVERT: T 175 GLU cc_start: 0.8675 (tp30) cc_final: 0.8218 (tp30) REVERT: T 179 LEU cc_start: 0.8198 (mp) cc_final: 0.7654 (mp) REVERT: T 232 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7562 (ttm110) REVERT: U 3 ARG cc_start: 0.7411 (tpp-160) cc_final: 0.6793 (mmt-90) REVERT: U 75 ASN cc_start: 0.8044 (m-40) cc_final: 0.7509 (t0) REVERT: U 228 ARG cc_start: 0.8080 (ptm-80) cc_final: 0.7491 (ptm-80) REVERT: V 166 ASP cc_start: 0.7791 (t0) cc_final: 0.7468 (t0) REVERT: V 172 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8230 (m-40) REVERT: W 87 MET cc_start: 0.8297 (ttp) cc_final: 0.7649 (ttp) REVERT: W 120 ILE cc_start: 0.8860 (mm) cc_final: 0.8456 (pt) REVERT: W 182 MET cc_start: 0.5958 (mmm) cc_final: 0.5438 (mmm) REVERT: W 203 MET cc_start: 0.3639 (mmt) cc_final: 0.2311 (mmt) REVERT: X 2 GLU cc_start: 0.6285 (mm-30) cc_final: 0.5716 (mm-30) REVERT: X 38 MET cc_start: 0.8444 (mmm) cc_final: 0.7413 (mmm) REVERT: X 62 LYS cc_start: 0.9055 (tmtt) cc_final: 0.8506 (tptp) REVERT: X 102 LEU cc_start: 0.8710 (mt) cc_final: 0.8329 (mm) REVERT: X 118 MET cc_start: 0.7758 (mtp) cc_final: 0.7193 (mpp) REVERT: Y 86 MET cc_start: 0.7713 (mtt) cc_final: 0.7252 (mtt) REVERT: Y 104 TRP cc_start: 0.4194 (t-100) cc_final: 0.3484 (t-100) REVERT: Y 190 ASP cc_start: 0.6286 (m-30) cc_final: 0.6000 (m-30) REVERT: Z 108 ASN cc_start: 0.8628 (m-40) cc_final: 0.8361 (t0) REVERT: Z 158 MET cc_start: 0.4184 (ptp) cc_final: 0.3962 (ptp) REVERT: Z 184 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7117 (mt-10) REVERT: Z 205 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: a 5 MET cc_start: 0.6823 (tpt) cc_final: 0.6491 (tpt) REVERT: a 103 MET cc_start: 0.8428 (tpp) cc_final: 0.8013 (mmt) REVERT: a 107 TRP cc_start: 0.8129 (m100) cc_final: 0.7268 (m100) REVERT: a 127 MET cc_start: 0.8484 (ptt) cc_final: 0.8267 (ptp) REVERT: a 183 SER cc_start: 0.9266 (t) cc_final: 0.8992 (p) REVERT: b 116 MET cc_start: 0.6141 (ttp) cc_final: 0.5813 (ttp) outliers start: 153 outliers final: 131 residues processed: 774 average time/residue: 0.5674 time to fit residues: 763.0484 Evaluate side-chains 792 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 652 time to evaluate : 6.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 215 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 101 ARG Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain H residue 193 ASN Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 172 ASN Chi-restraints excluded: chain J residue 30 ASP Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 MET Chi-restraints excluded: chain K residue 70 ASN Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 179 PHE Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain O residue 3 ARG Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 43 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 178 ASN Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 155 ASN Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 48 LYS Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 187 THR Chi-restraints excluded: chain Q residue 206 ILE Chi-restraints excluded: chain Q residue 217 LEU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 157 ASP Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain S residue 2 PHE Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 139 ASP Chi-restraints excluded: chain S residue 215 VAL Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 136 MET Chi-restraints excluded: chain T residue 144 ASP Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 84 THR Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 126 THR Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 146 GLU Chi-restraints excluded: chain U residue 195 VAL Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 172 ASN Chi-restraints excluded: chain V residue 179 SER Chi-restraints excluded: chain V residue 193 ASN Chi-restraints excluded: chain W residue 11 MET Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 121 CYS Chi-restraints excluded: chain W residue 138 SER Chi-restraints excluded: chain W residue 161 HIS Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain Y residue 31 VAL Chi-restraints excluded: chain Y residue 58 LEU Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Y residue 147 LEU Chi-restraints excluded: chain Z residue 127 VAL Chi-restraints excluded: chain Z residue 199 THR Chi-restraints excluded: chain Z residue 205 GLU Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 70 MET Chi-restraints excluded: chain a residue 154 LEU Chi-restraints excluded: chain b residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 360 optimal weight: 4.9990 chunk 580 optimal weight: 0.0170 chunk 354 optimal weight: 0.9980 chunk 275 optimal weight: 1.9990 chunk 403 optimal weight: 0.6980 chunk 608 optimal weight: 5.9990 chunk 560 optimal weight: 6.9990 chunk 484 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 374 optimal weight: 6.9990 chunk 297 optimal weight: 0.8980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 GLN C 54 GLN C 68 ASN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 ASN ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 ASN Q 92 GLN ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 150 GLN W 30 GLN ** X 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 53 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 49475 Z= 0.177 Angle : 0.625 15.606 66864 Z= 0.326 Chirality : 0.044 0.365 7506 Planarity : 0.004 0.050 8619 Dihedral : 5.094 74.695 6916 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.48 % Favored : 96.47 % Rotamer: Outliers : 2.67 % Allowed : 19.62 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.11), residues: 6184 helix: 1.51 (0.11), residues: 2222 sheet: 0.06 (0.14), residues: 1414 loop : -1.15 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP Y 184 HIS 0.005 0.001 HIS N 66 PHE 0.032 0.001 PHE X 56 TYR 0.020 0.001 TYR S 153 ARG 0.010 0.000 ARG R 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12368 Ramachandran restraints generated. 6184 Oldfield, 0 Emsley, 6184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 700 time to evaluate : 6.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 107 TRP cc_start: 0.7922 (m100) cc_final: 0.7222 (m100) REVERT: M 127 MET cc_start: 0.8341 (ptt) cc_final: 0.8112 (ptm) REVERT: A 172 PHE cc_start: 0.8617 (t80) cc_final: 0.8364 (t80) REVERT: B 156 TYR cc_start: 0.7725 (p90) cc_final: 0.7486 (p90) REVERT: B 174 MET cc_start: 0.8006 (mpp) cc_final: 0.7565 (tpt) REVERT: B 178 ASP cc_start: 0.8463 (t0) cc_final: 0.7592 (p0) REVERT: D 107 MET cc_start: 0.7801 (tpp) cc_final: 0.7213 (tpp) REVERT: E 88 MET cc_start: 0.8437 (mmp) cc_final: 0.8077 (mmm) REVERT: E 101 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.6768 (pmt-80) REVERT: E 196 ARG cc_start: 0.7434 (ttp-170) cc_final: 0.6433 (tpt-90) REVERT: F 81 LEU cc_start: 0.8942 (tp) cc_final: 0.8525 (mm) REVERT: G 3 ARG cc_start: 0.6692 (tpm170) cc_final: 0.5668 (mmm160) REVERT: G 63 SER cc_start: 0.8786 (m) cc_final: 0.8366 (p) REVERT: G 75 ASN cc_start: 0.7964 (m-40) cc_final: 0.7616 (t0) REVERT: G 130 GLU cc_start: 0.8511 (pm20) cc_final: 0.7811 (pm20) REVERT: H 109 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.6609 (m-70) REVERT: H 166 ASP cc_start: 0.7501 (t0) cc_final: 0.7220 (t0) REVERT: I 87 MET cc_start: 0.7918 (ttp) cc_final: 0.7343 (ttp) REVERT: I 105 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: I 121 CYS cc_start: 0.7580 (p) cc_final: 0.5609 (p) REVERT: I 145 MET cc_start: 0.7043 (mtt) cc_final: 0.6751 (mtt) REVERT: I 153 TRP cc_start: 0.7017 (t60) cc_final: 0.6346 (t60) REVERT: I 154 GLU cc_start: 0.7537 (mm-30) cc_final: 0.6957 (mm-30) REVERT: I 182 MET cc_start: 0.7887 (mtp) cc_final: 0.6487 (mtp) REVERT: J 34 LYS cc_start: 0.7667 (mmtt) cc_final: 0.7390 (tppt) REVERT: J 38 MET cc_start: 0.7965 (mmp) cc_final: 0.7455 (mmp) REVERT: K 70 ASN cc_start: 0.7939 (OUTLIER) cc_final: 0.7464 (t0) REVERT: K 82 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.6077 (mm) REVERT: K 85 ASN cc_start: 0.7957 (m-40) cc_final: 0.7749 (m-40) REVERT: K 100 MET cc_start: 0.7860 (ttm) cc_final: 0.7323 (mtt) REVERT: K 184 TRP cc_start: 0.7063 (p-90) cc_final: 0.6720 (p-90) REVERT: L 4 PRO cc_start: 0.8198 (Cg_endo) cc_final: 0.7849 (Cg_exo) REVERT: L 131 GLN cc_start: 0.8149 (pm20) cc_final: 0.7892 (pm20) REVERT: L 145 LEU cc_start: 0.8180 (mp) cc_final: 0.7951 (mp) REVERT: L 150 ASP cc_start: 0.7714 (t0) cc_final: 0.7407 (t0) REVERT: O 3 ARG cc_start: 0.4691 (OUTLIER) cc_final: 0.3803 (tpp-160) REVERT: Q 85 ASN cc_start: 0.8720 (m-40) cc_final: 0.8386 (t0) REVERT: Q 217 LEU cc_start: 0.1136 (OUTLIER) cc_final: 0.0635 (tp) REVERT: Q 234 LYS cc_start: 0.8895 (mmtm) cc_final: 0.7696 (tppt) REVERT: R 59 MET cc_start: 0.4447 (ppp) cc_final: 0.3903 (ppp) REVERT: R 107 MET cc_start: 0.7794 (tpp) cc_final: 0.7332 (tpp) REVERT: R 110 GLU cc_start: 0.8087 (tp30) cc_final: 0.7181 (tp30) REVERT: R 133 MET cc_start: 0.7053 (mmt) cc_final: 0.6368 (mmm) REVERT: S 2 PHE cc_start: 0.6323 (OUTLIER) cc_final: 0.5998 (m-80) REVERT: S 114 SER cc_start: 0.8779 (t) cc_final: 0.8509 (m) REVERT: S 140 MET cc_start: 0.6752 (mmm) cc_final: 0.6285 (mpp) REVERT: S 160 SER cc_start: 0.8834 (m) cc_final: 0.8375 (p) REVERT: S 179 PHE cc_start: 0.8250 (m-10) cc_final: 0.7623 (m-80) REVERT: T 175 GLU cc_start: 0.8639 (tp30) cc_final: 0.8269 (tp30) REVERT: T 179 LEU cc_start: 0.8142 (mp) cc_final: 0.7566 (mp) REVERT: T 232 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7557 (ttm110) REVERT: U 3 ARG cc_start: 0.7420 (tpp-160) cc_final: 0.6803 (mmt-90) REVERT: U 75 ASN cc_start: 0.7982 (m-40) cc_final: 0.7510 (t0) REVERT: U 228 ARG cc_start: 0.7934 (ptm-80) cc_final: 0.7366 (ptm-80) REVERT: V 166 ASP cc_start: 0.7649 (t0) cc_final: 0.7375 (t0) REVERT: V 172 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.8046 (m-40) REVERT: W 87 MET cc_start: 0.8270 (ttp) cc_final: 0.7630 (ttp) REVERT: W 120 ILE cc_start: 0.8864 (mm) cc_final: 0.8470 (pt) REVERT: W 153 TRP cc_start: 0.7278 (t60) cc_final: 0.6934 (t60) REVERT: W 154 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7160 (mm-30) REVERT: W 182 MET cc_start: 0.5909 (mmm) cc_final: 0.5462 (mmm) REVERT: W 203 MET cc_start: 0.3590 (mmt) cc_final: 0.2260 (mmt) REVERT: X 2 GLU cc_start: 0.6340 (mm-30) cc_final: 0.5618 (mm-30) REVERT: X 38 MET cc_start: 0.8464 (mmm) cc_final: 0.7926 (mmm) REVERT: X 62 LYS cc_start: 0.9062 (tmtt) cc_final: 0.8515 (tptp) REVERT: X 102 LEU cc_start: 0.8757 (mt) cc_final: 0.8345 (mm) REVERT: X 118 MET cc_start: 0.7726 (mtp) cc_final: 0.7239 (mpp) REVERT: Y 86 MET cc_start: 0.7674 (mtt) cc_final: 0.7197 (mtt) REVERT: Y 100 MET cc_start: 0.8007 (tpp) cc_final: 0.7329 (mtt) REVERT: Y 104 TRP cc_start: 0.4075 (t-100) cc_final: 0.3349 (t-100) REVERT: Y 190 ASP cc_start: 0.6218 (m-30) cc_final: 0.6004 (m-30) REVERT: Z 108 ASN cc_start: 0.8568 (m-40) cc_final: 0.8311 (t0) REVERT: Z 184 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7128 (mt-10) REVERT: Z 205 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7736 (pm20) REVERT: a 5 MET cc_start: 0.6681 (tpt) cc_final: 0.6429 (tpt) REVERT: a 103 MET cc_start: 0.8404 (tpp) cc_final: 0.7990 (mmt) REVERT: a 107 TRP cc_start: 0.8087 (m100) cc_final: 0.7218 (m100) REVERT: a 127 MET cc_start: 0.8431 (ptt) cc_final: 0.8147 (ptm) REVERT: a 183 SER cc_start: 0.9242 (t) cc_final: 0.8924 (p) outliers start: 126 outliers final: 100 residues processed: 777 average time/residue: 0.5686 time to fit residues: 766.3769 Evaluate side-chains 774 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 664 time to evaluate : 5.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 215 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 101 ARG Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 109 HIS Chi-restraints excluded: chain H residue 193 ASN Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 172 ASN Chi-restraints excluded: chain J residue 30 ASP Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 MET Chi-restraints excluded: chain K residue 70 ASN Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain O residue 3 ARG Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 43 VAL Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain Q residue 48 LYS Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 217 LEU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 157 ASP Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain S residue 2 PHE Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 215 VAL Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 136 MET Chi-restraints excluded: chain U residue 84 THR Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 126 THR Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 146 GLU Chi-restraints excluded: chain U residue 195 VAL Chi-restraints excluded: chain V residue 172 ASN Chi-restraints excluded: chain V residue 179 SER Chi-restraints excluded: chain V residue 193 ASN Chi-restraints excluded: chain W residue 11 MET Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 121 CYS Chi-restraints excluded: chain W residue 138 SER Chi-restraints excluded: chain W residue 161 HIS Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain Y residue 56 GLU Chi-restraints excluded: chain Y residue 58 LEU Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Y residue 147 LEU Chi-restraints excluded: chain Z residue 127 VAL Chi-restraints excluded: chain Z residue 199 THR Chi-restraints excluded: chain Z residue 205 GLU Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 70 MET Chi-restraints excluded: chain b residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 385 optimal weight: 0.9980 chunk 516 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 446 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 485 optimal weight: 0.9980 chunk 203 optimal weight: 0.9980 chunk 498 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 ASN L 108 ASN N 71 ASN R 182 GLN ** X 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.149925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.104431 restraints weight = 291706.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.108226 restraints weight = 98898.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.110241 restraints weight = 56134.722| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 49475 Z= 0.198 Angle : 0.634 15.333 66864 Z= 0.329 Chirality : 0.044 0.358 7506 Planarity : 0.004 0.050 8619 Dihedral : 5.036 72.978 6914 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.82 % Favored : 96.13 % Rotamer: Outliers : 2.67 % Allowed : 19.70 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.11), residues: 6184 helix: 1.56 (0.11), residues: 2222 sheet: 0.07 (0.14), residues: 1404 loop : -1.14 (0.12), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP Y 184 HIS 0.005 0.001 HIS N 66 PHE 0.025 0.001 PHE K 8 TYR 0.020 0.001 TYR T 58 ARG 0.013 0.000 ARG D 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13676.77 seconds wall clock time: 248 minutes 11.84 seconds (14891.84 seconds total)