Starting phenix.real_space_refine (version: dev) on Mon Feb 27 23:41:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nap_24277/02_2023/7nap_24277.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nap_24277/02_2023/7nap_24277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nap_24277/02_2023/7nap_24277.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nap_24277/02_2023/7nap_24277.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nap_24277/02_2023/7nap_24277.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nap_24277/02_2023/7nap_24277.pdb" } resolution = 3.2 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= 1.000 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 Process input model Symmetric amino acids flipped Residue "O ARG 90": "NH1" <-> "NH2" Residue "P ARG 8": "NH1" <-> "NH2" Residue "P GLU 22": "OE1" <-> "OE2" Residue "P PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 105": "OE1" <-> "OE2" Residue "Q TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 163": "NH1" <-> "NH2" Residue "Q PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 213": "NH1" <-> "NH2" Residue "R GLU 25": "OE1" <-> "OE2" Residue "R GLU 105": "OE1" <-> "OE2" Residue "S PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 101": "NH1" <-> "NH2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S GLU 173": "OE1" <-> "OE2" Residue "T GLU 93": "OE1" <-> "OE2" Residue "T PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 11": "NH1" <-> "NH2" Residue "U GLU 19": "OE1" <-> "OE2" Residue "U PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 88": "NH1" <-> "NH2" Residue "U PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 143": "NH1" <-> "NH2" Residue "W ARG 25": "NH1" <-> "NH2" Residue "W ARG 69": "NH1" <-> "NH2" Residue "W TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 79": "NH1" <-> "NH2" Residue "W GLU 164": "OE1" <-> "OE2" Residue "W GLU 190": "OE1" <-> "OE2" Residue "X GLU 2": "OE1" <-> "OE2" Residue "X GLU 49": "OE1" <-> "OE2" Residue "X GLU 58": "OE1" <-> "OE2" Residue "X GLU 74": "OE1" <-> "OE2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ARG 153": "NH1" <-> "NH2" Residue "Y PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 158": "NH1" <-> "NH2" Residue "Y GLU 181": "OE1" <-> "OE2" Residue "Y ARG 186": "NH1" <-> "NH2" Residue "Z ARG 99": "NH1" <-> "NH2" Residue "Z ARG 173": "NH1" <-> "NH2" Residue "Z GLU 205": "OE1" <-> "OE2" Residue "a ARG 100": "NH1" <-> "NH2" Residue "a PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 165": "OE1" <-> "OE2" Residue "b GLU 181": "OE1" <-> "OE2" Residue "k GLU 30": "OE1" <-> "OE2" Residue "k GLU 133": "OE1" <-> "OE2" Residue "j GLU 39": "OE1" <-> "OE2" Residue "j GLU 168": "OE1" <-> "OE2" Residue "j GLU 180": "OE1" <-> "OE2" Residue "j GLU 208": "OE1" <-> "OE2" Residue "m PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 27": "OE1" <-> "OE2" Residue "l ARG 210": "NH1" <-> "NH2" Residue "l ARG 213": "NH1" <-> "NH2" Residue "l TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 225": "OE1" <-> "OE2" Residue "n GLU 218": "OE1" <-> "OE2" Residue "p GLU 144": "OE1" <-> "OE2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 163": "NH1" <-> "NH2" Residue "C PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "D GLU 25": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "E PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G GLU 19": "OE1" <-> "OE2" Residue "G PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 143": "NH1" <-> "NH2" Residue "I ARG 25": "NH1" <-> "NH2" Residue "I ARG 69": "NH1" <-> "NH2" Residue "I TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 79": "NH1" <-> "NH2" Residue "I GLU 164": "OE1" <-> "OE2" Residue "I GLU 190": "OE1" <-> "OE2" Residue "J GLU 2": "OE1" <-> "OE2" Residue "J GLU 49": "OE1" <-> "OE2" Residue "J GLU 58": "OE1" <-> "OE2" Residue "J GLU 74": "OE1" <-> "OE2" Residue "J ARG 86": "NH1" <-> "NH2" Residue "J ARG 153": "NH1" <-> "NH2" Residue "K PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 158": "NH1" <-> "NH2" Residue "K GLU 181": "OE1" <-> "OE2" Residue "K ARG 186": "NH1" <-> "NH2" Residue "L ARG 99": "NH1" <-> "NH2" Residue "L ARG 173": "NH1" <-> "NH2" Residue "L GLU 205": "OE1" <-> "OE2" Residue "M ARG 100": "NH1" <-> "NH2" Residue "M PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 165": "OE1" <-> "OE2" Residue "N GLU 181": "OE1" <-> "OE2" Residue "d GLU 30": "OE1" <-> "OE2" Residue "d GLU 133": "OE1" <-> "OE2" Residue "c GLU 39": "OE1" <-> "OE2" Residue "c GLU 168": "OE1" <-> "OE2" Residue "c GLU 180": "OE1" <-> "OE2" Residue "c GLU 208": "OE1" <-> "OE2" Residue "f PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 27": "OE1" <-> "OE2" Residue "e ARG 210": "NH1" <-> "NH2" Residue "e ARG 213": "NH1" <-> "NH2" Residue "e TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 225": "OE1" <-> "OE2" Residue "g GLU 218": "OE1" <-> "OE2" Residue "i GLU 144": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 69762 Number of models: 1 Model: "" Number of chains: 42 Chain: "O" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1696 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 73 Chain: "P" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1793 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 5, 'TRANS': 243} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 114 Chain: "Q" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1703 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 6, 'TRANS': 228} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 86 Chain: "R" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1751 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 8, 'TRANS': 232} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "S" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1810 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 10, 'TRANS': 228} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "T" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1785 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 63 Chain: "U" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1769 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 8, 'TRANS': 230} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 74 Chain: "V" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1609 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 56 Chain: "W" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1564 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 26 Chain: "X" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1544 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 29 Chain: "Y" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1525 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "Z" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1599 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 44 Chain: "a" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1643 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "b" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1491 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "k" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1686 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "j" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 12, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "m" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1648 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "l" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1641 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "o" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1677 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 11, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 8, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "n" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1626 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "p" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1695 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1696 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1793 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 5, 'TRANS': 243} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 114 Chain: "C" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1703 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 6, 'TRANS': 228} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 86 Chain: "D" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1751 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 8, 'TRANS': 232} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "E" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1810 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 10, 'TRANS': 228} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "F" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1785 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 63 Chain: "G" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1769 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 8, 'TRANS': 230} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 74 Chain: "H" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1609 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 56 Chain: "I" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1564 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 26 Chain: "J" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1544 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 29 Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1525 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "L" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1599 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 44 Chain: "M" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1643 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "N" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1491 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "d" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1686 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "c" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 12, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "f" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1648 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "e" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1641 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "h" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1677 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 11, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 8, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "g" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1626 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "i" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1695 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Time building chain proxies: 28.72, per 1000 atoms: 0.41 Number of scatterers: 69762 At special positions: 0 Unit cell: (138.578, 134.932, 319.703, 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 358 16.00 O 12544 8.00 N 12120 7.00 C 44740 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: 23.67 Conformation dependent library (CDL) restraints added in 8.3 seconds 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17268 Finding SS restraints... Secondary structure from input PDB file: 256 helices and 70 sheets defined 53.1% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'O' and resid 3 through 8 removed outlier: 4.023A pdb=" N PHE O 7 " --> pdb=" O ARG O 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 31 removed outlier: 3.531A pdb=" N GLY O 31 " --> pdb=" O ALA O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 61 removed outlier: 3.623A 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 123 removed outlier: 3.649A pdb=" N GLN O 122 " --> pdb=" O GLN O 118 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER O 123 " --> pdb=" O GLU O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 177 Processing helix chain 'O' and resid 182 through 196 removed outlier: 4.043A pdb=" N HIS O 188 " --> pdb=" O GLU O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 221 through 230 Processing helix chain 'P' and resid 18 through 31 removed outlier: 3.517A pdb=" N GLU P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY P 29 " --> pdb=" O MET P 25 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS P 30 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA P 31 " --> pdb=" O ALA P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 102 Processing helix chain 'P' and resid 106 through 124 Processing helix chain 'P' and resid 167 through 179 removed outlier: 3.631A pdb=" N GLN P 177 " --> pdb=" O SER P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 185 through 201 Processing helix chain 'P' and resid 229 through 251 removed outlier: 3.827A pdb=" N LYS P 251 " --> pdb=" O ALA P 247 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 29 removed outlier: 3.821A pdb=" N GLU Q 20 " --> pdb=" O LEU Q 16 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS Q 27 " --> pdb=" O GLN Q 23 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS Q 28 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY Q 29 " --> pdb=" O ALA Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 59 Processing helix chain 'Q' and resid 76 through 99 Processing helix chain 'Q' and resid 103 through 121 removed outlier: 4.133A pdb=" N SER Q 121 " --> pdb=" O ARG Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 176 Processing helix chain 'Q' and resid 179 through 182 Processing helix chain 'Q' and resid 183 through 198 removed outlier: 3.764A pdb=" N VAL Q 198 " --> pdb=" O ALA Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 221 through 236 removed outlier: 3.649A pdb=" N LYS Q 236 " --> pdb=" O ILE Q 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 31 removed outlier: 3.761A pdb=" N GLU R 25 " --> pdb=" O LEU R 21 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 34 No H-bonds generated for 'chain 'R' and resid 32 through 34' Processing helix chain 'R' and resid 60 through 64 Processing helix chain 'R' and resid 81 through 104 Processing helix chain 'R' and resid 108 through 122 removed outlier: 3.571A pdb=" N GLN R 122 " --> pdb=" O ASN R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 125 No H-bonds generated for 'chain 'R' and resid 123 through 125' Processing helix chain 'R' and resid 173 through 185 removed outlier: 6.461A pdb=" N SER R 179 " --> pdb=" O GLU R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 206 Processing helix chain 'R' and resid 230 through 241 Processing helix chain 'S' and resid 19 through 32 removed outlier: 3.731A pdb=" N ALA S 28 " --> pdb=" O TYR S 24 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL S 29 " --> pdb=" O ALA S 25 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS S 30 " --> pdb=" O MET S 26 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN S 31 " --> pdb=" O GLU S 27 " (cutoff:3.500A) removed outlier: 3.845A 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 122 Proline residue: S 119 - end of helix Processing helix chain 'S' and resid 164 through 175 removed outlier: 4.395A pdb=" N ALA S 168 " --> pdb=" O ARG S 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 180 removed outlier: 3.929A pdb=" N PHE S 179 " --> pdb=" O HIS S 175 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET S 180 " --> pdb=" O MET S 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 175 through 180' Processing helix chain 'S' and resid 183 through 199 removed outlier: 3.765A pdb=" N THR S 198 " --> pdb=" O ALA S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 229 through 235 removed outlier: 4.310A pdb=" N GLY S 235 " --> pdb=" O PRO S 231 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 10 removed outlier: 4.263A pdb=" N ASP T 8 " --> pdb=" O THR T 5 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU T 9 " --> pdb=" O GLY T 6 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER T 10 " --> pdb=" O TYR T 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 5 through 10' Processing helix chain 'T' and resid 20 through 33 removed outlier: 3.783A pdb=" N GLU T 24 " --> pdb=" O VAL T 20 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL T 30 " --> pdb=" O ALA T 26 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU T 31 " --> pdb=" O MET T 27 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN T 32 " --> pdb=" O LYS T 28 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER T 33 " --> pdb=" O ALA T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 103 Processing helix chain 'T' and resid 107 through 125 removed outlier: 3.949A pdb=" N TYR T 122 " --> pdb=" O TYR T 118 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR T 123 " --> pdb=" O VAL T 119 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU T 124 " --> pdb=" O HIS T 120 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR T 125 " --> pdb=" O ALA T 121 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 178 Processing helix chain 'T' and resid 185 through 201 removed outlier: 4.293A pdb=" N LYS T 191 " --> pdb=" O ARG T 187 " (cutoff:3.500A) 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 removed outlier: 3.663A pdb=" N LYS T 244 " --> pdb=" O LYS T 240 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 34 removed outlier: 3.889A pdb=" N GLU U 26 " --> pdb=" O LEU U 22 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE U 32 " --> pdb=" O ALA U 28 " (cutoff:3.500A) removed outlier: 3.873A 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 110 through 128 Processing helix chain 'U' and resid 171 through 185 Processing helix chain 'U' and resid 190 through 207 Processing helix chain 'U' and resid 211 through 213 No H-bonds generated for 'chain 'U' and resid 211 through 213' Processing helix chain 'U' and resid 231 through 245 Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 91 removed outlier: 3.560A pdb=" N ALA V 79 " --> pdb=" O ARG V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 142 Processing helix chain 'V' and resid 147 through 166 Processing helix chain 'W' and resid 55 through 78 Processing helix chain 'W' and resid 82 through 97 removed outlier: 3.858A pdb=" N LYS W 97 " --> pdb=" O LEU W 93 " (cutoff:3.500A) Processing helix chain 'W' and resid 141 through 153 Processing helix chain 'W' and resid 158 through 176 removed outlier: 3.800A pdb=" N ARG W 176 " --> pdb=" O ASN W 172 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 72 Processing helix chain 'X' and resid 76 through 94 removed outlier: 3.831A pdb=" N ARG X 93 " --> pdb=" O ALA X 89 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER X 94 " --> pdb=" O ASP X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 133 through 147 removed outlier: 4.034A pdb=" N PHE X 137 " --> pdb=" O GLY X 133 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU X 138 " --> pdb=" O TYR X 134 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER X 141 " --> pdb=" O PHE X 137 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE X 142 " --> pdb=" O LEU X 138 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 171 Processing helix chain 'Y' and resid 48 through 71 Processing helix chain 'Y' and resid 75 through 90 removed outlier: 3.829A pdb=" N TYR Y 90 " --> pdb=" O MET Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 131 through 143 removed outlier: 3.905A pdb=" N GLY Y 137 " --> pdb=" O VAL Y 133 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL Y 138 " --> pdb=" O TYR Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 148 through 167 Processing helix chain 'Y' and resid 192 through 200 Processing helix chain 'Z' and resid 57 through 80 Processing helix chain 'Z' and resid 84 through 99 removed outlier: 3.965A pdb=" N ARG Z 99 " --> pdb=" O ILE Z 95 " (cutoff:3.500A) Processing helix chain 'Z' and resid 141 through 153 Proline residue: Z 147 - end of helix Processing helix chain 'Z' and resid 167 through 186 Processing helix chain 'a' and resid 57 through 78 Processing helix chain 'a' and resid 84 through 102 Processing helix chain 'a' and resid 141 through 157 removed outlier: 4.188A pdb=" N GLN a 147 " --> pdb=" O ALA a 143 " (cutoff:3.500A) Proline residue: a 148 - end of helix Processing helix chain 'a' and resid 161 through 180 Processing helix chain 'a' and resid 210 through 215 removed outlier: 3.862A pdb=" N MET a 214 " --> pdb=" O ASP a 210 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE a 215 " --> pdb=" O ILE a 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 210 through 215' Processing helix chain 'b' and resid 48 through 71 Processing helix chain 'b' and resid 75 through 90 Processing helix chain 'b' and resid 131 through 143 removed outlier: 3.787A pdb=" N ILE b 135 " --> pdb=" O GLY b 131 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLY b 137 " --> pdb=" O SER b 133 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR b 138 " --> pdb=" O TYR b 134 " (cutoff:3.500A) Processing helix chain 'b' and resid 148 through 167 Processing helix chain 'b' and resid 190 through 194 Processing helix chain 'k' and resid 10 through 34 Processing helix chain 'k' and resid 34 through 49 Processing helix chain 'k' and resid 50 through 53 Processing helix chain 'k' and resid 97 through 129 Proline residue: k 109 - end of helix Processing helix chain 'k' and resid 136 through 181 removed outlier: 4.520A pdb=" N VAL k 140 " --> pdb=" O ASN k 136 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE k 168 " --> pdb=" O ILE k 164 " (cutoff:3.500A) Processing helix chain 'k' and resid 185 through 223 Processing helix chain 'k' and resid 223 through 229 Processing helix chain 'j' and resid 7 through 31 Processing helix chain 'j' and resid 31 through 46 Processing helix chain 'j' and resid 107 through 138 Proline residue: j 119 - end of helix Processing helix chain 'j' and resid 147 through 191 removed outlier: 4.004A pdb=" N SER j 175 " --> pdb=" O HIS j 171 " (cutoff:3.500A) Processing helix chain 'j' and resid 195 through 239 removed outlier: 5.658A pdb=" N GLU j 235 " --> pdb=" O LEU j 231 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS j 236 " --> pdb=" O LYS j 232 " (cutoff:3.500A) Processing helix chain 'm' and resid 10 through 34 Processing helix chain 'm' and resid 34 through 49 removed outlier: 3.577A pdb=" N GLN m 38 " --> pdb=" O ARG m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 54 removed outlier: 3.856A pdb=" N VAL m 54 " --> pdb=" O SER m 51 " (cutoff:3.500A) Processing helix chain 'm' and resid 97 through 129 Proline residue: m 109 - end of helix Processing helix chain 'm' and resid 137 through 181 removed outlier: 4.152A pdb=" N PHE m 168 " --> pdb=" O ILE m 164 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER m 169 " --> pdb=" O SER m 165 " (cutoff:3.500A) Processing helix chain 'm' and resid 185 through 223 Processing helix chain 'm' and resid 223 through 229 Processing helix chain 'l' and resid 8 through 31 Processing helix chain 'l' and resid 31 through 46 Processing helix chain 'l' and resid 107 through 138 Proline residue: l 119 - end of helix Processing helix chain 'l' and resid 149 through 191 removed outlier: 3.765A pdb=" N SER l 175 " --> pdb=" O HIS l 171 " (cutoff:3.500A) Processing helix chain 'l' and resid 195 through 239 removed outlier: 5.581A pdb=" N GLU l 235 " --> pdb=" O LEU l 231 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LYS l 236 " --> pdb=" O LYS l 232 " (cutoff:3.500A) Processing helix chain 'o' and resid 10 through 34 Processing helix chain 'o' and resid 34 through 49 Processing helix chain 'o' and resid 56 through 61 removed outlier: 4.262A pdb=" N LEU o 60 " --> pdb=" O ASP o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 129 Proline residue: o 109 - end of helix Processing helix chain 'o' and resid 137 through 181 removed outlier: 4.239A pdb=" N PHE o 168 " --> pdb=" O ILE o 164 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER o 169 " --> pdb=" O SER o 165 " (cutoff:3.500A) Processing helix chain 'o' and resid 185 through 223 Processing helix chain 'o' and resid 223 through 229 Processing helix chain 'n' and resid 8 through 31 Processing helix chain 'n' and resid 31 through 46 Processing helix chain 'n' and resid 53 through 58 removed outlier: 3.922A pdb=" N LEU n 57 " --> pdb=" O ASN n 53 " (cutoff:3.500A) Processing helix chain 'n' and resid 107 through 138 Proline residue: n 119 - end of helix Processing helix chain 'n' and resid 149 through 191 removed outlier: 4.159A pdb=" N PHE n 178 " --> pdb=" O ILE n 174 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER n 179 " --> pdb=" O SER n 175 " (cutoff:3.500A) Processing helix chain 'n' and resid 195 through 239 removed outlier: 3.823A pdb=" N GLN n 199 " --> pdb=" O GLY n 195 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU n 235 " --> pdb=" O LEU n 231 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS n 236 " --> pdb=" O LYS n 232 " (cutoff:3.500A) Processing helix chain 'p' and resid 10 through 34 Processing helix chain 'p' and resid 34 through 49 Processing helix chain 'p' and resid 56 through 60 Processing helix chain 'p' and resid 97 through 129 Proline residue: p 109 - end of helix Processing helix chain 'p' and resid 137 through 181 removed outlier: 3.894A pdb=" N SER p 165 " --> pdb=" O GLN p 161 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE p 168 " --> pdb=" O ILE p 164 " (cutoff:3.500A) Processing helix chain 'p' and resid 185 through 223 Processing helix chain 'p' and resid 223 through 229 Processing helix chain 'A' and resid 4 through 8 Processing helix chain 'A' and resid 18 through 31 removed outlier: 3.531A pdb=" N GLY A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.624A pdb=" N VAL A 61 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 101 Processing helix chain 'A' and resid 105 through 123 removed outlier: 3.650A pdb=" N GLN A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.044A pdb=" N HIS A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'B' and resid 18 through 31 removed outlier: 3.517A pdb=" N GLU B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY B 29 " --> pdb=" O MET B 25 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 102 Processing helix chain 'B' and resid 106 through 124 Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.631A pdb=" N GLN B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 229 through 251 removed outlier: 3.827A pdb=" N LYS B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 29 removed outlier: 3.822A pdb=" N GLU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C 27 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 76 through 99 Processing helix chain 'C' and resid 103 through 121 removed outlier: 4.133A pdb=" N SER C 121 " --> pdb=" O ARG C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 176 Processing helix chain 'C' and resid 179 through 182 Processing helix chain 'C' and resid 183 through 198 removed outlier: 3.764A pdb=" N VAL C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 236 removed outlier: 3.649A pdb=" N LYS C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 31 removed outlier: 3.761A pdb=" N GLU D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 81 through 104 Processing helix chain 'D' and resid 108 through 122 removed outlier: 3.571A pdb=" N GLN D 122 " --> pdb=" O ASN D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 125 No H-bonds generated for 'chain 'D' and resid 123 through 125' Processing helix chain 'D' and resid 173 through 185 removed outlier: 6.462A pdb=" N SER D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 206 Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'E' and resid 19 through 32 removed outlier: 3.732A pdb=" N ALA E 28 " --> pdb=" O TYR E 24 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL E 29 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS E 30 " --> pdb=" O MET E 26 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN E 31 " --> pdb=" O GLU E 27 " (cutoff:3.500A) removed outlier: 3.845A 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 122 Proline residue: E 119 - end of helix Processing helix chain 'E' and resid 164 through 175 removed outlier: 4.395A pdb=" N ALA E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 180 removed outlier: 3.930A pdb=" N PHE E 179 " --> pdb=" O HIS E 175 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET E 180 " --> pdb=" O MET E 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 175 through 180' Processing helix chain 'E' and resid 183 through 199 removed outlier: 3.764A pdb=" N THR E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 235 removed outlier: 4.310A pdb=" N GLY E 235 " --> pdb=" O PRO E 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 10 removed outlier: 4.263A pdb=" N ASP F 8 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU F 9 " --> pdb=" O GLY F 6 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER F 10 " --> pdb=" O TYR F 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 5 through 10' Processing helix chain 'F' and resid 20 through 33 removed outlier: 3.783A pdb=" N GLU F 24 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU F 31 " --> pdb=" O MET F 27 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN F 32 " --> pdb=" O LYS F 28 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER F 33 " --> pdb=" O ALA F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 103 Processing helix chain 'F' and resid 107 through 125 removed outlier: 3.949A pdb=" N TYR F 122 " --> pdb=" O TYR F 118 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU F 124 " --> pdb=" O HIS F 120 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 178 Processing helix chain 'F' and resid 185 through 201 removed outlier: 4.294A 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: 3.664A pdb=" N LYS F 244 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 34 removed outlier: 3.890A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 3.874A 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 110 through 128 Processing helix chain 'G' and resid 171 through 185 Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 231 through 245 Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 91 removed outlier: 3.561A pdb=" N ALA H 79 " --> pdb=" O ARG H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 Processing helix chain 'H' and resid 147 through 166 Processing helix chain 'I' and resid 55 through 78 Processing helix chain 'I' and resid 82 through 97 removed outlier: 3.857A pdb=" N LYS I 97 " --> pdb=" O LEU I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 153 Processing helix chain 'I' and resid 158 through 176 removed outlier: 3.799A pdb=" N ARG I 176 " --> pdb=" O ASN I 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 72 Processing helix chain 'J' and resid 76 through 94 removed outlier: 3.831A pdb=" N ARG J 93 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER J 94 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 147 removed outlier: 4.034A pdb=" N PHE J 137 " --> pdb=" O GLY J 133 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU J 138 " --> pdb=" O TYR J 134 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER J 141 " --> pdb=" O PHE J 137 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE J 142 " --> pdb=" O LEU J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 171 Processing helix chain 'K' and resid 48 through 71 Processing helix chain 'K' and resid 75 through 90 removed outlier: 3.829A pdb=" N TYR K 90 " --> pdb=" O MET K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 143 removed outlier: 3.905A pdb=" N GLY K 137 " --> pdb=" O VAL K 133 " (cutoff:3.500A) removed outlier: 4.008A 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 Processing helix chain 'L' and resid 57 through 80 Processing helix chain 'L' and resid 84 through 99 removed outlier: 3.965A pdb=" N ARG L 99 " --> pdb=" O ILE L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 153 Proline residue: L 147 - end of helix Processing helix chain 'L' and resid 167 through 186 Processing helix chain 'M' and resid 57 through 78 Processing helix chain 'M' and resid 84 through 102 Processing helix chain 'M' and resid 141 through 157 removed outlier: 4.188A pdb=" N GLN M 147 " --> pdb=" O ALA M 143 " (cutoff:3.500A) Proline residue: M 148 - end of helix Processing helix chain 'M' and resid 161 through 180 Processing helix chain 'M' and resid 210 through 215 removed outlier: 3.862A pdb=" N MET M 214 " --> pdb=" O ASP M 210 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE M 215 " --> pdb=" O ILE M 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 210 through 215' Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 90 Processing helix chain 'N' and resid 131 through 143 removed outlier: 3.788A pdb=" N ILE N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLY N 137 " --> pdb=" O SER N 133 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR N 138 " --> pdb=" O TYR N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 167 Processing helix chain 'N' and resid 190 through 194 Processing helix chain 'd' and resid 10 through 34 Processing helix chain 'd' and resid 34 through 49 Processing helix chain 'd' and resid 50 through 53 Processing helix chain 'd' and resid 97 through 129 Proline residue: d 109 - end of helix Processing helix chain 'd' and resid 136 through 181 removed outlier: 4.521A pdb=" N VAL d 140 " --> pdb=" O ASN d 136 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE d 168 " --> pdb=" O ILE d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 185 through 223 Processing helix chain 'd' and resid 223 through 229 Processing helix chain 'c' and resid 7 through 31 Processing helix chain 'c' and resid 31 through 46 Processing helix chain 'c' and resid 107 through 138 Proline residue: c 119 - end of helix Processing helix chain 'c' and resid 147 through 191 removed outlier: 4.004A pdb=" N SER c 175 " --> pdb=" O HIS c 171 " (cutoff:3.500A) Processing helix chain 'c' and resid 195 through 239 removed outlier: 5.659A pdb=" N GLU c 235 " --> pdb=" O LEU c 231 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LYS c 236 " --> pdb=" O LYS c 232 " (cutoff:3.500A) Processing helix chain 'f' and resid 10 through 34 Processing helix chain 'f' and resid 34 through 49 removed outlier: 3.576A pdb=" N GLN f 38 " --> pdb=" O ARG f 34 " (cutoff:3.500A) Processing helix chain 'f' and resid 50 through 54 removed outlier: 3.855A pdb=" N VAL f 54 " --> pdb=" O SER f 51 " (cutoff:3.500A) Processing helix chain 'f' and resid 97 through 129 Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 137 through 181 removed outlier: 4.152A pdb=" N PHE f 168 " --> pdb=" O ILE f 164 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER f 169 " --> pdb=" O SER f 165 " (cutoff:3.500A) Processing helix chain 'f' and resid 185 through 223 Processing helix chain 'f' and resid 223 through 229 Processing helix chain 'e' and resid 8 through 31 Processing helix chain 'e' and resid 31 through 46 Processing helix chain 'e' and resid 107 through 138 Proline residue: e 119 - end of helix Processing helix chain 'e' and resid 149 through 191 removed outlier: 3.765A pdb=" N SER e 175 " --> pdb=" O HIS e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 195 through 239 removed outlier: 5.581A pdb=" N GLU e 235 " --> pdb=" O LEU e 231 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LYS e 236 " --> pdb=" O LYS e 232 " (cutoff:3.500A) Processing helix chain 'h' and resid 10 through 34 Processing helix chain 'h' and resid 34 through 49 Processing helix chain 'h' and resid 56 through 61 removed outlier: 4.263A pdb=" N LEU h 60 " --> pdb=" O ASP h 56 " (cutoff:3.500A) Processing helix chain 'h' and resid 97 through 129 Proline residue: h 109 - end of helix Processing helix chain 'h' and resid 137 through 181 removed outlier: 4.239A pdb=" N PHE h 168 " --> pdb=" O ILE h 164 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER h 169 " --> pdb=" O SER h 165 " (cutoff:3.500A) Processing helix chain 'h' and resid 185 through 223 Processing helix chain 'h' and resid 223 through 229 Processing helix chain 'g' and resid 8 through 31 Processing helix chain 'g' and resid 31 through 46 Processing helix chain 'g' and resid 53 through 58 removed outlier: 3.922A pdb=" N LEU g 57 " --> pdb=" O ASN g 53 " (cutoff:3.500A) Processing helix chain 'g' and resid 107 through 138 Proline residue: g 119 - end of helix Processing helix chain 'g' and resid 149 through 191 removed outlier: 4.159A pdb=" N PHE g 178 " --> pdb=" O ILE g 174 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER g 179 " --> pdb=" O SER g 175 " (cutoff:3.500A) Processing helix chain 'g' and resid 195 through 239 removed outlier: 3.824A pdb=" N GLN g 199 " --> pdb=" O GLY g 195 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLU g 235 " --> pdb=" O LEU g 231 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS g 236 " --> pdb=" O LYS g 232 " (cutoff:3.500A) Processing helix chain 'i' and resid 10 through 34 Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 56 through 60 Processing helix chain 'i' and resid 97 through 129 Proline residue: i 109 - end of helix Processing helix chain 'i' and resid 137 through 181 removed outlier: 3.895A pdb=" N SER i 165 " --> pdb=" O GLN i 161 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE i 168 " --> pdb=" O ILE i 164 " (cutoff:3.500A) Processing helix chain 'i' and resid 185 through 223 Processing helix chain 'i' and resid 223 through 229 Processing sheet with id=AA1, first strand: chain 'O' and resid 159 through 162 Processing sheet with id=AA2, first strand: chain 'O' and resid 65 through 66 Processing sheet with id=AA3, first strand: chain 'P' and resid 161 through 164 Processing sheet with id=AA4, first strand: chain 'P' and resid 65 through 69 removed outlier: 6.667A pdb=" N MET P 72 " --> pdb=" O LEU P 68 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU P 134 " --> pdb=" O SER P 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Q' and resid 158 through 161 Processing sheet with id=AA6, first strand: chain 'Q' and resid 63 through 64 Processing sheet with id=AA7, first strand: chain 'R' and resid 167 through 170 Processing sheet with id=AA8, first strand: chain 'R' and resid 67 through 69 Processing sheet with id=AA9, first strand: chain 'S' and resid 158 through 161 Processing sheet with id=AB1, first strand: chain 'S' and resid 63 through 65 Processing sheet with id=AB2, first strand: chain 'T' and resid 162 through 165 Processing sheet with id=AB3, first strand: chain 'T' and resid 66 through 70 removed outlier: 6.578A pdb=" N VAL T 73 " --> pdb=" O VAL T 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'U' and resid 165 through 169 removed outlier: 5.888A pdb=" N THR U 38 " --> pdb=" O GLN U 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'U' and resid 69 through 73 removed outlier: 6.659A pdb=" N ILE U 76 " --> pdb=" O ILE U 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'V' and resid 124 through 128 removed outlier: 6.375A pdb=" N THR V 2 " --> pdb=" O ASP V 17 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE V 173 " --> pdb=" O PRO V 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'V' and resid 19 through 22 removed outlier: 6.281A pdb=" N GLU V 22 " --> pdb=" O VAL V 26 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL V 26 " --> pdb=" O GLU V 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'V' and resid 34 through 36 Processing sheet with id=AB9, first strand: chain 'V' and resid 211 through 218 removed outlier: 4.622A pdb=" N VAL W 184 " --> pdb=" O LEU W 199 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ALA W 9 " --> pdb=" O ASP W 24 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'W' and resid 27 through 29 removed outlier: 6.877A pdb=" N PHE W 27 " --> pdb=" O VAL W 34 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'W' and resid 41 through 43 removed outlier: 4.392A pdb=" N ILE W 120 " --> pdb=" O THR W 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'X' and resid 129 through 132 removed outlier: 6.134A pdb=" N PHE X 178 " --> pdb=" O ASN X 193 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASN X 193 " --> pdb=" O PHE X 178 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL X 180 " --> pdb=" O LEU X 191 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'X' and resid 35 through 39 removed outlier: 6.825A pdb=" N ILE X 42 " --> pdb=" O MET X 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Y' and resid 125 through 129 removed outlier: 3.591A pdb=" N SER Y 188 " --> pdb=" O LEU Y 176 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N HIS Y 178 " --> pdb=" O ARG Y 186 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ARG Y 186 " --> pdb=" O HIS Y 178 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Y' and resid 20 through 22 removed outlier: 6.618A pdb=" N ALA Y 22 " --> pdb=" O ILE Y 26 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE Y 26 " --> pdb=" O ALA Y 22 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Y' and resid 34 through 35 Processing sheet with id=AC8, first strand: chain 'Y' and resid 34 through 35 Processing sheet with id=AC9, first strand: chain 'Z' and resid 135 through 139 removed outlier: 6.073A pdb=" N THR Z 11 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 29 through 31 removed outlier: 6.417A pdb=" N GLU Z 31 " --> pdb=" O ILE Z 35 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ILE Z 35 " --> pdb=" O GLU Z 31 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Z' and resid 43 through 47 removed outlier: 6.661A pdb=" N THR Z 50 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN Z 108 " --> pdb=" O PHE Z 124 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL Z 121 " --> pdb=" O ASP Z 133 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'a' and resid 7 through 8 removed outlier: 6.647A pdb=" N THR a 49 " --> pdb=" O VAL a 45 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'a' and resid 7 through 8 Processing sheet with id=AD5, first strand: chain 'a' and resid 136 through 138 Processing sheet with id=AD6, first strand: chain 'b' and resid 125 through 129 removed outlier: 6.070A pdb=" N THR b 2 " --> pdb=" O ASP b 17 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'b' and resid 20 through 22 removed outlier: 7.311A pdb=" N THR b 20 " --> pdb=" O ALA b 27 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'b' and resid 34 through 36 Processing sheet with id=AD9, first strand: chain 'A' and resid 159 through 162 Processing sheet with id=AE1, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AE2, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AE3, first strand: chain 'B' and resid 65 through 69 removed outlier: 6.667A pdb=" N MET B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 134 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AE5, first strand: chain 'C' and resid 63 through 64 Processing sheet with id=AE6, first strand: chain 'D' and resid 167 through 170 Processing sheet with id=AE7, first strand: chain 'D' and resid 67 through 69 Processing sheet with id=AE8, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AE9, first strand: chain 'E' and resid 63 through 65 Processing sheet with id=AF1, first strand: chain 'F' and resid 162 through 165 Processing sheet with id=AF2, first strand: chain 'F' and resid 66 through 70 removed outlier: 6.578A pdb=" N VAL F 73 " --> pdb=" O VAL F 69 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.889A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 69 through 73 removed outlier: 6.659A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 124 through 128 removed outlier: 6.376A pdb=" N THR H 2 " --> pdb=" O ASP H 17 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE H 173 " --> pdb=" O PRO H 188 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.281A pdb=" N GLU H 22 " --> pdb=" O VAL H 26 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL H 26 " --> pdb=" O GLU H 22 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 34 through 36 Processing sheet with id=AF8, first strand: chain 'H' and resid 211 through 218 removed outlier: 4.621A pdb=" N VAL I 184 " --> pdb=" O LEU I 199 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ALA I 9 " --> pdb=" O ASP I 24 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 27 through 29 removed outlier: 6.876A pdb=" N PHE I 27 " --> pdb=" O VAL I 34 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 41 through 43 removed outlier: 4.393A pdb=" N ILE I 120 " --> pdb=" O THR I 132 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 129 through 132 removed outlier: 6.134A pdb=" N PHE J 178 " --> pdb=" O ASN J 193 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASN J 193 " --> pdb=" O PHE J 178 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL J 180 " --> pdb=" O LEU J 191 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 35 through 39 removed outlier: 6.825A pdb=" N ILE J 42 " --> pdb=" O MET J 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 125 through 129 removed outlier: 3.592A pdb=" N SER K 188 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N HIS K 178 " --> pdb=" O ARG K 186 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ARG K 186 " --> pdb=" O HIS K 178 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 20 through 22 removed outlier: 6.617A pdb=" N ALA K 22 " --> pdb=" O ILE K 26 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE K 26 " --> pdb=" O ALA K 22 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 34 through 35 Processing sheet with id=AG7, first strand: chain 'K' and resid 34 through 35 Processing sheet with id=AG8, first strand: chain 'L' and resid 135 through 139 removed outlier: 6.073A pdb=" N THR L 11 " --> pdb=" O ASP L 26 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 29 through 31 removed outlier: 6.418A pdb=" N GLU L 31 " --> pdb=" O ILE L 35 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ILE L 35 " --> pdb=" O GLU L 31 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 43 through 47 removed outlier: 6.661A pdb=" N THR L 50 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN L 108 " --> pdb=" O PHE L 124 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL L 121 " --> pdb=" O ASP L 133 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 7 through 8 removed outlier: 6.647A pdb=" N THR M 49 " --> pdb=" O VAL M 45 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'M' and resid 7 through 8 Processing sheet with id=AH4, first strand: chain 'M' and resid 136 through 138 Processing sheet with id=AH5, first strand: chain 'N' and resid 125 through 129 removed outlier: 6.070A pdb=" N THR N 2 " --> pdb=" O ASP N 17 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'N' and resid 20 through 22 removed outlier: 7.311A pdb=" N THR N 20 " --> pdb=" O ALA N 27 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'N' and resid 34 through 36 4716 hydrogen bonds defined for protein. 13788 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: 27.05 Time building geometry restraints manager: 25.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22671 1.34 - 1.46: 12142 1.46 - 1.58: 35675 1.58 - 1.69: 0 1.69 - 1.81: 594 Bond restraints: 71082 Sorted by residual: bond pdb=" N MET X 1 " pdb=" CA MET X 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N GLN g 7 " pdb=" CA GLN g 7 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" N ARG O 3 " pdb=" CA ARG O 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N ARG L 1 " pdb=" CA ARG L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 ... (remaining 71077 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.09: 1509 106.09 - 113.14: 39005 113.14 - 120.18: 24409 120.18 - 127.23: 30913 127.23 - 134.28: 616 Bond angle restraints: 96452 Sorted by residual: angle pdb=" N ASP L 191 " pdb=" CA ASP L 191 " pdb=" CB ASP L 191 " ideal model delta sigma weight residual 114.17 109.58 4.59 1.14e+00 7.69e-01 1.62e+01 angle pdb=" N ASP Z 191 " pdb=" CA ASP Z 191 " pdb=" CB ASP Z 191 " ideal model delta sigma weight residual 114.17 109.62 4.55 1.14e+00 7.69e-01 1.59e+01 angle pdb=" N VAL R 12 " pdb=" CA VAL R 12 " pdb=" C VAL R 12 " ideal model delta sigma weight residual 110.21 106.51 3.70 1.13e+00 7.83e-01 1.07e+01 angle pdb=" N VAL D 12 " pdb=" CA VAL D 12 " pdb=" C VAL D 12 " ideal model delta sigma weight residual 110.21 106.52 3.69 1.13e+00 7.83e-01 1.07e+01 angle pdb=" C ILE I 29 " pdb=" N GLN I 30 " pdb=" CA GLN I 30 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.70e+00 ... (remaining 96447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 39465 17.80 - 35.59: 2732 35.59 - 53.39: 345 53.39 - 71.19: 122 71.19 - 88.99: 60 Dihedral angle restraints: 42724 sinusoidal: 15870 harmonic: 26854 Sorted by residual: dihedral pdb=" CA ARG H 187 " pdb=" C ARG H 187 " pdb=" N PRO H 188 " pdb=" CA PRO H 188 " ideal model delta harmonic sigma weight residual -180.00 -121.78 -58.22 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA ARG V 187 " pdb=" C ARG V 187 " pdb=" N PRO V 188 " pdb=" CA PRO V 188 " ideal model delta harmonic sigma weight residual -180.00 -121.80 -58.20 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA ARG R 5 " pdb=" C ARG R 5 " pdb=" N SER R 6 " pdb=" CA SER R 6 " ideal model delta harmonic sigma weight residual -180.00 -127.07 -52.93 0 5.00e+00 4.00e-02 1.12e+02 ... (remaining 42721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 8166 0.045 - 0.090: 2327 0.090 - 0.135: 653 0.135 - 0.180: 72 0.180 - 0.225: 4 Chirality restraints: 11222 Sorted by residual: chirality pdb=" CG LEU N 202 " pdb=" CB LEU N 202 " pdb=" CD1 LEU N 202 " pdb=" CD2 LEU N 202 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CG LEU b 202 " pdb=" CB LEU b 202 " pdb=" CD1 LEU b 202 " pdb=" CD2 LEU b 202 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB VAL Z 127 " pdb=" CA VAL Z 127 " pdb=" CG1 VAL Z 127 " pdb=" CG2 VAL Z 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.53e-01 ... (remaining 11219 not shown) Planarity restraints: 12306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS S 148 " 0.057 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO S 149 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO S 149 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO S 149 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 148 " -0.057 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO E 149 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO E 149 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 149 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP W 158 " 0.056 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO W 159 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO W 159 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO W 159 " 0.047 5.00e-02 4.00e+02 ... (remaining 12303 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 622 2.65 - 3.21: 67000 3.21 - 3.78: 113719 3.78 - 4.34: 155441 4.34 - 4.90: 258537 Nonbonded interactions: 595319 Sorted by model distance: nonbonded pdb=" OG SER b 124 " pdb=" OH TYR b 143 " model vdw 2.090 2.440 nonbonded pdb=" OG SER N 124 " pdb=" OH TYR N 143 " model vdw 2.090 2.440 nonbonded pdb=" O THR Y 44 " pdb=" OG1 THR Y 99 " model vdw 2.092 2.440 nonbonded pdb=" O THR K 44 " pdb=" OG1 THR K 99 " model vdw 2.093 2.440 nonbonded pdb=" OG1 THR H 213 " pdb=" OG1 THR I 198 " model vdw 2.115 2.440 ... (remaining 595314 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' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } ncs_group { reference = (chain 'c' and (resid 7 through 55 or (resid 56 and (name N or name CA or name C \ or name O or name CB )) or resid 57 through 249)) selection = (chain 'e' and (resid 7 through 121 or (resid 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 through 142 or (resid 143 and (name N or \ name CA or name C or name O or name CB )) or resid 144 through 153 or (resid 15 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 155 through \ 157 or (resid 158 and (name N or name CA or name C or name O or name CB )) or re \ sid 159 through 244 or (resid 245 and (name N or name CA or name C or name O or \ name CB )) or resid 246 or (resid 247 and (name N or name CA or name C or name O \ or name CB )) or resid 248 through 249)) selection = (chain 'g' and (resid 7 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 105 or (resid 106 and (name N or na \ me CA or name C or name O or name CB )) or resid 107 through 246 or (resid 247 a \ nd (name N or name CA or name C or name O or name CB )) or resid 248 through 249 \ )) selection = (chain 'j' and (resid 7 through 55 or (resid 56 and (name N or name CA or name C \ or name O or name CB )) or resid 57 through 249)) selection = (chain 'l' and (resid 7 through 121 or (resid 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 through 142 or (resid 143 and (name N or \ name CA or name C or name O or name CB )) or resid 144 through 153 or (resid 15 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 155 through \ 157 or (resid 158 and (name N or name CA or name C or name O or name CB )) or re \ sid 159 through 244 or (resid 245 and (name N or name CA or name C or name O or \ name CB )) or resid 246 or (resid 247 and (name N or name CA or name C or name O \ or name CB )) or resid 248 through 249)) selection = (chain 'n' and (resid 7 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 105 or (resid 106 and (name N or na \ me CA or name C or name O or name CB )) or resid 107 through 246 or (resid 247 a \ nd (name N or name CA or name C or name O or name CB )) or resid 248 through 249 \ )) } ncs_group { reference = (chain 'd' and (resid 8 through 28 or (resid 29 through 30 and (name N or name C \ A or name C or name O or name CB )) or resid 31 through 58 or (resid 59 and (nam \ e N or name CA or name C or name O or name CB )) or resid 60 through 92 or (resi \ d 93 and (name N or name CA or name C or name O or name CB )) or resid 94 throug \ h 233)) selection = (chain 'f' and (resid 8 through 28 or (resid 29 through 30 and (name N or name C \ A or name C or name O or name CB )) or resid 31 through 58 or (resid 59 and (nam \ e N or name CA or name C or name O or name CB )) or resid 60 through 92 or (resi \ d 93 and (name N or name CA or name C or name O or name CB )) or resid 94 throug \ h 165 or (resid 166 and (name N or name CA or name C or name O or name CB )) or \ resid 167 through 233)) selection = (chain 'h' and (resid 8 through 58 or (resid 59 and (name N or name CA or name C \ or name O or name CB )) or resid 60 through 147 or (resid 148 and (name N or na \ me CA or name C or name O or name CB )) or resid 149 through 165 or (resid 166 a \ nd (name N or name CA or name C or name O or name CB )) or resid 167 through 233 \ )) selection = (chain 'i' and (resid 8 through 13 or (resid 14 through 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 through 28 or (resid 29 through \ 30 and (name N or name CA or name C or name O or name CB )) or resid 31 through \ 92 or (resid 93 and (name N or name CA or name C or name O or name CB )) or resi \ d 94 through 147 or (resid 148 and (name N or name CA or name C or name O or nam \ e CB )) or resid 149 through 233)) selection = (chain 'k' and (resid 8 through 28 or (resid 29 through 30 and (name N or name C \ A or name C or name O or name CB )) or resid 31 through 58 or (resid 59 and (nam \ e N or name CA or name C or name O or name CB )) or resid 60 through 92 or (resi \ d 93 and (name N or name CA or name C or name O or name CB )) or resid 94 throug \ h 233)) selection = (chain 'm' and (resid 8 through 28 or (resid 29 through 30 and (name N or name C \ A or name C or name O or name CB )) or resid 31 through 58 or (resid 59 and (nam \ e N or name CA or name C or name O or name CB )) or resid 60 through 92 or (resi \ d 93 and (name N or name CA or name C or name O or name CB )) or resid 94 throug \ h 165 or (resid 166 and (name N or name CA or name C or name O or name CB )) or \ resid 167 through 233)) selection = (chain 'o' and (resid 8 through 58 or (resid 59 and (name N or name CA or name C \ or name O or name CB )) or resid 60 through 147 or (resid 148 and (name N or na \ me CA or name C or name O or name CB )) or resid 149 through 165 or (resid 166 a \ nd (name N or name CA or name C or name O or name CB )) or resid 167 through 233 \ )) selection = (chain 'p' and (resid 8 through 13 or (resid 14 through 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 through 28 or (resid 29 through \ 30 and (name N or name CA or name C or name O or name CB )) or resid 31 through \ 92 or (resid 93 and (name N or name CA or name C or name O or name CB )) or resi \ d 94 through 147 or (resid 148 and (name N or name CA or name C or name O or nam \ e CB )) or resid 149 through 233)) } 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 358 5.16 5 C 44740 2.51 5 N 12120 2.21 5 O 12544 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 16.200 Check model and map are aligned: 0.820 Process input model: 143.730 Find NCS groups from input model: 6.970 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Set scattering table: 0.500 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 : 0.005 0.051 71082 Z= 0.342 Angle : 0.743 8.036 96452 Z= 0.403 Chirality : 0.045 0.225 11222 Planarity : 0.006 0.087 12306 Dihedral : 13.060 88.985 25456 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.24 % Favored : 98.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.08), residues: 9128 helix: 1.74 (0.07), residues: 4456 sheet: 0.37 (0.12), residues: 1478 loop : -0.20 (0.10), residues: 3194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2458 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2458 time to evaluate : 6.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2458 average time/residue: 0.7637 time to fit residues: 3073.9935 Evaluate side-chains 1473 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1473 time to evaluate : 6.480 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.6297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 765 optimal weight: 20.0000 chunk 686 optimal weight: 6.9990 chunk 381 optimal weight: 0.7980 chunk 234 optimal weight: 0.8980 chunk 463 optimal weight: 0.9990 chunk 366 optimal weight: 5.9990 chunk 710 optimal weight: 0.0570 chunk 274 optimal weight: 4.9990 chunk 431 optimal weight: 6.9990 chunk 528 optimal weight: 9.9990 chunk 822 optimal weight: 8.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 94 GLN O 95 GLN ** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 188 HIS Q 18 GLN Q 120 GLN ** S 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 90 GLN ** T 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN U 34 GLN U 90 GLN U 172 GLN V 85 GLN W 60 GLN W 161 HIS X 63 ASN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 ASN Y 62 GLN Y 70 ASN Y 151 GLN Z 8 ASN Z 79 ASN Z 131 GLN ** Z 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 69 GLN ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 187 GLN b 193 GLN k 136 ASN k 161 GLN k 183 HIS j 202 HIS ** m 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 136 ASN m 143 GLN l 136 GLN l 153 GLN ** o 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 143 GLN n 27 ASN ** n 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 136 GLN n 146 ASN p 16 GLN ** p 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS A 95 GLN B 109 GLN B 146 GLN B 166 ASN B 167 ASN C 205 ASN D 122 GLN E 20 HIS E 60 GLN E 65 HIS E 68 ASN F 147 GLN G 224 ASN H 57 GLN ** I 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN I 161 HIS I 172 ASN ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN J 63 ASN J 99 HIS J 101 ASN K 38 ASN L 8 ASN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN N 123 GLN d 16 GLN d 126 GLN d 143 GLN d 183 HIS c 27 ASN c 56 ASN c 129 ASN c 164 HIS c 233 ASN f 22 GLN f 127 HIS f 161 GLN f 229 ASN e 127 GLN e 136 GLN e 138 GLN e 171 HIS h 23 ASN g 136 GLN g 193 HIS i 22 GLN i 143 GLN i 151 ASN i 161 GLN i 183 HIS Total number of N/Q/H flips: 88 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 71082 Z= 0.243 Angle : 0.643 9.627 96452 Z= 0.341 Chirality : 0.044 0.224 11222 Planarity : 0.005 0.080 12306 Dihedral : 4.837 51.374 10044 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.64 % Favored : 98.33 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.08), residues: 9128 helix: 2.23 (0.07), residues: 4458 sheet: 0.53 (0.12), residues: 1478 loop : -0.06 (0.11), residues: 3192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1788 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1620 time to evaluate : 6.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 168 outliers final: 76 residues processed: 1711 average time/residue: 0.7005 time to fit residues: 2008.2545 Evaluate side-chains 1446 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1370 time to evaluate : 6.545 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 0 residues processed: 76 average time/residue: 0.5377 time to fit residues: 84.7663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 457 optimal weight: 8.9990 chunk 255 optimal weight: 9.9990 chunk 684 optimal weight: 3.9990 chunk 560 optimal weight: 8.9990 chunk 226 optimal weight: 0.0870 chunk 824 optimal weight: 6.9990 chunk 890 optimal weight: 8.9990 chunk 734 optimal weight: 4.9990 chunk 817 optimal weight: 6.9990 chunk 280 optimal weight: 5.9990 chunk 661 optimal weight: 7.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 95 GLN P 95 GLN S 90 GLN U 24 GLN X 87 ASN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 175 ASN a 81 HIS ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 77 HIS ** b 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 ASN m 44 ASN m 136 ASN l 136 GLN l 193 HIS o 45 GLN o 48 GLN ** o 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 136 GLN n 146 ASN ** n 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 233 ASN ** p 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN B 109 GLN D 97 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN G 128 ASN ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 HIS M 108 ASN M 157 GLN d 127 HIS c 146 ASN ** c 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 127 HIS ** f 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 193 HIS e 199 GLN g 173 GLN g 233 ASN i 126 GLN ** i 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.084 71082 Z= 0.463 Angle : 0.699 12.047 96452 Z= 0.374 Chirality : 0.046 0.256 11222 Planarity : 0.005 0.074 12306 Dihedral : 4.814 52.252 10044 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.25 % Favored : 97.73 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.09), residues: 9128 helix: 2.15 (0.07), residues: 4474 sheet: 0.34 (0.12), residues: 1530 loop : -0.06 (0.11), residues: 3124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1529 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1357 time to evaluate : 6.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 172 outliers final: 95 residues processed: 1460 average time/residue: 0.7190 time to fit residues: 1774.8197 Evaluate side-chains 1312 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1217 time to evaluate : 6.709 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 0 residues processed: 95 average time/residue: 0.5663 time to fit residues: 112.1549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 814 optimal weight: 0.9980 chunk 619 optimal weight: 0.9990 chunk 427 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 393 optimal weight: 3.9990 chunk 553 optimal weight: 1.9990 chunk 827 optimal weight: 10.0000 chunk 875 optimal weight: 2.9990 chunk 432 optimal weight: 8.9990 chunk 783 optimal weight: 7.9990 chunk 236 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 95 GLN S 16 GLN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 60 GLN X 87 ASN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 175 ASN a 65 GLN ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 ASN ** j 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 126 GLN ** l 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 GLN ** o 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 136 GLN ** n 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 193 HIS ** p 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN G 24 GLN H 62 ASN I 32 GLN ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 126 GLN c 146 ASN ** c 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 127 HIS e 138 GLN i 151 ASN ** i 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 71082 Z= 0.258 Angle : 0.612 10.510 96452 Z= 0.326 Chirality : 0.043 0.312 11222 Planarity : 0.004 0.070 12306 Dihedral : 4.617 49.461 10044 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.09), residues: 9128 helix: 2.30 (0.07), residues: 4496 sheet: 0.27 (0.13), residues: 1488 loop : -0.05 (0.11), residues: 3144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1472 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1365 time to evaluate : 6.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 59 residues processed: 1424 average time/residue: 0.7045 time to fit residues: 1693.3148 Evaluate side-chains 1297 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1238 time to evaluate : 6.448 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.5389 time to fit residues: 68.2842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 729 optimal weight: 0.8980 chunk 497 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 652 optimal weight: 5.9990 chunk 361 optimal weight: 10.0000 chunk 747 optimal weight: 3.9990 chunk 605 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 447 optimal weight: 5.9990 chunk 786 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 16 GLN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 175 HIS ** T 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 60 GLN X 87 ASN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 22 GLN k 136 ASN ** j 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 GLN ** o 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 136 GLN n 173 GLN ** n 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN E 90 GLN ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 ASN ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 GLN d 126 GLN ** c 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 71082 Z= 0.279 Angle : 0.612 11.174 96452 Z= 0.326 Chirality : 0.043 0.314 11222 Planarity : 0.004 0.069 12306 Dihedral : 4.542 51.640 10044 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.09), residues: 9128 helix: 2.30 (0.07), residues: 4504 sheet: 0.18 (0.13), residues: 1498 loop : -0.05 (0.11), residues: 3126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1424 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1319 time to evaluate : 6.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 57 residues processed: 1385 average time/residue: 0.6909 time to fit residues: 1618.7098 Evaluate side-chains 1285 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1228 time to evaluate : 6.480 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.5413 time to fit residues: 67.0028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 294 optimal weight: 0.8980 chunk 788 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 514 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 chunk 876 optimal weight: 6.9990 chunk 727 optimal weight: 2.9990 chunk 405 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 289 optimal weight: 6.9990 chunk 460 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 146 GLN Q 54 GLN ** S 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 12 HIS W 60 GLN X 87 ASN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 ASN a 65 GLN ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 ASN ** j 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 191 GLN m 161 GLN o 45 GLN ** n 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 136 GLN ** n 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN E 90 GLN E 146 GLN E 175 HIS H 62 ASN I 64 GLN ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 126 GLN c 233 ASN ** f 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 151 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 71082 Z= 0.255 Angle : 0.609 9.422 96452 Z= 0.324 Chirality : 0.042 0.334 11222 Planarity : 0.004 0.068 12306 Dihedral : 4.475 49.787 10044 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.09), residues: 9128 helix: 2.33 (0.07), residues: 4494 sheet: 0.07 (0.13), residues: 1522 loop : -0.02 (0.11), residues: 3112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1449 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1355 time to evaluate : 6.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 48 residues processed: 1407 average time/residue: 0.6976 time to fit residues: 1661.3891 Evaluate side-chains 1304 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1256 time to evaluate : 6.515 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.5317 time to fit residues: 56.8067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 845 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 499 optimal weight: 6.9990 chunk 640 optimal weight: 0.9980 chunk 495 optimal weight: 10.0000 chunk 737 optimal weight: 5.9990 chunk 489 optimal weight: 4.9990 chunk 873 optimal weight: 3.9990 chunk 546 optimal weight: 4.9990 chunk 532 optimal weight: 0.4980 chunk 403 optimal weight: 2.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 54 GLN ** S 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 128 ASN U 150 GLN W 60 GLN X 87 ASN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 ASN ** j 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 202 HIS m 48 GLN o 45 GLN ** o 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 173 GLN ** n 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN C 85 ASN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN E 90 GLN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 ASN ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 161 GLN ** e 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 143 GLN i 161 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 71082 Z= 0.313 Angle : 0.638 11.259 96452 Z= 0.339 Chirality : 0.043 0.303 11222 Planarity : 0.004 0.073 12306 Dihedral : 4.508 48.863 10044 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.09), residues: 9128 helix: 2.27 (0.07), residues: 4500 sheet: 0.04 (0.13), residues: 1528 loop : -0.08 (0.11), residues: 3100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1371 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1291 time to evaluate : 6.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 43 residues processed: 1333 average time/residue: 0.7123 time to fit residues: 1620.8881 Evaluate side-chains 1259 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1216 time to evaluate : 6.532 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.5447 time to fit residues: 52.9932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 540 optimal weight: 0.9980 chunk 348 optimal weight: 10.0000 chunk 521 optimal weight: 0.6980 chunk 263 optimal weight: 6.9990 chunk 171 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 555 optimal weight: 5.9990 chunk 594 optimal weight: 0.9990 chunk 431 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 686 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 54 GLN ** S 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 128 ASN W 60 GLN X 87 ASN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 ASN Y 151 GLN Z 152 GLN ** Z 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 ASN ** j 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 GLN ** n 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 136 GLN ** n 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN E 59 HIS E 68 ASN E 90 GLN E 146 GLN ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 ASN ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 191 GLN ** e 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 143 GLN ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 71082 Z= 0.197 Angle : 0.620 9.585 96452 Z= 0.328 Chirality : 0.042 0.313 11222 Planarity : 0.004 0.064 12306 Dihedral : 4.402 48.178 10044 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.09), residues: 9128 helix: 2.31 (0.07), residues: 4514 sheet: 0.05 (0.13), residues: 1518 loop : -0.12 (0.11), residues: 3096 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1454 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1406 time to evaluate : 6.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 18 residues processed: 1423 average time/residue: 0.7064 time to fit residues: 1705.1803 Evaluate side-chains 1295 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1277 time to evaluate : 6.563 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.5595 time to fit residues: 27.1363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 794 optimal weight: 0.9990 chunk 836 optimal weight: 10.0000 chunk 763 optimal weight: 4.9990 chunk 813 optimal weight: 0.8980 chunk 489 optimal weight: 1.9990 chunk 354 optimal weight: 10.0000 chunk 638 optimal weight: 10.0000 chunk 249 optimal weight: 7.9990 chunk 735 optimal weight: 0.9990 chunk 769 optimal weight: 7.9990 chunk 810 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 118 GLN Q 54 GLN ** S 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 60 GLN ** W 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 ASN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 ASN ** j 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 GLN n 115 GLN ** n 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 136 GLN n 147 ASN ** n 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 223 ASN ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN C 85 ASN E 68 ASN E 146 GLN ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN J 87 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 ASN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 213 HIS f 161 GLN f 229 ASN ** e 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 143 GLN ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 71082 Z= 0.217 Angle : 0.648 12.982 96452 Z= 0.343 Chirality : 0.043 0.308 11222 Planarity : 0.004 0.083 12306 Dihedral : 4.372 46.972 10044 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.09), residues: 9128 helix: 2.25 (0.07), residues: 4534 sheet: 0.04 (0.13), residues: 1518 loop : -0.14 (0.11), residues: 3076 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1380 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1346 time to evaluate : 6.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 21 residues processed: 1358 average time/residue: 0.7121 time to fit residues: 1643.9418 Evaluate side-chains 1293 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1272 time to evaluate : 6.592 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.5211 time to fit residues: 29.6777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 534 optimal weight: 0.6980 chunk 860 optimal weight: 5.9990 chunk 525 optimal weight: 4.9990 chunk 408 optimal weight: 3.9990 chunk 598 optimal weight: 5.9990 chunk 902 optimal weight: 5.9990 chunk 830 optimal weight: 6.9990 chunk 718 optimal weight: 7.9990 chunk 74 optimal weight: 0.3980 chunk 555 optimal weight: 7.9990 chunk 440 optimal weight: 0.9980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 143 HIS ** T 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 60 GLN ** W 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 ASN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 ASN ** j 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 126 GLN ** l 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 GLN o 161 GLN o 192 HIS n 115 GLN ** n 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 147 ASN ** n 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN E 68 ASN E 146 GLN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 GLN J 61 GLN J 87 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 ASN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 213 HIS c 146 ASN c 199 GLN ** c 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 229 ASN ** e 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 71082 Z= 0.287 Angle : 0.682 11.809 96452 Z= 0.361 Chirality : 0.043 0.273 11222 Planarity : 0.004 0.110 12306 Dihedral : 4.435 47.109 10044 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.78 % Favored : 97.21 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.09), residues: 9128 helix: 2.22 (0.07), residues: 4518 sheet: 0.02 (0.13), residues: 1522 loop : -0.20 (0.11), residues: 3088 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18256 Ramachandran restraints generated. 9128 Oldfield, 0 Emsley, 9128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1312 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1294 time to evaluate : 7.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 1302 average time/residue: 0.7134 time to fit residues: 1579.0094 Evaluate side-chains 1263 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1255 time to evaluate : 6.605 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5426 time to fit residues: 16.8478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 570 optimal weight: 0.8980 chunk 765 optimal weight: 0.5980 chunk 220 optimal weight: 2.9990 chunk 662 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 719 optimal weight: 0.8980 chunk 301 optimal weight: 0.8980 chunk 739 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 35 HIS W 60 GLN ** W 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 ASN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 ASN ** j 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 126 GLN ** l 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 147 ASN ** n 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN E 68 ASN G 12 HIS ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 ASN ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 213 HIS d 161 GLN ** c 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 48 GLN f 229 ASN ** e 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 22 GLN ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 161 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.066851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.054069 restraints weight = 228507.206| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.33 r_work: 0.2758 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 71082 Z= 0.206 Angle : 0.664 12.209 96452 Z= 0.350 Chirality : 0.043 0.265 11222 Planarity : 0.004 0.063 12306 Dihedral : 4.376 46.258 10044 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.09), residues: 9128 helix: 2.21 (0.07), residues: 4514 sheet: 0.08 (0.13), residues: 1524 loop : -0.24 (0.11), residues: 3090 =============================================================================== Job complete usr+sys time: 24252.72 seconds wall clock time: 422 minutes 15.53 seconds (25335.53 seconds total)