Starting phenix.real_space_refine on Sat Feb 17 15:32:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nap_24277/02_2024/7nap_24277.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nap_24277/02_2024/7nap_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_2024/7nap_24277.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nap_24277/02_2024/7nap_24277.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nap_24277/02_2024/7nap_24277.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nap_24277/02_2024/7nap_24277.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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 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. 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: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 26.90, per 1000 atoms: 0.39 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: 21.20 Conformation dependent library (CDL) restraints added in 9.6 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: 4.85 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: 25.80 Time building geometry restraints manager: 23.32 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 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 13.680 Check model and map are aligned: 0.770 Set scattering table: 0.490 Process input model: 139.150 Find NCS groups from input model: 6.530 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 % Allowed : 1.41 % Favored : 98.59 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 215 HIS 0.009 0.002 HIS R 73 PHE 0.022 0.002 PHE W 68 TYR 0.030 0.002 TYR H 42 ARG 0.006 0.001 ARG f 188 *********************** 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 : 6.064 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 REVERT: O 108 GLN cc_start: 0.8578 (mm110) cc_final: 0.8320 (mm-40) REVERT: P 6 ASP cc_start: 0.8564 (p0) cc_final: 0.8285 (p0) REVERT: P 128 ARG cc_start: 0.8798 (ptt-90) cc_final: 0.8465 (ptt-90) REVERT: Q 13 ASP cc_start: 0.8481 (m-30) cc_final: 0.8248 (m-30) REVERT: Q 67 ASP cc_start: 0.8111 (p0) cc_final: 0.7525 (p0) REVERT: Q 118 TYR cc_start: 0.9265 (m-80) cc_final: 0.9024 (m-10) REVERT: R 73 HIS cc_start: 0.7100 (p-80) cc_final: 0.6788 (p-80) REVERT: R 107 MET cc_start: 0.8023 (mtp) cc_final: 0.7789 (mtm) REVERT: R 135 ARG cc_start: 0.9023 (ptt90) cc_final: 0.8713 (ptt-90) REVERT: S 9 ASP cc_start: 0.8180 (t70) cc_final: 0.7672 (t70) REVERT: S 67 ASP cc_start: 0.8408 (t70) cc_final: 0.8043 (t0) REVERT: S 100 ASP cc_start: 0.9039 (t0) cc_final: 0.8525 (t0) REVERT: S 152 ASN cc_start: 0.8478 (t0) cc_final: 0.8170 (t0) REVERT: S 179 PHE cc_start: 0.8646 (m-10) cc_final: 0.8013 (m-80) REVERT: T 17 ASP cc_start: 0.8292 (p0) cc_final: 0.7966 (p0) REVERT: T 93 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8094 (mt-10) REVERT: T 167 LYS cc_start: 0.9106 (ttpt) cc_final: 0.8823 (ttmm) REVERT: T 173 LYS cc_start: 0.9371 (mtpp) cc_final: 0.9136 (mtmm) REVERT: U 9 PHE cc_start: 0.8783 (m-80) cc_final: 0.8554 (m-10) REVERT: U 125 TYR cc_start: 0.8755 (m-80) cc_final: 0.7415 (m-80) REVERT: U 138 MET cc_start: 0.7834 (ttm) cc_final: 0.7626 (ttm) REVERT: V 30 ASN cc_start: 0.8629 (t0) cc_final: 0.8384 (t0) REVERT: V 51 ASP cc_start: 0.8645 (m-30) cc_final: 0.8213 (m-30) REVERT: V 146 MET cc_start: 0.8197 (mtm) cc_final: 0.7640 (mtm) REVERT: W 112 ASP cc_start: 0.8828 (t70) cc_final: 0.8363 (t0) REVERT: W 192 ASP cc_start: 0.8541 (p0) cc_final: 0.8264 (p0) REVERT: W 193 LYS cc_start: 0.9006 (pttt) cc_final: 0.8587 (ptpp) REVERT: X 18 ASP cc_start: 0.8364 (p0) cc_final: 0.7829 (p0) REVERT: X 108 ASP cc_start: 0.7448 (t0) cc_final: 0.7229 (t0) REVERT: Y 44 THR cc_start: 0.8789 (p) cc_final: 0.8412 (p) REVERT: Y 140 ASP cc_start: 0.8194 (m-30) cc_final: 0.7622 (m-30) REVERT: Z 44 TYR cc_start: 0.8866 (m-80) cc_final: 0.8580 (m-80) REVERT: Z 184 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7733 (mm-30) REVERT: a 5 MET cc_start: 0.8118 (mmt) cc_final: 0.7682 (mmm) REVERT: a 26 MET cc_start: 0.8069 (mtp) cc_final: 0.7866 (mtt) REVERT: a 73 ASP cc_start: 0.8438 (p0) cc_final: 0.8010 (p0) REVERT: a 79 ASP cc_start: 0.8718 (p0) cc_final: 0.8499 (p0) REVERT: a 104 ASN cc_start: 0.8926 (t0) cc_final: 0.8431 (t0) REVERT: a 108 ASN cc_start: 0.8324 (m-40) cc_final: 0.8059 (m-40) REVERT: k 34 ARG cc_start: 0.8484 (mtt90) cc_final: 0.7919 (mtt90) REVERT: k 185 MET cc_start: 0.8624 (mmp) cc_final: 0.8150 (mmp) REVERT: k 217 TYR cc_start: 0.9200 (t80) cc_final: 0.8927 (t80) REVERT: j 11 GLN cc_start: 0.8487 (tt0) cc_final: 0.8243 (tp-100) REVERT: j 15 ASP cc_start: 0.8438 (m-30) cc_final: 0.7492 (m-30) REVERT: j 123 ASP cc_start: 0.8470 (m-30) cc_final: 0.8077 (m-30) REVERT: j 146 ASN cc_start: 0.8526 (t0) cc_final: 0.8179 (t0) REVERT: j 170 PHE cc_start: 0.9346 (m-10) cc_final: 0.9015 (m-80) REVERT: j 196 ASP cc_start: 0.7739 (t70) cc_final: 0.7435 (t0) REVERT: j 199 GLN cc_start: 0.9141 (tp-100) cc_final: 0.8563 (tp-100) REVERT: j 202 HIS cc_start: 0.8790 (m90) cc_final: 0.7904 (m-70) REVERT: j 228 ASP cc_start: 0.9118 (t70) cc_final: 0.8652 (t0) REVERT: m 180 LYS cc_start: 0.8976 (tptp) cc_final: 0.8745 (tptp) REVERT: m 217 TYR cc_start: 0.8515 (t80) cc_final: 0.7108 (t80) REVERT: l 11 GLN cc_start: 0.8403 (tt0) cc_final: 0.8154 (tp40) REVERT: l 32 TYR cc_start: 0.8663 (t80) cc_final: 0.7674 (t80) REVERT: l 123 ASP cc_start: 0.8628 (m-30) cc_final: 0.8289 (t0) REVERT: l 157 PHE cc_start: 0.8166 (m-80) cc_final: 0.7840 (m-80) REVERT: l 191 GLN cc_start: 0.9302 (mp10) cc_final: 0.8842 (mp10) REVERT: l 196 ASP cc_start: 0.8576 (m-30) cc_final: 0.8362 (m-30) REVERT: l 215 MET cc_start: 0.9174 (mtt) cc_final: 0.8846 (mtp) REVERT: o 57 LEU cc_start: 0.8838 (mp) cc_final: 0.7981 (mt) REVERT: o 181 GLU cc_start: 0.9037 (mp0) cc_final: 0.8730 (mp0) REVERT: o 199 TYR cc_start: 0.8292 (t80) cc_final: 0.8028 (t80) REVERT: o 236 PRO cc_start: 0.9203 (Cg_exo) cc_final: 0.8863 (Cg_endo) REVERT: n 129 ASN cc_start: 0.9456 (m-40) cc_final: 0.9074 (m-40) REVERT: n 132 THR cc_start: 0.9543 (m) cc_final: 0.9186 (p) REVERT: n 146 ASN cc_start: 0.8484 (m-40) cc_final: 0.8120 (t0) REVERT: n 164 HIS cc_start: 0.8895 (t70) cc_final: 0.7927 (t-90) REVERT: n 176 LYS cc_start: 0.9212 (pttt) cc_final: 0.8727 (ptpp) REVERT: n 203 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8417 (tp30) REVERT: n 212 ILE cc_start: 0.9106 (mt) cc_final: 0.8764 (mm) REVERT: n 215 MET cc_start: 0.8608 (mtt) cc_final: 0.7538 (mtm) REVERT: p 42 TYR cc_start: 0.9010 (t80) cc_final: 0.8570 (t80) REVERT: p 97 ASN cc_start: 0.8463 (t0) cc_final: 0.8047 (t0) REVERT: p 122 ILE cc_start: 0.9478 (mt) cc_final: 0.9273 (mt) REVERT: p 142 ILE cc_start: 0.9519 (mt) cc_final: 0.9300 (tt) REVERT: p 185 MET cc_start: 0.7322 (mmm) cc_final: 0.7104 (mmp) REVERT: p 186 ASP cc_start: 0.7527 (t0) cc_final: 0.6686 (t0) REVERT: p 223 ASN cc_start: 0.9327 (m-40) cc_final: 0.9052 (m-40) REVERT: A 6 SER cc_start: 0.9184 (m) cc_final: 0.8908 (t) REVERT: A 7 PHE cc_start: 0.9148 (m-80) cc_final: 0.8619 (m-80) REVERT: A 187 ILE cc_start: 0.8790 (pt) cc_final: 0.8468 (mt) REVERT: A 198 PHE cc_start: 0.6956 (m-80) cc_final: 0.5943 (m-80) REVERT: B 22 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7660 (mt-10) REVERT: B 26 GLU cc_start: 0.8714 (tp30) cc_final: 0.8381 (mm-30) REVERT: B 108 GLU cc_start: 0.7724 (tt0) cc_final: 0.7513 (tt0) REVERT: C 3 TYR cc_start: 0.9220 (m-80) cc_final: 0.8994 (m-10) REVERT: C 91 CYS cc_start: 0.8483 (m) cc_final: 0.8207 (m) REVERT: D 52 LYS cc_start: 0.8832 (mttt) cc_final: 0.8033 (mmtp) REVERT: D 74 ILE cc_start: 0.9299 (mt) cc_final: 0.9028 (mt) REVERT: D 157 ASP cc_start: 0.7613 (p0) cc_final: 0.7253 (p0) REVERT: D 189 MET cc_start: 0.7278 (ptm) cc_final: 0.6392 (ptm) REVERT: E 14 SER cc_start: 0.9114 (t) cc_final: 0.8751 (p) REVERT: E 94 ASP cc_start: 0.8160 (m-30) cc_final: 0.7836 (m-30) REVERT: E 100 ASP cc_start: 0.8894 (t0) cc_final: 0.8526 (t0) REVERT: F 24 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7782 (mt-10) REVERT: F 135 PHE cc_start: 0.9036 (p90) cc_final: 0.8819 (p90) REVERT: F 136 MET cc_start: 0.7807 (mtm) cc_final: 0.7444 (mtm) REVERT: G 9 PHE cc_start: 0.8734 (m-80) cc_final: 0.8355 (m-10) REVERT: G 39 SER cc_start: 0.9043 (p) cc_final: 0.8839 (m) REVERT: G 96 TYR cc_start: 0.9192 (t80) cc_final: 0.8952 (t80) REVERT: G 116 LYS cc_start: 0.8887 (tttt) cc_final: 0.8604 (tttm) REVERT: G 144 ASP cc_start: 0.8184 (t0) cc_final: 0.6885 (t0) REVERT: H 24 MET cc_start: 0.8359 (mmm) cc_final: 0.8092 (mmp) REVERT: H 93 TYR cc_start: 0.8567 (m-80) cc_final: 0.8334 (m-10) REVERT: H 124 TYR cc_start: 0.8678 (p90) cc_final: 0.7978 (p90) REVERT: H 140 ASP cc_start: 0.8729 (t0) cc_final: 0.8385 (t70) REVERT: H 146 MET cc_start: 0.8518 (mtm) cc_final: 0.8147 (mtp) REVERT: H 216 ILE cc_start: 0.9444 (mt) cc_final: 0.9096 (mt) REVERT: I 44 MET cc_start: 0.8392 (mmm) cc_final: 0.7970 (mmp) REVERT: I 73 TYR cc_start: 0.8597 (t80) cc_final: 0.8210 (t80) REVERT: I 141 CYS cc_start: 0.7912 (p) cc_final: 0.7501 (p) REVERT: I 164 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7504 (tp30) REVERT: I 176 ARG cc_start: 0.8445 (mmm160) cc_final: 0.7444 (mmt180) REVERT: J 38 MET cc_start: 0.8397 (mmp) cc_final: 0.8077 (mmm) REVERT: J 90 ASP cc_start: 0.8386 (m-30) cc_final: 0.8155 (m-30) REVERT: J 169 LYS cc_start: 0.9071 (tttp) cc_final: 0.8869 (tttm) REVERT: K 140 ASP cc_start: 0.7936 (m-30) cc_final: 0.7688 (m-30) REVERT: L 60 ASP cc_start: 0.8053 (m-30) cc_final: 0.7707 (m-30) REVERT: L 83 MET cc_start: 0.8219 (mtp) cc_final: 0.7599 (mtp) REVERT: L 163 HIS cc_start: 0.7649 (m-70) cc_final: 0.7432 (m-70) REVERT: L 193 LEU cc_start: 0.9075 (tp) cc_final: 0.8756 (tp) REVERT: M 108 ASN cc_start: 0.7924 (m-40) cc_final: 0.7709 (m-40) REVERT: N 71 ASN cc_start: 0.8665 (t0) cc_final: 0.8368 (t0) REVERT: N 110 GLN cc_start: 0.8371 (mt0) cc_final: 0.8003 (mt0) REVERT: N 167 ASP cc_start: 0.8306 (t0) cc_final: 0.8020 (t0) REVERT: d 42 TYR cc_start: 0.8756 (t80) cc_final: 0.8521 (t80) REVERT: d 156 LYS cc_start: 0.9205 (mmtm) cc_final: 0.8932 (mmtp) REVERT: d 158 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8248 (mt-10) REVERT: d 161 GLN cc_start: 0.8949 (pt0) cc_final: 0.8733 (pp30) REVERT: d 185 MET cc_start: 0.8761 (mmp) cc_final: 0.8431 (mmp) REVERT: d 208 ASP cc_start: 0.8925 (m-30) cc_final: 0.8470 (m-30) REVERT: c 17 PHE cc_start: 0.8553 (t80) cc_final: 0.8224 (t80) REVERT: c 43 PHE cc_start: 0.8832 (t80) cc_final: 0.8539 (t80) REVERT: c 116 ARG cc_start: 0.8658 (mtp180) cc_final: 0.7916 (mmm-85) REVERT: c 123 ASP cc_start: 0.8600 (m-30) cc_final: 0.8279 (m-30) REVERT: c 138 GLN cc_start: 0.9141 (mm110) cc_final: 0.8911 (mt0) REVERT: c 183 ASP cc_start: 0.9183 (m-30) cc_final: 0.8883 (m-30) REVERT: c 199 GLN cc_start: 0.9014 (tp-100) cc_final: 0.8716 (tp-100) REVERT: c 203 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8090 (mm-30) REVERT: c 211 ASP cc_start: 0.8829 (t0) cc_final: 0.8569 (t0) REVERT: c 217 MET cc_start: 0.8931 (mtp) cc_final: 0.8683 (mtp) REVERT: c 221 ASN cc_start: 0.9271 (m-40) cc_final: 0.9036 (m110) REVERT: c 233 ASN cc_start: 0.9217 (m-40) cc_final: 0.8910 (m110) REVERT: f 97 ASN cc_start: 0.8237 (t0) cc_final: 0.7237 (t0) REVERT: f 136 ASN cc_start: 0.8300 (t0) cc_final: 0.7664 (t0) REVERT: e 15 ASP cc_start: 0.8482 (m-30) cc_final: 0.7752 (m-30) REVERT: e 218 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8469 (tp30) REVERT: h 166 LYS cc_start: 0.9106 (pttp) cc_final: 0.8857 (ptmt) REVERT: h 210 ARG cc_start: 0.9211 (ttp-170) cc_final: 0.8930 (ttp80) REVERT: h 212 PHE cc_start: 0.8803 (m-10) cc_final: 0.8066 (m-10) REVERT: g 187 LYS cc_start: 0.9194 (mttt) cc_final: 0.8931 (mttt) REVERT: g 215 MET cc_start: 0.8490 (mtt) cc_final: 0.8210 (mtp) REVERT: g 228 ASP cc_start: 0.8959 (t70) cc_final: 0.8698 (t0) REVERT: i 23 ASN cc_start: 0.8726 (m110) cc_final: 0.8166 (m-40) REVERT: i 115 LYS cc_start: 0.9031 (ttmt) cc_final: 0.8828 (ttpt) REVERT: i 134 ASP cc_start: 0.7110 (m-30) cc_final: 0.6877 (m-30) REVERT: i 156 LYS cc_start: 0.9113 (mmmt) cc_final: 0.8910 (mmtp) REVERT: i 194 ARG cc_start: 0.8858 (mmt180) cc_final: 0.8357 (mmt180) REVERT: i 217 TYR cc_start: 0.8882 (t80) cc_final: 0.8676 (t80) outliers start: 0 outliers final: 0 residues processed: 2458 average time/residue: 0.7200 time to fit residues: 2884.0185 Evaluate side-chains 1514 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1514 time to evaluate : 6.049 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.0980 chunk 528 optimal weight: 7.9990 chunk 822 optimal weight: 7.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- 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 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 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 b 187 GLN b 193 GLN k 136 ASN ** k 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 183 HIS j 199 GLN ** m 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 136 ASN m 143 GLN l 136 GLN l 153 GLN ** o 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 143 GLN n 27 ASN n 136 GLN p 16 GLN ** p 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 183 HIS A 87 HIS A 95 GLN B 109 GLN B 146 GLN B 167 ASN C 205 ASN D 122 GLN E 20 HIS ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 M 81 HIS N 123 GLN d 16 GLN d 126 GLN d 143 GLN d 183 HIS c 27 ASN ** c 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 ASN c 129 ASN c 164 HIS 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: 83 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 71082 Z= 0.208 Angle : 0.624 9.257 96452 Z= 0.331 Chirality : 0.043 0.214 11222 Planarity : 0.005 0.080 12306 Dihedral : 4.813 51.507 10044 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.68 % Favored : 98.30 % Rotamer: Outliers : 2.22 % Allowed : 11.45 % Favored : 86.33 % 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: 1.76 (0.08), residues: 9128 helix: 2.26 (0.07), residues: 4456 sheet: 0.54 (0.12), residues: 1474 loop : -0.04 (0.11), residues: 3198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 104 HIS 0.006 0.001 HIS E 65 PHE 0.028 0.002 PHE b 125 TYR 0.025 0.002 TYR h 199 ARG 0.011 0.001 ARG o 21 *********************** 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 1845 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1691 time to evaluate : 6.125 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: O 174 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7747 (tp30) REVERT: P 6 ASP cc_start: 0.8733 (p0) cc_final: 0.8332 (p0) REVERT: P 25 MET cc_start: 0.8986 (mtt) cc_final: 0.8517 (mtp) REVERT: P 174 MET cc_start: 0.8503 (mtp) cc_final: 0.7949 (ttp) REVERT: P 178 ASP cc_start: 0.8182 (m-30) cc_final: 0.7831 (m-30) REVERT: Q 55 ASP cc_start: 0.8380 (t0) cc_final: 0.8136 (t0) REVERT: Q 146 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8340 (tm-30) REVERT: R 51 GLU cc_start: 0.6579 (tm-30) cc_final: 0.6183 (tm-30) REVERT: R 73 HIS cc_start: 0.7627 (p-80) cc_final: 0.7425 (p90) REVERT: R 107 MET cc_start: 0.7964 (mtp) cc_final: 0.7747 (mtm) REVERT: R 135 ARG cc_start: 0.9128 (ptt90) cc_final: 0.8729 (ptt-90) REVERT: S 9 ASP cc_start: 0.8435 (t70) cc_final: 0.8055 (t70) REVERT: S 90 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7537 (tp40) REVERT: S 94 ASP cc_start: 0.8166 (m-30) cc_final: 0.7734 (m-30) REVERT: S 100 ASP cc_start: 0.9032 (t0) cc_final: 0.8461 (t0) REVERT: S 152 ASN cc_start: 0.8580 (t0) cc_final: 0.8269 (t0) REVERT: S 171 TYR cc_start: 0.8993 (t80) cc_final: 0.8508 (t80) REVERT: S 178 GLU cc_start: 0.8736 (mp0) cc_final: 0.8444 (pm20) REVERT: S 179 PHE cc_start: 0.8711 (m-10) cc_final: 0.8033 (m-80) REVERT: T 27 MET cc_start: 0.8807 (mmm) cc_final: 0.8465 (mmm) REVERT: T 31 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8344 (mm-30) REVERT: T 73 VAL cc_start: 0.9352 (OUTLIER) cc_final: 0.9062 (m) REVERT: U 17 SER cc_start: 0.9028 (OUTLIER) cc_final: 0.8263 (t) REVERT: U 83 MET cc_start: 0.7975 (mtt) cc_final: 0.7660 (mtt) REVERT: U 125 TYR cc_start: 0.8687 (m-80) cc_final: 0.8068 (m-80) REVERT: U 235 ILE cc_start: 0.8947 (mt) cc_final: 0.8745 (tp) REVERT: V 135 MET cc_start: 0.8663 (tpp) cc_final: 0.8107 (tpp) REVERT: V 150 GLU cc_start: 0.7621 (tt0) cc_final: 0.7311 (tt0) REVERT: W 203 MET cc_start: 0.7935 (mmm) cc_final: 0.7573 (mmm) REVERT: X 2 GLU cc_start: 0.8310 (mp0) cc_final: 0.8082 (mp0) REVERT: X 18 ASP cc_start: 0.8166 (p0) cc_final: 0.7807 (p0) REVERT: X 27 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8193 (tm-30) REVERT: X 166 GLU cc_start: 0.8145 (tp30) cc_final: 0.7729 (tp30) REVERT: Y 107 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7638 (mpp80) REVERT: Z 54 CYS cc_start: 0.8294 (m) cc_final: 0.8010 (p) REVERT: Z 186 ASP cc_start: 0.8643 (t0) cc_final: 0.8382 (t0) REVERT: a 104 ASN cc_start: 0.9007 (t0) cc_final: 0.8503 (t0) REVERT: k 185 MET cc_start: 0.8590 (mmp) cc_final: 0.8384 (mmp) REVERT: k 217 TYR cc_start: 0.9107 (t80) cc_final: 0.8556 (t80) REVERT: j 120 GLU cc_start: 0.8823 (mp0) cc_final: 0.8604 (mp0) REVERT: j 123 ASP cc_start: 0.8440 (m-30) cc_final: 0.8025 (m-30) REVERT: j 146 ASN cc_start: 0.8570 (t0) cc_final: 0.8152 (t0) REVERT: j 170 PHE cc_start: 0.9201 (m-10) cc_final: 0.8925 (m-80) REVERT: j 196 ASP cc_start: 0.7771 (t70) cc_final: 0.7523 (t0) REVERT: j 199 GLN cc_start: 0.9325 (tp40) cc_final: 0.8826 (tp-100) REVERT: j 210 ARG cc_start: 0.8178 (mtm-85) cc_final: 0.7807 (mtm-85) REVERT: j 218 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8385 (tt0) REVERT: j 228 ASP cc_start: 0.9238 (t70) cc_final: 0.8731 (t0) REVERT: m 21 ARG cc_start: 0.8998 (mtp85) cc_final: 0.8729 (mtp85) REVERT: m 185 MET cc_start: 0.8770 (mmm) cc_final: 0.7969 (mmm) REVERT: m 217 TYR cc_start: 0.8377 (t80) cc_final: 0.7347 (t80) REVERT: l 11 GLN cc_start: 0.8368 (tt0) cc_final: 0.8096 (tp40) REVERT: l 157 PHE cc_start: 0.8047 (m-80) cc_final: 0.7677 (m-80) REVERT: l 176 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.8695 (tppp) REVERT: l 191 GLN cc_start: 0.9352 (mp10) cc_final: 0.9120 (mp10) REVERT: o 23 ASN cc_start: 0.8906 (m110) cc_final: 0.8624 (m110) REVERT: o 126 GLN cc_start: 0.9165 (mt0) cc_final: 0.8951 (mt0) REVERT: o 136 ASN cc_start: 0.8629 (m-40) cc_final: 0.8387 (t0) REVERT: o 229 ASN cc_start: 0.9075 (t0) cc_final: 0.8831 (t0) REVERT: n 146 ASN cc_start: 0.8599 (m-40) cc_final: 0.8189 (t0) REVERT: n 164 HIS cc_start: 0.8491 (t70) cc_final: 0.8137 (t-90) REVERT: n 217 MET cc_start: 0.9025 (tpp) cc_final: 0.8767 (mmm) REVERT: p 14 ARG cc_start: 0.8298 (ttm110) cc_final: 0.7746 (mtt-85) REVERT: p 23 ASN cc_start: 0.9142 (m110) cc_final: 0.8734 (m110) REVERT: p 32 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9016 (pp) REVERT: p 97 ASN cc_start: 0.8369 (t0) cc_final: 0.8164 (t0) REVERT: p 112 TRP cc_start: 0.8269 (m100) cc_final: 0.8013 (m100) REVERT: p 142 ILE cc_start: 0.9476 (mt) cc_final: 0.9108 (tt) REVERT: p 223 ASN cc_start: 0.9390 (m-40) cc_final: 0.9074 (m-40) REVERT: A 6 SER cc_start: 0.9285 (m) cc_final: 0.8606 (t) REVERT: A 7 PHE cc_start: 0.9093 (m-80) cc_final: 0.8760 (m-80) REVERT: A 187 ILE cc_start: 0.8652 (pt) cc_final: 0.8339 (mt) REVERT: B 6 ASP cc_start: 0.7784 (p0) cc_final: 0.7143 (p0) REVERT: B 30 HIS cc_start: 0.8390 (m-70) cc_final: 0.7572 (m170) REVERT: B 67 LYS cc_start: 0.8999 (ttpt) cc_final: 0.8503 (tttp) REVERT: B 136 TYR cc_start: 0.8605 (m-80) cc_final: 0.8331 (m-80) REVERT: C 3 TYR cc_start: 0.9232 (m-80) cc_final: 0.8964 (m-10) REVERT: C 67 ASP cc_start: 0.8095 (p0) cc_final: 0.7880 (p0) REVERT: C 90 GLU cc_start: 0.8359 (tp30) cc_final: 0.7914 (tp30) REVERT: D 78 MET cc_start: 0.7844 (ppp) cc_final: 0.7635 (ppp) REVERT: D 186 HIS cc_start: 0.7288 (p90) cc_final: 0.6983 (p90) REVERT: D 216 GLU cc_start: 0.7510 (tt0) cc_final: 0.6886 (tt0) REVERT: E 27 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8474 (mm-30) REVERT: E 30 LYS cc_start: 0.9182 (mtmm) cc_final: 0.8928 (mtmm) REVERT: E 80 ASP cc_start: 0.8350 (m-30) cc_final: 0.7781 (m-30) REVERT: E 91 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8170 (mm-30) REVERT: E 94 ASP cc_start: 0.8159 (m-30) cc_final: 0.7835 (m-30) REVERT: E 100 ASP cc_start: 0.8856 (t0) cc_final: 0.8385 (t0) REVERT: E 154 PHE cc_start: 0.8786 (m-80) cc_final: 0.8480 (m-80) REVERT: E 178 GLU cc_start: 0.8479 (mp0) cc_final: 0.7937 (pm20) REVERT: G 9 PHE cc_start: 0.8736 (m-80) cc_final: 0.8410 (m-10) REVERT: H 57 GLN cc_start: 0.8654 (mt0) cc_final: 0.8365 (mt0) REVERT: H 124 TYR cc_start: 0.8773 (p90) cc_final: 0.7914 (p90) REVERT: H 140 ASP cc_start: 0.8715 (t0) cc_final: 0.8080 (t70) REVERT: H 141 LYS cc_start: 0.9077 (mttm) cc_final: 0.8836 (mttp) REVERT: H 157 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8387 (mm-30) REVERT: I 73 TYR cc_start: 0.8810 (t80) cc_final: 0.8427 (t80) REVERT: I 151 SER cc_start: 0.9044 (p) cc_final: 0.8768 (p) REVERT: I 157 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8092 (mpp) REVERT: I 164 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7498 (tp30) REVERT: I 197 ARG cc_start: 0.8403 (mtt90) cc_final: 0.7900 (mtt90) REVERT: I 203 MET cc_start: 0.8388 (mmp) cc_final: 0.8115 (mmp) REVERT: J 2 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7400 (pt0) REVERT: J 38 MET cc_start: 0.8693 (mmp) cc_final: 0.8482 (mmm) REVERT: J 68 LYS cc_start: 0.9491 (tttp) cc_final: 0.9154 (tppt) REVERT: J 169 LYS cc_start: 0.9089 (tttp) cc_final: 0.8855 (tttm) REVERT: J 196 PHE cc_start: 0.8454 (m-80) cc_final: 0.7803 (m-80) REVERT: K 44 THR cc_start: 0.9049 (p) cc_final: 0.8792 (t) REVERT: L 60 ASP cc_start: 0.8105 (m-30) cc_final: 0.7864 (m-30) REVERT: L 131 GLN cc_start: 0.8218 (pm20) cc_final: 0.7991 (pm20) REVERT: L 146 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7271 (tm-30) REVERT: L 163 HIS cc_start: 0.7722 (m-70) cc_final: 0.7504 (m-70) REVERT: M 74 GLU cc_start: 0.7700 (pp20) cc_final: 0.6921 (pp20) REVERT: M 75 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8151 (mm-30) REVERT: M 96 MET cc_start: 0.8699 (mmm) cc_final: 0.8140 (mtp) REVERT: N 28 ASN cc_start: 0.8477 (t0) cc_final: 0.8262 (t0) REVERT: N 71 ASN cc_start: 0.8621 (t0) cc_final: 0.8331 (t0) REVERT: N 84 LYS cc_start: 0.9133 (ttpp) cc_final: 0.8796 (ttmt) REVERT: N 167 ASP cc_start: 0.8303 (t0) cc_final: 0.7989 (t0) REVERT: d 33 TYR cc_start: 0.8989 (m-10) cc_final: 0.8724 (m-10) REVERT: d 38 GLN cc_start: 0.9066 (mp10) cc_final: 0.8793 (mm-40) REVERT: d 156 LYS cc_start: 0.9158 (mmtm) cc_final: 0.8755 (mmtp) REVERT: d 208 ASP cc_start: 0.8785 (m-30) cc_final: 0.8440 (m-30) REVERT: c 11 GLN cc_start: 0.8281 (pp30) cc_final: 0.8003 (pp30) REVERT: c 115 GLN cc_start: 0.9291 (tt0) cc_final: 0.8972 (tm-30) REVERT: c 123 ASP cc_start: 0.8704 (m-30) cc_final: 0.8393 (m-30) REVERT: c 178 PHE cc_start: 0.8961 (m-10) cc_final: 0.8756 (m-80) REVERT: c 180 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8330 (mt-10) REVERT: c 203 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8201 (mm-30) REVERT: c 208 GLU cc_start: 0.8292 (tp30) cc_final: 0.7819 (tp30) REVERT: c 221 ASN cc_start: 0.9287 (m-40) cc_final: 0.9027 (m110) REVERT: f 22 GLN cc_start: 0.8508 (mt0) cc_final: 0.8297 (pt0) REVERT: f 97 ASN cc_start: 0.8302 (t0) cc_final: 0.7843 (t0) REVERT: f 136 ASN cc_start: 0.8243 (t0) cc_final: 0.7661 (t0) REVERT: f 194 ARG cc_start: 0.9092 (mmt90) cc_final: 0.8884 (mmt90) REVERT: e 127 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8923 (mm-40) REVERT: e 211 ASP cc_start: 0.9270 (m-30) cc_final: 0.8905 (m-30) REVERT: e 217 MET cc_start: 0.8774 (mmm) cc_final: 0.8437 (tpt) REVERT: h 25 PHE cc_start: 0.8911 (m-10) cc_final: 0.8523 (m-80) REVERT: h 136 ASN cc_start: 0.8695 (t0) cc_final: 0.8477 (t0) REVERT: h 151 ASN cc_start: 0.9522 (m-40) cc_final: 0.9203 (m110) REVERT: h 186 ASP cc_start: 0.8365 (m-30) cc_final: 0.7740 (t0) REVERT: h 208 ASP cc_start: 0.8774 (t0) cc_final: 0.7877 (t0) REVERT: h 210 ARG cc_start: 0.9199 (ttp-170) cc_final: 0.8861 (ttp80) REVERT: h 212 PHE cc_start: 0.8957 (m-10) cc_final: 0.8575 (m-80) REVERT: g 170 PHE cc_start: 0.8737 (m-10) cc_final: 0.8328 (m-80) REVERT: g 191 GLN cc_start: 0.9096 (mp10) cc_final: 0.8791 (mp10) REVERT: g 208 GLU cc_start: 0.8988 (tp30) cc_final: 0.8584 (tp30) REVERT: g 210 ARG cc_start: 0.8913 (mtt-85) cc_final: 0.8682 (mtt-85) REVERT: g 211 ASP cc_start: 0.9234 (t0) cc_final: 0.9026 (t0) REVERT: g 215 MET cc_start: 0.8476 (mtt) cc_final: 0.8012 (mtt) REVERT: g 228 ASP cc_start: 0.9012 (t70) cc_final: 0.8767 (t0) REVERT: g 233 ASN cc_start: 0.9170 (m-40) cc_final: 0.8870 (m110) REVERT: i 23 ASN cc_start: 0.8697 (m110) cc_final: 0.8383 (m-40) REVERT: i 112 TRP cc_start: 0.8214 (m100) cc_final: 0.7802 (m100) REVERT: i 156 LYS cc_start: 0.9090 (mmmt) cc_final: 0.8849 (mmtp) REVERT: i 173 ASP cc_start: 0.8967 (t0) cc_final: 0.8759 (m-30) outliers start: 154 outliers final: 72 residues processed: 1780 average time/residue: 0.7276 time to fit residues: 2192.1864 Evaluate side-chains 1508 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1428 time to evaluate : 6.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 174 GLU Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain Q residue 82 ILE Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 106 SER Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain W residue 72 LEU Chi-restraints excluded: chain W residue 114 LYS Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain Y residue 38 ASN Chi-restraints excluded: chain Y residue 107 ARG Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Z residue 48 ASP Chi-restraints excluded: chain a residue 39 ILE Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain b residue 62 GLN Chi-restraints excluded: chain b residue 93 ASP Chi-restraints excluded: chain b residue 94 LEU Chi-restraints excluded: chain k residue 186 ASP Chi-restraints excluded: chain j residue 164 HIS Chi-restraints excluded: chain j residue 179 SER Chi-restraints excluded: chain m residue 32 LEU Chi-restraints excluded: chain m residue 184 VAL Chi-restraints excluded: chain l residue 176 LYS Chi-restraints excluded: chain o residue 183 HIS Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain p residue 32 LEU Chi-restraints excluded: chain p residue 165 SER Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 133 CYS Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 154 CYS Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain I residue 157 MET Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain K residue 93 MET Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 121 ILE Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 54 CYS Chi-restraints excluded: chain L residue 203 ILE Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain f residue 118 CYS Chi-restraints excluded: chain f residue 179 SER Chi-restraints excluded: chain f residue 183 HIS Chi-restraints excluded: chain f residue 184 VAL Chi-restraints excluded: chain e residue 127 GLN Chi-restraints excluded: chain e residue 144 ASP Chi-restraints excluded: chain h residue 206 VAL Chi-restraints excluded: chain i residue 34 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 457 optimal weight: 0.9980 chunk 255 optimal weight: 10.0000 chunk 684 optimal weight: 0.9980 chunk 560 optimal weight: 7.9990 chunk 226 optimal weight: 0.4980 chunk 824 optimal weight: 7.9990 chunk 890 optimal weight: 10.0000 chunk 734 optimal weight: 0.9990 chunk 817 optimal weight: 8.9990 chunk 280 optimal weight: 5.9990 chunk 661 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** U 24 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 Y 175 ASN ** Z 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 81 HIS b 77 HIS k 136 ASN k 161 GLN j 11 GLN j 136 GLN ** m 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 136 ASN ** o 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 GLN o 48 GLN ** o 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 136 GLN ** n 164 HIS ** 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 95 GLN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN E 60 GLN E 65 HIS F 63 ASN G 24 GLN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN L 8 ASN ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN M 157 GLN c 146 ASN c 233 ASN f 127 HIS ** e 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 138 GLN e 199 GLN h 136 ASN ** g 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 126 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 71082 Z= 0.188 Angle : 0.580 8.369 96452 Z= 0.307 Chirality : 0.042 0.284 11222 Planarity : 0.004 0.077 12306 Dihedral : 4.533 48.316 10044 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.90 % Favored : 98.08 % Rotamer: Outliers : 2.48 % Allowed : 13.22 % Favored : 84.30 % 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: 1.87 (0.08), residues: 9128 helix: 2.41 (0.07), residues: 4482 sheet: 0.51 (0.13), residues: 1476 loop : -0.05 (0.11), residues: 3170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP i 124 HIS 0.006 0.001 HIS U 12 PHE 0.030 0.001 PHE F 135 TYR 0.026 0.001 TYR I 73 ARG 0.010 0.001 ARG o 21 *********************** 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 1702 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1530 time to evaluate : 6.115 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: O 174 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7788 (tp30) REVERT: P 6 ASP cc_start: 0.8774 (p0) cc_final: 0.8393 (p0) REVERT: P 22 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8170 (mm-30) REVERT: P 25 MET cc_start: 0.9043 (mtt) cc_final: 0.8797 (mtp) REVERT: P 26 GLU cc_start: 0.8685 (tp30) cc_final: 0.8333 (tp30) REVERT: P 159 TRP cc_start: 0.9081 (m100) cc_final: 0.8846 (m100) REVERT: P 174 MET cc_start: 0.8474 (mtp) cc_final: 0.8201 (ttm) REVERT: P 178 ASP cc_start: 0.8175 (m-30) cc_final: 0.7764 (m-30) REVERT: Q 55 ASP cc_start: 0.8410 (t0) cc_final: 0.8192 (t0) REVERT: Q 60 ARG cc_start: 0.7731 (ptt-90) cc_final: 0.7525 (ptp-170) REVERT: Q 67 ASP cc_start: 0.8105 (p0) cc_final: 0.7884 (p0) REVERT: Q 92 GLN cc_start: 0.9373 (mm-40) cc_final: 0.8892 (mm-40) REVERT: Q 116 GLN cc_start: 0.8694 (tt0) cc_final: 0.8483 (tt0) REVERT: Q 146 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8494 (tm-30) REVERT: R 26 TYR cc_start: 0.9347 (m-10) cc_final: 0.9127 (m-10) REVERT: R 73 HIS cc_start: 0.7830 (p-80) cc_final: 0.7508 (p90) REVERT: R 135 ARG cc_start: 0.9147 (ptt90) cc_final: 0.8826 (ptt-90) REVERT: S 9 ASP cc_start: 0.8449 (t70) cc_final: 0.8080 (t70) REVERT: S 90 GLN cc_start: 0.8161 (tp-100) cc_final: 0.6528 (tp40) REVERT: S 94 ASP cc_start: 0.8062 (m-30) cc_final: 0.7207 (m-30) REVERT: S 100 ASP cc_start: 0.9065 (t0) cc_final: 0.8483 (t0) REVERT: S 179 PHE cc_start: 0.8713 (m-10) cc_final: 0.8069 (m-80) REVERT: T 27 MET cc_start: 0.8803 (mmm) cc_final: 0.8507 (mmm) REVERT: T 31 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8325 (mm-30) REVERT: T 73 VAL cc_start: 0.9380 (OUTLIER) cc_final: 0.9115 (m) REVERT: T 150 MET cc_start: 0.8608 (tmm) cc_final: 0.8405 (tmm) REVERT: U 125 TYR cc_start: 0.8630 (m-80) cc_final: 0.7688 (m-80) REVERT: U 131 MET cc_start: 0.7682 (ptp) cc_final: 0.7410 (ttp) REVERT: U 138 MET cc_start: 0.7869 (ttm) cc_final: 0.7634 (ttm) REVERT: U 235 ILE cc_start: 0.8870 (mt) cc_final: 0.8668 (tp) REVERT: V 30 ASN cc_start: 0.8499 (t0) cc_final: 0.8288 (t0) REVERT: V 135 MET cc_start: 0.8528 (tpp) cc_final: 0.8069 (tpp) REVERT: W 49 TYR cc_start: 0.8673 (m-80) cc_final: 0.8457 (m-80) REVERT: W 145 MET cc_start: 0.8156 (mtm) cc_final: 0.7726 (mtm) REVERT: W 171 LEU cc_start: 0.9501 (mt) cc_final: 0.8718 (mm) REVERT: W 203 MET cc_start: 0.8043 (mmm) cc_final: 0.7713 (mmm) REVERT: X 18 ASP cc_start: 0.7956 (p0) cc_final: 0.7614 (p0) REVERT: X 27 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8199 (tm-30) REVERT: X 141 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8464 (t) REVERT: X 165 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8083 (mp0) REVERT: X 166 GLU cc_start: 0.8356 (tp30) cc_final: 0.8120 (tp30) REVERT: Y 107 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7486 (mpp80) REVERT: Z 44 TYR cc_start: 0.8966 (m-80) cc_final: 0.8722 (m-80) REVERT: Z 186 ASP cc_start: 0.8705 (t0) cc_final: 0.8426 (t0) REVERT: a 10 SER cc_start: 0.8615 (m) cc_final: 0.8363 (p) REVERT: a 104 ASN cc_start: 0.8995 (t0) cc_final: 0.8549 (t0) REVERT: b 31 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8323 (p) REVERT: k 161 GLN cc_start: 0.8632 (pt0) cc_final: 0.8425 (pm20) REVERT: k 217 TYR cc_start: 0.9160 (t80) cc_final: 0.8677 (t80) REVERT: j 11 GLN cc_start: 0.8936 (tm130) cc_final: 0.8319 (tm-30) REVERT: j 15 ASP cc_start: 0.8642 (m-30) cc_final: 0.7961 (m-30) REVERT: j 123 ASP cc_start: 0.8514 (m-30) cc_final: 0.8103 (m-30) REVERT: j 146 ASN cc_start: 0.8565 (t0) cc_final: 0.8110 (t0) REVERT: j 173 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8490 (tm-30) REVERT: j 196 ASP cc_start: 0.7828 (t70) cc_final: 0.7613 (t0) REVERT: j 199 GLN cc_start: 0.9174 (tp40) cc_final: 0.8789 (tp-100) REVERT: j 213 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8250 (ttm-80) REVERT: j 218 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: j 227 TYR cc_start: 0.9243 (t80) cc_final: 0.8680 (t80) REVERT: j 228 ASP cc_start: 0.9263 (t70) cc_final: 0.8774 (t0) REVERT: m 42 TYR cc_start: 0.8777 (t80) cc_final: 0.8489 (t80) REVERT: m 48 GLN cc_start: 0.8917 (pt0) cc_final: 0.8398 (pm20) REVERT: m 158 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7821 (tm-30) REVERT: m 217 TYR cc_start: 0.8323 (t80) cc_final: 0.7552 (t80) REVERT: l 11 GLN cc_start: 0.8372 (tt0) cc_final: 0.8164 (tp40) REVERT: l 157 PHE cc_start: 0.8071 (m-80) cc_final: 0.7738 (m-80) REVERT: l 191 GLN cc_start: 0.9363 (mp10) cc_final: 0.9128 (mp10) REVERT: l 215 MET cc_start: 0.9078 (mtm) cc_final: 0.8649 (mtp) REVERT: l 247 MET cc_start: 0.6871 (tpp) cc_final: 0.6650 (tpp) REVERT: o 23 ASN cc_start: 0.8823 (m110) cc_final: 0.8455 (m110) REVERT: o 42 TYR cc_start: 0.8635 (t80) cc_final: 0.8426 (t80) REVERT: o 126 GLN cc_start: 0.9135 (mt0) cc_final: 0.8885 (mt0) REVERT: o 136 ASN cc_start: 0.8653 (m-40) cc_final: 0.8395 (t0) REVERT: o 199 TYR cc_start: 0.8151 (t80) cc_final: 0.7836 (t80) REVERT: o 203 ARG cc_start: 0.9236 (ttp80) cc_final: 0.8958 (mtp85) REVERT: n 43 PHE cc_start: 0.8781 (t80) cc_final: 0.8312 (t80) REVERT: n 116 ARG cc_start: 0.8802 (ttt180) cc_final: 0.8257 (ttt180) REVERT: n 180 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8197 (mp0) REVERT: n 191 GLN cc_start: 0.9211 (mt0) cc_final: 0.8976 (pt0) REVERT: n 199 GLN cc_start: 0.9121 (tp40) cc_final: 0.8876 (tm-30) REVERT: n 215 MET cc_start: 0.8908 (mtm) cc_final: 0.8445 (mmm) REVERT: n 217 MET cc_start: 0.8956 (tpp) cc_final: 0.8685 (mmm) REVERT: p 22 GLN cc_start: 0.7855 (pp30) cc_final: 0.7620 (pp30) REVERT: p 23 ASN cc_start: 0.9126 (m110) cc_final: 0.8701 (m-40) REVERT: p 97 ASN cc_start: 0.8292 (t0) cc_final: 0.7950 (t0) REVERT: p 112 TRP cc_start: 0.8274 (m100) cc_final: 0.7928 (m100) REVERT: p 122 ILE cc_start: 0.9566 (mt) cc_final: 0.9345 (mt) REVERT: p 185 MET cc_start: 0.8101 (mmp) cc_final: 0.7766 (mmm) REVERT: A 6 SER cc_start: 0.9002 (m) cc_final: 0.8534 (t) REVERT: A 7 PHE cc_start: 0.9113 (m-80) cc_final: 0.8733 (m-80) REVERT: A 102 GLU cc_start: 0.8294 (tp30) cc_final: 0.8088 (tp30) REVERT: B 6 ASP cc_start: 0.7483 (p0) cc_final: 0.7156 (p0) REVERT: B 30 HIS cc_start: 0.8283 (m-70) cc_final: 0.7865 (m170) REVERT: B 67 LYS cc_start: 0.8977 (ttpt) cc_final: 0.8539 (tttp) REVERT: B 108 GLU cc_start: 0.8175 (tp30) cc_final: 0.7509 (tp30) REVERT: C 3 TYR cc_start: 0.9237 (m-80) cc_final: 0.8957 (m-10) REVERT: C 90 GLU cc_start: 0.8356 (tp30) cc_final: 0.7866 (tp30) REVERT: C 105 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7766 (tm-30) REVERT: C 116 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8654 (tp40) REVERT: C 120 GLN cc_start: 0.8313 (pt0) cc_final: 0.7408 (pt0) REVERT: D 13 ASN cc_start: 0.8569 (m-40) cc_final: 0.8248 (t0) REVERT: D 21 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9134 (tt) REVERT: E 30 LYS cc_start: 0.9225 (mtmm) cc_final: 0.8936 (mtmm) REVERT: E 80 ASP cc_start: 0.8354 (m-30) cc_final: 0.8122 (m-30) REVERT: E 91 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8202 (mm-30) REVERT: E 100 ASP cc_start: 0.8852 (t0) cc_final: 0.8349 (t0) REVERT: E 154 PHE cc_start: 0.8783 (m-80) cc_final: 0.8562 (m-80) REVERT: G 9 PHE cc_start: 0.8722 (m-80) cc_final: 0.8415 (m-10) REVERT: G 26 GLU cc_start: 0.8756 (mp0) cc_final: 0.8553 (mp0) REVERT: H 124 TYR cc_start: 0.8742 (p90) cc_final: 0.7851 (p90) REVERT: H 157 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8432 (mm-30) REVERT: H 202 TYR cc_start: 0.7072 (m-80) cc_final: 0.6801 (m-80) REVERT: I 30 GLN cc_start: 0.8321 (tp40) cc_final: 0.8117 (tp-100) REVERT: I 33 MET cc_start: 0.7973 (tmm) cc_final: 0.7719 (ttp) REVERT: I 64 GLN cc_start: 0.8805 (mt0) cc_final: 0.8600 (mt0) REVERT: I 95 TYR cc_start: 0.9177 (t80) cc_final: 0.8840 (t80) REVERT: I 157 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7926 (mpp) REVERT: I 164 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7441 (tp30) REVERT: I 175 ASP cc_start: 0.8048 (m-30) cc_final: 0.7788 (m-30) REVERT: I 182 MET cc_start: 0.8760 (mmm) cc_final: 0.7922 (mmm) REVERT: J 38 MET cc_start: 0.8657 (mmp) cc_final: 0.8304 (mmp) REVERT: J 61 GLN cc_start: 0.9302 (tt0) cc_final: 0.8923 (tt0) REVERT: J 68 LYS cc_start: 0.9546 (tttp) cc_final: 0.9196 (tppt) REVERT: J 196 PHE cc_start: 0.8426 (m-80) cc_final: 0.8055 (m-80) REVERT: L 60 ASP cc_start: 0.7978 (m-30) cc_final: 0.7746 (m-30) REVERT: L 131 GLN cc_start: 0.8314 (pm20) cc_final: 0.8026 (pm20) REVERT: L 146 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7622 (tm-30) REVERT: L 177 ASP cc_start: 0.7616 (m-30) cc_final: 0.7406 (m-30) REVERT: M 74 GLU cc_start: 0.7845 (pp20) cc_final: 0.6750 (pp20) REVERT: M 75 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7955 (mm-30) REVERT: M 96 MET cc_start: 0.8581 (mmm) cc_final: 0.8009 (mtp) REVERT: M 133 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8132 (mt-10) REVERT: M 137 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9038 (mt) REVERT: N 28 ASN cc_start: 0.8384 (t0) cc_final: 0.8082 (t0) REVERT: N 164 MET cc_start: 0.8227 (mtm) cc_final: 0.7953 (mtp) REVERT: N 167 ASP cc_start: 0.8214 (t0) cc_final: 0.7943 (t0) REVERT: d 38 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8813 (mm-40) REVERT: d 156 LYS cc_start: 0.9183 (mmtm) cc_final: 0.8893 (mmtp) REVERT: d 208 ASP cc_start: 0.8787 (m-30) cc_final: 0.8361 (m-30) REVERT: c 115 GLN cc_start: 0.9238 (tt0) cc_final: 0.8922 (tm-30) REVERT: c 123 ASP cc_start: 0.8740 (m-30) cc_final: 0.8400 (m-30) REVERT: c 217 MET cc_start: 0.9065 (ttp) cc_final: 0.8656 (ttm) REVERT: c 221 ASN cc_start: 0.9310 (m-40) cc_final: 0.9083 (m110) REVERT: f 22 GLN cc_start: 0.8477 (mt0) cc_final: 0.8227 (pt0) REVERT: f 48 GLN cc_start: 0.8799 (mt0) cc_final: 0.8472 (mt0) REVERT: f 97 ASN cc_start: 0.8355 (t0) cc_final: 0.7931 (t0) REVERT: f 136 ASN cc_start: 0.8267 (t0) cc_final: 0.7646 (t0) REVERT: e 11 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8004 (tm-30) REVERT: e 15 ASP cc_start: 0.8645 (m-30) cc_final: 0.8159 (m-30) REVERT: e 153 GLN cc_start: 0.9108 (mt0) cc_final: 0.8699 (mp10) REVERT: e 211 ASP cc_start: 0.9252 (m-30) cc_final: 0.8835 (m-30) REVERT: e 217 MET cc_start: 0.8673 (mmm) cc_final: 0.8361 (tpt) REVERT: h 25 PHE cc_start: 0.8950 (m-10) cc_final: 0.8573 (m-10) REVERT: h 136 ASN cc_start: 0.8784 (t0) cc_final: 0.8484 (t0) REVERT: h 151 ASN cc_start: 0.9581 (m-40) cc_final: 0.9242 (m110) REVERT: h 210 ARG cc_start: 0.9176 (ttp-170) cc_final: 0.8851 (ttp80) REVERT: h 212 PHE cc_start: 0.8978 (m-10) cc_final: 0.8602 (m-80) REVERT: g 123 ASP cc_start: 0.8813 (m-30) cc_final: 0.8464 (p0) REVERT: g 170 PHE cc_start: 0.8806 (m-10) cc_final: 0.8576 (m-80) REVERT: g 191 GLN cc_start: 0.9144 (mp10) cc_final: 0.8655 (mp10) REVERT: g 208 GLU cc_start: 0.9097 (tp30) cc_final: 0.8656 (tp30) REVERT: g 210 ARG cc_start: 0.8881 (mtt-85) cc_final: 0.8624 (mtt-85) REVERT: g 213 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8354 (ttt-90) REVERT: g 215 MET cc_start: 0.8523 (mtt) cc_final: 0.7677 (mtt) REVERT: g 228 ASP cc_start: 0.9015 (t70) cc_final: 0.8806 (t0) REVERT: g 233 ASN cc_start: 0.9157 (m-40) cc_final: 0.8816 (m110) REVERT: i 23 ASN cc_start: 0.8676 (m110) cc_final: 0.8320 (m-40) REVERT: i 151 ASN cc_start: 0.8915 (m110) cc_final: 0.8712 (m110) REVERT: i 156 LYS cc_start: 0.9051 (mmmt) cc_final: 0.8827 (mttt) outliers start: 172 outliers final: 95 residues processed: 1623 average time/residue: 0.6761 time to fit residues: 1844.7441 Evaluate side-chains 1489 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1382 time to evaluate : 7.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 174 GLU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain Q residue 7 ILE Chi-restraints excluded: chain Q residue 82 ILE Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 147 THR Chi-restraints excluded: chain S residue 228 ASP Chi-restraints excluded: chain S residue 236 LEU Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 78 CYS Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain W residue 151 SER Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain Y residue 38 ASN Chi-restraints excluded: chain Y residue 107 ARG Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Y residue 175 ASN Chi-restraints excluded: chain Z residue 48 ASP Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 62 GLN Chi-restraints excluded: chain b residue 93 ASP Chi-restraints excluded: chain b residue 94 LEU Chi-restraints excluded: chain k residue 186 ASP Chi-restraints excluded: chain k residue 238 MET Chi-restraints excluded: chain j residue 50 ASN Chi-restraints excluded: chain j residue 164 HIS Chi-restraints excluded: chain j residue 213 ARG Chi-restraints excluded: chain j residue 218 GLU Chi-restraints excluded: chain m residue 32 LEU Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 170 GLU Chi-restraints excluded: chain o residue 183 HIS Chi-restraints excluded: chain n residue 113 LEU Chi-restraints excluded: chain n residue 161 THR Chi-restraints excluded: chain p residue 65 ASP Chi-restraints excluded: chain p residue 118 CYS Chi-restraints excluded: chain p residue 134 ASP Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 133 CYS Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 154 CYS Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain I residue 146 TYR Chi-restraints excluded: chain I residue 157 MET Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 93 MET Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 121 ILE Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 54 CYS Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 137 LEU Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain d residue 38 GLN Chi-restraints excluded: chain f residue 118 CYS Chi-restraints excluded: chain f residue 134 ASP Chi-restraints excluded: chain f residue 185 MET Chi-restraints excluded: chain f residue 208 ASP Chi-restraints excluded: chain e residue 144 ASP Chi-restraints excluded: chain h residue 206 VAL Chi-restraints excluded: chain g residue 213 ARG Chi-restraints excluded: chain i residue 118 CYS Chi-restraints excluded: chain i residue 185 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 814 optimal weight: 3.9990 chunk 619 optimal weight: 0.1980 chunk 427 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 393 optimal weight: 10.0000 chunk 553 optimal weight: 1.9990 chunk 827 optimal weight: 7.9990 chunk 875 optimal weight: 2.9990 chunk 432 optimal weight: 7.9990 chunk 783 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 32 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 Y 175 ASN ** Z 108 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 136 ASN j 191 GLN m 44 ASN m 136 ASN l 193 HIS ** o 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 GLN ** o 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 129 ASN n 136 GLN ** n 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 193 HIS ** p 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 223 ASN A 95 GLN C 85 ASN D 97 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN F 101 ASN G 128 ASN ** I 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN L 8 ASN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 146 ASN e 127 GLN e 138 GLN e 193 HIS ** i 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3752 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= 0.323 Angle : 0.622 11.488 96452 Z= 0.330 Chirality : 0.043 0.283 11222 Planarity : 0.004 0.077 12306 Dihedral : 4.498 51.539 10044 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.26 % Favored : 97.73 % Rotamer: Outliers : 3.20 % Allowed : 13.93 % Favored : 82.87 % 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: 1.84 (0.09), residues: 9128 helix: 2.40 (0.07), residues: 4478 sheet: 0.40 (0.13), residues: 1484 loop : -0.04 (0.11), residues: 3166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP T 215 HIS 0.007 0.001 HIS S 175 PHE 0.030 0.002 PHE j 170 TYR 0.033 0.002 TYR U 160 ARG 0.014 0.001 ARG A 176 *********************** 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 1601 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1379 time to evaluate : 6.206 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: O 174 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7872 (tp30) REVERT: P 6 ASP cc_start: 0.8667 (p0) cc_final: 0.8325 (p0) REVERT: P 25 MET cc_start: 0.9137 (mtt) cc_final: 0.8880 (mtp) REVERT: P 26 GLU cc_start: 0.8725 (tp30) cc_final: 0.8391 (tp30) REVERT: P 174 MET cc_start: 0.8628 (mtp) cc_final: 0.8108 (ttm) REVERT: P 178 ASP cc_start: 0.8254 (m-30) cc_final: 0.7794 (m-30) REVERT: Q 55 ASP cc_start: 0.8417 (t0) cc_final: 0.8216 (t0) REVERT: Q 66 ASP cc_start: 0.7969 (t0) cc_final: 0.7599 (t70) REVERT: Q 67 ASP cc_start: 0.8092 (p0) cc_final: 0.7776 (p0) REVERT: Q 71 MET cc_start: 0.8476 (ptp) cc_final: 0.8252 (ptm) REVERT: Q 116 GLN cc_start: 0.8838 (tt0) cc_final: 0.8554 (tt0) REVERT: S 9 ASP cc_start: 0.8442 (t70) cc_final: 0.8156 (t70) REVERT: S 90 GLN cc_start: 0.8429 (tp-100) cc_final: 0.6714 (tp40) REVERT: S 94 ASP cc_start: 0.8171 (m-30) cc_final: 0.7269 (m-30) REVERT: S 100 ASP cc_start: 0.9135 (t0) cc_final: 0.8516 (t0) REVERT: S 138 ASP cc_start: 0.8079 (p0) cc_final: 0.7846 (p0) REVERT: S 179 PHE cc_start: 0.8876 (m-10) cc_final: 0.8288 (m-80) REVERT: T 27 MET cc_start: 0.8835 (mmm) cc_final: 0.8537 (mmm) REVERT: T 73 VAL cc_start: 0.9487 (OUTLIER) cc_final: 0.9212 (m) REVERT: U 83 MET cc_start: 0.8347 (mtt) cc_final: 0.7835 (mtt) REVERT: U 86 ASP cc_start: 0.8524 (m-30) cc_final: 0.8206 (m-30) REVERT: U 125 TYR cc_start: 0.8728 (m-80) cc_final: 0.7937 (m-10) REVERT: U 189 TRP cc_start: 0.8549 (m-10) cc_final: 0.8149 (m-10) REVERT: V 135 MET cc_start: 0.8584 (tpp) cc_final: 0.8120 (tpp) REVERT: W 171 LEU cc_start: 0.9317 (mt) cc_final: 0.8958 (mm) REVERT: X 18 ASP cc_start: 0.8110 (p0) cc_final: 0.7655 (p0) REVERT: X 27 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8223 (tm-30) REVERT: X 37 LYS cc_start: 0.8761 (ptmt) cc_final: 0.8493 (tttp) REVERT: X 69 MET cc_start: 0.8730 (mmm) cc_final: 0.8333 (mmm) REVERT: X 141 SER cc_start: 0.8992 (OUTLIER) cc_final: 0.8612 (t) REVERT: X 166 GLU cc_start: 0.8489 (tp30) cc_final: 0.8204 (tp30) REVERT: Y 33 LYS cc_start: 0.8949 (mttm) cc_final: 0.8537 (mttt) REVERT: Y 107 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7682 (mpp80) REVERT: Z 186 ASP cc_start: 0.8803 (t0) cc_final: 0.8534 (t0) REVERT: a 10 SER cc_start: 0.8830 (m) cc_final: 0.8591 (p) REVERT: a 104 ASN cc_start: 0.9101 (t0) cc_final: 0.8582 (t0) REVERT: a 110 MET cc_start: 0.8037 (mtm) cc_final: 0.7812 (mtm) REVERT: k 26 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8684 (tm-30) REVERT: k 33 TYR cc_start: 0.9308 (m-10) cc_final: 0.9075 (m-10) REVERT: k 126 GLN cc_start: 0.9189 (mt0) cc_final: 0.8974 (mt0) REVERT: k 208 ASP cc_start: 0.8998 (m-30) cc_final: 0.8745 (m-30) REVERT: k 217 TYR cc_start: 0.9199 (t80) cc_final: 0.8741 (t80) REVERT: j 11 GLN cc_start: 0.8827 (tm130) cc_final: 0.7835 (tm-30) REVERT: j 15 ASP cc_start: 0.8413 (m-30) cc_final: 0.7511 (m-30) REVERT: j 120 GLU cc_start: 0.8879 (mp0) cc_final: 0.8551 (mp0) REVERT: j 123 ASP cc_start: 0.8588 (m-30) cc_final: 0.8191 (m-30) REVERT: j 146 ASN cc_start: 0.8727 (t0) cc_final: 0.8261 (t0) REVERT: j 170 PHE cc_start: 0.9031 (m-80) cc_final: 0.8715 (m-80) REVERT: j 199 GLN cc_start: 0.9217 (tp40) cc_final: 0.8709 (tp-100) REVERT: j 203 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8610 (mm-30) REVERT: j 210 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.8053 (mtm-85) REVERT: j 213 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8278 (ttm-80) REVERT: j 218 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: j 228 ASP cc_start: 0.9324 (t70) cc_final: 0.8890 (t0) REVERT: m 42 TYR cc_start: 0.8843 (t80) cc_final: 0.8628 (t80) REVERT: m 48 GLN cc_start: 0.9002 (pt0) cc_final: 0.8408 (pm20) REVERT: m 217 TYR cc_start: 0.8715 (t80) cc_final: 0.8159 (t80) REVERT: l 157 PHE cc_start: 0.8319 (m-80) cc_final: 0.8026 (m-80) REVERT: l 191 GLN cc_start: 0.9413 (mp10) cc_final: 0.9139 (mp10) REVERT: l 215 MET cc_start: 0.9057 (mtm) cc_final: 0.8761 (mtp) REVERT: o 42 TYR cc_start: 0.8662 (t80) cc_final: 0.8432 (t80) REVERT: o 58 THR cc_start: 0.8946 (p) cc_final: 0.8710 (p) REVERT: o 136 ASN cc_start: 0.8780 (m-40) cc_final: 0.8496 (t0) REVERT: o 199 TYR cc_start: 0.8460 (t80) cc_final: 0.8251 (t80) REVERT: n 43 PHE cc_start: 0.8902 (t80) cc_final: 0.8170 (t80) REVERT: n 116 ARG cc_start: 0.8873 (ttt180) cc_final: 0.8034 (ttt180) REVERT: n 146 ASN cc_start: 0.8158 (t0) cc_final: 0.7490 (t0) REVERT: n 170 PHE cc_start: 0.8807 (m-10) cc_final: 0.8424 (m-80) REVERT: n 191 GLN cc_start: 0.9194 (mt0) cc_final: 0.8945 (pt0) REVERT: n 203 GLU cc_start: 0.8583 (tp30) cc_final: 0.8229 (tp30) REVERT: n 217 MET cc_start: 0.8921 (tpp) cc_final: 0.8589 (mmm) REVERT: n 218 GLU cc_start: 0.9030 (tp30) cc_final: 0.8628 (tp30) REVERT: n 241 ARG cc_start: 0.9219 (tpp80) cc_final: 0.8940 (tpp80) REVERT: p 23 ASN cc_start: 0.9176 (m110) cc_final: 0.8886 (m110) REVERT: p 34 ARG cc_start: 0.8401 (ptp90) cc_final: 0.8118 (ptp90) REVERT: p 97 ASN cc_start: 0.8433 (t0) cc_final: 0.8091 (t0) REVERT: p 185 MET cc_start: 0.8223 (mmp) cc_final: 0.7823 (mmm) REVERT: A 6 SER cc_start: 0.9044 (m) cc_final: 0.8558 (t) REVERT: A 7 PHE cc_start: 0.9155 (m-80) cc_final: 0.8864 (m-80) REVERT: B 6 ASP cc_start: 0.7742 (p0) cc_final: 0.7365 (p0) REVERT: B 67 LYS cc_start: 0.8968 (ttpt) cc_final: 0.8531 (tttp) REVERT: B 108 GLU cc_start: 0.8468 (tp30) cc_final: 0.7731 (tp30) REVERT: C 3 TYR cc_start: 0.9339 (m-80) cc_final: 0.9064 (m-10) REVERT: C 67 ASP cc_start: 0.8366 (p0) cc_final: 0.8135 (p0) REVERT: C 90 GLU cc_start: 0.8537 (tp30) cc_final: 0.8311 (tp30) REVERT: C 105 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7897 (tm-30) REVERT: D 21 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9187 (tt) REVERT: D 52 LYS cc_start: 0.9205 (mmtp) cc_final: 0.8803 (mmtp) REVERT: D 135 ARG cc_start: 0.9254 (ptt-90) cc_final: 0.8941 (ptt-90) REVERT: D 216 GLU cc_start: 0.7517 (tt0) cc_final: 0.7110 (mt-10) REVERT: E 30 LYS cc_start: 0.9277 (mtmm) cc_final: 0.8952 (mtmm) REVERT: E 80 ASP cc_start: 0.8670 (m-30) cc_final: 0.8384 (m-30) REVERT: E 91 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8353 (mm-30) REVERT: E 100 ASP cc_start: 0.8887 (t0) cc_final: 0.8364 (t0) REVERT: E 176 MET cc_start: 0.8219 (ttp) cc_final: 0.7996 (ppp) REVERT: G 9 PHE cc_start: 0.8818 (m-80) cc_final: 0.8472 (m-10) REVERT: G 11 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.7859 (ptp-110) REVERT: G 22 LEU cc_start: 0.8663 (mt) cc_final: 0.8254 (mp) REVERT: G 26 GLU cc_start: 0.8837 (mp0) cc_final: 0.8557 (mp0) REVERT: G 159 TYR cc_start: 0.7696 (t80) cc_final: 0.7285 (t80) REVERT: H 57 GLN cc_start: 0.8500 (mt0) cc_final: 0.8295 (mt0) REVERT: H 124 TYR cc_start: 0.8997 (p90) cc_final: 0.8169 (p90) REVERT: H 157 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8435 (mm-30) REVERT: H 202 TYR cc_start: 0.7100 (m-80) cc_final: 0.6824 (m-80) REVERT: H 214 GLU cc_start: 0.8591 (tp30) cc_final: 0.8230 (tp30) REVERT: I 95 TYR cc_start: 0.9335 (t80) cc_final: 0.8994 (t80) REVERT: I 157 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7868 (mpp) REVERT: I 164 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7722 (tp30) REVERT: I 175 ASP cc_start: 0.8067 (m-30) cc_final: 0.7851 (m-30) REVERT: I 197 ARG cc_start: 0.8227 (mtt90) cc_final: 0.7620 (mtt90) REVERT: J 31 ASP cc_start: 0.8608 (p0) cc_final: 0.8246 (p0) REVERT: J 34 LYS cc_start: 0.8567 (mttp) cc_final: 0.8208 (mttp) REVERT: J 38 MET cc_start: 0.8598 (mmp) cc_final: 0.8352 (mmm) REVERT: J 68 LYS cc_start: 0.9569 (tttp) cc_final: 0.9237 (tppt) REVERT: J 166 GLU cc_start: 0.8631 (tp30) cc_final: 0.8385 (tp30) REVERT: K 119 ASN cc_start: 0.9010 (OUTLIER) cc_final: 0.8373 (m-40) REVERT: L 60 ASP cc_start: 0.8462 (m-30) cc_final: 0.8200 (m-30) REVERT: L 131 GLN cc_start: 0.8511 (pm20) cc_final: 0.8165 (pm20) REVERT: L 146 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7658 (tm-30) REVERT: M 47 ASN cc_start: 0.8900 (t0) cc_final: 0.8664 (t0) REVERT: M 74 GLU cc_start: 0.7952 (pp20) cc_final: 0.6812 (pp20) REVERT: M 75 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7974 (mm-30) REVERT: M 96 MET cc_start: 0.8649 (mmm) cc_final: 0.7792 (mtp) REVERT: M 133 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8173 (mt-10) REVERT: N 28 ASN cc_start: 0.8523 (t0) cc_final: 0.8135 (t0) REVERT: N 164 MET cc_start: 0.8402 (mtm) cc_final: 0.8086 (mtp) REVERT: N 167 ASP cc_start: 0.8315 (t0) cc_final: 0.8106 (t0) REVERT: N 193 GLN cc_start: 0.8662 (mt0) cc_final: 0.8448 (mt0) REVERT: d 38 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.8907 (mm-40) REVERT: d 42 TYR cc_start: 0.9144 (t80) cc_final: 0.8848 (t80) REVERT: d 47 LEU cc_start: 0.9305 (mt) cc_final: 0.9013 (pp) REVERT: d 208 ASP cc_start: 0.8829 (m-30) cc_final: 0.8486 (m-30) REVERT: d 229 ASN cc_start: 0.8893 (t0) cc_final: 0.8625 (m-40) REVERT: c 115 GLN cc_start: 0.9263 (tt0) cc_final: 0.8877 (tm-30) REVERT: c 123 ASP cc_start: 0.8782 (m-30) cc_final: 0.8413 (m-30) REVERT: c 199 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8457 (tp-100) REVERT: c 217 MET cc_start: 0.9203 (ttp) cc_final: 0.8769 (ttm) REVERT: c 220 ARG cc_start: 0.9630 (ttp80) cc_final: 0.9399 (ttp80) REVERT: c 221 ASN cc_start: 0.9317 (m-40) cc_final: 0.9046 (m-40) REVERT: f 22 GLN cc_start: 0.8460 (mt0) cc_final: 0.8160 (pt0) REVERT: f 97 ASN cc_start: 0.8454 (t0) cc_final: 0.8052 (t0) REVERT: f 136 ASN cc_start: 0.8528 (t0) cc_final: 0.7888 (t0) REVERT: e 15 ASP cc_start: 0.8656 (m-30) cc_final: 0.8334 (m-30) REVERT: e 211 ASP cc_start: 0.9274 (m-30) cc_final: 0.8855 (m-30) REVERT: h 25 PHE cc_start: 0.8960 (m-10) cc_final: 0.8567 (m-10) REVERT: h 136 ASN cc_start: 0.8857 (t0) cc_final: 0.8470 (t0) REVERT: h 151 ASN cc_start: 0.9585 (m-40) cc_final: 0.9194 (m110) REVERT: h 210 ARG cc_start: 0.9182 (ttp-170) cc_final: 0.8851 (ttp80) REVERT: h 212 PHE cc_start: 0.8936 (m-10) cc_final: 0.8616 (m-80) REVERT: g 170 PHE cc_start: 0.8960 (m-10) cc_final: 0.8672 (m-80) REVERT: g 191 GLN cc_start: 0.9054 (mp10) cc_final: 0.8644 (mp10) REVERT: g 208 GLU cc_start: 0.9152 (tp30) cc_final: 0.8925 (tp30) REVERT: g 211 ASP cc_start: 0.9198 (t0) cc_final: 0.8974 (t0) REVERT: g 215 MET cc_start: 0.8528 (mtt) cc_final: 0.7895 (mtt) REVERT: g 233 ASN cc_start: 0.9292 (m-40) cc_final: 0.8929 (m110) REVERT: i 23 ASN cc_start: 0.8756 (m110) cc_final: 0.8451 (m-40) REVERT: i 112 TRP cc_start: 0.7778 (m100) cc_final: 0.7210 (m100) REVERT: i 151 ASN cc_start: 0.9029 (m110) cc_final: 0.8775 (m110) outliers start: 222 outliers final: 155 residues processed: 1518 average time/residue: 0.6692 time to fit residues: 1706.5857 Evaluate side-chains 1467 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1302 time to evaluate : 6.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 174 GLU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain Q residue 7 ILE Chi-restraints excluded: chain Q residue 82 ILE Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain Q residue 148 ASP Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 106 SER Chi-restraints excluded: chain S residue 147 THR Chi-restraints excluded: chain S residue 228 ASP Chi-restraints excluded: chain S residue 236 LEU Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 78 CYS Chi-restraints excluded: chain V residue 82 MET Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain W residue 92 ASN Chi-restraints excluded: chain W residue 134 ASP Chi-restraints excluded: chain W residue 136 VAL Chi-restraints excluded: chain W residue 151 SER Chi-restraints excluded: chain W residue 154 GLU Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 63 CYS Chi-restraints excluded: chain Y residue 74 ILE Chi-restraints excluded: chain Y residue 107 ARG Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Z residue 48 ASP Chi-restraints excluded: chain a residue 3 ASN Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 155 GLU Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 200 GLU Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 62 GLN Chi-restraints excluded: chain b residue 93 ASP Chi-restraints excluded: chain b residue 94 LEU Chi-restraints excluded: chain k residue 16 GLN Chi-restraints excluded: chain k residue 36 LEU Chi-restraints excluded: chain k residue 40 ILE Chi-restraints excluded: chain k residue 186 ASP Chi-restraints excluded: chain k residue 238 MET Chi-restraints excluded: chain j residue 26 GLU Chi-restraints excluded: chain j residue 50 ASN Chi-restraints excluded: chain j residue 144 ASP Chi-restraints excluded: chain j residue 164 HIS Chi-restraints excluded: chain j residue 179 SER Chi-restraints excluded: chain j residue 183 ASP Chi-restraints excluded: chain j residue 213 ARG Chi-restraints excluded: chain j residue 218 GLU Chi-restraints excluded: chain m residue 32 LEU Chi-restraints excluded: chain m residue 184 VAL Chi-restraints excluded: chain l residue 41 ASP Chi-restraints excluded: chain o residue 183 HIS Chi-restraints excluded: chain n residue 162 SER Chi-restraints excluded: chain p residue 118 CYS Chi-restraints excluded: chain p residue 134 ASP Chi-restraints excluded: chain p residue 208 ASP Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain E residue 65 HIS Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 133 CYS Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 154 CYS Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain I residue 157 MET Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 121 ILE Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 54 CYS Chi-restraints excluded: chain L residue 144 MET Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain d residue 38 GLN Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 169 SER Chi-restraints excluded: chain c residue 26 GLU Chi-restraints excluded: chain c residue 203 GLU Chi-restraints excluded: chain c residue 248 ILE Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 118 CYS Chi-restraints excluded: chain f residue 134 ASP Chi-restraints excluded: chain f residue 183 HIS Chi-restraints excluded: chain f residue 184 VAL Chi-restraints excluded: chain f residue 185 MET Chi-restraints excluded: chain f residue 208 ASP Chi-restraints excluded: chain f residue 209 LEU Chi-restraints excluded: chain e residue 41 ASP Chi-restraints excluded: chain e residue 113 LEU Chi-restraints excluded: chain e residue 144 ASP Chi-restraints excluded: chain e residue 157 PHE Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain g residue 213 ARG Chi-restraints excluded: chain i residue 118 CYS Chi-restraints excluded: chain i residue 134 ASP Chi-restraints excluded: chain i residue 185 MET Chi-restraints excluded: chain i residue 208 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 729 optimal weight: 0.3980 chunk 497 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 652 optimal weight: 0.9980 chunk 361 optimal weight: 3.9990 chunk 747 optimal weight: 3.9990 chunk 605 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 447 optimal weight: 8.9990 chunk 786 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 95 GLN P 146 GLN ** S 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 175 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** ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 123 GLN k 136 ASN m 161 GLN o 45 GLN n 136 GLN ** n 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN C 85 ASN C 116 GLN E 16 GLN E 90 GLN H 35 HIS I 64 GLN ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN c 146 ASN c 199 GLN e 115 GLN e 138 GLN ** i 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 143 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 71082 Z= 0.237 Angle : 0.579 11.340 96452 Z= 0.308 Chirality : 0.042 0.306 11222 Planarity : 0.004 0.071 12306 Dihedral : 4.386 49.772 10044 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.97 % Allowed : 15.61 % Favored : 81.42 % 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: 1.90 (0.09), residues: 9128 helix: 2.46 (0.07), residues: 4504 sheet: 0.37 (0.13), residues: 1470 loop : -0.02 (0.11), residues: 3154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP T 215 HIS 0.005 0.001 HIS k 192 PHE 0.024 0.001 PHE n 170 TYR 0.034 0.001 TYR U 160 ARG 0.008 0.001 ARG i 14 *********************** 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 1621 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1415 time to evaluate : 6.146 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: O 7 PHE cc_start: 0.9133 (m-80) cc_final: 0.8876 (m-80) REVERT: O 174 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7945 (tp30) REVERT: O 202 MET cc_start: 0.7555 (ttp) cc_final: 0.7299 (ttm) REVERT: P 25 MET cc_start: 0.9082 (mtt) cc_final: 0.8822 (mtp) REVERT: P 26 GLU cc_start: 0.8690 (tp30) cc_final: 0.8364 (tp30) REVERT: P 174 MET cc_start: 0.8658 (mtp) cc_final: 0.8331 (ttm) REVERT: P 178 ASP cc_start: 0.8269 (m-30) cc_final: 0.7793 (m-30) REVERT: Q 66 ASP cc_start: 0.7999 (t0) cc_final: 0.7691 (t0) REVERT: Q 67 ASP cc_start: 0.8117 (p0) cc_final: 0.7878 (p0) REVERT: Q 116 GLN cc_start: 0.8726 (tt0) cc_final: 0.8469 (tt0) REVERT: S 9 ASP cc_start: 0.8501 (t70) cc_final: 0.8237 (t70) REVERT: S 90 GLN cc_start: 0.8435 (tp-100) cc_final: 0.6745 (tp40) REVERT: S 94 ASP cc_start: 0.8162 (m-30) cc_final: 0.7284 (m-30) REVERT: S 100 ASP cc_start: 0.9098 (t0) cc_final: 0.8487 (t0) REVERT: S 138 ASP cc_start: 0.8161 (p0) cc_final: 0.7907 (p0) REVERT: S 178 GLU cc_start: 0.8714 (pm20) cc_final: 0.8439 (pm20) REVERT: S 179 PHE cc_start: 0.8768 (m-10) cc_final: 0.8174 (m-80) REVERT: T 27 MET cc_start: 0.8814 (mmm) cc_final: 0.8526 (mmm) REVERT: T 73 VAL cc_start: 0.9463 (OUTLIER) cc_final: 0.9154 (m) REVERT: U 53 GLN cc_start: 0.8276 (mt0) cc_final: 0.7977 (mt0) REVERT: U 83 MET cc_start: 0.8286 (mtt) cc_final: 0.7729 (mtt) REVERT: U 86 ASP cc_start: 0.8473 (m-30) cc_final: 0.8121 (m-30) REVERT: U 125 TYR cc_start: 0.8680 (m-80) cc_final: 0.7828 (m-80) REVERT: U 216 GLU cc_start: 0.6948 (mp0) cc_final: 0.6470 (mp0) REVERT: V 8 TYR cc_start: 0.8743 (p90) cc_final: 0.8463 (p90) REVERT: V 135 MET cc_start: 0.8563 (tpp) cc_final: 0.8057 (tpp) REVERT: W 57 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8505 (p) REVERT: W 145 MET cc_start: 0.8298 (mtp) cc_final: 0.7996 (mtm) REVERT: W 192 ASP cc_start: 0.8645 (p0) cc_final: 0.8431 (p0) REVERT: X 18 ASP cc_start: 0.7988 (p0) cc_final: 0.7613 (p0) REVERT: X 27 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8186 (tm-30) REVERT: X 37 LYS cc_start: 0.8780 (ptmt) cc_final: 0.8486 (tttp) REVERT: X 69 MET cc_start: 0.8750 (mmm) cc_final: 0.8278 (mmm) REVERT: X 166 GLU cc_start: 0.8381 (tp30) cc_final: 0.8142 (tp30) REVERT: Y 33 LYS cc_start: 0.8846 (mttm) cc_final: 0.8416 (mttt) REVERT: Y 67 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8520 (tm-30) REVERT: Y 107 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7810 (mpp80) REVERT: Z 157 ASN cc_start: 0.8372 (m-40) cc_final: 0.7945 (m-40) REVERT: Z 186 ASP cc_start: 0.8754 (t0) cc_final: 0.8470 (t0) REVERT: a 10 SER cc_start: 0.8865 (m) cc_final: 0.8615 (p) REVERT: a 104 ASN cc_start: 0.9030 (t0) cc_final: 0.8499 (t0) REVERT: a 110 MET cc_start: 0.8144 (mtm) cc_final: 0.7889 (mtm) REVERT: k 26 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8311 (tm-30) REVERT: k 208 ASP cc_start: 0.8965 (m-30) cc_final: 0.8667 (m-30) REVERT: k 217 TYR cc_start: 0.9174 (t80) cc_final: 0.8639 (t80) REVERT: j 11 GLN cc_start: 0.8885 (tm130) cc_final: 0.8434 (tp40) REVERT: j 15 ASP cc_start: 0.8530 (m-30) cc_final: 0.8019 (m-30) REVERT: j 116 ARG cc_start: 0.8748 (mtp85) cc_final: 0.8428 (mtp85) REVERT: j 120 GLU cc_start: 0.8867 (mp0) cc_final: 0.8504 (mp0) REVERT: j 123 ASP cc_start: 0.8577 (m-30) cc_final: 0.8164 (m-30) REVERT: j 146 ASN cc_start: 0.8700 (t0) cc_final: 0.8165 (t0) REVERT: j 170 PHE cc_start: 0.8939 (m-80) cc_final: 0.8610 (m-80) REVERT: j 199 GLN cc_start: 0.9294 (tp40) cc_final: 0.8801 (tp-100) REVERT: j 202 HIS cc_start: 0.8640 (m90) cc_final: 0.8348 (m-70) REVERT: j 210 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7725 (mtm-85) REVERT: j 213 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8111 (ttt-90) REVERT: j 218 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: j 228 ASP cc_start: 0.9312 (t70) cc_final: 0.8911 (t0) REVERT: m 48 GLN cc_start: 0.9008 (pt0) cc_final: 0.8808 (pt0) REVERT: m 155 THR cc_start: 0.9608 (p) cc_final: 0.9390 (t) REVERT: l 157 PHE cc_start: 0.8348 (m-80) cc_final: 0.7968 (m-80) REVERT: l 215 MET cc_start: 0.9028 (mtm) cc_final: 0.8712 (mtp) REVERT: o 42 TYR cc_start: 0.8715 (t80) cc_final: 0.8386 (t80) REVERT: o 136 ASN cc_start: 0.8773 (m-40) cc_final: 0.8550 (t0) REVERT: n 43 PHE cc_start: 0.8910 (t80) cc_final: 0.8096 (t80) REVERT: n 116 ARG cc_start: 0.8834 (ttt180) cc_final: 0.7895 (ttt180) REVERT: n 146 ASN cc_start: 0.8213 (t0) cc_final: 0.7931 (t0) REVERT: n 218 GLU cc_start: 0.9026 (tp30) cc_final: 0.8750 (tp30) REVERT: n 241 ARG cc_start: 0.9224 (tpp80) cc_final: 0.8459 (tpp80) REVERT: p 23 ASN cc_start: 0.9140 (m110) cc_final: 0.8830 (m-40) REVERT: p 34 ARG cc_start: 0.8439 (ptp90) cc_final: 0.8190 (ptp90) REVERT: p 97 ASN cc_start: 0.8413 (t0) cc_final: 0.8095 (t0) REVERT: p 112 TRP cc_start: 0.8281 (m100) cc_final: 0.8018 (m100) REVERT: p 194 ARG cc_start: 0.9080 (mmt90) cc_final: 0.8833 (mmt90) REVERT: A 6 SER cc_start: 0.9023 (m) cc_final: 0.8489 (t) REVERT: A 7 PHE cc_start: 0.9159 (m-80) cc_final: 0.8858 (m-80) REVERT: B 6 ASP cc_start: 0.7840 (p0) cc_final: 0.7511 (p0) REVERT: B 30 HIS cc_start: 0.8388 (m-70) cc_final: 0.7978 (m-70) REVERT: B 64 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8504 (mtpt) REVERT: B 67 LYS cc_start: 0.8841 (ttpt) cc_final: 0.8364 (tttp) REVERT: B 108 GLU cc_start: 0.8507 (tp30) cc_final: 0.7853 (tp30) REVERT: B 160 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8165 (mppt) REVERT: C 3 TYR cc_start: 0.9331 (m-80) cc_final: 0.8999 (m-10) REVERT: C 90 GLU cc_start: 0.8400 (tp30) cc_final: 0.8141 (tp30) REVERT: C 105 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7857 (tm-30) REVERT: D 52 LYS cc_start: 0.9208 (mmtp) cc_final: 0.8716 (mmtp) REVERT: D 216 GLU cc_start: 0.7520 (tt0) cc_final: 0.6980 (mt-10) REVERT: E 30 LYS cc_start: 0.9273 (mtmm) cc_final: 0.8932 (mtmm) REVERT: E 91 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8328 (mm-30) REVERT: E 100 ASP cc_start: 0.8868 (t0) cc_final: 0.8287 (t0) REVERT: G 9 PHE cc_start: 0.8864 (m-80) cc_final: 0.8459 (m-10) REVERT: G 19 GLU cc_start: 0.7670 (pm20) cc_final: 0.7405 (pm20) REVERT: G 22 LEU cc_start: 0.8567 (mt) cc_final: 0.8114 (mp) REVERT: G 26 GLU cc_start: 0.8787 (mp0) cc_final: 0.8574 (mp0) REVERT: G 131 MET cc_start: 0.7326 (mpp) cc_final: 0.7007 (mpp) REVERT: G 159 TYR cc_start: 0.7674 (t80) cc_final: 0.7246 (t80) REVERT: G 234 GLU cc_start: 0.8640 (mp0) cc_final: 0.8402 (mp0) REVERT: H 124 TYR cc_start: 0.8896 (p90) cc_final: 0.8058 (p90) REVERT: H 157 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8424 (mm-30) REVERT: H 202 TYR cc_start: 0.7104 (m-80) cc_final: 0.6832 (m-80) REVERT: H 214 GLU cc_start: 0.8598 (tp30) cc_final: 0.8221 (tp30) REVERT: I 65 ARG cc_start: 0.8574 (mtp85) cc_final: 0.8216 (mtp85) REVERT: I 95 TYR cc_start: 0.9330 (t80) cc_final: 0.9019 (t80) REVERT: I 157 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7872 (mtp) REVERT: I 175 ASP cc_start: 0.8077 (m-30) cc_final: 0.7861 (m-30) REVERT: I 197 ARG cc_start: 0.8268 (mtt90) cc_final: 0.7572 (mtt90) REVERT: J 18 ASP cc_start: 0.7610 (p0) cc_final: 0.7308 (p0) REVERT: J 31 ASP cc_start: 0.8533 (p0) cc_final: 0.8222 (p0) REVERT: J 34 LYS cc_start: 0.8438 (mttp) cc_final: 0.8107 (mttp) REVERT: J 38 MET cc_start: 0.8584 (mmp) cc_final: 0.8306 (mmm) REVERT: J 68 LYS cc_start: 0.9562 (tttp) cc_final: 0.9236 (tppt) REVERT: J 166 GLU cc_start: 0.8746 (tp30) cc_final: 0.8543 (tp30) REVERT: L 60 ASP cc_start: 0.8372 (m-30) cc_final: 0.8160 (m-30) REVERT: L 131 GLN cc_start: 0.8462 (pm20) cc_final: 0.8149 (pm20) REVERT: L 146 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7710 (tm-30) REVERT: L 159 GLN cc_start: 0.8620 (tt0) cc_final: 0.8348 (tt0) REVERT: M 47 ASN cc_start: 0.8865 (t0) cc_final: 0.8612 (t0) REVERT: M 96 MET cc_start: 0.8707 (mmm) cc_final: 0.7610 (mtp) REVERT: M 133 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8280 (mt-10) REVERT: N 28 ASN cc_start: 0.8480 (t0) cc_final: 0.8170 (t0) REVERT: N 71 ASN cc_start: 0.8825 (t0) cc_final: 0.8500 (t0) REVERT: N 164 MET cc_start: 0.8271 (mtm) cc_final: 0.7950 (mtp) REVERT: d 38 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8943 (mm-40) REVERT: d 42 TYR cc_start: 0.9144 (t80) cc_final: 0.8836 (t80) REVERT: d 208 ASP cc_start: 0.8810 (m-30) cc_final: 0.8414 (m-30) REVERT: d 229 ASN cc_start: 0.8874 (t0) cc_final: 0.8619 (m-40) REVERT: c 115 GLN cc_start: 0.9290 (tt0) cc_final: 0.8949 (tm-30) REVERT: c 123 ASP cc_start: 0.8764 (m-30) cc_final: 0.8405 (m-30) REVERT: c 133 THR cc_start: 0.9640 (m) cc_final: 0.9396 (p) REVERT: c 199 GLN cc_start: 0.8998 (tp40) cc_final: 0.8569 (tp-100) REVERT: c 217 MET cc_start: 0.9196 (ttp) cc_final: 0.8752 (ttm) REVERT: c 221 ASN cc_start: 0.9334 (m-40) cc_final: 0.9037 (m110) REVERT: f 22 GLN cc_start: 0.8440 (mt0) cc_final: 0.8117 (mt0) REVERT: f 48 GLN cc_start: 0.8791 (mt0) cc_final: 0.8533 (mt0) REVERT: f 97 ASN cc_start: 0.8373 (t0) cc_final: 0.7990 (t0) REVERT: f 136 ASN cc_start: 0.8482 (t0) cc_final: 0.7924 (t0) REVERT: e 211 ASP cc_start: 0.9252 (m-30) cc_final: 0.8825 (m-30) REVERT: h 25 PHE cc_start: 0.8945 (m-10) cc_final: 0.8606 (m-10) REVERT: h 136 ASN cc_start: 0.8875 (t0) cc_final: 0.8413 (t0) REVERT: h 151 ASN cc_start: 0.9597 (m-40) cc_final: 0.9203 (m110) REVERT: h 194 ARG cc_start: 0.9058 (tpp80) cc_final: 0.8804 (tpp80) REVERT: h 210 ARG cc_start: 0.9173 (ttp-170) cc_final: 0.8846 (ttp80) REVERT: h 212 PHE cc_start: 0.8952 (m-10) cc_final: 0.8624 (m-80) REVERT: g 123 ASP cc_start: 0.9041 (m-30) cc_final: 0.8776 (p0) REVERT: g 191 GLN cc_start: 0.9034 (mp10) cc_final: 0.8703 (mp10) REVERT: g 208 GLU cc_start: 0.9092 (tp30) cc_final: 0.8830 (tp30) REVERT: g 213 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8383 (ttt-90) REVERT: g 215 MET cc_start: 0.8590 (mtt) cc_final: 0.7889 (mtt) REVERT: g 233 ASN cc_start: 0.9268 (m-40) cc_final: 0.8913 (m110) REVERT: i 23 ASN cc_start: 0.8718 (m110) cc_final: 0.8448 (m-40) REVERT: i 42 TYR cc_start: 0.8473 (t80) cc_final: 0.8265 (t80) REVERT: i 117 LYS cc_start: 0.9378 (mmmt) cc_final: 0.9004 (mmtp) REVERT: i 188 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8203 (mtp85) outliers start: 206 outliers final: 143 residues processed: 1540 average time/residue: 0.6973 time to fit residues: 1820.9276 Evaluate side-chains 1484 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1329 time to evaluate : 6.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 174 GLU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 72 MET Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain Q residue 7 ILE Chi-restraints excluded: chain Q residue 82 ILE Chi-restraints excluded: chain Q residue 148 ASP Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 106 SER Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 147 THR Chi-restraints excluded: chain S residue 228 ASP Chi-restraints excluded: chain S residue 236 LEU Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 78 CYS Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 72 LEU Chi-restraints excluded: chain W residue 136 VAL Chi-restraints excluded: chain W residue 151 SER Chi-restraints excluded: chain W residue 154 GLU Chi-restraints excluded: chain W residue 164 GLU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 107 ARG Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Z residue 48 ASP Chi-restraints excluded: chain Z residue 159 GLN Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 200 GLU Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 17 ASP Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 62 GLN Chi-restraints excluded: chain b residue 93 ASP Chi-restraints excluded: chain b residue 94 LEU Chi-restraints excluded: chain b residue 123 GLN Chi-restraints excluded: chain k residue 16 GLN Chi-restraints excluded: chain k residue 36 LEU Chi-restraints excluded: chain k residue 40 ILE Chi-restraints excluded: chain k residue 186 ASP Chi-restraints excluded: chain k residue 238 MET Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 26 GLU Chi-restraints excluded: chain j residue 50 ASN Chi-restraints excluded: chain j residue 105 ASN Chi-restraints excluded: chain j residue 164 HIS Chi-restraints excluded: chain j residue 179 SER Chi-restraints excluded: chain j residue 213 ARG Chi-restraints excluded: chain j residue 218 GLU Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 169 SER Chi-restraints excluded: chain m residue 184 VAL Chi-restraints excluded: chain o residue 183 HIS Chi-restraints excluded: chain n residue 123 ASP Chi-restraints excluded: chain n residue 161 THR Chi-restraints excluded: chain p residue 118 CYS Chi-restraints excluded: chain p residue 125 ILE Chi-restraints excluded: chain p residue 134 ASP Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 70 CYS Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 133 CYS Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 154 CYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain I residue 157 MET Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 121 ILE Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 54 CYS Chi-restraints excluded: chain L residue 144 MET Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain d residue 38 GLN Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 169 SER Chi-restraints excluded: chain c residue 26 GLU Chi-restraints excluded: chain c residue 56 ASN Chi-restraints excluded: chain c residue 248 ILE Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 118 CYS Chi-restraints excluded: chain f residue 183 HIS Chi-restraints excluded: chain f residue 184 VAL Chi-restraints excluded: chain f residue 185 MET Chi-restraints excluded: chain f residue 208 ASP Chi-restraints excluded: chain f residue 209 LEU Chi-restraints excluded: chain e residue 41 ASP Chi-restraints excluded: chain e residue 144 ASP Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain e residue 178 PHE Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain g residue 213 ARG Chi-restraints excluded: chain i residue 118 CYS Chi-restraints excluded: chain i residue 134 ASP Chi-restraints excluded: chain i residue 185 MET Chi-restraints excluded: chain i residue 188 ARG Chi-restraints excluded: chain i residue 208 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 294 optimal weight: 4.9990 chunk 788 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 514 optimal weight: 0.7980 chunk 216 optimal weight: 0.8980 chunk 876 optimal weight: 0.9980 chunk 727 optimal weight: 3.9990 chunk 405 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 289 optimal weight: 8.9990 chunk 460 optimal weight: 0.9980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 16 GLN U 12 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** ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 162 GLN k 136 ASN j 191 GLN o 45 GLN ** n 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 138 GLN ** g 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 143 GLN i 151 ASN ** i 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 71082 Z= 0.218 Angle : 0.580 9.343 96452 Z= 0.308 Chirality : 0.042 0.270 11222 Planarity : 0.004 0.069 12306 Dihedral : 4.321 49.022 10044 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.03 % Allowed : 16.13 % Favored : 80.84 % 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: 1.90 (0.09), residues: 9128 helix: 2.47 (0.07), residues: 4490 sheet: 0.29 (0.13), residues: 1492 loop : 0.01 (0.11), residues: 3146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP T 215 HIS 0.004 0.001 HIS k 192 PHE 0.039 0.001 PHE n 170 TYR 0.037 0.001 TYR Q 110 ARG 0.013 0.001 ARG P 8 *********************** 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 1591 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1381 time to evaluate : 6.153 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: O 7 PHE cc_start: 0.9120 (m-80) cc_final: 0.8863 (m-80) REVERT: O 174 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7940 (tp30) REVERT: O 202 MET cc_start: 0.7612 (ttp) cc_final: 0.7287 (ttm) REVERT: P 25 MET cc_start: 0.9045 (mtt) cc_final: 0.8654 (mtp) REVERT: P 26 GLU cc_start: 0.8681 (tp30) cc_final: 0.8362 (tp30) REVERT: P 174 MET cc_start: 0.8680 (mtp) cc_final: 0.8361 (ttm) REVERT: P 178 ASP cc_start: 0.8291 (m-30) cc_final: 0.7873 (m-30) REVERT: Q 66 ASP cc_start: 0.7917 (t0) cc_final: 0.7623 (t0) REVERT: Q 67 ASP cc_start: 0.8094 (p0) cc_final: 0.7853 (p0) REVERT: Q 116 GLN cc_start: 0.8732 (tt0) cc_final: 0.8428 (tt0) REVERT: S 9 ASP cc_start: 0.8512 (t70) cc_final: 0.8251 (t70) REVERT: S 90 GLN cc_start: 0.8445 (tp-100) cc_final: 0.6748 (tp40) REVERT: S 94 ASP cc_start: 0.8189 (m-30) cc_final: 0.7328 (m-30) REVERT: S 100 ASP cc_start: 0.9101 (t0) cc_final: 0.8474 (t0) REVERT: S 137 TYR cc_start: 0.8804 (t80) cc_final: 0.7930 (t80) REVERT: S 178 GLU cc_start: 0.8658 (pm20) cc_final: 0.8421 (pm20) REVERT: S 179 PHE cc_start: 0.8828 (m-10) cc_final: 0.8299 (m-80) REVERT: T 27 MET cc_start: 0.8799 (mmm) cc_final: 0.8519 (mmm) REVERT: T 73 VAL cc_start: 0.9455 (OUTLIER) cc_final: 0.9138 (m) REVERT: U 53 GLN cc_start: 0.8203 (mt0) cc_final: 0.7914 (mt0) REVERT: U 83 MET cc_start: 0.8292 (mtt) cc_final: 0.8062 (mtt) REVERT: U 86 ASP cc_start: 0.8485 (m-30) cc_final: 0.8272 (m-30) REVERT: U 125 TYR cc_start: 0.8631 (m-80) cc_final: 0.8158 (m-80) REVERT: U 131 MET cc_start: 0.7539 (ttp) cc_final: 0.7067 (ttp) REVERT: U 216 GLU cc_start: 0.7150 (mp0) cc_final: 0.6666 (mp0) REVERT: V 8 TYR cc_start: 0.8770 (p90) cc_final: 0.8485 (p90) REVERT: V 135 MET cc_start: 0.8536 (tpp) cc_final: 0.8055 (tpp) REVERT: V 157 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8278 (mm-30) REVERT: W 57 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8518 (p) REVERT: W 192 ASP cc_start: 0.8705 (p0) cc_final: 0.8466 (p0) REVERT: X 18 ASP cc_start: 0.7883 (p0) cc_final: 0.7491 (p0) REVERT: X 27 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8157 (tm-30) REVERT: X 37 LYS cc_start: 0.8809 (ptmt) cc_final: 0.8505 (tttp) REVERT: X 69 MET cc_start: 0.8756 (mmm) cc_final: 0.8231 (mmm) REVERT: Y 67 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8666 (tm-30) REVERT: Y 107 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7829 (mpp80) REVERT: Z 157 ASN cc_start: 0.8189 (m-40) cc_final: 0.7744 (m-40) REVERT: Z 186 ASP cc_start: 0.8719 (t0) cc_final: 0.8430 (t0) REVERT: a 2 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8189 (mp10) REVERT: a 10 SER cc_start: 0.8806 (m) cc_final: 0.8542 (p) REVERT: a 96 MET cc_start: 0.8810 (mmm) cc_final: 0.8448 (mtt) REVERT: a 104 ASN cc_start: 0.9023 (t0) cc_final: 0.8645 (t0) REVERT: a 110 MET cc_start: 0.8161 (mtm) cc_final: 0.6937 (mtm) REVERT: k 26 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8341 (tm-30) REVERT: k 44 ASN cc_start: 0.8937 (p0) cc_final: 0.8641 (p0) REVERT: k 208 ASP cc_start: 0.8997 (m-30) cc_final: 0.8725 (m-30) REVERT: k 217 TYR cc_start: 0.9163 (t80) cc_final: 0.8636 (t80) REVERT: j 11 GLN cc_start: 0.8899 (tm130) cc_final: 0.8447 (tp40) REVERT: j 15 ASP cc_start: 0.8543 (m-30) cc_final: 0.7982 (m-30) REVERT: j 116 ARG cc_start: 0.8772 (mtp85) cc_final: 0.8537 (mtp85) REVERT: j 120 GLU cc_start: 0.8852 (mp0) cc_final: 0.8487 (mp0) REVERT: j 123 ASP cc_start: 0.8568 (m-30) cc_final: 0.8142 (m-30) REVERT: j 146 ASN cc_start: 0.8707 (t0) cc_final: 0.8156 (t0) REVERT: j 170 PHE cc_start: 0.8841 (m-80) cc_final: 0.8618 (m-80) REVERT: j 199 GLN cc_start: 0.9216 (tp40) cc_final: 0.8872 (tp-100) REVERT: j 202 HIS cc_start: 0.8636 (m90) cc_final: 0.8323 (m-70) REVERT: j 210 ARG cc_start: 0.8252 (mtm-85) cc_final: 0.7695 (mtm-85) REVERT: j 213 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8171 (ttt-90) REVERT: j 218 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8557 (tt0) REVERT: j 227 TYR cc_start: 0.9327 (t80) cc_final: 0.8784 (t80) REVERT: j 228 ASP cc_start: 0.9317 (t70) cc_final: 0.8898 (t0) REVERT: m 42 TYR cc_start: 0.8820 (t80) cc_final: 0.8612 (t80) REVERT: m 48 GLN cc_start: 0.9009 (pt0) cc_final: 0.8793 (pt0) REVERT: m 155 THR cc_start: 0.9601 (p) cc_final: 0.9392 (t) REVERT: l 15 ASP cc_start: 0.8614 (m-30) cc_final: 0.8376 (m-30) REVERT: l 157 PHE cc_start: 0.8276 (m-80) cc_final: 0.7962 (m-80) REVERT: l 215 MET cc_start: 0.8995 (mtm) cc_final: 0.8732 (mtp) REVERT: o 42 TYR cc_start: 0.8763 (t80) cc_final: 0.8413 (t80) REVERT: o 126 GLN cc_start: 0.9228 (mt0) cc_final: 0.8989 (mt0) REVERT: n 43 PHE cc_start: 0.8949 (t80) cc_final: 0.8180 (t80) REVERT: n 116 ARG cc_start: 0.8855 (ttt180) cc_final: 0.8093 (ttt180) REVERT: n 146 ASN cc_start: 0.8199 (t0) cc_final: 0.7755 (t0) REVERT: n 199 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8592 (tm-30) REVERT: n 211 ASP cc_start: 0.8186 (t0) cc_final: 0.7732 (t0) REVERT: n 217 MET cc_start: 0.9000 (tpp) cc_final: 0.8618 (mmm) REVERT: n 218 GLU cc_start: 0.8875 (tp30) cc_final: 0.8652 (mm-30) REVERT: p 23 ASN cc_start: 0.9115 (m110) cc_final: 0.8854 (m-40) REVERT: p 34 ARG cc_start: 0.8463 (ptp90) cc_final: 0.8223 (ptp90) REVERT: p 97 ASN cc_start: 0.8373 (t0) cc_final: 0.8057 (t0) REVERT: p 112 TRP cc_start: 0.8268 (m100) cc_final: 0.7922 (m100) REVERT: p 194 ARG cc_start: 0.9096 (mmt90) cc_final: 0.8874 (mmt90) REVERT: A 6 SER cc_start: 0.9012 (m) cc_final: 0.8473 (t) REVERT: A 7 PHE cc_start: 0.9214 (m-80) cc_final: 0.8920 (m-80) REVERT: A 187 ILE cc_start: 0.8954 (pt) cc_final: 0.8701 (mt) REVERT: B 6 ASP cc_start: 0.7858 (p0) cc_final: 0.7499 (p0) REVERT: B 30 HIS cc_start: 0.8361 (m-70) cc_final: 0.8048 (m-70) REVERT: B 64 LYS cc_start: 0.8842 (mtpt) cc_final: 0.8534 (mtpt) REVERT: B 67 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8332 (tttp) REVERT: B 108 GLU cc_start: 0.8516 (tp30) cc_final: 0.7861 (tp30) REVERT: B 160 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8167 (mppt) REVERT: C 3 TYR cc_start: 0.9323 (m-80) cc_final: 0.9009 (m-10) REVERT: C 90 GLU cc_start: 0.8366 (tp30) cc_final: 0.8053 (tp30) REVERT: C 105 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7834 (tm-30) REVERT: C 116 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8692 (tp40) REVERT: D 52 LYS cc_start: 0.9196 (mmtp) cc_final: 0.8595 (mmtp) REVERT: D 156 MET cc_start: 0.8448 (tmm) cc_final: 0.7840 (tmm) REVERT: D 216 GLU cc_start: 0.7525 (tt0) cc_final: 0.6952 (mt-10) REVERT: E 30 LYS cc_start: 0.9286 (mtmm) cc_final: 0.9083 (mtmm) REVERT: E 91 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8351 (mm-30) REVERT: E 100 ASP cc_start: 0.8861 (t0) cc_final: 0.8317 (t0) REVERT: E 128 TYR cc_start: 0.9064 (m-10) cc_final: 0.8739 (m-10) REVERT: E 186 GLU cc_start: 0.8897 (mp0) cc_final: 0.8646 (mp0) REVERT: G 9 PHE cc_start: 0.8783 (m-80) cc_final: 0.8429 (m-10) REVERT: G 11 ARG cc_start: 0.8323 (mtm-85) cc_final: 0.7795 (ptp-110) REVERT: G 22 LEU cc_start: 0.8480 (mt) cc_final: 0.7966 (mp) REVERT: G 26 GLU cc_start: 0.8760 (mp0) cc_final: 0.8515 (mp0) REVERT: G 159 TYR cc_start: 0.7566 (t80) cc_final: 0.7144 (t80) REVERT: H 124 TYR cc_start: 0.8887 (p90) cc_final: 0.8043 (p90) REVERT: H 157 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8395 (mm-30) REVERT: H 202 TYR cc_start: 0.7133 (m-80) cc_final: 0.6858 (m-80) REVERT: H 214 GLU cc_start: 0.8543 (tp30) cc_final: 0.8211 (tp30) REVERT: I 33 MET cc_start: 0.8592 (tmm) cc_final: 0.8254 (ttp) REVERT: I 44 MET cc_start: 0.8451 (mmm) cc_final: 0.8208 (mmp) REVERT: I 73 TYR cc_start: 0.8777 (t80) cc_final: 0.8358 (t80) REVERT: I 95 TYR cc_start: 0.9356 (t80) cc_final: 0.9041 (t80) REVERT: I 157 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7866 (mtp) REVERT: I 182 MET cc_start: 0.8510 (mmm) cc_final: 0.7957 (mmm) REVERT: I 197 ARG cc_start: 0.8216 (mtt90) cc_final: 0.7523 (mtt90) REVERT: I 203 MET cc_start: 0.8241 (mmp) cc_final: 0.7781 (mmp) REVERT: J 27 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7871 (tm-30) REVERT: J 31 ASP cc_start: 0.8526 (p0) cc_final: 0.8232 (p0) REVERT: J 38 MET cc_start: 0.8536 (mmp) cc_final: 0.8294 (mmm) REVERT: J 68 LYS cc_start: 0.9571 (tttp) cc_final: 0.9243 (tppt) REVERT: K 119 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8316 (m-40) REVERT: L 131 GLN cc_start: 0.8411 (pm20) cc_final: 0.8112 (pm20) REVERT: L 146 GLN cc_start: 0.8364 (tm-30) cc_final: 0.7884 (tm-30) REVERT: L 159 GLN cc_start: 0.8620 (tt0) cc_final: 0.8375 (tt0) REVERT: M 47 ASN cc_start: 0.8869 (t0) cc_final: 0.8603 (t0) REVERT: M 96 MET cc_start: 0.8680 (mmm) cc_final: 0.7661 (mtp) REVERT: M 133 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8257 (mt-10) REVERT: N 28 ASN cc_start: 0.8482 (t0) cc_final: 0.8189 (t0) REVERT: N 164 MET cc_start: 0.8260 (mtm) cc_final: 0.7971 (mtp) REVERT: d 22 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8613 (mm-40) REVERT: d 208 ASP cc_start: 0.8784 (m-30) cc_final: 0.8446 (m-30) REVERT: d 229 ASN cc_start: 0.8866 (t0) cc_final: 0.8633 (m-40) REVERT: c 115 GLN cc_start: 0.9292 (tt0) cc_final: 0.9011 (tm-30) REVERT: c 123 ASP cc_start: 0.8745 (m-30) cc_final: 0.8387 (m-30) REVERT: c 133 THR cc_start: 0.9639 (m) cc_final: 0.9412 (p) REVERT: c 199 GLN cc_start: 0.8972 (tp40) cc_final: 0.8536 (tp-100) REVERT: c 217 MET cc_start: 0.9155 (ttp) cc_final: 0.8840 (ttm) REVERT: c 221 ASN cc_start: 0.9305 (m-40) cc_final: 0.9020 (m-40) REVERT: f 22 GLN cc_start: 0.8463 (mt0) cc_final: 0.8169 (mt0) REVERT: f 97 ASN cc_start: 0.8363 (t0) cc_final: 0.7998 (t0) REVERT: f 136 ASN cc_start: 0.8501 (t0) cc_final: 0.7930 (t0) REVERT: e 211 ASP cc_start: 0.9243 (m-30) cc_final: 0.8804 (m-30) REVERT: h 25 PHE cc_start: 0.8941 (m-10) cc_final: 0.8573 (m-10) REVERT: h 136 ASN cc_start: 0.8908 (t0) cc_final: 0.8448 (t0) REVERT: h 151 ASN cc_start: 0.9606 (m-40) cc_final: 0.9232 (m110) REVERT: h 194 ARG cc_start: 0.9025 (tpp80) cc_final: 0.8726 (tpp80) REVERT: h 210 ARG cc_start: 0.9160 (ttp-170) cc_final: 0.8846 (ttp80) REVERT: h 212 PHE cc_start: 0.8963 (m-10) cc_final: 0.8595 (m-80) REVERT: g 123 ASP cc_start: 0.8985 (m-30) cc_final: 0.8756 (p0) REVERT: g 191 GLN cc_start: 0.9019 (mp10) cc_final: 0.8791 (mp10) REVERT: g 208 GLU cc_start: 0.9103 (tp30) cc_final: 0.8872 (tp30) REVERT: g 211 ASP cc_start: 0.9141 (t0) cc_final: 0.8652 (t0) REVERT: g 215 MET cc_start: 0.8594 (mtt) cc_final: 0.8379 (mtm) REVERT: g 233 ASN cc_start: 0.9259 (m-40) cc_final: 0.8891 (m110) REVERT: i 23 ASN cc_start: 0.8718 (m110) cc_final: 0.8431 (m-40) REVERT: i 45 GLN cc_start: 0.7925 (pp30) cc_final: 0.7724 (pp30) REVERT: i 117 LYS cc_start: 0.9387 (mmmt) cc_final: 0.9036 (mmtp) REVERT: i 149 ARG cc_start: 0.8920 (tpp-160) cc_final: 0.8463 (tpp-160) outliers start: 210 outliers final: 154 residues processed: 1509 average time/residue: 0.6537 time to fit residues: 1666.1443 Evaluate side-chains 1484 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1319 time to evaluate : 6.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 174 GLU Chi-restraints excluded: chain O residue 212 CYS Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 72 MET Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain Q residue 7 ILE Chi-restraints excluded: chain Q residue 82 ILE Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain Q residue 148 ASP Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 106 SER Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 147 THR Chi-restraints excluded: chain S residue 228 ASP Chi-restraints excluded: chain S residue 236 LEU Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 72 LEU Chi-restraints excluded: chain W residue 92 ASN Chi-restraints excluded: chain W residue 134 ASP Chi-restraints excluded: chain W residue 136 VAL Chi-restraints excluded: chain W residue 151 SER Chi-restraints excluded: chain W residue 154 GLU Chi-restraints excluded: chain W residue 164 GLU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 107 ARG Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 48 ASP Chi-restraints excluded: chain Z residue 159 GLN Chi-restraints excluded: chain a residue 2 GLN Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 133 GLU Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 200 GLU Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 17 ASP Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 62 GLN Chi-restraints excluded: chain b residue 93 ASP Chi-restraints excluded: chain b residue 94 LEU Chi-restraints excluded: chain k residue 16 GLN Chi-restraints excluded: chain k residue 36 LEU Chi-restraints excluded: chain k residue 40 ILE Chi-restraints excluded: chain k residue 169 SER Chi-restraints excluded: chain k residue 186 ASP Chi-restraints excluded: chain k residue 238 MET Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 50 ASN Chi-restraints excluded: chain j residue 105 ASN Chi-restraints excluded: chain j residue 144 ASP Chi-restraints excluded: chain j residue 164 HIS Chi-restraints excluded: chain j residue 179 SER Chi-restraints excluded: chain j residue 183 ASP Chi-restraints excluded: chain j residue 191 GLN Chi-restraints excluded: chain j residue 213 ARG Chi-restraints excluded: chain j residue 218 GLU Chi-restraints excluded: chain m residue 184 VAL Chi-restraints excluded: chain n residue 162 SER Chi-restraints excluded: chain p residue 118 CYS Chi-restraints excluded: chain p residue 125 ILE Chi-restraints excluded: chain p residue 134 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 133 CYS Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 154 CYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 157 MET Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 121 ILE Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 54 CYS Chi-restraints excluded: chain L residue 144 MET Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 169 SER Chi-restraints excluded: chain c residue 26 GLU Chi-restraints excluded: chain c residue 56 ASN Chi-restraints excluded: chain c residue 171 HIS Chi-restraints excluded: chain c residue 203 GLU Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 118 CYS Chi-restraints excluded: chain f residue 184 VAL Chi-restraints excluded: chain f residue 185 MET Chi-restraints excluded: chain f residue 208 ASP Chi-restraints excluded: chain f residue 209 LEU Chi-restraints excluded: chain e residue 41 ASP Chi-restraints excluded: chain e residue 144 ASP Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain e residue 178 PHE Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain h residue 206 VAL Chi-restraints excluded: chain g residue 213 ARG Chi-restraints excluded: chain i residue 118 CYS Chi-restraints excluded: chain i residue 134 ASP Chi-restraints excluded: chain i residue 185 MET Chi-restraints excluded: chain i residue 208 ASP Chi-restraints excluded: chain i residue 238 MET 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: 5.9990 chunk 499 optimal weight: 0.0970 chunk 640 optimal weight: 10.0000 chunk 495 optimal weight: 0.1980 chunk 737 optimal weight: 3.9990 chunk 489 optimal weight: 0.4980 chunk 873 optimal weight: 7.9990 chunk 546 optimal weight: 6.9990 chunk 532 optimal weight: 0.4980 chunk 403 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 16 GLN ** 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** ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 ASN m 126 GLN o 45 GLN ** n 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 23 ASN ** p 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN I 32 GLN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN L 80 ASN ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 138 GLN f 48 GLN e 138 GLN ** g 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 45 GLN ** 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: 0.8517 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 71082 Z= 0.174 Angle : 0.575 9.293 96452 Z= 0.305 Chirality : 0.041 0.278 11222 Planarity : 0.004 0.066 12306 Dihedral : 4.244 47.499 10044 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.55 % Allowed : 17.42 % Favored : 80.03 % 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: 1.91 (0.09), residues: 9128 helix: 2.50 (0.07), residues: 4500 sheet: 0.25 (0.13), residues: 1502 loop : 0.00 (0.11), residues: 3126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP T 215 HIS 0.003 0.001 HIS k 192 PHE 0.033 0.001 PHE b 125 TYR 0.035 0.001 TYR Q 110 ARG 0.007 0.000 ARG o 149 *********************** 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 1625 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1448 time to evaluate : 6.088 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: O 7 PHE cc_start: 0.9089 (m-80) cc_final: 0.8838 (m-80) REVERT: O 174 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7990 (tp30) REVERT: P 25 MET cc_start: 0.9013 (mtt) cc_final: 0.8692 (mtp) REVERT: P 26 GLU cc_start: 0.8621 (tp30) cc_final: 0.8296 (tp30) REVERT: P 174 MET cc_start: 0.8625 (mtp) cc_final: 0.8364 (ttm) REVERT: P 178 ASP cc_start: 0.8302 (m-30) cc_final: 0.7896 (m-30) REVERT: Q 66 ASP cc_start: 0.7761 (t0) cc_final: 0.7475 (t70) REVERT: Q 116 GLN cc_start: 0.8642 (tt0) cc_final: 0.8348 (tt0) REVERT: R 104 ASN cc_start: 0.9336 (t0) cc_final: 0.9074 (t0) REVERT: S 9 ASP cc_start: 0.8462 (t70) cc_final: 0.8094 (t70) REVERT: S 90 GLN cc_start: 0.8374 (tp-100) cc_final: 0.6632 (tp40) REVERT: S 94 ASP cc_start: 0.8158 (m-30) cc_final: 0.7299 (m-30) REVERT: S 100 ASP cc_start: 0.9084 (t0) cc_final: 0.8461 (t0) REVERT: S 137 TYR cc_start: 0.8760 (t80) cc_final: 0.7933 (t80) REVERT: S 178 GLU cc_start: 0.8601 (pm20) cc_final: 0.8176 (pm20) REVERT: S 179 PHE cc_start: 0.8717 (m-10) cc_final: 0.8219 (m-80) REVERT: T 27 MET cc_start: 0.8764 (mmm) cc_final: 0.8536 (mmm) REVERT: U 53 GLN cc_start: 0.8148 (mt0) cc_final: 0.7894 (mt0) REVERT: U 83 MET cc_start: 0.8253 (mtt) cc_final: 0.8000 (mtt) REVERT: U 86 ASP cc_start: 0.8450 (m-30) cc_final: 0.8206 (m-30) REVERT: U 125 TYR cc_start: 0.8577 (m-80) cc_final: 0.8069 (m-80) REVERT: U 216 GLU cc_start: 0.7117 (mp0) cc_final: 0.6883 (mp0) REVERT: V 8 TYR cc_start: 0.8673 (p90) cc_final: 0.8394 (p90) REVERT: V 111 TYR cc_start: 0.8991 (m-80) cc_final: 0.8615 (m-10) REVERT: V 157 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8217 (mm-30) REVERT: W 33 MET cc_start: 0.8455 (tmm) cc_final: 0.8183 (tmm) REVERT: W 57 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8305 (t) REVERT: W 192 ASP cc_start: 0.8682 (p0) cc_final: 0.8464 (p0) REVERT: X 18 ASP cc_start: 0.7649 (p0) cc_final: 0.7313 (p0) REVERT: X 27 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8070 (tm-30) REVERT: X 37 LYS cc_start: 0.8820 (ptmt) cc_final: 0.8467 (tttp) REVERT: X 69 MET cc_start: 0.8689 (mmm) cc_final: 0.8094 (mmm) REVERT: X 108 ASP cc_start: 0.7883 (p0) cc_final: 0.6628 (p0) REVERT: X 144 ASP cc_start: 0.8484 (m-30) cc_final: 0.8233 (m-30) REVERT: Y 67 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8684 (tm-30) REVERT: Y 107 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7885 (mpp80) REVERT: Z 186 ASP cc_start: 0.8677 (t0) cc_final: 0.8364 (t0) REVERT: a 2 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8197 (mp10) REVERT: a 10 SER cc_start: 0.8677 (m) cc_final: 0.8371 (p) REVERT: a 96 MET cc_start: 0.8766 (mmm) cc_final: 0.8360 (mmm) REVERT: a 104 ASN cc_start: 0.8970 (t0) cc_final: 0.8583 (t0) REVERT: a 110 MET cc_start: 0.8036 (mtm) cc_final: 0.7805 (mtm) REVERT: k 26 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8285 (tm-30) REVERT: k 44 ASN cc_start: 0.8920 (p0) cc_final: 0.8632 (p0) REVERT: k 208 ASP cc_start: 0.9002 (m-30) cc_final: 0.8696 (m-30) REVERT: k 217 TYR cc_start: 0.9152 (t80) cc_final: 0.8469 (t80) REVERT: j 11 GLN cc_start: 0.8928 (tm130) cc_final: 0.8577 (tp40) REVERT: j 15 ASP cc_start: 0.8568 (m-30) cc_final: 0.8229 (m-30) REVERT: j 116 ARG cc_start: 0.8835 (mtp85) cc_final: 0.8621 (mtp85) REVERT: j 120 GLU cc_start: 0.8837 (mp0) cc_final: 0.8518 (mp0) REVERT: j 123 ASP cc_start: 0.8494 (m-30) cc_final: 0.8073 (m-30) REVERT: j 146 ASN cc_start: 0.8702 (t0) cc_final: 0.8126 (t0) REVERT: j 180 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8711 (mt-10) REVERT: j 199 GLN cc_start: 0.9242 (tp40) cc_final: 0.8818 (tp-100) REVERT: j 202 HIS cc_start: 0.8617 (m90) cc_final: 0.8322 (m-70) REVERT: j 213 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8077 (ttm-80) REVERT: j 218 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8617 (tt0) REVERT: j 227 TYR cc_start: 0.9297 (t80) cc_final: 0.8812 (t80) REVERT: j 228 ASP cc_start: 0.9298 (t70) cc_final: 0.8808 (t0) REVERT: m 22 GLN cc_start: 0.8779 (mt0) cc_final: 0.8554 (mt0) REVERT: m 48 GLN cc_start: 0.9043 (pt0) cc_final: 0.8800 (pt0) REVERT: m 155 THR cc_start: 0.9566 (p) cc_final: 0.9346 (t) REVERT: m 203 ARG cc_start: 0.9158 (ttm-80) cc_final: 0.8933 (ttm-80) REVERT: l 136 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8913 (mm110) REVERT: l 157 PHE cc_start: 0.8234 (m-80) cc_final: 0.7809 (m-80) REVERT: l 215 MET cc_start: 0.8964 (mtm) cc_final: 0.8708 (mtp) REVERT: o 23 ASN cc_start: 0.8546 (m110) cc_final: 0.8324 (m110) REVERT: o 42 TYR cc_start: 0.8752 (t80) cc_final: 0.8374 (t80) REVERT: o 126 GLN cc_start: 0.9225 (mt0) cc_final: 0.8985 (mt0) REVERT: n 11 GLN cc_start: 0.8940 (tp40) cc_final: 0.8715 (tp40) REVERT: n 43 PHE cc_start: 0.8953 (t80) cc_final: 0.8138 (t80) REVERT: n 116 ARG cc_start: 0.8848 (ttt180) cc_final: 0.8049 (ttt180) REVERT: n 146 ASN cc_start: 0.8190 (t0) cc_final: 0.7715 (t0) REVERT: n 180 GLU cc_start: 0.8997 (tp30) cc_final: 0.8015 (tp30) REVERT: n 183 ASP cc_start: 0.9002 (m-30) cc_final: 0.8738 (p0) REVERT: n 199 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8520 (tm-30) REVERT: n 211 ASP cc_start: 0.8465 (t0) cc_final: 0.8210 (t0) REVERT: n 217 MET cc_start: 0.8958 (tpp) cc_final: 0.8675 (tpp) REVERT: n 221 ASN cc_start: 0.9073 (m-40) cc_final: 0.8792 (m110) REVERT: p 23 ASN cc_start: 0.9090 (m-40) cc_final: 0.8878 (m-40) REVERT: p 34 ARG cc_start: 0.8417 (ptp90) cc_final: 0.8143 (ptp90) REVERT: p 97 ASN cc_start: 0.8316 (t0) cc_final: 0.8003 (t0) REVERT: p 112 TRP cc_start: 0.8199 (m100) cc_final: 0.7788 (m100) REVERT: p 185 MET cc_start: 0.8240 (mmm) cc_final: 0.7300 (mmp) REVERT: p 194 ARG cc_start: 0.9097 (mmt90) cc_final: 0.8889 (mmt90) REVERT: A 6 SER cc_start: 0.9024 (m) cc_final: 0.8487 (t) REVERT: A 7 PHE cc_start: 0.9142 (m-80) cc_final: 0.8844 (m-80) REVERT: A 142 ARG cc_start: 0.8401 (ptm-80) cc_final: 0.7985 (ptm160) REVERT: A 187 ILE cc_start: 0.8947 (pt) cc_final: 0.8706 (mt) REVERT: B 6 ASP cc_start: 0.7843 (p0) cc_final: 0.7488 (p0) REVERT: B 30 HIS cc_start: 0.8373 (m-70) cc_final: 0.8056 (m-70) REVERT: B 50 ARG cc_start: 0.8393 (mmm-85) cc_final: 0.8014 (mtm-85) REVERT: B 64 LYS cc_start: 0.8866 (mtpt) cc_final: 0.8615 (mtpt) REVERT: B 67 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8314 (tttp) REVERT: B 108 GLU cc_start: 0.8455 (tp30) cc_final: 0.7794 (tp30) REVERT: B 160 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8426 (mppt) REVERT: C 3 TYR cc_start: 0.9259 (m-80) cc_final: 0.8911 (m-10) REVERT: C 90 GLU cc_start: 0.8305 (tp30) cc_final: 0.7857 (tp30) REVERT: C 105 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7801 (tm-30) REVERT: C 116 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8731 (tp40) REVERT: D 52 LYS cc_start: 0.9162 (mmtp) cc_final: 0.8532 (mmtp) REVERT: D 216 GLU cc_start: 0.7480 (tt0) cc_final: 0.7023 (mt-10) REVERT: E 27 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8369 (mp0) REVERT: E 50 LYS cc_start: 0.9000 (mtmt) cc_final: 0.8758 (mtmm) REVERT: E 91 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8326 (mm-30) REVERT: E 100 ASP cc_start: 0.8851 (t0) cc_final: 0.8283 (t0) REVERT: E 128 TYR cc_start: 0.8961 (m-10) cc_final: 0.8603 (m-10) REVERT: E 186 GLU cc_start: 0.8874 (mp0) cc_final: 0.8667 (mp0) REVERT: G 11 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.7692 (ptp-110) REVERT: G 19 GLU cc_start: 0.7840 (pm20) cc_final: 0.7605 (pm20) REVERT: G 22 LEU cc_start: 0.8426 (mt) cc_final: 0.7967 (mp) REVERT: G 26 GLU cc_start: 0.8741 (mp0) cc_final: 0.8458 (mp0) REVERT: G 159 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.7048 (t80) REVERT: H 18 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8699 (p) REVERT: H 124 TYR cc_start: 0.8804 (p90) cc_final: 0.7947 (p90) REVERT: H 157 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8427 (mm-30) REVERT: H 202 TYR cc_start: 0.7094 (m-80) cc_final: 0.6805 (m-80) REVERT: H 214 GLU cc_start: 0.8540 (tp30) cc_final: 0.8228 (tp30) REVERT: I 33 MET cc_start: 0.8571 (tmm) cc_final: 0.8199 (ttp) REVERT: I 65 ARG cc_start: 0.8504 (mtp85) cc_final: 0.8057 (mtp85) REVERT: I 73 TYR cc_start: 0.8650 (t80) cc_final: 0.8298 (t80) REVERT: I 95 TYR cc_start: 0.9325 (t80) cc_final: 0.9041 (t80) REVERT: I 182 MET cc_start: 0.8418 (mmm) cc_final: 0.7987 (mmm) REVERT: I 197 ARG cc_start: 0.8251 (mtt90) cc_final: 0.7559 (mtt90) REVERT: I 203 MET cc_start: 0.8170 (mmp) cc_final: 0.7694 (mmp) REVERT: J 27 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7772 (tm-30) REVERT: J 31 ASP cc_start: 0.8510 (p0) cc_final: 0.8224 (p0) REVERT: J 36 PHE cc_start: 0.8755 (m-80) cc_final: 0.8432 (m-80) REVERT: J 61 GLN cc_start: 0.9251 (tt0) cc_final: 0.8862 (tt0) REVERT: J 68 LYS cc_start: 0.9516 (tttp) cc_final: 0.9178 (tppt) REVERT: L 131 GLN cc_start: 0.8358 (pm20) cc_final: 0.8126 (pm20) REVERT: L 146 GLN cc_start: 0.8338 (tm-30) cc_final: 0.8030 (tm-30) REVERT: L 159 GLN cc_start: 0.8658 (tt0) cc_final: 0.8416 (tt0) REVERT: M 12 LEU cc_start: 0.9299 (mt) cc_final: 0.8986 (mt) REVERT: M 47 ASN cc_start: 0.8832 (t0) cc_final: 0.8557 (t0) REVERT: M 96 MET cc_start: 0.8663 (mmm) cc_final: 0.7608 (mtp) REVERT: M 133 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8247 (mt-10) REVERT: N 28 ASN cc_start: 0.8461 (t0) cc_final: 0.8255 (t0) REVERT: N 136 TYR cc_start: 0.8564 (m-80) cc_final: 0.8351 (m-80) REVERT: N 164 MET cc_start: 0.8136 (mtm) cc_final: 0.7901 (mtp) REVERT: d 42 TYR cc_start: 0.9127 (t80) cc_final: 0.8811 (t80) REVERT: d 208 ASP cc_start: 0.8809 (m-30) cc_final: 0.8488 (m-30) REVERT: c 115 GLN cc_start: 0.9259 (tt0) cc_final: 0.8998 (tm-30) REVERT: c 123 ASP cc_start: 0.8730 (m-30) cc_final: 0.8355 (m-30) REVERT: c 133 THR cc_start: 0.9623 (m) cc_final: 0.9390 (p) REVERT: c 199 GLN cc_start: 0.8861 (tp40) cc_final: 0.8404 (tp-100) REVERT: c 217 MET cc_start: 0.9149 (ttp) cc_final: 0.8833 (ttm) REVERT: c 221 ASN cc_start: 0.9252 (m-40) cc_final: 0.8987 (m-40) REVERT: f 97 ASN cc_start: 0.8315 (t0) cc_final: 0.7971 (t0) REVERT: f 136 ASN cc_start: 0.8465 (t0) cc_final: 0.7875 (t0) REVERT: e 211 ASP cc_start: 0.9221 (m-30) cc_final: 0.8735 (m-30) REVERT: e 217 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8347 (tpt) REVERT: h 25 PHE cc_start: 0.8939 (m-10) cc_final: 0.8555 (m-10) REVERT: h 136 ASN cc_start: 0.8918 (t0) cc_final: 0.8434 (t0) REVERT: h 151 ASN cc_start: 0.9600 (m-40) cc_final: 0.9232 (m110) REVERT: h 186 ASP cc_start: 0.8116 (m-30) cc_final: 0.7502 (m-30) REVERT: h 194 ARG cc_start: 0.8996 (tpp80) cc_final: 0.8742 (tpp80) REVERT: h 210 ARG cc_start: 0.9146 (ttp-170) cc_final: 0.8850 (ttp80) REVERT: h 212 PHE cc_start: 0.8975 (m-10) cc_final: 0.8600 (m-80) REVERT: g 43 PHE cc_start: 0.8953 (t80) cc_final: 0.8710 (t80) REVERT: g 123 ASP cc_start: 0.8971 (m-30) cc_final: 0.8771 (p0) REVERT: g 191 GLN cc_start: 0.9008 (mp10) cc_final: 0.8805 (mp10) REVERT: g 211 ASP cc_start: 0.9184 (t0) cc_final: 0.8694 (t0) REVERT: g 215 MET cc_start: 0.8590 (mtt) cc_final: 0.8353 (ttm) REVERT: i 23 ASN cc_start: 0.8723 (m110) cc_final: 0.8459 (m-40) REVERT: i 45 GLN cc_start: 0.7958 (pp30) cc_final: 0.7685 (pp30) REVERT: i 117 LYS cc_start: 0.9354 (mmmt) cc_final: 0.9064 (mmtp) outliers start: 177 outliers final: 123 residues processed: 1548 average time/residue: 0.6527 time to fit residues: 1708.7898 Evaluate side-chains 1485 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1350 time to evaluate : 6.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 174 GLU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 72 MET Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 147 THR Chi-restraints excluded: chain S residue 228 ASP Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 161 CYS Chi-restraints excluded: chain U residue 217 VAL Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 72 LEU Chi-restraints excluded: chain W residue 136 VAL Chi-restraints excluded: chain W residue 151 SER Chi-restraints excluded: chain W residue 154 GLU Chi-restraints excluded: chain W residue 164 GLU Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 107 ARG Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 48 ASP Chi-restraints excluded: chain Z residue 159 GLN Chi-restraints excluded: chain a residue 2 GLN Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 200 GLU Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 62 GLN Chi-restraints excluded: chain b residue 93 ASP Chi-restraints excluded: chain b residue 94 LEU Chi-restraints excluded: chain k residue 16 GLN Chi-restraints excluded: chain k residue 36 LEU Chi-restraints excluded: chain k residue 40 ILE Chi-restraints excluded: chain k residue 169 SER Chi-restraints excluded: chain k residue 186 ASP Chi-restraints excluded: chain k residue 238 MET Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 50 ASN Chi-restraints excluded: chain j residue 105 ASN Chi-restraints excluded: chain j residue 144 ASP Chi-restraints excluded: chain j residue 164 HIS Chi-restraints excluded: chain j residue 183 ASP Chi-restraints excluded: chain j residue 213 ARG Chi-restraints excluded: chain j residue 218 GLU Chi-restraints excluded: chain m residue 184 VAL Chi-restraints excluded: chain p residue 118 CYS Chi-restraints excluded: chain p residue 134 ASP Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 154 CYS Chi-restraints excluded: chain G residue 159 TYR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 54 CYS Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 144 MET Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 169 SER Chi-restraints excluded: chain c residue 26 GLU Chi-restraints excluded: chain c residue 56 ASN Chi-restraints excluded: chain c residue 171 HIS Chi-restraints excluded: chain c residue 203 GLU Chi-restraints excluded: chain c residue 248 ILE Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 118 CYS Chi-restraints excluded: chain f residue 165 SER Chi-restraints excluded: chain f residue 184 VAL Chi-restraints excluded: chain f residue 185 MET Chi-restraints excluded: chain f residue 208 ASP Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain e residue 178 PHE Chi-restraints excluded: chain e residue 217 MET Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain h residue 206 VAL Chi-restraints excluded: chain g residue 213 ARG Chi-restraints excluded: chain i residue 118 CYS Chi-restraints excluded: chain i residue 208 ASP Chi-restraints excluded: chain i residue 238 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 540 optimal weight: 0.0670 chunk 348 optimal weight: 7.9990 chunk 521 optimal weight: 0.0770 chunk 263 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 chunk 555 optimal weight: 6.9990 chunk 594 optimal weight: 0.6980 chunk 431 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 686 optimal weight: 10.0000 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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** T 63 ASN U 150 GLN 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** Y 151 GLN ** Z 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 188 GLN k 136 ASN m 126 GLN ** l 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 GLN n 138 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN E 68 ASN ** J 55 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** N 123 GLN c 138 GLN f 161 GLN e 138 GLN g 233 ASN ** i 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 71082 Z= 0.172 Angle : 0.588 13.717 96452 Z= 0.309 Chirality : 0.042 0.276 11222 Planarity : 0.004 0.061 12306 Dihedral : 4.194 45.955 10044 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.47 % Allowed : 18.08 % Favored : 79.46 % 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: 1.89 (0.09), residues: 9128 helix: 2.48 (0.07), residues: 4494 sheet: 0.27 (0.13), residues: 1502 loop : -0.00 (0.11), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP U 189 HIS 0.003 0.000 HIS k 192 PHE 0.030 0.001 PHE n 170 TYR 0.033 0.001 TYR Q 110 ARG 0.011 0.000 ARG A 176 *********************** 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 1635 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1464 time to evaluate : 6.156 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: O 7 PHE cc_start: 0.9056 (m-80) cc_final: 0.8809 (m-80) REVERT: O 162 MET cc_start: 0.8349 (mtm) cc_final: 0.7923 (mtm) REVERT: O 174 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8063 (tp30) REVERT: P 25 MET cc_start: 0.9043 (mtt) cc_final: 0.8748 (mtp) REVERT: P 26 GLU cc_start: 0.8584 (tp30) cc_final: 0.8247 (tp30) REVERT: P 108 GLU cc_start: 0.7991 (tp30) cc_final: 0.7785 (tp30) REVERT: P 174 MET cc_start: 0.8651 (mtp) cc_final: 0.8410 (ttm) REVERT: P 178 ASP cc_start: 0.8316 (m-30) cc_final: 0.7925 (m-30) REVERT: Q 116 GLN cc_start: 0.8716 (tt0) cc_final: 0.8440 (tt0) REVERT: R 5 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7114 (tpt90) REVERT: R 86 LYS cc_start: 0.8989 (mttm) cc_final: 0.8661 (ptpp) REVERT: R 104 ASN cc_start: 0.9345 (t0) cc_final: 0.9062 (t0) REVERT: S 9 ASP cc_start: 0.8469 (t70) cc_final: 0.8104 (t70) REVERT: S 90 GLN cc_start: 0.8426 (tp-100) cc_final: 0.6715 (tp40) REVERT: S 94 ASP cc_start: 0.8050 (m-30) cc_final: 0.7220 (m-30) REVERT: S 100 ASP cc_start: 0.9070 (t0) cc_final: 0.8454 (t0) REVERT: S 137 TYR cc_start: 0.8741 (t80) cc_final: 0.7985 (t80) REVERT: S 178 GLU cc_start: 0.8584 (pm20) cc_final: 0.8216 (pm20) REVERT: S 179 PHE cc_start: 0.8644 (m-10) cc_final: 0.8139 (m-80) REVERT: T 27 MET cc_start: 0.8718 (mmm) cc_final: 0.8508 (mmm) REVERT: U 53 GLN cc_start: 0.8119 (mt0) cc_final: 0.7836 (mt0) REVERT: U 83 MET cc_start: 0.8275 (mtt) cc_final: 0.8030 (mtt) REVERT: U 86 ASP cc_start: 0.8417 (m-30) cc_final: 0.8166 (m-30) REVERT: U 125 TYR cc_start: 0.8571 (m-80) cc_final: 0.8031 (m-80) REVERT: U 131 MET cc_start: 0.7464 (ttp) cc_final: 0.6892 (ttm) REVERT: U 216 GLU cc_start: 0.7164 (mp0) cc_final: 0.6936 (mp0) REVERT: V 80 ASN cc_start: 0.8659 (t0) cc_final: 0.8211 (t0) REVERT: V 111 TYR cc_start: 0.8875 (m-80) cc_final: 0.8617 (m-10) REVERT: W 57 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8140 (t) REVERT: W 145 MET cc_start: 0.8231 (mtp) cc_final: 0.7949 (mtm) REVERT: W 192 ASP cc_start: 0.8678 (p0) cc_final: 0.8441 (p0) REVERT: X 18 ASP cc_start: 0.7473 (p0) cc_final: 0.7176 (p0) REVERT: X 27 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8071 (tm-30) REVERT: X 37 LYS cc_start: 0.8818 (ptmt) cc_final: 0.8445 (tttp) REVERT: X 69 MET cc_start: 0.8694 (mmm) cc_final: 0.8176 (mmm) REVERT: X 108 ASP cc_start: 0.7865 (p0) cc_final: 0.5970 (p0) REVERT: X 144 ASP cc_start: 0.8418 (m-30) cc_final: 0.8201 (m-30) REVERT: Y 67 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8663 (tm-30) REVERT: Y 107 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7861 (mpp80) REVERT: Z 75 TYR cc_start: 0.8629 (t80) cc_final: 0.8416 (t80) REVERT: Z 186 ASP cc_start: 0.8617 (t0) cc_final: 0.8270 (t0) REVERT: a 2 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8208 (mp10) REVERT: a 96 MET cc_start: 0.8825 (mmm) cc_final: 0.8338 (mmm) REVERT: a 103 MET cc_start: 0.8897 (mmm) cc_final: 0.8695 (mmt) REVERT: a 104 ASN cc_start: 0.8943 (t0) cc_final: 0.8538 (t0) REVERT: a 110 MET cc_start: 0.8073 (mtm) cc_final: 0.7850 (mtm) REVERT: k 26 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8243 (tm-30) REVERT: k 44 ASN cc_start: 0.8923 (p0) cc_final: 0.8634 (p0) REVERT: k 208 ASP cc_start: 0.9007 (m-30) cc_final: 0.8694 (m-30) REVERT: k 217 TYR cc_start: 0.9148 (t80) cc_final: 0.8492 (t80) REVERT: j 11 GLN cc_start: 0.8887 (tm130) cc_final: 0.8631 (tp40) REVERT: j 15 ASP cc_start: 0.8584 (m-30) cc_final: 0.8273 (m-30) REVERT: j 123 ASP cc_start: 0.8470 (m-30) cc_final: 0.8030 (m-30) REVERT: j 132 THR cc_start: 0.9134 (m) cc_final: 0.8728 (m) REVERT: j 146 ASN cc_start: 0.8638 (t0) cc_final: 0.8046 (t0) REVERT: j 170 PHE cc_start: 0.8749 (m-10) cc_final: 0.8538 (m-80) REVERT: j 180 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8346 (mp0) REVERT: j 199 GLN cc_start: 0.9165 (tp40) cc_final: 0.8608 (tp-100) REVERT: j 202 HIS cc_start: 0.8560 (m90) cc_final: 0.8283 (m-70) REVERT: j 203 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8295 (mm-30) REVERT: j 210 ARG cc_start: 0.8310 (mtm-85) cc_final: 0.8055 (mtm-85) REVERT: j 213 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8072 (ttm-80) REVERT: j 227 TYR cc_start: 0.9270 (t80) cc_final: 0.8901 (t80) REVERT: j 228 ASP cc_start: 0.9285 (t70) cc_final: 0.8827 (t0) REVERT: m 48 GLN cc_start: 0.9024 (pt0) cc_final: 0.8740 (pt0) REVERT: m 203 ARG cc_start: 0.9102 (ttm-80) cc_final: 0.8852 (ttm-80) REVERT: l 157 PHE cc_start: 0.8244 (m-80) cc_final: 0.7857 (m-80) REVERT: l 215 MET cc_start: 0.8913 (mtm) cc_final: 0.8635 (mtp) REVERT: l 247 MET cc_start: 0.7514 (tpp) cc_final: 0.7274 (tpp) REVERT: o 19 VAL cc_start: 0.9256 (m) cc_final: 0.8878 (p) REVERT: o 21 ARG cc_start: 0.9225 (mtp-110) cc_final: 0.8932 (mtp85) REVERT: o 23 ASN cc_start: 0.8859 (m110) cc_final: 0.8274 (m110) REVERT: o 42 TYR cc_start: 0.8750 (t80) cc_final: 0.8325 (t80) REVERT: o 126 GLN cc_start: 0.9233 (mt0) cc_final: 0.8962 (mt0) REVERT: n 43 PHE cc_start: 0.8960 (t80) cc_final: 0.8160 (t80) REVERT: n 116 ARG cc_start: 0.8843 (ttt180) cc_final: 0.8090 (ttt180) REVERT: n 129 ASN cc_start: 0.9282 (m110) cc_final: 0.9009 (m-40) REVERT: n 146 ASN cc_start: 0.8095 (t0) cc_final: 0.7683 (t0) REVERT: n 180 GLU cc_start: 0.9060 (tp30) cc_final: 0.8074 (tp30) REVERT: n 183 ASP cc_start: 0.8966 (m-30) cc_final: 0.8708 (p0) REVERT: n 199 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8468 (tm-30) REVERT: n 211 ASP cc_start: 0.8387 (t0) cc_final: 0.8044 (t0) REVERT: n 217 MET cc_start: 0.8933 (tpp) cc_final: 0.8518 (mmm) REVERT: n 218 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8501 (tp30) REVERT: n 221 ASN cc_start: 0.9120 (m-40) cc_final: 0.8772 (m110) REVERT: p 97 ASN cc_start: 0.8293 (t0) cc_final: 0.7981 (t0) REVERT: p 185 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7974 (mpp) REVERT: A 7 PHE cc_start: 0.9086 (m-80) cc_final: 0.8843 (m-80) REVERT: A 142 ARG cc_start: 0.8381 (ptm-80) cc_final: 0.8013 (ptm160) REVERT: A 187 ILE cc_start: 0.8945 (pt) cc_final: 0.8697 (mt) REVERT: B 6 ASP cc_start: 0.7922 (p0) cc_final: 0.7546 (p0) REVERT: B 30 HIS cc_start: 0.8369 (m-70) cc_final: 0.8092 (m-70) REVERT: B 50 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7891 (mtm-85) REVERT: B 64 LYS cc_start: 0.8907 (mtpt) cc_final: 0.8695 (mttt) REVERT: B 67 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8346 (tttp) REVERT: B 108 GLU cc_start: 0.8444 (tp30) cc_final: 0.7809 (tp30) REVERT: B 160 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8416 (mppt) REVERT: C 3 TYR cc_start: 0.9199 (m-80) cc_final: 0.8858 (m-10) REVERT: C 23 GLN cc_start: 0.9000 (mt0) cc_final: 0.8733 (mt0) REVERT: C 90 GLU cc_start: 0.8090 (tp30) cc_final: 0.7695 (tp30) REVERT: C 105 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7792 (tm-30) REVERT: D 52 LYS cc_start: 0.9114 (mmtp) cc_final: 0.8483 (mmtp) REVERT: D 216 GLU cc_start: 0.7481 (tt0) cc_final: 0.7011 (mt-10) REVERT: E 14 SER cc_start: 0.8627 (t) cc_final: 0.8266 (p) REVERT: E 27 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: E 50 LYS cc_start: 0.8998 (mtmt) cc_final: 0.8764 (mtmm) REVERT: E 91 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8324 (mm-30) REVERT: E 100 ASP cc_start: 0.8842 (t0) cc_final: 0.8270 (t0) REVERT: E 146 GLN cc_start: 0.8123 (tt0) cc_final: 0.7816 (tm-30) REVERT: F 13 THR cc_start: 0.9326 (m) cc_final: 0.9001 (p) REVERT: G 22 LEU cc_start: 0.8396 (mt) cc_final: 0.7848 (mp) REVERT: G 26 GLU cc_start: 0.8747 (mp0) cc_final: 0.8434 (mp0) REVERT: G 159 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.7103 (t80) REVERT: H 124 TYR cc_start: 0.8704 (p90) cc_final: 0.7874 (p90) REVERT: H 157 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8410 (mm-30) REVERT: H 202 TYR cc_start: 0.7133 (m-80) cc_final: 0.6900 (m-80) REVERT: H 214 GLU cc_start: 0.8509 (tp30) cc_final: 0.8195 (tp30) REVERT: I 33 MET cc_start: 0.8589 (tmm) cc_final: 0.8248 (ttp) REVERT: I 58 ASP cc_start: 0.8486 (m-30) cc_final: 0.8106 (t0) REVERT: I 65 ARG cc_start: 0.8456 (mtp85) cc_final: 0.8004 (mtp85) REVERT: I 73 TYR cc_start: 0.8633 (t80) cc_final: 0.8312 (t80) REVERT: I 95 TYR cc_start: 0.9299 (t80) cc_final: 0.9042 (t80) REVERT: I 143 GLU cc_start: 0.8524 (mp0) cc_final: 0.8172 (mp0) REVERT: I 153 TRP cc_start: 0.9164 (t60) cc_final: 0.8793 (t60) REVERT: I 182 MET cc_start: 0.8402 (mmm) cc_final: 0.8001 (mmm) REVERT: I 197 ARG cc_start: 0.8246 (mtt90) cc_final: 0.7560 (mtt90) REVERT: I 203 MET cc_start: 0.8072 (mmp) cc_final: 0.7556 (mmp) REVERT: J 27 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7759 (tm-30) REVERT: J 31 ASP cc_start: 0.8509 (p0) cc_final: 0.8235 (p0) REVERT: J 36 PHE cc_start: 0.8617 (m-80) cc_final: 0.8412 (m-80) REVERT: J 38 MET cc_start: 0.8478 (mmm) cc_final: 0.7911 (mmm) REVERT: J 68 LYS cc_start: 0.9338 (tttp) cc_final: 0.8865 (tppt) REVERT: K 119 ASN cc_start: 0.8904 (OUTLIER) cc_final: 0.8300 (m110) REVERT: L 159 GLN cc_start: 0.8588 (tt0) cc_final: 0.8369 (tt0) REVERT: L 184 GLU cc_start: 0.8391 (tp30) cc_final: 0.8048 (tp30) REVERT: M 26 MET cc_start: 0.7872 (mtp) cc_final: 0.7548 (mtm) REVERT: M 47 ASN cc_start: 0.8830 (t0) cc_final: 0.8513 (t0) REVERT: M 96 MET cc_start: 0.8643 (mmm) cc_final: 0.7650 (mtp) REVERT: M 127 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8245 (ttp) REVERT: M 133 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8204 (mt-10) REVERT: N 28 ASN cc_start: 0.8445 (t0) cc_final: 0.8242 (t0) REVERT: d 42 TYR cc_start: 0.9099 (t80) cc_final: 0.8743 (t80) REVERT: d 208 ASP cc_start: 0.8783 (m-30) cc_final: 0.8463 (m-30) REVERT: c 11 GLN cc_start: 0.8554 (pp30) cc_final: 0.7772 (tm-30) REVERT: c 46 GLU cc_start: 0.8893 (pt0) cc_final: 0.8642 (pm20) REVERT: c 115 GLN cc_start: 0.9259 (tt0) cc_final: 0.9002 (tm-30) REVERT: c 123 ASP cc_start: 0.8712 (m-30) cc_final: 0.8355 (m-30) REVERT: c 133 THR cc_start: 0.9626 (m) cc_final: 0.9388 (p) REVERT: c 186 THR cc_start: 0.9422 (m) cc_final: 0.9141 (p) REVERT: c 199 GLN cc_start: 0.8841 (tp40) cc_final: 0.8362 (tp-100) REVERT: c 215 MET cc_start: 0.9046 (mmm) cc_final: 0.8766 (mmt) REVERT: c 217 MET cc_start: 0.9138 (ttp) cc_final: 0.8888 (ttm) REVERT: c 221 ASN cc_start: 0.9199 (m-40) cc_final: 0.8985 (m-40) REVERT: f 22 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8471 (mt0) REVERT: f 97 ASN cc_start: 0.8246 (t0) cc_final: 0.7895 (t0) REVERT: f 136 ASN cc_start: 0.8446 (t0) cc_final: 0.7790 (t0) REVERT: f 229 ASN cc_start: 0.8935 (t0) cc_final: 0.8657 (t0) REVERT: e 211 ASP cc_start: 0.9173 (m-30) cc_final: 0.8703 (m-30) REVERT: h 25 PHE cc_start: 0.8938 (m-10) cc_final: 0.8543 (m-10) REVERT: h 26 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8747 (mm-40) REVERT: h 33 TYR cc_start: 0.8999 (m-80) cc_final: 0.8447 (m-80) REVERT: h 136 ASN cc_start: 0.8921 (t0) cc_final: 0.8462 (t0) REVERT: h 151 ASN cc_start: 0.9591 (m-40) cc_final: 0.9225 (m110) REVERT: h 186 ASP cc_start: 0.8205 (m-30) cc_final: 0.7836 (t0) REVERT: h 194 ARG cc_start: 0.8949 (tpp80) cc_final: 0.8722 (tpp80) REVERT: h 210 ARG cc_start: 0.9113 (ttp-170) cc_final: 0.8825 (ttp80) REVERT: h 212 PHE cc_start: 0.8981 (m-10) cc_final: 0.8609 (m-80) REVERT: g 191 GLN cc_start: 0.8958 (mp10) cc_final: 0.8683 (mp10) REVERT: g 211 ASP cc_start: 0.9176 (t0) cc_final: 0.8831 (t0) REVERT: i 23 ASN cc_start: 0.8719 (m110) cc_final: 0.8475 (m-40) REVERT: i 117 LYS cc_start: 0.9291 (mmmt) cc_final: 0.9025 (mmtp) REVERT: i 145 LYS cc_start: 0.9421 (tppp) cc_final: 0.9177 (tppt) outliers start: 171 outliers final: 126 residues processed: 1559 average time/residue: 0.6973 time to fit residues: 1847.9555 Evaluate side-chains 1505 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1367 time to evaluate : 6.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 174 GLU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 72 MET Chi-restraints excluded: chain Q residue 7 ILE Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 147 THR Chi-restraints excluded: chain S residue 228 ASP Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 217 VAL Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 72 LEU Chi-restraints excluded: chain W residue 92 ASN Chi-restraints excluded: chain W residue 136 VAL Chi-restraints excluded: chain W residue 151 SER Chi-restraints excluded: chain W residue 154 GLU Chi-restraints excluded: chain W residue 164 GLU Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 107 ARG Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 48 ASP Chi-restraints excluded: chain Z residue 159 GLN Chi-restraints excluded: chain a residue 2 GLN Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 200 GLU Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 93 ASP Chi-restraints excluded: chain b residue 94 LEU Chi-restraints excluded: chain k residue 16 GLN Chi-restraints excluded: chain k residue 36 LEU Chi-restraints excluded: chain k residue 40 ILE Chi-restraints excluded: chain k residue 169 SER Chi-restraints excluded: chain k residue 186 ASP Chi-restraints excluded: chain k residue 238 MET Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 50 ASN Chi-restraints excluded: chain j residue 105 ASN Chi-restraints excluded: chain j residue 144 ASP Chi-restraints excluded: chain j residue 164 HIS Chi-restraints excluded: chain j residue 213 ARG Chi-restraints excluded: chain m residue 184 VAL Chi-restraints excluded: chain p residue 118 CYS Chi-restraints excluded: chain p residue 125 ILE Chi-restraints excluded: chain p residue 134 ASP Chi-restraints excluded: chain p residue 185 MET Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 133 CYS Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 154 CYS Chi-restraints excluded: chain G residue 159 TYR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 54 CYS Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 144 MET Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 134 ASP Chi-restraints excluded: chain d residue 169 SER Chi-restraints excluded: chain c residue 26 GLU Chi-restraints excluded: chain c residue 56 ASN Chi-restraints excluded: chain c residue 171 HIS Chi-restraints excluded: chain c residue 203 GLU Chi-restraints excluded: chain c residue 248 ILE Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 118 CYS Chi-restraints excluded: chain f residue 127 HIS Chi-restraints excluded: chain f residue 165 SER Chi-restraints excluded: chain f residue 184 VAL Chi-restraints excluded: chain f residue 185 MET Chi-restraints excluded: chain f residue 208 ASP Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain e residue 178 PHE Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain h residue 206 VAL Chi-restraints excluded: chain g residue 121 ILE Chi-restraints excluded: chain g residue 213 ARG Chi-restraints excluded: chain i residue 118 CYS Chi-restraints excluded: chain i residue 208 ASP Chi-restraints excluded: chain i residue 238 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 794 optimal weight: 0.9980 chunk 836 optimal weight: 5.9990 chunk 763 optimal weight: 6.9990 chunk 813 optimal weight: 0.9990 chunk 489 optimal weight: 7.9990 chunk 354 optimal weight: 9.9990 chunk 638 optimal weight: 9.9990 chunk 249 optimal weight: 8.9990 chunk 735 optimal weight: 1.9990 chunk 769 optimal weight: 6.9990 chunk 810 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN 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** Z 152 GLN Z 157 ASN b 123 GLN k 136 ASN ** j 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 173 GLN ** 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 147 ASN ** p 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN ** A 101 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** K 38 ASN L 77 HIS L 80 ASN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 126 GLN d 161 GLN f 26 GLN e 146 ASN ** i 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 71082 Z= 0.273 Angle : 0.626 13.210 96452 Z= 0.329 Chirality : 0.043 0.364 11222 Planarity : 0.004 0.064 12306 Dihedral : 4.266 46.411 10044 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.49 % Allowed : 18.57 % Favored : 78.94 % Cbeta Deviations : 0.01 % 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: 1.83 (0.09), residues: 9128 helix: 2.43 (0.07), residues: 4500 sheet: 0.20 (0.13), residues: 1510 loop : -0.01 (0.11), residues: 3118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP U 189 HIS 0.004 0.001 HIS k 192 PHE 0.037 0.001 PHE n 170 TYR 0.037 0.001 TYR U 160 ARG 0.009 0.001 ARG P 8 *********************** 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 1520 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1347 time to evaluate : 6.154 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: O 7 PHE cc_start: 0.9118 (m-80) cc_final: 0.8888 (m-80) REVERT: O 174 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: O 206 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8282 (p0) REVERT: P 25 MET cc_start: 0.9015 (mtt) cc_final: 0.8678 (mtp) REVERT: P 26 GLU cc_start: 0.8646 (tp30) cc_final: 0.8327 (tp30) REVERT: P 108 GLU cc_start: 0.8153 (tp30) cc_final: 0.7927 (tp30) REVERT: P 174 MET cc_start: 0.8667 (mtp) cc_final: 0.8358 (ttm) REVERT: P 178 ASP cc_start: 0.8368 (m-30) cc_final: 0.7952 (m-30) REVERT: Q 116 GLN cc_start: 0.8814 (tt0) cc_final: 0.8563 (tt0) REVERT: R 5 ARG cc_start: 0.7967 (ttp80) cc_final: 0.7706 (ttp80) REVERT: R 86 LYS cc_start: 0.9036 (mttm) cc_final: 0.8703 (ptpp) REVERT: R 104 ASN cc_start: 0.9345 (t0) cc_final: 0.9067 (t0) REVERT: S 9 ASP cc_start: 0.8567 (t70) cc_final: 0.8174 (t70) REVERT: S 90 GLN cc_start: 0.8555 (tp-100) cc_final: 0.7049 (tp40) REVERT: S 94 ASP cc_start: 0.8168 (m-30) cc_final: 0.7074 (m-30) REVERT: S 100 ASP cc_start: 0.9095 (t0) cc_final: 0.8485 (t0) REVERT: S 137 TYR cc_start: 0.8873 (t80) cc_final: 0.7986 (t80) REVERT: S 178 GLU cc_start: 0.8667 (pm20) cc_final: 0.8295 (pm20) REVERT: S 179 PHE cc_start: 0.8734 (m-10) cc_final: 0.8232 (m-80) REVERT: T 27 MET cc_start: 0.8762 (mmm) cc_final: 0.8526 (mmm) REVERT: U 53 GLN cc_start: 0.8145 (mt0) cc_final: 0.7837 (mt0) REVERT: U 83 MET cc_start: 0.8321 (mtt) cc_final: 0.8097 (mtt) REVERT: U 86 ASP cc_start: 0.8500 (m-30) cc_final: 0.8284 (m-30) REVERT: U 125 TYR cc_start: 0.8630 (m-80) cc_final: 0.8136 (m-80) REVERT: U 216 GLU cc_start: 0.7137 (mp0) cc_final: 0.6809 (mp0) REVERT: V 8 TYR cc_start: 0.8745 (p90) cc_final: 0.8472 (p90) REVERT: W 57 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8468 (p) REVERT: W 145 MET cc_start: 0.8302 (mtp) cc_final: 0.7975 (mtm) REVERT: X 18 ASP cc_start: 0.7709 (p0) cc_final: 0.7373 (p0) REVERT: X 27 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8156 (tm-30) REVERT: X 37 LYS cc_start: 0.8887 (ptmt) cc_final: 0.8518 (tttp) REVERT: X 58 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8477 (mm-30) REVERT: X 69 MET cc_start: 0.8729 (mmm) cc_final: 0.8222 (mmm) REVERT: X 144 ASP cc_start: 0.8554 (m-30) cc_final: 0.8294 (m-30) REVERT: Y 67 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8673 (tm-30) REVERT: Y 107 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8028 (mpp80) REVERT: Z 186 ASP cc_start: 0.8760 (t0) cc_final: 0.8513 (t0) REVERT: a 2 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8209 (mp10) REVERT: a 10 SER cc_start: 0.8678 (m) cc_final: 0.8386 (p) REVERT: a 104 ASN cc_start: 0.8993 (t0) cc_final: 0.8587 (t0) REVERT: a 110 MET cc_start: 0.8093 (mtm) cc_final: 0.7882 (mtm) REVERT: k 26 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8303 (tm-30) REVERT: k 44 ASN cc_start: 0.8934 (p0) cc_final: 0.8650 (p0) REVERT: k 208 ASP cc_start: 0.9027 (m-30) cc_final: 0.8731 (m-30) REVERT: j 116 ARG cc_start: 0.8745 (mtp85) cc_final: 0.8163 (ttm110) REVERT: j 120 GLU cc_start: 0.8831 (mp0) cc_final: 0.8487 (mp0) REVERT: j 123 ASP cc_start: 0.8433 (m-30) cc_final: 0.8091 (m-30) REVERT: j 146 ASN cc_start: 0.8715 (t0) cc_final: 0.8108 (t0) REVERT: j 180 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8313 (mp0) REVERT: j 199 GLN cc_start: 0.9193 (tp40) cc_final: 0.8653 (tp-100) REVERT: j 203 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8340 (mm-30) REVERT: j 210 ARG cc_start: 0.8364 (mtm-85) cc_final: 0.7832 (mtm-85) REVERT: j 213 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8303 (ttm-80) REVERT: j 227 TYR cc_start: 0.9373 (t80) cc_final: 0.8880 (t80) REVERT: j 228 ASP cc_start: 0.9332 (t70) cc_final: 0.8805 (t0) REVERT: m 48 GLN cc_start: 0.9047 (pt0) cc_final: 0.8774 (pt0) REVERT: m 203 ARG cc_start: 0.9095 (ttm-80) cc_final: 0.8844 (ttm-80) REVERT: l 157 PHE cc_start: 0.8430 (m-80) cc_final: 0.8126 (m-80) REVERT: l 211 ASP cc_start: 0.9300 (t0) cc_final: 0.8853 (t0) REVERT: l 215 MET cc_start: 0.8955 (mtm) cc_final: 0.8641 (mtp) REVERT: l 247 MET cc_start: 0.7492 (tpp) cc_final: 0.7269 (tpp) REVERT: o 21 ARG cc_start: 0.9243 (mtp-110) cc_final: 0.8953 (mtp85) REVERT: o 42 TYR cc_start: 0.8812 (t80) cc_final: 0.8396 (t80) REVERT: o 45 GLN cc_start: 0.9048 (pt0) cc_final: 0.8832 (pt0) REVERT: o 126 GLN cc_start: 0.9231 (mt0) cc_final: 0.9004 (mt0) REVERT: n 146 ASN cc_start: 0.8153 (t0) cc_final: 0.7739 (t0) REVERT: n 180 GLU cc_start: 0.9116 (tp30) cc_final: 0.8101 (tp30) REVERT: n 183 ASP cc_start: 0.8974 (m-30) cc_final: 0.8708 (p0) REVERT: p 23 ASN cc_start: 0.9206 (m-40) cc_final: 0.8971 (m-40) REVERT: p 97 ASN cc_start: 0.8428 (t0) cc_final: 0.8137 (t0) REVERT: p 112 TRP cc_start: 0.8444 (m100) cc_final: 0.8034 (m100) REVERT: p 185 MET cc_start: 0.8190 (mmm) cc_final: 0.7969 (mpp) REVERT: A 142 ARG cc_start: 0.8384 (ptm-80) cc_final: 0.7993 (ptm160) REVERT: B 6 ASP cc_start: 0.7912 (p0) cc_final: 0.7410 (p0) REVERT: B 50 ARG cc_start: 0.8272 (mmm-85) cc_final: 0.8056 (mtm-85) REVERT: B 64 LYS cc_start: 0.8913 (mtpt) cc_final: 0.8688 (mttt) REVERT: B 67 LYS cc_start: 0.8841 (ttpt) cc_final: 0.8432 (tttp) REVERT: B 108 GLU cc_start: 0.8493 (tp30) cc_final: 0.7822 (tp30) REVERT: B 160 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8420 (mppt) REVERT: C 3 TYR cc_start: 0.9268 (m-80) cc_final: 0.9008 (m-10) REVERT: C 90 GLU cc_start: 0.8177 (tp30) cc_final: 0.7886 (tp30) REVERT: C 105 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7849 (tm-30) REVERT: D 13 ASN cc_start: 0.8580 (m-40) cc_final: 0.8342 (t0) REVERT: D 52 LYS cc_start: 0.9161 (mmtp) cc_final: 0.8459 (mmtp) REVERT: D 216 GLU cc_start: 0.7511 (tt0) cc_final: 0.7005 (mt-10) REVERT: E 14 SER cc_start: 0.8575 (t) cc_final: 0.8180 (p) REVERT: E 27 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8272 (mp0) REVERT: E 50 LYS cc_start: 0.9080 (mtmt) cc_final: 0.8830 (mtmm) REVERT: E 91 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8353 (mm-30) REVERT: E 100 ASP cc_start: 0.8872 (t0) cc_final: 0.8306 (t0) REVERT: E 128 TYR cc_start: 0.8974 (m-10) cc_final: 0.8605 (m-10) REVERT: F 13 THR cc_start: 0.9376 (m) cc_final: 0.8999 (p) REVERT: G 11 ARG cc_start: 0.8159 (mtm-85) cc_final: 0.7753 (ptp-110) REVERT: G 22 LEU cc_start: 0.8448 (mt) cc_final: 0.7860 (mp) REVERT: G 26 GLU cc_start: 0.8681 (mp0) cc_final: 0.8300 (mp0) REVERT: G 159 TYR cc_start: 0.7515 (t80) cc_final: 0.7167 (t80) REVERT: H 18 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8748 (p) REVERT: H 124 TYR cc_start: 0.8894 (p90) cc_final: 0.8051 (p90) REVERT: H 157 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8428 (mm-30) REVERT: H 202 TYR cc_start: 0.7367 (m-80) cc_final: 0.7048 (m-80) REVERT: H 214 GLU cc_start: 0.8568 (tp30) cc_final: 0.8250 (tp30) REVERT: I 33 MET cc_start: 0.8634 (tmm) cc_final: 0.8240 (ttp) REVERT: I 58 ASP cc_start: 0.8550 (m-30) cc_final: 0.8136 (t0) REVERT: I 73 TYR cc_start: 0.8836 (t80) cc_final: 0.8435 (t80) REVERT: I 95 TYR cc_start: 0.9326 (t80) cc_final: 0.9074 (t80) REVERT: I 182 MET cc_start: 0.8493 (mmm) cc_final: 0.8021 (mmm) REVERT: I 197 ARG cc_start: 0.8245 (mtt90) cc_final: 0.7497 (mtt90) REVERT: I 203 MET cc_start: 0.8223 (mmp) cc_final: 0.7748 (mmp) REVERT: J 27 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7836 (tm-30) REVERT: J 31 ASP cc_start: 0.8503 (p0) cc_final: 0.8200 (p0) REVERT: J 38 MET cc_start: 0.8567 (mmm) cc_final: 0.8165 (mmm) REVERT: J 68 LYS cc_start: 0.9362 (tttp) cc_final: 0.8912 (tppt) REVERT: K 119 ASN cc_start: 0.8887 (OUTLIER) cc_final: 0.8298 (m110) REVERT: L 146 GLN cc_start: 0.8473 (tm-30) cc_final: 0.7900 (tm-30) REVERT: L 159 GLN cc_start: 0.8620 (tt0) cc_final: 0.8375 (tt0) REVERT: L 184 GLU cc_start: 0.8482 (tp30) cc_final: 0.8122 (tp30) REVERT: M 47 ASN cc_start: 0.8908 (t0) cc_final: 0.8594 (t0) REVERT: M 96 MET cc_start: 0.8714 (mmm) cc_final: 0.7664 (mtp) REVERT: M 127 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8217 (ttp) REVERT: N 28 ASN cc_start: 0.8596 (t0) cc_final: 0.8378 (t0) REVERT: d 42 TYR cc_start: 0.9145 (t80) cc_final: 0.8821 (t80) REVERT: d 208 ASP cc_start: 0.8835 (m-30) cc_final: 0.8488 (m-30) REVERT: c 46 GLU cc_start: 0.8756 (pt0) cc_final: 0.8475 (pm20) REVERT: c 115 GLN cc_start: 0.9244 (tt0) cc_final: 0.8969 (tm-30) REVERT: c 123 ASP cc_start: 0.8739 (m-30) cc_final: 0.8358 (m-30) REVERT: c 133 THR cc_start: 0.9625 (m) cc_final: 0.9350 (p) REVERT: c 199 GLN cc_start: 0.8920 (tp40) cc_final: 0.8430 (tp-100) REVERT: c 211 ASP cc_start: 0.9203 (t0) cc_final: 0.8707 (t0) REVERT: c 215 MET cc_start: 0.9261 (mmm) cc_final: 0.8929 (mmt) REVERT: c 217 MET cc_start: 0.9121 (ttp) cc_final: 0.8834 (ttm) REVERT: c 221 ASN cc_start: 0.9219 (m-40) cc_final: 0.9002 (m-40) REVERT: f 22 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8483 (mt0) REVERT: f 97 ASN cc_start: 0.8339 (t0) cc_final: 0.7980 (t0) REVERT: f 136 ASN cc_start: 0.8469 (t0) cc_final: 0.7956 (t0) REVERT: f 229 ASN cc_start: 0.8961 (t0) cc_final: 0.8678 (t0) REVERT: e 211 ASP cc_start: 0.9210 (m-30) cc_final: 0.8766 (m-30) REVERT: h 26 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8758 (mm-40) REVERT: h 136 ASN cc_start: 0.8929 (t0) cc_final: 0.8456 (t0) REVERT: h 151 ASN cc_start: 0.9592 (m-40) cc_final: 0.9213 (m110) REVERT: h 186 ASP cc_start: 0.8110 (m-30) cc_final: 0.7463 (m-30) REVERT: h 194 ARG cc_start: 0.9005 (tpp80) cc_final: 0.8747 (tpp80) REVERT: h 210 ARG cc_start: 0.9151 (ttp-170) cc_final: 0.8860 (ttp80) REVERT: h 212 PHE cc_start: 0.8966 (m-10) cc_final: 0.8627 (m-80) REVERT: g 123 ASP cc_start: 0.9029 (m-30) cc_final: 0.8759 (p0) REVERT: g 171 HIS cc_start: 0.8259 (OUTLIER) cc_final: 0.7957 (t-170) REVERT: g 180 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8369 (mp0) REVERT: i 117 LYS cc_start: 0.9321 (mmmt) cc_final: 0.9068 (mmtp) REVERT: i 145 LYS cc_start: 0.9393 (tppp) cc_final: 0.9131 (tppt) REVERT: i 149 ARG cc_start: 0.8858 (tpp-160) cc_final: 0.8440 (tpp-160) outliers start: 173 outliers final: 141 residues processed: 1452 average time/residue: 0.6564 time to fit residues: 1607.3001 Evaluate side-chains 1459 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1305 time to evaluate : 6.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 174 GLU Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 72 MET Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 82 ILE Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain Q residue 148 ASP Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 106 SER Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 147 THR Chi-restraints excluded: chain S residue 228 ASP Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 161 CYS Chi-restraints excluded: chain U residue 217 VAL Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 72 LEU Chi-restraints excluded: chain W residue 92 ASN Chi-restraints excluded: chain W residue 136 VAL Chi-restraints excluded: chain W residue 151 SER Chi-restraints excluded: chain W residue 154 GLU Chi-restraints excluded: chain W residue 164 GLU Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 107 ARG Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 48 ASP Chi-restraints excluded: chain Z residue 159 GLN Chi-restraints excluded: chain a residue 2 GLN Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 133 GLU Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 200 GLU Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 93 ASP Chi-restraints excluded: chain b residue 94 LEU Chi-restraints excluded: chain b residue 123 GLN Chi-restraints excluded: chain k residue 16 GLN Chi-restraints excluded: chain k residue 36 LEU Chi-restraints excluded: chain k residue 40 ILE Chi-restraints excluded: chain k residue 169 SER Chi-restraints excluded: chain k residue 186 ASP Chi-restraints excluded: chain k residue 238 MET Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 50 ASN Chi-restraints excluded: chain j residue 105 ASN Chi-restraints excluded: chain j residue 144 ASP Chi-restraints excluded: chain j residue 164 HIS Chi-restraints excluded: chain j residue 213 ARG Chi-restraints excluded: chain m residue 184 VAL Chi-restraints excluded: chain n residue 162 SER Chi-restraints excluded: chain p residue 118 CYS Chi-restraints excluded: chain p residue 125 ILE Chi-restraints excluded: chain p residue 134 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 133 CYS Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 154 CYS Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 54 CYS Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 144 MET Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 134 ASP Chi-restraints excluded: chain d residue 169 SER Chi-restraints excluded: chain c residue 26 GLU Chi-restraints excluded: chain c residue 56 ASN Chi-restraints excluded: chain c residue 203 GLU Chi-restraints excluded: chain c residue 248 ILE Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 118 CYS Chi-restraints excluded: chain f residue 165 SER Chi-restraints excluded: chain f residue 184 VAL Chi-restraints excluded: chain f residue 185 MET Chi-restraints excluded: chain f residue 208 ASP Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain e residue 178 PHE Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain h residue 206 VAL Chi-restraints excluded: chain g residue 121 ILE Chi-restraints excluded: chain g residue 171 HIS Chi-restraints excluded: chain g residue 213 ARG Chi-restraints excluded: chain i residue 118 CYS Chi-restraints excluded: chain i residue 134 ASP Chi-restraints excluded: chain i residue 238 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 534 optimal weight: 6.9990 chunk 860 optimal weight: 5.9990 chunk 525 optimal weight: 0.8980 chunk 408 optimal weight: 0.7980 chunk 598 optimal weight: 6.9990 chunk 902 optimal weight: 6.9990 chunk 830 optimal weight: 3.9990 chunk 718 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 555 optimal weight: 5.9990 chunk 440 optimal weight: 0.7980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** l 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 147 ASN ** p 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN E 146 GLN I 168 GLN J 55 GLN J 61 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 ASN ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 126 GLN ** c 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 161 GLN i 151 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 71082 Z= 0.221 Angle : 0.629 11.831 96452 Z= 0.331 Chirality : 0.043 0.326 11222 Planarity : 0.004 0.063 12306 Dihedral : 4.272 46.198 10044 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.31 % Allowed : 19.19 % Favored : 78.50 % 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: 1.79 (0.09), residues: 9128 helix: 2.40 (0.07), residues: 4502 sheet: 0.19 (0.13), residues: 1504 loop : -0.05 (0.11), residues: 3122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP U 189 HIS 0.004 0.001 HIS n 164 PHE 0.029 0.001 PHE Y 126 TYR 0.043 0.001 TYR Q 110 ARG 0.014 0.001 ARG n 213 ********************** 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 1526 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1366 time to evaluate : 6.164 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: O 7 PHE cc_start: 0.9100 (m-80) cc_final: 0.8888 (m-80) REVERT: O 162 MET cc_start: 0.8226 (mtm) cc_final: 0.7967 (mtm) REVERT: O 174 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7894 (tp30) REVERT: P 15 GLU cc_start: 0.8632 (pm20) cc_final: 0.8384 (pm20) REVERT: P 25 MET cc_start: 0.8993 (mtt) cc_final: 0.8653 (mtp) REVERT: P 26 GLU cc_start: 0.8611 (tp30) cc_final: 0.8287 (tp30) REVERT: P 178 ASP cc_start: 0.8387 (m-30) cc_final: 0.8061 (m-30) REVERT: Q 116 GLN cc_start: 0.8821 (tt0) cc_final: 0.8524 (tt0) REVERT: R 86 LYS cc_start: 0.8989 (mttm) cc_final: 0.8749 (ptpp) REVERT: R 104 ASN cc_start: 0.9330 (t0) cc_final: 0.9071 (t0) REVERT: S 9 ASP cc_start: 0.8496 (t70) cc_final: 0.8105 (t70) REVERT: S 90 GLN cc_start: 0.8475 (tp-100) cc_final: 0.6981 (tp40) REVERT: S 94 ASP cc_start: 0.8156 (m-30) cc_final: 0.7065 (m-30) REVERT: S 100 ASP cc_start: 0.9103 (t0) cc_final: 0.8478 (t0) REVERT: S 137 TYR cc_start: 0.8870 (t80) cc_final: 0.8053 (t80) REVERT: S 178 GLU cc_start: 0.8629 (pm20) cc_final: 0.8275 (pm20) REVERT: S 179 PHE cc_start: 0.8694 (m-10) cc_final: 0.8201 (m-80) REVERT: T 27 MET cc_start: 0.8757 (mmm) cc_final: 0.8522 (mmm) REVERT: U 53 GLN cc_start: 0.8115 (mt0) cc_final: 0.7789 (mt0) REVERT: U 83 MET cc_start: 0.8291 (mtt) cc_final: 0.8063 (mtt) REVERT: U 86 ASP cc_start: 0.8462 (m-30) cc_final: 0.8238 (m-30) REVERT: U 125 TYR cc_start: 0.8608 (m-80) cc_final: 0.8128 (m-80) REVERT: U 216 GLU cc_start: 0.7145 (mp0) cc_final: 0.6837 (mp0) REVERT: V 8 TYR cc_start: 0.8715 (p90) cc_final: 0.8441 (p90) REVERT: V 80 ASN cc_start: 0.8684 (t0) cc_final: 0.8284 (t0) REVERT: V 111 TYR cc_start: 0.8963 (m-80) cc_final: 0.8622 (m-10) REVERT: V 198 ARG cc_start: 0.8412 (ttm110) cc_final: 0.8038 (ttm170) REVERT: W 33 MET cc_start: 0.8593 (tmm) cc_final: 0.8361 (tmm) REVERT: W 57 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8488 (p) REVERT: W 145 MET cc_start: 0.8260 (mtp) cc_final: 0.7960 (mtm) REVERT: X 18 ASP cc_start: 0.7667 (p0) cc_final: 0.7345 (p0) REVERT: X 27 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8087 (tm-30) REVERT: X 37 LYS cc_start: 0.8869 (ptmt) cc_final: 0.8564 (tttp) REVERT: X 58 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8486 (mm-30) REVERT: X 69 MET cc_start: 0.8717 (mmm) cc_final: 0.8209 (mmm) REVERT: X 144 ASP cc_start: 0.8519 (m-30) cc_final: 0.8241 (m-30) REVERT: Y 67 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8688 (tm-30) REVERT: Y 107 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8006 (mpp80) REVERT: Z 169 ASP cc_start: 0.8625 (p0) cc_final: 0.8418 (p0) REVERT: Z 186 ASP cc_start: 0.8668 (t0) cc_final: 0.8395 (t0) REVERT: a 2 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8229 (mp10) REVERT: a 10 SER cc_start: 0.8608 (m) cc_final: 0.8332 (p) REVERT: a 96 MET cc_start: 0.8763 (mmm) cc_final: 0.8216 (mtt) REVERT: a 104 ASN cc_start: 0.8972 (t0) cc_final: 0.8569 (t0) REVERT: a 110 MET cc_start: 0.8099 (mtm) cc_final: 0.6920 (mtm) REVERT: k 26 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8294 (tm-30) REVERT: k 44 ASN cc_start: 0.8871 (p0) cc_final: 0.8571 (p0) REVERT: k 208 ASP cc_start: 0.9020 (m-30) cc_final: 0.8718 (m-30) REVERT: j 11 GLN cc_start: 0.8824 (tp40) cc_final: 0.8175 (tp-100) REVERT: j 116 ARG cc_start: 0.8737 (mtp85) cc_final: 0.8294 (ttm110) REVERT: j 123 ASP cc_start: 0.8423 (m-30) cc_final: 0.8065 (m-30) REVERT: j 132 THR cc_start: 0.9078 (m) cc_final: 0.8741 (m) REVERT: j 146 ASN cc_start: 0.8706 (t0) cc_final: 0.8096 (t0) REVERT: j 180 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8567 (mp0) REVERT: j 199 GLN cc_start: 0.9217 (tp40) cc_final: 0.8693 (tp-100) REVERT: j 203 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8305 (mm-30) REVERT: j 210 ARG cc_start: 0.8346 (mtm-85) cc_final: 0.8052 (mtm-85) REVERT: j 213 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7974 (ttm-80) REVERT: j 227 TYR cc_start: 0.9357 (t80) cc_final: 0.8861 (t80) REVERT: j 228 ASP cc_start: 0.9319 (t70) cc_final: 0.8797 (t0) REVERT: m 48 GLN cc_start: 0.9066 (pt0) cc_final: 0.8787 (pt0) REVERT: m 203 ARG cc_start: 0.9065 (ttm-80) cc_final: 0.8805 (ttm-80) REVERT: l 127 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8462 (mm-40) REVERT: l 157 PHE cc_start: 0.8351 (m-80) cc_final: 0.8063 (m-80) REVERT: l 247 MET cc_start: 0.7507 (tpp) cc_final: 0.7286 (tpp) REVERT: o 21 ARG cc_start: 0.9222 (mtp-110) cc_final: 0.8930 (mtp85) REVERT: o 23 ASN cc_start: 0.8437 (m110) cc_final: 0.8203 (m110) REVERT: o 42 TYR cc_start: 0.8879 (t80) cc_final: 0.8514 (t80) REVERT: o 126 GLN cc_start: 0.9227 (mt0) cc_final: 0.8993 (mt0) REVERT: n 146 ASN cc_start: 0.8112 (t0) cc_final: 0.7704 (t0) REVERT: n 180 GLU cc_start: 0.9114 (tp30) cc_final: 0.8100 (tp30) REVERT: n 183 ASP cc_start: 0.8964 (m-30) cc_final: 0.8758 (p0) REVERT: n 211 ASP cc_start: 0.8348 (t0) cc_final: 0.8079 (t0) REVERT: n 217 MET cc_start: 0.8935 (tpp) cc_final: 0.8621 (mmm) REVERT: p 97 ASN cc_start: 0.8414 (t0) cc_final: 0.8128 (t0) REVERT: p 185 MET cc_start: 0.8177 (mmm) cc_final: 0.7929 (mpp) REVERT: A 142 ARG cc_start: 0.8355 (ptm-80) cc_final: 0.7985 (ptm160) REVERT: B 6 ASP cc_start: 0.7913 (p0) cc_final: 0.7566 (p0) REVERT: B 50 ARG cc_start: 0.8267 (mmm-85) cc_final: 0.8044 (mtm-85) REVERT: B 64 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8696 (mttt) REVERT: B 108 GLU cc_start: 0.8447 (tp30) cc_final: 0.7792 (tp30) REVERT: B 160 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8431 (mppt) REVERT: C 3 TYR cc_start: 0.9244 (m-80) cc_final: 0.8991 (m-10) REVERT: C 90 GLU cc_start: 0.8114 (tp30) cc_final: 0.7793 (tp30) REVERT: C 105 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7819 (tm-30) REVERT: D 52 LYS cc_start: 0.9189 (mmtp) cc_final: 0.8605 (mmtp) REVERT: D 216 GLU cc_start: 0.7487 (tt0) cc_final: 0.6932 (mt-10) REVERT: E 14 SER cc_start: 0.8249 (t) cc_final: 0.7871 (p) REVERT: E 27 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8288 (mp0) REVERT: E 50 LYS cc_start: 0.9081 (mtmt) cc_final: 0.8828 (mtmm) REVERT: E 91 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8308 (mm-30) REVERT: E 100 ASP cc_start: 0.8857 (t0) cc_final: 0.8276 (t0) REVERT: F 13 THR cc_start: 0.9322 (m) cc_final: 0.9017 (p) REVERT: F 75 MET cc_start: 0.8303 (ttt) cc_final: 0.7900 (ttt) REVERT: G 11 ARG cc_start: 0.8135 (mtm-85) cc_final: 0.7765 (ptp-110) REVERT: G 26 GLU cc_start: 0.8655 (mp0) cc_final: 0.8272 (mp0) REVERT: G 159 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.7110 (t80) REVERT: H 18 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8662 (p) REVERT: H 124 TYR cc_start: 0.8840 (p90) cc_final: 0.8020 (p90) REVERT: H 157 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8409 (mm-30) REVERT: H 202 TYR cc_start: 0.7371 (m-80) cc_final: 0.7115 (m-80) REVERT: H 214 GLU cc_start: 0.8527 (tp30) cc_final: 0.8201 (tp30) REVERT: I 33 MET cc_start: 0.8608 (tmm) cc_final: 0.8211 (ttp) REVERT: I 58 ASP cc_start: 0.8552 (m-30) cc_final: 0.8132 (t0) REVERT: I 65 ARG cc_start: 0.8563 (mtp85) cc_final: 0.8135 (mtp85) REVERT: I 73 TYR cc_start: 0.8767 (t80) cc_final: 0.8419 (t80) REVERT: I 95 TYR cc_start: 0.9357 (t80) cc_final: 0.9075 (t80) REVERT: I 148 MET cc_start: 0.9343 (mmm) cc_final: 0.9063 (mmp) REVERT: I 153 TRP cc_start: 0.9179 (t60) cc_final: 0.8778 (t60) REVERT: I 182 MET cc_start: 0.8479 (mmm) cc_final: 0.8034 (mmm) REVERT: I 197 ARG cc_start: 0.8255 (mtt90) cc_final: 0.7495 (mtt90) REVERT: I 203 MET cc_start: 0.8149 (mmp) cc_final: 0.7668 (mmp) REVERT: J 27 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7921 (tm-30) REVERT: J 31 ASP cc_start: 0.8494 (p0) cc_final: 0.8200 (p0) REVERT: J 38 MET cc_start: 0.8589 (mmm) cc_final: 0.8244 (mmm) REVERT: J 68 LYS cc_start: 0.9319 (tttp) cc_final: 0.8880 (tppt) REVERT: K 119 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8293 (m110) REVERT: L 146 GLN cc_start: 0.8469 (tm-30) cc_final: 0.7893 (tm-30) REVERT: L 184 GLU cc_start: 0.8463 (tp30) cc_final: 0.8136 (tp30) REVERT: M 26 MET cc_start: 0.7868 (mtp) cc_final: 0.7566 (mtm) REVERT: M 47 ASN cc_start: 0.8897 (t0) cc_final: 0.8569 (t0) REVERT: M 96 MET cc_start: 0.8704 (mmm) cc_final: 0.7621 (mtp) REVERT: M 127 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8296 (ttp) REVERT: M 133 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8302 (mt-10) REVERT: N 28 ASN cc_start: 0.8518 (t0) cc_final: 0.8303 (t0) REVERT: d 42 TYR cc_start: 0.9143 (t80) cc_final: 0.8801 (t80) REVERT: d 208 ASP cc_start: 0.8794 (m-30) cc_final: 0.8468 (m-30) REVERT: d 238 MET cc_start: 0.8150 (mmt) cc_final: 0.7722 (mmp) REVERT: c 56 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8367 (p0) REVERT: c 115 GLN cc_start: 0.9240 (tt0) cc_final: 0.8993 (tm-30) REVERT: c 123 ASP cc_start: 0.8728 (m-30) cc_final: 0.8343 (m-30) REVERT: c 133 THR cc_start: 0.9626 (m) cc_final: 0.9358 (p) REVERT: c 164 HIS cc_start: 0.8716 (t-90) cc_final: 0.8223 (t-90) REVERT: c 199 GLN cc_start: 0.8912 (tp40) cc_final: 0.8419 (tp-100) REVERT: c 211 ASP cc_start: 0.9108 (t0) cc_final: 0.8657 (t0) REVERT: c 215 MET cc_start: 0.9226 (mmm) cc_final: 0.8652 (mmt) REVERT: f 97 ASN cc_start: 0.8292 (t0) cc_final: 0.7952 (t0) REVERT: f 136 ASN cc_start: 0.8493 (t0) cc_final: 0.7999 (t0) REVERT: f 229 ASN cc_start: 0.8955 (t0) cc_final: 0.8670 (t0) REVERT: e 211 ASP cc_start: 0.9202 (m-30) cc_final: 0.8745 (m-30) REVERT: h 25 PHE cc_start: 0.8984 (m-80) cc_final: 0.8719 (m-10) REVERT: h 26 GLN cc_start: 0.9163 (mm-40) cc_final: 0.8747 (mm-40) REVERT: h 33 TYR cc_start: 0.9006 (m-80) cc_final: 0.8377 (m-80) REVERT: h 136 ASN cc_start: 0.8921 (t0) cc_final: 0.8450 (t0) REVERT: h 151 ASN cc_start: 0.9581 (m-40) cc_final: 0.9188 (m110) REVERT: h 194 ARG cc_start: 0.9001 (tpp80) cc_final: 0.8753 (tpp80) REVERT: h 210 ARG cc_start: 0.9142 (ttp-170) cc_final: 0.8850 (ttp80) REVERT: h 212 PHE cc_start: 0.8971 (m-10) cc_final: 0.8632 (m-80) REVERT: g 123 ASP cc_start: 0.9002 (m-30) cc_final: 0.8666 (p0) REVERT: g 171 HIS cc_start: 0.8307 (OUTLIER) cc_final: 0.8010 (t70) REVERT: i 117 LYS cc_start: 0.9296 (mmmt) cc_final: 0.9082 (mmtp) REVERT: i 145 LYS cc_start: 0.9399 (tppp) cc_final: 0.9145 (tppt) outliers start: 160 outliers final: 133 residues processed: 1461 average time/residue: 0.6530 time to fit residues: 1607.6976 Evaluate side-chains 1465 residues out of total 7856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1318 time to evaluate : 6.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 174 GLU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 72 MET Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain Q residue 148 ASP Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 106 SER Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 147 THR Chi-restraints excluded: chain S residue 228 ASP Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 161 CYS Chi-restraints excluded: chain U residue 217 VAL Chi-restraints excluded: chain V residue 82 MET Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 72 LEU Chi-restraints excluded: chain W residue 92 ASN Chi-restraints excluded: chain W residue 136 VAL Chi-restraints excluded: chain W residue 151 SER Chi-restraints excluded: chain W residue 154 GLU Chi-restraints excluded: chain W residue 164 GLU Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 107 ARG Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 48 ASP Chi-restraints excluded: chain a residue 2 GLN Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 133 GLU Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 200 GLU Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 93 ASP Chi-restraints excluded: chain b residue 94 LEU Chi-restraints excluded: chain k residue 16 GLN Chi-restraints excluded: chain k residue 36 LEU Chi-restraints excluded: chain k residue 40 ILE Chi-restraints excluded: chain k residue 169 SER Chi-restraints excluded: chain k residue 186 ASP Chi-restraints excluded: chain k residue 238 MET Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 50 ASN Chi-restraints excluded: chain j residue 105 ASN Chi-restraints excluded: chain j residue 144 ASP Chi-restraints excluded: chain j residue 164 HIS Chi-restraints excluded: chain j residue 213 ARG Chi-restraints excluded: chain m residue 184 VAL Chi-restraints excluded: chain l residue 144 ASP Chi-restraints excluded: chain n residue 113 LEU Chi-restraints excluded: chain n residue 162 SER Chi-restraints excluded: chain p residue 118 CYS Chi-restraints excluded: chain p residue 125 ILE Chi-restraints excluded: chain p residue 134 ASP Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 133 CYS Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 154 CYS Chi-restraints excluded: chain G residue 159 TYR Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 54 CYS Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 169 SER Chi-restraints excluded: chain c residue 26 GLU Chi-restraints excluded: chain c residue 56 ASN Chi-restraints excluded: chain c residue 203 GLU Chi-restraints excluded: chain c residue 248 ILE Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 118 CYS Chi-restraints excluded: chain f residue 165 SER Chi-restraints excluded: chain f residue 184 VAL Chi-restraints excluded: chain f residue 185 MET Chi-restraints excluded: chain f residue 208 ASP Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain e residue 178 PHE Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain h residue 206 VAL Chi-restraints excluded: chain g residue 121 ILE Chi-restraints excluded: chain g residue 171 HIS Chi-restraints excluded: chain g residue 213 ARG Chi-restraints excluded: chain i residue 118 CYS Chi-restraints excluded: chain i residue 134 ASP Chi-restraints excluded: chain i residue 238 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 570 optimal weight: 0.9990 chunk 765 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 662 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 719 optimal weight: 0.5980 chunk 301 optimal weight: 3.9990 chunk 739 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 60 GLN W 80 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 k 136 ASN ** j 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 126 GLN ** l 173 GLN ** 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 147 ASN ** n 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN E 146 GLN J 55 GLN J 61 GLN J 87 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 ASN ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 53 ASN d 126 GLN ** c 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 22 GLN ** f 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 48 GLN i 22 GLN i 44 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.066379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.053588 restraints weight = 228829.682| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.31 r_work: 0.2747 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 71082 Z= 0.240 Angle : 0.635 11.201 96452 Z= 0.334 Chirality : 0.043 0.312 11222 Planarity : 0.004 0.066 12306 Dihedral : 4.290 45.878 10044 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.41 % Allowed : 19.23 % Favored : 78.36 % 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: 1.74 (0.09), residues: 9128 helix: 2.35 (0.07), residues: 4498 sheet: 0.18 (0.13), residues: 1500 loop : -0.08 (0.11), residues: 3130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 215 HIS 0.004 0.001 HIS n 164 PHE 0.052 0.001 PHE c 170 TYR 0.042 0.001 TYR Q 110 ARG 0.014 0.001 ARG n 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24443.62 seconds wall clock time: 425 minutes 25.94 seconds (25525.94 seconds total)