Starting phenix.real_space_refine (version: dev) on Thu Dec 22 11:41:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r70_4738/12_2022/6r70_4738.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r70_4738/12_2022/6r70_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_4738/12_2022/6r70_4738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r70_4738/12_2022/6r70_4738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r70_4738/12_2022/6r70_4738.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r70_4738/12_2022/6r70_4738.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 41.41, per 1000 atoms: 0.85 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: 17.48 Conformation dependent library (CDL) restraints added in 11.8 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: 2.92 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: 20.79 Time building geometry restraints manager: 18.97 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 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. 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 15.790 Check model and map are aligned: 0.740 Convert atoms to be neutral: 0.370 Process input model: 139.440 Find NCS groups from input model: 5.060 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 : 4.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.67 % Favored : 96.07 % Rotamer Outliers : 0.52 % 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 *********************** 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 : 5.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 1156 average time/residue: 0.6072 time to fit residues: 1136.6509 Evaluate side-chains 713 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 705 time to evaluate : 5.792 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4573 time to fit residues: 14.1713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 515 optimal weight: 6.9990 chunk 463 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 312 optimal weight: 0.9980 chunk 247 optimal weight: 7.9990 chunk 478 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 291 optimal weight: 0.8980 chunk 356 optimal weight: 6.9990 chunk 554 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 108 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 D 155 HIS E 16 GLN F 63 ASN F 72 HIS ** F 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN H 35 HIS H 172 ASN I 64 GLN ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 GLN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 GLN 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 N 110 GLN ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN 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 63 ASN 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 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: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 49475 Z= 0.233 Angle : 0.692 16.118 66864 Z= 0.372 Chirality : 0.046 0.265 7506 Planarity : 0.005 0.086 8619 Dihedral : 5.974 50.982 6908 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer Outliers : 1.85 % 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: -1.12 (0.10), residues: 6184 helix: -0.17 (0.10), residues: 2249 sheet: -0.38 (0.13), residues: 1399 loop : -1.37 (0.11), residues: 2536 *********************** 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 893 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 808 time to evaluate : 5.407 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 outliers start: 85 outliers final: 47 residues processed: 845 average time/residue: 0.5656 time to fit residues: 805.8683 Evaluate side-chains 728 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 681 time to evaluate : 5.523 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.4396 time to fit residues: 45.8433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 308 optimal weight: 0.6980 chunk 172 optimal weight: 4.9990 chunk 461 optimal weight: 2.9990 chunk 377 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 555 optimal weight: 3.9990 chunk 600 optimal weight: 2.9990 chunk 495 optimal weight: 2.9990 chunk 551 optimal weight: 9.9990 chunk 189 optimal weight: 3.9990 chunk 445 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 61 GLN A 94 GLN ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN ** F 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN G 238 HIS H 57 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 172 ASN W 172 ASN ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 ASN X 99 HIS A ** X 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 53 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 49475 Z= 0.381 Angle : 0.721 16.797 66864 Z= 0.384 Chirality : 0.047 0.346 7506 Planarity : 0.005 0.064 8619 Dihedral : 5.748 44.547 6908 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.16 % Favored : 95.77 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.12 % 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: -0.77 (0.10), residues: 6184 helix: 0.42 (0.11), residues: 2251 sheet: -0.35 (0.13), residues: 1393 loop : -1.38 (0.11), residues: 2540 *********************** 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 818 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 721 time to evaluate : 5.469 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 outliers start: 97 outliers final: 61 residues processed: 773 average time/residue: 0.5509 time to fit residues: 728.8966 Evaluate side-chains 724 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 663 time to evaluate : 5.515 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.4314 time to fit residues: 57.3136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 549 optimal weight: 4.9990 chunk 417 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 265 optimal weight: 0.7980 chunk 373 optimal weight: 9.9990 chunk 557 optimal weight: 0.0980 chunk 590 optimal weight: 5.9990 chunk 291 optimal weight: 2.9990 chunk 528 optimal weight: 20.0000 chunk 159 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 108 ASN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 55 GLN ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 186 ASN ** Z 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 53 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 49475 Z= 0.227 Angle : 0.631 16.676 66864 Z= 0.336 Chirality : 0.044 0.341 7506 Planarity : 0.004 0.056 8619 Dihedral : 5.394 48.453 6908 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.38 % Favored : 96.57 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.05 % Twisted Proline : 0.51 % 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: -0.39 (0.10), residues: 6184 helix: 0.89 (0.11), residues: 2250 sheet: -0.20 (0.13), residues: 1376 loop : -1.29 (0.12), residues: 2558 *********************** 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 817 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 742 time to evaluate : 5.261 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 outliers start: 75 outliers final: 37 residues processed: 777 average time/residue: 0.5506 time to fit residues: 732.6180 Evaluate side-chains 698 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 661 time to evaluate : 5.508 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.4305 time to fit residues: 38.1380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 491 optimal weight: 9.9990 chunk 335 optimal weight: 0.0370 chunk 8 optimal weight: 1.9990 chunk 439 optimal weight: 0.0050 chunk 243 optimal weight: 9.9990 chunk 503 optimal weight: 6.9990 chunk 408 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 301 optimal weight: 0.7980 chunk 530 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 108 ASN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** F 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 ASN G 53 GLN ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 HIS ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 227 HIS ** U 150 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 Y 162 GLN Z 157 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 49475 Z= 0.182 Angle : 0.609 16.706 66864 Z= 0.322 Chirality : 0.044 0.387 7506 Planarity : 0.004 0.051 8619 Dihedral : 5.182 66.733 6908 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.26 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.05 % Twisted Proline : 0.51 % 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: -0.13 (0.10), residues: 6184 helix: 1.17 (0.11), residues: 2246 sheet: -0.11 (0.13), residues: 1399 loop : -1.18 (0.12), residues: 2539 *********************** 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 764 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 717 time to evaluate : 5.542 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 outliers start: 47 outliers final: 25 residues processed: 741 average time/residue: 0.5713 time to fit residues: 727.1432 Evaluate side-chains 679 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 654 time to evaluate : 5.685 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.5386 time to fit residues: 34.3560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 198 optimal weight: 0.5980 chunk 531 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 346 optimal weight: 0.5980 chunk 145 optimal weight: 0.9980 chunk 591 optimal weight: 0.5980 chunk 490 optimal weight: 9.9990 chunk 273 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 310 optimal weight: 5.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS F 180 GLN G 53 GLN ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 215 GLN ** 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** ** U 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 57 GLN W 92 ASN ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 49475 Z= 0.250 Angle : 0.639 16.777 66864 Z= 0.335 Chirality : 0.045 0.362 7506 Planarity : 0.004 0.052 8619 Dihedral : 5.217 84.312 6908 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.98 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.05 % Twisted Proline : 0.51 % 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: -0.08 (0.11), residues: 6184 helix: 1.23 (0.11), residues: 2240 sheet: -0.08 (0.13), residues: 1392 loop : -1.17 (0.12), residues: 2552 *********************** 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 738 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 677 time to evaluate : 5.562 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 outliers start: 61 outliers final: 30 residues processed: 709 average time/residue: 0.5654 time to fit residues: 685.2629 Evaluate side-chains 677 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 647 time to evaluate : 5.965 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.4222 time to fit residues: 31.6708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 569 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 336 optimal weight: 6.9990 chunk 431 optimal weight: 2.9990 chunk 334 optimal weight: 0.8980 chunk 497 optimal weight: 8.9990 chunk 330 optimal weight: 0.5980 chunk 588 optimal weight: 1.9990 chunk 368 optimal weight: 3.9990 chunk 359 optimal weight: 6.9990 chunk 271 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** 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** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** S 21 GLN ** S 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 150 GLN ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 49475 Z= 0.242 Angle : 0.634 16.816 66864 Z= 0.332 Chirality : 0.045 0.333 7506 Planarity : 0.004 0.063 8619 Dihedral : 5.183 87.025 6908 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.92 % Favored : 96.03 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.05 % Twisted Proline : 0.51 % 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: -0.01 (0.11), residues: 6184 helix: 1.30 (0.11), residues: 2232 sheet: -0.04 (0.14), residues: 1392 loop : -1.12 (0.12), residues: 2560 *********************** 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 725 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 677 time to evaluate : 6.045 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 outliers start: 48 outliers final: 26 residues processed: 698 average time/residue: 0.5771 time to fit residues: 687.5011 Evaluate side-chains 664 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 638 time to evaluate : 5.501 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.4448 time to fit residues: 29.3160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 364 optimal weight: 0.9990 chunk 235 optimal weight: 0.9990 chunk 351 optimal weight: 6.9990 chunk 177 optimal weight: 0.8980 chunk 115 optimal weight: 0.0980 chunk 114 optimal weight: 1.9990 chunk 374 optimal weight: 10.0000 chunk 401 optimal weight: 3.9990 chunk 291 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 462 optimal weight: 6.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** 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 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 ASN ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 ASN P 109 GLN ** Q 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 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** ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 92 ASN ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 49475 Z= 0.198 Angle : 0.624 16.865 66864 Z= 0.326 Chirality : 0.044 0.356 7506 Planarity : 0.004 0.059 8619 Dihedral : 5.084 79.766 6908 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.28 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.05 % 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: 0.07 (0.11), residues: 6184 helix: 1.42 (0.11), residues: 2218 sheet: -0.03 (0.14), residues: 1411 loop : -1.12 (0.12), residues: 2555 *********************** 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 722 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 688 time to evaluate : 5.633 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 outliers start: 34 outliers final: 19 residues processed: 704 average time/residue: 0.5710 time to fit residues: 689.2402 Evaluate side-chains 670 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 651 time to evaluate : 5.478 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4288 time to fit residues: 22.8695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 535 optimal weight: 10.0000 chunk 564 optimal weight: 3.9990 chunk 514 optimal weight: 7.9990 chunk 548 optimal weight: 6.9990 chunk 330 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 430 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 495 optimal weight: 8.9990 chunk 519 optimal weight: 9.9990 chunk 546 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN C 92 GLN C 122 ASN ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 HIS ** Q 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 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** ** S 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 90 GLN W 30 GLN ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 110 HIS X 132 HIS ** Z 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 147 GLN b 53 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.115 49475 Z= 0.547 Angle : 0.816 17.151 66864 Z= 0.425 Chirality : 0.051 0.317 7506 Planarity : 0.006 0.089 8619 Dihedral : 5.658 71.188 6908 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.45 % Favored : 94.50 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.10), residues: 6184 helix: 0.85 (0.11), residues: 2225 sheet: -0.29 (0.14), residues: 1392 loop : -1.37 (0.12), residues: 2567 *********************** 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 688 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 649 time to evaluate : 5.633 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 outliers start: 39 outliers final: 30 residues processed: 665 average time/residue: 0.5817 time to fit residues: 663.8268 Evaluate side-chains 640 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 610 time to evaluate : 5.576 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.4580 time to fit residues: 33.0672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 360 optimal weight: 3.9990 chunk 580 optimal weight: 4.9990 chunk 354 optimal weight: 0.8980 chunk 275 optimal weight: 4.9990 chunk 403 optimal weight: 0.9980 chunk 608 optimal weight: 0.9990 chunk 560 optimal weight: 4.9990 chunk 484 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 374 optimal weight: 2.9990 chunk 297 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 165 ASN ** 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** ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 HIS ** 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** ** S 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 175 HIS U 90 GLN ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 92 ASN ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 147 GLN b 53 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4579 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= 0.207 Angle : 0.672 16.831 66864 Z= 0.349 Chirality : 0.045 0.327 7506 Planarity : 0.004 0.070 8619 Dihedral : 5.295 71.684 6908 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.69 % Favored : 96.26 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.11), residues: 6184 helix: 1.25 (0.11), residues: 2221 sheet: -0.11 (0.14), residues: 1382 loop : -1.23 (0.12), residues: 2581 ********************** 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 680 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 669 time to evaluate : 5.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 670 average time/residue: 0.5678 time to fit residues: 649.0555 Evaluate side-chains 641 residues out of total 5118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 637 time to evaluate : 5.661 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4210 time to fit residues: 10.8422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 385 optimal weight: 0.0370 chunk 516 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 446 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 485 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 498 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- 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** ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 8 GLN ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 147 GLN b 53 GLN b 158 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.147526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.102031 restraints weight = 284040.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.105792 restraints weight = 98895.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107005 restraints weight = 59507.750| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4057 r_free = 0.4057 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4056 r_free = 0.4056 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 49475 Z= 0.326 Angle : 0.703 17.010 66864 Z= 0.366 Chirality : 0.046 0.337 7506 Planarity : 0.005 0.073 8619 Dihedral : 5.320 70.506 6908 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.59 % Favored : 95.36 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.11), residues: 6184 helix: 1.21 (0.11), residues: 2219 sheet: -0.23 (0.14), residues: 1403 loop : -1.23 (0.12), residues: 2562 =============================================================================== Job complete usr+sys time: 12368.89 seconds wall clock time: 222 minutes 24.78 seconds (13344.78 seconds total)