Starting phenix.real_space_refine on Sat Feb 24 18:03:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvr_27013/02_2024/8cvr_27013_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvr_27013/02_2024/8cvr_27013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvr_27013/02_2024/8cvr_27013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvr_27013/02_2024/8cvr_27013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvr_27013/02_2024/8cvr_27013_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvr_27013/02_2024/8cvr_27013_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.035 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 282 5.16 5 C 29167 2.51 5 N 8030 2.21 5 O 8107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 88": "NH1" <-> "NH2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E GLU 236": "OE1" <-> "OE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H GLU 86": "OE1" <-> "OE2" Residue "H GLU 182": "OE1" <-> "OE2" Residue "I TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 144": "NH1" <-> "NH2" Residue "I GLU 149": "OE1" <-> "OE2" Residue "I GLU 221": "OE1" <-> "OE2" Residue "J ARG 25": "NH1" <-> "NH2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 79": "NH1" <-> "NH2" Residue "K ARG 86": "NH1" <-> "NH2" Residue "K ARG 153": "NH1" <-> "NH2" Residue "K GLU 158": "OE1" <-> "OE2" Residue "L ARG 159": "NH1" <-> "NH2" Residue "L ARG 187": "NH1" <-> "NH2" Residue "M TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 99": "NH1" <-> "NH2" Residue "M ARG 173": "NH1" <-> "NH2" Residue "M GLU 205": "OE1" <-> "OE2" Residue "N ARG 100": "NH1" <-> "NH2" Residue "O ARG 88": "NH1" <-> "NH2" Residue "P ARG 90": "NH1" <-> "NH2" Residue "P GLU 102": "OE1" <-> "OE2" Residue "P TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 163": "NH1" <-> "NH2" Residue "R ARG 213": "NH1" <-> "NH2" Residue "S GLU 69": "OE1" <-> "OE2" Residue "T ARG 101": "NH1" <-> "NH2" Residue "V PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 182": "OE1" <-> "OE2" Residue "W ARG 144": "NH1" <-> "NH2" Residue "X ARG 25": "NH1" <-> "NH2" Residue "X ARG 69": "NH1" <-> "NH2" Residue "X ARG 79": "NH1" <-> "NH2" Residue "X GLU 143": "OE1" <-> "OE2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ARG 153": "NH1" <-> "NH2" Residue "Y GLU 158": "OE1" <-> "OE2" Residue "Z GLU 37": "OE1" <-> "OE2" Residue "Z GLU 57": "OE1" <-> "OE2" Residue "Z GLU 68": "OE1" <-> "OE2" Residue "Z ARG 159": "NH1" <-> "NH2" Residue "Z ARG 187": "NH1" <-> "NH2" Residue "a ARG 99": "NH1" <-> "NH2" Residue "a ARG 173": "NH1" <-> "NH2" Residue "b ARG 100": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 45586 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1738 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "B" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1662 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1786 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 18, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 109 Chain: "D" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1633 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 6, 'TRANS': 225} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "E" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1660 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 13, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 84 Chain: "F" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1704 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "G" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1760 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 77 Chain: "H" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1469 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 34 Chain: "I" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1580 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "J" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1546 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 34 Chain: "K" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1509 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "L" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1504 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 39 Chain: "M" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1584 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 205} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP%COO:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 55 Chain: "N" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1568 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 7, 'TRANS': 204} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "O" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1734 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "P" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1662 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 96 Chain: "Q" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1786 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 18, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 109 Chain: "R" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1633 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 6, 'TRANS': 225} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "S" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1660 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 13, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 84 Chain: "T" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1707 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "U" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1760 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 77 Chain: "V" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1465 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "W" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1576 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "X" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1534 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "Y" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1506 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "Z" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1500 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 39 Chain: "a" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1584 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 205} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP%COO:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 55 Chain: "b" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1572 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 204} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "H" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'LDZ': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'LDZ': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'LDZ': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'LDZ': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'LDZ': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'LDZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 23.57, per 1000 atoms: 0.52 Number of scatterers: 45586 At special positions: 0 Unit cell: (130.38, 132.5, 174.9, 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 282 16.00 O 8107 8.00 N 8030 7.00 C 29167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.94 Conformation dependent library (CDL) restraints added in 9.4 seconds 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 159 helices and 67 sheets defined 34.9% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.93 Creating SS restraints... Processing helix chain 'A' and resid 23 through 26 No H-bonds generated for 'chain 'A' and resid 23 through 26' Processing helix chain 'A' and resid 84 through 105 Processing helix chain 'A' and resid 111 through 127 removed outlier: 3.708A pdb=" N TYR A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 Processing helix chain 'A' and resid 192 through 206 Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'B' and resid 19 through 30 Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 79 through 100 Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.565A pdb=" N TYR B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.579A pdb=" N ILE B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.624A pdb=" N HIS C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 101 Processing helix chain 'C' and resid 107 through 122 removed outlier: 3.984A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 177 Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 230 through 247 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 56 through 59 Processing helix chain 'D' and resid 77 through 97 Processing helix chain 'D' and resid 104 through 119 Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 179 through 181 No H-bonds generated for 'chain 'D' and resid 179 through 181' Processing helix chain 'D' and resid 184 through 198 removed outlier: 3.644A pdb=" N ILE D 192 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 232 Processing helix chain 'E' and resid 22 through 33 removed outlier: 3.534A pdb=" N ILE E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 63 No H-bonds generated for 'chain 'E' and resid 61 through 63' Processing helix chain 'E' and resid 82 through 103 removed outlier: 4.559A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 119 removed outlier: 3.523A pdb=" N LEU E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 removed outlier: 6.381A pdb=" N SER E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 205 Processing helix chain 'E' and resid 231 through 240 removed outlier: 3.614A pdb=" N ASP E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 31 removed outlier: 3.642A pdb=" N ALA F 28 " --> pdb=" O TYR F 24 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS F 30 " --> pdb=" O MET F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 98 Processing helix chain 'F' and resid 105 through 121 Proline residue: F 119 - end of helix Processing helix chain 'F' and resid 165 through 178 removed outlier: 5.198A pdb=" N SER F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 198 Processing helix chain 'F' and resid 226 through 233 Proline residue: F 231 - end of helix Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.636A pdb=" N VAL G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 101 Processing helix chain 'G' and resid 108 through 122 removed outlier: 3.704A pdb=" N TYR G 122 " --> pdb=" O TYR G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 178 removed outlier: 3.606A pdb=" N LYS G 178 " --> pdb=" O THR G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 183 No H-bonds generated for 'chain 'G' and resid 181 through 183' Processing helix chain 'G' and resid 186 through 200 removed outlier: 3.586A pdb=" N LYS G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 242 Processing helix chain 'H' and resid 50 through 71 Processing helix chain 'H' and resid 77 through 90 Processing helix chain 'H' and resid 133 through 143 removed outlier: 5.605A pdb=" N GLY H 138 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR H 139 " --> pdb=" O TYR H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 165 Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'I' and resid 50 through 71 Processing helix chain 'I' and resid 77 through 90 Processing helix chain 'I' and resid 132 through 142 Processing helix chain 'I' and resid 149 through 166 Processing helix chain 'J' and resid 2 through 4 No H-bonds generated for 'chain 'J' and resid 2 through 4' Processing helix chain 'J' and resid 56 through 77 Processing helix chain 'J' and resid 83 through 97 removed outlier: 4.111A pdb=" N LYS J 97 " --> pdb=" O LEU J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 152 removed outlier: 4.026A pdb=" N SER J 151 " --> pdb=" O GLY J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 176 removed outlier: 3.528A pdb=" N ASP J 175 " --> pdb=" O LEU J 171 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG J 176 " --> pdb=" O ASN J 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 71 Processing helix chain 'K' and resid 77 through 89 Processing helix chain 'K' and resid 135 through 137 No H-bonds generated for 'chain 'K' and resid 135 through 137' Processing helix chain 'K' and resid 140 through 146 Processing helix chain 'K' and resid 153 through 170 removed outlier: 3.537A pdb=" N VAL K 157 " --> pdb=" O ARG K 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 71 Processing helix chain 'L' and resid 77 through 91 removed outlier: 3.608A pdb=" N GLN L 90 " --> pdb=" O ASN L 86 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR L 91 " --> pdb=" O MET L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 143 removed outlier: 3.901A pdb=" N VAL L 139 " --> pdb=" O TYR L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 167 removed outlier: 3.603A pdb=" N ARG L 167 " --> pdb=" O GLN L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 193 through 199 removed outlier: 3.566A pdb=" N GLU L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 79 Processing helix chain 'M' and resid 85 through 102 removed outlier: 4.074A pdb=" N ARG M 99 " --> pdb=" O ILE M 95 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG M 100 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N PHE M 101 " --> pdb=" O TYR M 97 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE M 102 " --> pdb=" O SER M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 152 Proline residue: M 147 - end of helix Processing helix chain 'M' and resid 168 through 183 Processing helix chain 'N' and resid 57 through 77 removed outlier: 3.692A pdb=" N LEU N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 101 Processing helix chain 'N' and resid 140 through 145 removed outlier: 3.600A pdb=" N LEU N 145 " --> pdb=" O GLY N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 156 Processing helix chain 'N' and resid 162 through 179 Processing helix chain 'O' and resid 23 through 31 removed outlier: 3.550A pdb=" N LYS O 30 " --> pdb=" O GLU O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'O' and resid 84 through 105 Processing helix chain 'O' and resid 111 through 127 removed outlier: 3.620A pdb=" N TYR O 125 " --> pdb=" O ILE O 121 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR O 126 " --> pdb=" O SER O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 186 removed outlier: 3.604A pdb=" N LYS O 181 " --> pdb=" O SER O 177 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS O 182 " --> pdb=" O PHE O 178 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS O 184 " --> pdb=" O GLU O 180 " (cutoff:3.500A) Processing helix chain 'O' and resid 192 through 205 removed outlier: 3.601A pdb=" N LEU O 202 " --> pdb=" O ILE O 199 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL O 205 " --> pdb=" O LEU O 202 " (cutoff:3.500A) Processing helix chain 'O' and resid 232 through 241 Processing helix chain 'P' and resid 19 through 29 Processing helix chain 'P' and resid 79 through 100 Processing helix chain 'P' and resid 106 through 121 removed outlier: 3.507A pdb=" N VAL P 116 " --> pdb=" O ARG P 112 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR P 121 " --> pdb=" O MET P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 176 Processing helix chain 'P' and resid 183 through 197 removed outlier: 3.718A pdb=" N SER P 197 " --> pdb=" O THR P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 230 Processing helix chain 'Q' and resid 19 through 30 removed outlier: 3.588A pdb=" N HIS Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 101 Processing helix chain 'Q' and resid 107 through 122 removed outlier: 3.544A pdb=" N THR Q 122 " --> pdb=" O LYS Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 176 Processing helix chain 'Q' and resid 186 through 200 removed outlier: 4.032A pdb=" N ILE Q 194 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 230 through 246 Processing helix chain 'R' and resid 17 through 27 Processing helix chain 'R' and resid 56 through 58 No H-bonds generated for 'chain 'R' and resid 56 through 58' Processing helix chain 'R' and resid 77 through 98 Processing helix chain 'R' and resid 104 through 119 removed outlier: 4.084A pdb=" N THR R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 175 Processing helix chain 'R' and resid 179 through 181 No H-bonds generated for 'chain 'R' and resid 179 through 181' Processing helix chain 'R' and resid 184 through 196 Processing helix chain 'R' and resid 222 through 231 Processing helix chain 'S' and resid 22 through 33 removed outlier: 3.738A pdb=" N LEU S 33 " --> pdb=" O GLU S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 63 No H-bonds generated for 'chain 'S' and resid 61 through 63' Processing helix chain 'S' and resid 82 through 103 removed outlier: 4.309A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 117 Processing helix chain 'S' and resid 174 through 183 removed outlier: 6.287A pdb=" N SER S 179 " --> pdb=" O GLU S 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 205 Processing helix chain 'S' and resid 231 through 240 removed outlier: 3.513A pdb=" N ASP S 240 " --> pdb=" O GLU S 236 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 31 removed outlier: 3.918A pdb=" N VAL T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS T 30 " --> pdb=" O MET T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 98 Processing helix chain 'T' and resid 105 through 120 removed outlier: 3.531A pdb=" N ILE T 118 " --> pdb=" O SER T 114 " (cutoff:3.500A) Proline residue: T 119 - end of helix Processing helix chain 'T' and resid 165 through 179 removed outlier: 5.224A pdb=" N SER T 177 " --> pdb=" O GLU T 173 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU T 178 " --> pdb=" O ARG T 174 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE T 179 " --> pdb=" O HIS T 175 " (cutoff:3.500A) Processing helix chain 'T' and resid 184 through 198 removed outlier: 3.510A pdb=" N THR T 198 " --> pdb=" O ALA T 194 " (cutoff:3.500A) Processing helix chain 'T' and resid 226 through 233 Proline residue: T 231 - end of helix Processing helix chain 'U' and resid 21 through 32 removed outlier: 3.810A pdb=" N VAL U 30 " --> pdb=" O ALA U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 101 Processing helix chain 'U' and resid 108 through 122 removed outlier: 3.606A pdb=" N TYR U 122 " --> pdb=" O TYR U 118 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 178 Processing helix chain 'U' and resid 186 through 200 removed outlier: 4.505A pdb=" N LYS U 191 " --> pdb=" O ARG U 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU U 192 " --> pdb=" O ASP U 188 " (cutoff:3.500A) Processing helix chain 'U' and resid 229 through 243 Processing helix chain 'V' and resid 50 through 70 Processing helix chain 'V' and resid 77 through 90 Processing helix chain 'V' and resid 133 through 143 removed outlier: 3.680A pdb=" N TYR V 137 " --> pdb=" O SER V 134 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLY V 138 " --> pdb=" O TYR V 135 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR V 143 " --> pdb=" O VAL V 140 " (cutoff:3.500A) Processing helix chain 'V' and resid 150 through 167 Processing helix chain 'V' and resid 192 through 194 No H-bonds generated for 'chain 'V' and resid 192 through 194' Processing helix chain 'W' and resid 50 through 53 No H-bonds generated for 'chain 'W' and resid 50 through 53' Processing helix chain 'W' and resid 56 through 71 Processing helix chain 'W' and resid 77 through 90 removed outlier: 3.945A pdb=" N ARG W 90 " --> pdb=" O GLN W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 142 Processing helix chain 'W' and resid 149 through 166 Processing helix chain 'X' and resid 56 through 77 Processing helix chain 'X' and resid 83 through 97 removed outlier: 3.718A pdb=" N LYS X 97 " --> pdb=" O LEU X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 152 Processing helix chain 'X' and resid 159 through 173 Processing helix chain 'Y' and resid 52 through 71 Processing helix chain 'Y' and resid 77 through 89 Processing helix chain 'Y' and resid 134 through 138 Processing helix chain 'Y' and resid 140 through 146 Processing helix chain 'Y' and resid 153 through 170 Processing helix chain 'Z' and resid 50 through 71 Processing helix chain 'Z' and resid 77 through 91 removed outlier: 3.713A pdb=" N GLN Z 90 " --> pdb=" O ASN Z 86 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR Z 91 " --> pdb=" O MET Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 133 through 143 removed outlier: 3.673A pdb=" N GLY Z 138 " --> pdb=" O VAL Z 134 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL Z 139 " --> pdb=" O TYR Z 135 " (cutoff:3.500A) Processing helix chain 'Z' and resid 150 through 167 Processing helix chain 'Z' and resid 193 through 199 Processing helix chain 'a' and resid 58 through 79 Processing helix chain 'a' and resid 85 through 99 removed outlier: 3.821A pdb=" N ARG a 99 " --> pdb=" O ILE a 95 " (cutoff:3.500A) Processing helix chain 'a' and resid 142 through 152 Proline residue: a 147 - end of helix removed outlier: 3.901A pdb=" N ASN a 151 " --> pdb=" O PRO a 147 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 185 Processing helix chain 'b' and resid 57 through 76 Processing helix chain 'b' and resid 85 through 101 Processing helix chain 'b' and resid 140 through 145 Processing helix chain 'b' and resid 147 through 156 Processing helix chain 'b' and resid 162 through 179 Processing sheet with id= A, first strand: chain 'A' and resid 165 through 169 removed outlier: 6.194A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 53 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 148 through 154 removed outlier: 6.600A pdb=" N CYS A 78 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS A 71 " --> pdb=" O CYS A 78 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N MET A 80 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU A 69 " --> pdb=" O MET A 80 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 159 through 162 Processing sheet with id= D, first strand: chain 'B' and resid 71 through 77 removed outlier: 4.191A pdb=" N LEU B 145 " --> pdb=" O TRP B 157 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 161 through 164 Processing sheet with id= F, first strand: chain 'C' and resid 72 through 78 removed outlier: 4.164A pdb=" N LEU C 147 " --> pdb=" O TRP C 159 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 158 through 161 Processing sheet with id= H, first strand: chain 'D' and resid 69 through 75 removed outlier: 4.210A pdb=" N LEU D 144 " --> pdb=" O TRP D 156 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 167 through 170 Processing sheet with id= J, first strand: chain 'E' and resid 67 through 69 Processing sheet with id= K, first strand: chain 'F' and resid 158 through 161 Processing sheet with id= L, first strand: chain 'F' and resid 63 through 65 Processing sheet with id= M, first strand: chain 'G' and resid 162 through 165 Processing sheet with id= N, first strand: chain 'G' and resid 157 through 159 removed outlier: 6.801A pdb=" N MET G 75 " --> pdb=" O ASN G 68 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ASN G 68 " --> pdb=" O MET G 75 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL G 77 " --> pdb=" O LEU G 66 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU G 66 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 126 through 130 Processing sheet with id= P, first strand: chain 'H' and resid 35 through 37 removed outlier: 4.057A pdb=" N VAL H 112 " --> pdb=" O GLN H 124 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 21 through 23 removed outlier: 6.644A pdb=" N THR H 23 " --> pdb=" O ILE H 27 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE H 27 " --> pdb=" O THR H 23 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 125 through 129 Processing sheet with id= S, first strand: chain 'I' and resid 120 through 122 removed outlier: 5.990A pdb=" N CYS I 44 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N PHE I 37 " --> pdb=" O CYS I 44 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLY I 46 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE I 35 " --> pdb=" O GLY I 46 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 21 through 23 removed outlier: 5.830A pdb=" N GLU I 23 " --> pdb=" O VAL I 27 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL I 27 " --> pdb=" O GLU I 23 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 135 through 139 removed outlier: 5.752A pdb=" N ALA J 9 " --> pdb=" O ASP J 24 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL J 184 " --> pdb=" O LEU J 199 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 41 through 43 removed outlier: 4.642A pdb=" N ILE J 120 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR J 132 " --> pdb=" O ILE J 120 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 27 through 29 removed outlier: 6.210A pdb=" N ILE J 29 " --> pdb=" O MET J 33 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N MET J 33 " --> pdb=" O ILE J 29 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 129 through 132 removed outlier: 4.452A pdb=" N VAL K 180 " --> pdb=" O LEU K 191 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 35 through 37 Processing sheet with id= Z, first strand: chain 'L' and resid 126 through 130 removed outlier: 6.626A pdb=" N HIS L 179 " --> pdb=" O ARG L 187 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ARG L 187 " --> pdb=" O HIS L 179 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 35 through 37 removed outlier: 3.658A pdb=" N MET L 101 " --> pdb=" O THR L 45 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 21 through 23 removed outlier: 6.279A pdb=" N ALA L 23 " --> pdb=" O ILE L 27 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'M' and resid 135 through 139 removed outlier: 5.674A pdb=" N THR M 11 " --> pdb=" O ASP M 26 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 130 through 133 removed outlier: 3.664A pdb=" N VAL M 121 " --> pdb=" O ASP M 133 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN M 108 " --> pdb=" O PHE M 124 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE M 52 " --> pdb=" O LYS M 45 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LYS M 45 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N CYS M 54 " --> pdb=" O CYS M 43 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N CYS M 43 " --> pdb=" O CYS M 54 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'M' and resid 29 through 31 removed outlier: 6.300A pdb=" N GLU M 31 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE M 35 " --> pdb=" O GLU M 31 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'N' and resid 136 through 138 removed outlier: 3.627A pdb=" N GLY N 19 " --> pdb=" O PHE N 16 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 42 through 44 Processing sheet with id= AH, first strand: chain 'N' and resid 28 through 30 removed outlier: 6.568A pdb=" N TYR N 30 " --> pdb=" O ALA N 34 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'O' and resid 165 through 169 removed outlier: 5.615A pdb=" N THR O 38 " --> pdb=" O GLN O 53 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'O' and resid 160 through 163 removed outlier: 4.147A pdb=" N VAL O 151 " --> pdb=" O PHE O 163 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N CYS O 78 " --> pdb=" O LYS O 71 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LYS O 71 " --> pdb=" O CYS O 78 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET O 80 " --> pdb=" O LEU O 69 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU O 69 " --> pdb=" O MET O 80 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'P' and resid 159 through 162 Processing sheet with id= AL, first strand: chain 'P' and resid 71 through 77 Processing sheet with id= AM, first strand: chain 'Q' and resid 161 through 164 Processing sheet with id= AN, first strand: chain 'Q' and resid 65 through 67 removed outlier: 4.102A pdb=" N LEU Q 147 " --> pdb=" O TRP Q 159 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'R' and resid 158 through 161 removed outlier: 3.691A pdb=" N VAL R 41 " --> pdb=" O MET R 211 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'R' and resid 69 through 75 Processing sheet with id= AQ, first strand: chain 'S' and resid 167 through 170 Processing sheet with id= AR, first strand: chain 'S' and resid 162 through 164 removed outlier: 6.538A pdb=" N CYS S 76 " --> pdb=" O GLU S 69 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLU S 69 " --> pdb=" O CYS S 76 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N MET S 78 " --> pdb=" O ILE S 67 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE S 67 " --> pdb=" O MET S 78 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'T' and resid 158 through 161 Processing sheet with id= AT, first strand: chain 'T' and resid 153 through 156 removed outlier: 3.983A pdb=" N ILE T 144 " --> pdb=" O CYS T 156 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE T 72 " --> pdb=" O HIS T 65 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N HIS T 65 " --> pdb=" O ILE T 72 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE T 74 " --> pdb=" O ILE T 63 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE T 63 " --> pdb=" O ILE T 74 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'U' and resid 162 through 165 Processing sheet with id= AV, first strand: chain 'U' and resid 66 through 68 removed outlier: 4.241A pdb=" N LEU U 148 " --> pdb=" O TYR U 160 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'V' and resid 126 through 129 Processing sheet with id= AX, first strand: chain 'V' and resid 35 through 37 removed outlier: 4.204A pdb=" N VAL V 112 " --> pdb=" O GLN V 124 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'W' and resid 125 through 128 Processing sheet with id= AZ, first strand: chain 'W' and resid 120 through 122 removed outlier: 6.138A pdb=" N CYS W 44 " --> pdb=" O PHE W 37 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N PHE W 37 " --> pdb=" O CYS W 44 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLY W 46 " --> pdb=" O ILE W 35 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE W 35 " --> pdb=" O GLY W 46 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'W' and resid 21 through 23 removed outlier: 5.761A pdb=" N GLU W 23 " --> pdb=" O VAL W 27 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL W 27 " --> pdb=" O GLU W 23 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'X' and resid 135 through 139 removed outlier: 6.022A pdb=" N ALA X 9 " --> pdb=" O ASP X 24 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL X 184 " --> pdb=" O LEU X 199 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'X' and resid 41 through 43 removed outlier: 3.643A pdb=" N ALA X 53 " --> pdb=" O GLU X 105 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE X 120 " --> pdb=" O THR X 132 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR X 132 " --> pdb=" O ILE X 120 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'X' and resid 27 through 29 removed outlier: 6.158A pdb=" N ILE X 29 " --> pdb=" O MET X 33 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N MET X 33 " --> pdb=" O ILE X 29 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'Y' and resid 129 through 132 removed outlier: 4.565A pdb=" N VAL Y 180 " --> pdb=" O LEU Y 191 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'Y' and resid 35 through 37 Processing sheet with id= BG, first strand: chain 'Z' and resid 126 through 130 removed outlier: 3.595A pdb=" N SER Z 189 " --> pdb=" O LEU Z 177 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N HIS Z 179 " --> pdb=" O ARG Z 187 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ARG Z 187 " --> pdb=" O HIS Z 179 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG Z 181 " --> pdb=" O TRP Z 185 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N TRP Z 185 " --> pdb=" O ARG Z 181 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'Z' and resid 121 through 123 removed outlier: 3.610A pdb=" N MET Z 101 " --> pdb=" O THR Z 45 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY Z 44 " --> pdb=" O GLU Z 37 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLU Z 37 " --> pdb=" O GLY Z 44 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N MET Z 46 " --> pdb=" O VAL Z 35 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL Z 35 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'Z' and resid 21 through 23 removed outlier: 6.639A pdb=" N ALA Z 23 " --> pdb=" O ILE Z 27 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE Z 27 " --> pdb=" O ALA Z 23 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'a' and resid 135 through 139 removed outlier: 5.544A pdb=" N THR a 11 " --> pdb=" O ASP a 26 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'a' and resid 130 through 133 removed outlier: 3.506A pdb=" N VAL a 121 " --> pdb=" O ASP a 133 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN a 108 " --> pdb=" O PHE a 124 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR a 50 " --> pdb=" O THR a 47 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE a 52 " --> pdb=" O LYS a 45 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LYS a 45 " --> pdb=" O ILE a 52 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N CYS a 54 " --> pdb=" O CYS a 43 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N CYS a 43 " --> pdb=" O CYS a 54 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'a' and resid 29 through 31 removed outlier: 6.240A pdb=" N GLU a 31 " --> pdb=" O ILE a 35 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE a 35 " --> pdb=" O GLU a 31 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'b' and resid 136 through 138 removed outlier: 3.676A pdb=" N ILE b 189 " --> pdb=" O GLU b 200 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'b' and resid 42 through 44 Processing sheet with id= BO, first strand: chain 'b' and resid 28 through 30 removed outlier: 6.595A pdb=" N TYR b 30 " --> pdb=" O ALA b 34 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA b 34 " --> pdb=" O TYR b 30 " (cutoff:3.500A) 2449 hydrogen bonds defined for protein. 6966 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.17 Time building geometry restraints manager: 19.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 7181 1.31 - 1.43: 12345 1.43 - 1.56: 26437 1.56 - 1.69: 0 1.69 - 1.82: 465 Bond restraints: 46428 Sorted by residual: bond pdb=" C15 LDZ V 301 " pdb=" N16 LDZ V 301 " ideal model delta sigma weight residual 1.340 1.455 -0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C12 LDZ I 301 " pdb=" N13 LDZ I 301 " ideal model delta sigma weight residual 1.340 1.454 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C12 LDZ L 301 " pdb=" N13 LDZ L 301 " ideal model delta sigma weight residual 1.340 1.454 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C15 LDZ L 301 " pdb=" N16 LDZ L 301 " ideal model delta sigma weight residual 1.340 1.453 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C9 LDZ L 301 " pdb=" N10 LDZ L 301 " ideal model delta sigma weight residual 1.345 1.455 -0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 46423 not shown) Histogram of bond angle deviations from ideal: 99.38 - 106.39: 1237 106.39 - 113.39: 25005 113.39 - 120.40: 21014 120.40 - 127.40: 15585 127.40 - 134.41: 185 Bond angle restraints: 63026 Sorted by residual: angle pdb=" N ILE I 38 " pdb=" CA ILE I 38 " pdb=" C ILE I 38 " ideal model delta sigma weight residual 111.90 105.47 6.43 8.10e-01 1.52e+00 6.29e+01 angle pdb=" N ILE W 38 " pdb=" CA ILE W 38 " pdb=" C ILE W 38 " ideal model delta sigma weight residual 111.81 105.32 6.49 8.60e-01 1.35e+00 5.70e+01 angle pdb=" N LYS B 158 " pdb=" CA LYS B 158 " pdb=" C LYS B 158 " ideal model delta sigma weight residual 113.41 104.69 8.72 1.22e+00 6.72e-01 5.11e+01 angle pdb=" N LYS P 158 " pdb=" CA LYS P 158 " pdb=" C LYS P 158 " ideal model delta sigma weight residual 113.41 104.77 8.64 1.22e+00 6.72e-01 5.01e+01 angle pdb=" N LYS C 160 " pdb=" CA LYS C 160 " pdb=" C LYS C 160 " ideal model delta sigma weight residual 113.41 105.24 8.17 1.22e+00 6.72e-01 4.48e+01 ... (remaining 63021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.59: 27076 32.59 - 65.17: 517 65.17 - 97.76: 24 97.76 - 130.34: 2 130.34 - 162.93: 5 Dihedral angle restraints: 27624 sinusoidal: 9742 harmonic: 17882 Sorted by residual: dihedral pdb=" C GLN a 131 " pdb=" N GLN a 131 " pdb=" CA GLN a 131 " pdb=" CB GLN a 131 " ideal model delta harmonic sigma weight residual -122.60 -108.03 -14.57 0 2.50e+00 1.60e-01 3.40e+01 dihedral pdb=" C17 LDZ H 301 " pdb=" C18 LDZ H 301 " pdb=" C19 LDZ H 301 " pdb=" C21 LDZ H 301 " ideal model delta sinusoidal sigma weight residual -53.33 109.60 -162.93 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C17 LDZ W 301 " pdb=" C18 LDZ W 301 " pdb=" C19 LDZ W 301 " pdb=" C21 LDZ W 301 " ideal model delta sinusoidal sigma weight residual 306.67 157.48 149.19 1 3.00e+01 1.11e-03 1.98e+01 ... (remaining 27621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3056 0.072 - 0.145: 3364 0.145 - 0.217: 901 0.217 - 0.289: 40 0.289 - 0.362: 3 Chirality restraints: 7364 Sorted by residual: chirality pdb=" CA GLN a 131 " pdb=" N GLN a 131 " pdb=" C GLN a 131 " pdb=" CB GLN a 131 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" C17 LDZ I 301 " pdb=" C18 LDZ I 301 " pdb=" C22 LDZ I 301 " pdb=" N16 LDZ I 301 " both_signs ideal model delta sigma weight residual False -2.35 -2.67 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C17 LDZ Z 301 " pdb=" C18 LDZ Z 301 " pdb=" C22 LDZ Z 301 " pdb=" N16 LDZ Z 301 " both_signs ideal model delta sigma weight residual False -2.35 -2.65 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 7361 not shown) Planarity restraints: 8010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 74 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" C CYS C 74 " -0.032 2.00e-02 2.50e+03 pdb=" O CYS C 74 " 0.012 2.00e-02 2.50e+03 pdb=" N SER C 75 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 160 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.02e+00 pdb=" C TYR A 160 " 0.025 2.00e-02 2.50e+03 pdb=" O TYR A 160 " -0.009 2.00e-02 2.50e+03 pdb=" N CYS A 161 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR U 104 " -0.013 2.00e-02 2.50e+03 9.50e-03 1.81e+00 pdb=" CG TYR U 104 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR U 104 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR U 104 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR U 104 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR U 104 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR U 104 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR U 104 " -0.001 2.00e-02 2.50e+03 ... (remaining 8007 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 12784 2.82 - 3.34: 42881 3.34 - 3.86: 80177 3.86 - 4.38: 99797 4.38 - 4.90: 164234 Nonbonded interactions: 399873 Sorted by model distance: nonbonded pdb=" O THR b 205 " pdb=" N THR b 207 " model vdw 2.299 2.520 nonbonded pdb=" OH TYR Z 41 " pdb=" O ILE Z 75 " model vdw 2.312 2.440 nonbonded pdb=" O ARG C 3 " pdb=" NH2 ARG C 8 " model vdw 2.333 2.520 nonbonded pdb=" OD2 ASP F 9 " pdb=" OG1 THR F 11 " model vdw 2.339 2.440 nonbonded pdb=" O ILE C 65 " pdb=" O CYS C 74 " model vdw 2.353 3.040 ... (remaining 399868 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 213 or (resid 214 and (name N or name CA or name \ C or name O or name CB )) or resid 215 through 242)) 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' and (resid 4 through 139 or (resid 140 and (name N or name CA or name \ C or name O or name CB )) or resid 141 through 236)) } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = (chain 'H' and (resid 2 through 193 or (resid 194 and (name N or name CA or name \ C or name O or name CB )) or resid 195 through 203 or resid 301)) selection = chain 'V' } ncs_group { reference = (chain 'I' and (resid 2 through 220 or (resid 221 and (name N or name CA or name \ C or name O or name CB )) or resid 301)) selection = chain 'W' } ncs_group { reference = (chain 'J' and (resid 1 through 76 or (resid 77 and (name N or name CA or name C \ or name O or name CB )) or resid 78 through 95 or (resid 96 and (name N or name \ CA or name C or name O or name CB )) or resid 97 through 133 or (resid 134 and \ (name N or name CA or name C or name O or name CB )) or resid 135 through 148 or \ (resid 149 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 0 through 204)) selection = chain 'X' } ncs_group { reference = (chain 'K' and (resid 1 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB )) or resid 34 through 196)) selection = chain 'Y' } ncs_group { reference = (chain 'L' and (resid 2 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 201 or resid 301)) selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = (chain 'b' and (resid 1 through 73 or (resid 74 through 75 and (name N or name C \ A or name C or name O or name CB )) or resid 76 through 212)) } 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 9.690 Check model and map are aligned: 0.680 Set scattering table: 0.460 Process input model: 122.180 Find NCS groups from input model: 5.090 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.115 46428 Z= 0.815 Angle : 1.534 10.674 63026 Z= 1.179 Chirality : 0.099 0.362 7364 Planarity : 0.003 0.019 8010 Dihedral : 12.610 162.931 16208 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.63 % Allowed : 3.58 % Favored : 95.78 % Rotamer: Outliers : 5.28 % Allowed : 7.06 % Favored : 87.66 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.33 (0.09), residues: 6142 helix: -0.27 (0.10), residues: 2296 sheet: -0.23 (0.12), residues: 1458 loop : -1.83 (0.11), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 100 HIS 0.009 0.001 HIS T 59 PHE 0.020 0.002 PHE L 7 TYR 0.023 0.002 TYR U 104 ARG 0.006 0.001 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1443 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1217 time to evaluate : 4.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8266 (mmp) cc_final: 0.8039 (mmp) REVERT: C 75 SER cc_start: 0.8516 (t) cc_final: 0.8213 (t) REVERT: C 198 ASN cc_start: 0.8585 (t0) cc_final: 0.8351 (t0) REVERT: J 40 LYS cc_start: 0.8638 (mttt) cc_final: 0.8421 (mttp) REVERT: J 177 ASP cc_start: 0.7794 (t0) cc_final: 0.7297 (t0) REVERT: O 80 MET cc_start: 0.8587 (mmm) cc_final: 0.8387 (mmm) REVERT: S 32 LYS cc_start: 0.8307 (mttt) cc_final: 0.8057 (mtmt) REVERT: V 111 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8304 (mt0) REVERT: b 188 GLN cc_start: 0.8449 (mt0) cc_final: 0.8243 (mt0) outliers start: 226 outliers final: 42 residues processed: 1335 average time/residue: 1.7147 time to fit residues: 2774.9013 Evaluate side-chains 941 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 898 time to evaluate : 4.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain O residue 19 GLU Chi-restraints excluded: chain O residue 182 LYS Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 93 GLU Chi-restraints excluded: chain U residue 148 LEU Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain V residue 111 GLN Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain b residue 154 LEU Chi-restraints excluded: chain b residue 169 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 515 optimal weight: 0.9980 chunk 462 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 311 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 478 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 290 optimal weight: 0.7980 chunk 355 optimal weight: 0.9990 chunk 553 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 224 ASN B 108 GLN B 111 GLN C 40 ASN C 100 GLN C 109 GLN C 123 GLN C 146 GLN C 167 ASN C 198 ASN D 122 ASN E 13 ASN E 97 GLN E 99 HIS E 118 ASN E 182 GLN E 225 ASN F 21 GLN F 60 GLN F 68 ASN F 152 ASN G 68 ASN G 101 ASN H 107 GLN H 111 GLN H 194 GLN J 6 ASN J 17 ASN J 64 GLN K 82 ASN K 87 ASN K 101 ASN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN L 39 ASN L 90 GLN L 163 GLN M 79 ASN M 108 ASN M 157 ASN M 159 GLN M 163 HIS N 69 GLN N 89 HIS N 157 GLN N 188 GLN O 24 GLN O 193 GLN P 95 GLN P 108 GLN Q 40 ASN Q 167 ASN R 122 ASN R 146 GLN S 114 GLN S 152 GLN S 186 HIS S 225 ASN T 86 ASN T 90 GLN T 121 GLN T 152 ASN U 32 ASN U 101 ASN V 78 HIS W 81 ASN W 117 HIS X 92 ASN X 156 ASN Y 8 GLN Y 55 GLN Y 63 ASN Y 82 ASN Y 87 ASN Y 101 ASN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 168 GLN Y 189 HIS Y 193 ASN Z 120 ASN Z 152 GLN ** Z 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 176 ASN a 8 ASN a 108 ASN a 146 GLN a 157 ASN a 159 GLN a 163 HIS b 47 ASN b 69 GLN b 89 HIS b 108 ASN b 188 GLN Total number of N/Q/H flips: 92 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 46428 Z= 0.195 Angle : 0.568 9.411 63026 Z= 0.302 Chirality : 0.043 0.334 7364 Planarity : 0.004 0.053 8010 Dihedral : 8.688 166.026 7034 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.30 % Favored : 97.59 % Rotamer: Outliers : 3.81 % Allowed : 15.26 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.21 (0.10), residues: 6142 helix: 1.40 (0.11), residues: 2302 sheet: 0.11 (0.12), residues: 1562 loop : -1.10 (0.12), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 56 HIS 0.007 0.001 HIS T 65 PHE 0.026 0.002 PHE O 210 TYR 0.020 0.001 TYR F 171 ARG 0.009 0.001 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 918 time to evaluate : 5.660 Fit side-chains revert: symmetry clash REVERT: C 198 ASN cc_start: 0.9031 (t0) cc_final: 0.8805 (t0) REVERT: E 20 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7078 (mtp180) REVERT: K 111 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7211 (mm-30) REVERT: M 74 MET cc_start: 0.8594 (mtp) cc_final: 0.8337 (mtp) REVERT: M 114 ASP cc_start: 0.7803 (p0) cc_final: 0.7507 (p0) REVERT: N 26 MET cc_start: 0.8514 (mtp) cc_final: 0.8251 (mtp) REVERT: O 10 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7732 (p0) REVERT: O 120 ASP cc_start: 0.7588 (m-30) cc_final: 0.7335 (m-30) REVERT: P 195 LYS cc_start: 0.8810 (ttpt) cc_final: 0.8561 (ttmt) REVERT: T 178 GLU cc_start: 0.7763 (pt0) cc_final: 0.7247 (pt0) outliers start: 163 outliers final: 53 residues processed: 1014 average time/residue: 1.6388 time to fit residues: 2030.9892 Evaluate side-chains 896 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 841 time to evaluate : 5.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 197 LYS Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 182 LYS Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain T residue 229 VAL Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain X residue 130 MET Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain b residue 169 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 307 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 chunk 461 optimal weight: 5.9990 chunk 377 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 554 optimal weight: 2.9990 chunk 599 optimal weight: 4.9990 chunk 494 optimal weight: 7.9990 chunk 550 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 445 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN D 122 ASN D 154 HIS E 118 ASN E 182 GLN E 225 ASN G 101 ASN G 180 GLN H 107 GLN I 31 ASN J 17 ASN K 27 GLN K 63 ASN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 189 HIS K 193 ASN L 39 ASN L 120 ASN L 176 ASN M 131 GLN M 159 GLN M 163 HIS N 157 GLN O 24 GLN P 95 GLN Q 146 GLN Q 198 ASN S 13 ASN S 114 GLN S 221 GLN S 227 HIS T 60 GLN T 152 ASN U 110 HIS X 156 ASN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 39 ASN Z 120 ASN Z 152 GLN Z 163 GLN a 151 ASN a 157 ASN b 47 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 46428 Z= 0.442 Angle : 0.604 10.967 63026 Z= 0.317 Chirality : 0.046 0.315 7364 Planarity : 0.004 0.039 8010 Dihedral : 8.407 167.472 7003 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.29 % Favored : 96.61 % Rotamer: Outliers : 3.51 % Allowed : 16.57 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.56 (0.10), residues: 6142 helix: 1.69 (0.11), residues: 2294 sheet: 0.30 (0.13), residues: 1556 loop : -0.91 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 56 HIS 0.008 0.001 HIS T 65 PHE 0.035 0.002 PHE A 191 TYR 0.023 0.002 TYR R 153 ARG 0.006 0.001 ARG Z 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 818 time to evaluate : 5.382 Fit side-chains revert: symmetry clash REVERT: E 20 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7150 (mtp180) REVERT: F 61 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8125 (mttm) REVERT: J 60 GLN cc_start: 0.8572 (mt0) cc_final: 0.8350 (mt0) REVERT: J 138 SER cc_start: 0.8887 (t) cc_final: 0.8681 (p) REVERT: K 111 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7220 (mm-30) REVERT: L 94 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.8001 (mtm) REVERT: M 74 MET cc_start: 0.8698 (mtp) cc_final: 0.8454 (mtp) REVERT: M 114 ASP cc_start: 0.8005 (p0) cc_final: 0.7637 (p0) REVERT: N 26 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8196 (mtp) REVERT: O 120 ASP cc_start: 0.7754 (m-30) cc_final: 0.7491 (m-30) REVERT: P 195 LYS cc_start: 0.8939 (ttpt) cc_final: 0.8730 (ttmt) REVERT: S 182 GLN cc_start: 0.8292 (tm-30) cc_final: 0.7691 (tp40) REVERT: X 193 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8540 (ptmm) outliers start: 150 outliers final: 76 residues processed: 905 average time/residue: 1.7424 time to fit residues: 1908.4668 Evaluate side-chains 866 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 785 time to evaluate : 5.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 25 MET Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 182 LYS Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 193 THR Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain S residue 29 GLU Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 229 VAL Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain X residue 11 MET Chi-restraints excluded: chain X residue 130 MET Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain X residue 180 SER Chi-restraints excluded: chain X residue 193 LYS Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Y residue 179 SER Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 38 ILE Chi-restraints excluded: chain Z residue 54 SER Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain b residue 169 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 548 optimal weight: 7.9990 chunk 417 optimal weight: 1.9990 chunk 288 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 264 optimal weight: 0.9990 chunk 372 optimal weight: 8.9990 chunk 556 optimal weight: 0.8980 chunk 589 optimal weight: 4.9990 chunk 290 optimal weight: 1.9990 chunk 527 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 188 HIS D 85 ASN D 122 ASN E 118 ASN E 182 GLN E 221 GLN F 68 ASN G 32 ASN G 97 ASN G 101 ASN H 107 GLN H 155 GLN I 31 ASN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN L 39 ASN M 159 GLN P 95 GLN Q 198 ASN S 114 GLN T 86 ASN T 121 GLN V 188 GLN X 156 ASN Y 55 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 30 GLN Z 39 ASN Z 152 GLN a 157 ASN b 47 ASN b 108 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 46428 Z= 0.176 Angle : 0.503 10.061 63026 Z= 0.265 Chirality : 0.042 0.301 7364 Planarity : 0.004 0.039 8010 Dihedral : 8.068 167.773 6995 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.31 % Favored : 97.62 % Rotamer: Outliers : 3.04 % Allowed : 18.23 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.96 (0.11), residues: 6142 helix: 2.11 (0.11), residues: 2280 sheet: 0.44 (0.13), residues: 1540 loop : -0.70 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 100 HIS 0.005 0.001 HIS T 65 PHE 0.016 0.001 PHE X 68 TYR 0.020 0.001 TYR R 153 ARG 0.009 0.000 ARG W 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 854 time to evaluate : 5.114 Fit side-chains revert: symmetry clash REVERT: D 157 LYS cc_start: 0.8886 (mttt) cc_final: 0.8648 (mttt) REVERT: E 20 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7202 (mtp180) REVERT: J 60 GLN cc_start: 0.8506 (mt0) cc_final: 0.8290 (mt0) REVERT: K 111 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7158 (mm-30) REVERT: M 74 MET cc_start: 0.8663 (mtp) cc_final: 0.8450 (mtp) REVERT: M 114 ASP cc_start: 0.8084 (p0) cc_final: 0.7822 (p0) REVERT: N 26 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8202 (mtp) REVERT: O 120 ASP cc_start: 0.7746 (m-30) cc_final: 0.7448 (m-30) REVERT: P 195 LYS cc_start: 0.8872 (ttpt) cc_final: 0.8667 (ttmt) REVERT: R 23 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.8037 (mt0) REVERT: S 182 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7716 (tp-100) outliers start: 130 outliers final: 57 residues processed: 925 average time/residue: 1.7099 time to fit residues: 1925.4069 Evaluate side-chains 868 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 808 time to evaluate : 5.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 182 LYS Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 23 GLN Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain S residue 29 GLU Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 229 VAL Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain X residue 130 MET Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain X residue 180 SER Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 54 SER Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 169 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 491 optimal weight: 9.9990 chunk 334 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 439 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 chunk 503 optimal weight: 5.9990 chunk 407 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 301 optimal weight: 4.9990 chunk 529 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 ASN E 118 ASN F 68 ASN F 152 ASN F 166 GLN G 97 ASN G 101 ASN H 107 GLN H 155 GLN K 27 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN L 120 ASN M 80 ASN M 108 ASN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 159 GLN N 47 ASN P 95 GLN Q 198 ASN S 114 GLN ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 ASN X 156 ASN Y 55 GLN Y 65 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 30 GLN Z 39 ASN Z 152 GLN a 157 ASN a 159 GLN b 108 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 46428 Z= 0.541 Angle : 0.621 11.720 63026 Z= 0.324 Chirality : 0.047 0.304 7364 Planarity : 0.004 0.045 8010 Dihedral : 8.198 167.876 6991 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 3.25 % Allowed : 18.49 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.88 (0.11), residues: 6142 helix: 1.97 (0.11), residues: 2288 sheet: 0.42 (0.13), residues: 1546 loop : -0.69 (0.13), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 56 HIS 0.006 0.001 HIS T 59 PHE 0.022 0.002 PHE X 68 TYR 0.025 0.002 TYR R 153 ARG 0.009 0.001 ARG W 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 767 time to evaluate : 4.854 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8183 (mttp) REVERT: B 101 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7795 (mp10) REVERT: D 157 LYS cc_start: 0.8950 (mttt) cc_final: 0.8692 (mttt) REVERT: E 20 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7138 (mtp180) REVERT: F 166 GLN cc_start: 0.7969 (tp40) cc_final: 0.7717 (tp-100) REVERT: J 60 GLN cc_start: 0.8628 (mt0) cc_final: 0.8420 (mt0) REVERT: M 114 ASP cc_start: 0.8180 (p0) cc_final: 0.7910 (p0) REVERT: N 26 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8231 (mtp) REVERT: N 110 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7320 (mtm) REVERT: P 195 LYS cc_start: 0.8960 (ttpt) cc_final: 0.8752 (ttmt) REVERT: S 182 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8079 (tm-30) outliers start: 139 outliers final: 86 residues processed: 853 average time/residue: 1.7570 time to fit residues: 1813.5589 Evaluate side-chains 847 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 756 time to evaluate : 5.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 25 MET Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain S residue 29 GLU Chi-restraints excluded: chain S residue 196 LYS Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 229 VAL Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain V residue 87 MET Chi-restraints excluded: chain V residue 188 GLN Chi-restraints excluded: chain W residue 13 ILE Chi-restraints excluded: chain X residue 130 MET Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain X residue 180 SER Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain Z residue 38 ILE Chi-restraints excluded: chain Z residue 54 SER Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 193 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 198 optimal weight: 1.9990 chunk 530 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 346 optimal weight: 5.9990 chunk 145 optimal weight: 0.5980 chunk 590 optimal weight: 4.9990 chunk 489 optimal weight: 1.9990 chunk 273 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 309 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN D 122 ASN E 118 ASN F 68 ASN G 97 ASN H 107 GLN H 155 GLN I 92 GLN K 27 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN M 108 ASN M 159 GLN N 47 ASN P 95 GLN S 13 ASN S 114 GLN ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 ASN T 121 GLN V 188 GLN X 156 ASN Y 27 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 30 GLN Z 39 ASN Z 71 ASN Z 163 GLN a 157 ASN a 159 GLN b 108 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 46428 Z= 0.192 Angle : 0.515 11.129 63026 Z= 0.271 Chirality : 0.042 0.290 7364 Planarity : 0.004 0.037 8010 Dihedral : 7.960 168.885 6987 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.52 % Favored : 97.41 % Rotamer: Outliers : 2.59 % Allowed : 19.35 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.15 (0.11), residues: 6142 helix: 2.27 (0.11), residues: 2274 sheet: 0.49 (0.13), residues: 1534 loop : -0.55 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 100 HIS 0.004 0.001 HIS T 65 PHE 0.021 0.001 PHE B 172 TYR 0.020 0.001 TYR R 153 ARG 0.007 0.000 ARG W 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 807 time to evaluate : 5.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 201 MET cc_start: 0.7905 (ttm) cc_final: 0.7650 (mtp) REVERT: E 20 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7212 (mtp180) REVERT: E 221 GLN cc_start: 0.8464 (mt0) cc_final: 0.8171 (mm-40) REVERT: J 60 GLN cc_start: 0.8505 (mt0) cc_final: 0.8275 (mt0) REVERT: K 111 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7120 (mm-30) REVERT: M 114 ASP cc_start: 0.8168 (p0) cc_final: 0.7898 (p0) REVERT: N 26 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8210 (mtp) REVERT: O 117 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7430 (mmp80) REVERT: P 49 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8440 (ptmt) REVERT: P 195 LYS cc_start: 0.8915 (ttpt) cc_final: 0.8706 (ttmt) REVERT: S 182 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7793 (tp40) outliers start: 111 outliers final: 64 residues processed: 877 average time/residue: 1.7377 time to fit residues: 1855.4335 Evaluate side-chains 859 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 792 time to evaluate : 5.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 117 ARG Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain S residue 29 GLU Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 229 VAL Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain X residue 130 MET Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 54 SER Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 169 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 569 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 336 optimal weight: 3.9990 chunk 431 optimal weight: 5.9990 chunk 333 optimal weight: 4.9990 chunk 496 optimal weight: 2.9990 chunk 329 optimal weight: 7.9990 chunk 587 optimal weight: 7.9990 chunk 367 optimal weight: 10.0000 chunk 358 optimal weight: 5.9990 chunk 271 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 ASN E 118 ASN G 97 ASN H 107 GLN H 155 GLN J 64 GLN K 27 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN M 108 ASN M 159 GLN N 47 ASN P 95 GLN Q 198 ASN S 114 GLN ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 225 ASN T 21 GLN T 86 ASN V 188 GLN X 156 ASN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 30 GLN Z 39 ASN Z 120 ASN a 157 ASN a 159 GLN b 108 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 46428 Z= 0.440 Angle : 0.580 10.985 63026 Z= 0.303 Chirality : 0.045 0.300 7364 Planarity : 0.004 0.039 8010 Dihedral : 8.010 169.195 6986 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.09 % Favored : 96.86 % Rotamer: Outliers : 3.06 % Allowed : 19.26 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.07 (0.11), residues: 6142 helix: 2.15 (0.11), residues: 2286 sheet: 0.49 (0.13), residues: 1540 loop : -0.57 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 56 HIS 0.005 0.001 HIS J 187 PHE 0.021 0.001 PHE X 68 TYR 0.024 0.001 TYR R 153 ARG 0.007 0.000 ARG P 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 783 time to evaluate : 5.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8146 (mttp) REVERT: C 201 MET cc_start: 0.7894 (ttm) cc_final: 0.7688 (mtp) REVERT: E 20 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7233 (mtp180) REVERT: E 204 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8231 (tp-100) REVERT: E 221 GLN cc_start: 0.8501 (mt0) cc_final: 0.8143 (mm-40) REVERT: J 60 GLN cc_start: 0.8602 (mt0) cc_final: 0.8390 (mt0) REVERT: K 111 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7148 (mm-30) REVERT: M 114 ASP cc_start: 0.8210 (p0) cc_final: 0.7923 (p0) REVERT: O 117 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7506 (mmp80) REVERT: P 195 LYS cc_start: 0.8946 (ttpt) cc_final: 0.8721 (ttmt) REVERT: S 29 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: S 182 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8126 (tm-30) REVERT: b 110 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7100 (mtm) outliers start: 131 outliers final: 85 residues processed: 870 average time/residue: 1.7856 time to fit residues: 1903.1495 Evaluate side-chains 860 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 770 time to evaluate : 5.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 25 MET Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 19 GLU Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 117 ARG Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 168 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain S residue 29 GLU Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 229 VAL Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain W residue 212 VAL Chi-restraints excluded: chain X residue 11 MET Chi-restraints excluded: chain X residue 130 MET Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 54 SER Chi-restraints excluded: chain Z residue 98 MET Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 183 ASP Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 110 MET Chi-restraints excluded: chain b residue 169 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 363 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 351 optimal weight: 5.9990 chunk 177 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 373 optimal weight: 3.9990 chunk 400 optimal weight: 1.9990 chunk 290 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 462 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN D 122 ASN E 118 ASN G 97 ASN H 107 GLN H 155 GLN I 31 ASN K 27 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN M 108 ASN M 159 GLN N 47 ASN P 95 GLN S 13 ASN S 114 GLN ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 121 GLN V 188 GLN X 156 ASN Y 27 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 30 GLN Z 39 ASN a 131 GLN a 157 ASN a 159 GLN b 108 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 46428 Z= 0.201 Angle : 0.520 12.735 63026 Z= 0.273 Chirality : 0.042 0.287 7364 Planarity : 0.004 0.039 8010 Dihedral : 7.873 170.335 6986 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.72 % Favored : 97.23 % Rotamer: Outliers : 2.52 % Allowed : 20.03 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.24 (0.11), residues: 6142 helix: 2.31 (0.11), residues: 2284 sheet: 0.55 (0.13), residues: 1530 loop : -0.48 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 100 HIS 0.004 0.001 HIS F 65 PHE 0.017 0.001 PHE X 68 TYR 0.020 0.001 TYR R 153 ARG 0.008 0.000 ARG P 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 802 time to evaluate : 4.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 20 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7161 (mtp180) REVERT: E 204 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8149 (tp-100) REVERT: E 221 GLN cc_start: 0.8460 (mt0) cc_final: 0.8193 (mm-40) REVERT: J 60 GLN cc_start: 0.8527 (mt0) cc_final: 0.8314 (mt0) REVERT: J 79 ARG cc_start: 0.8379 (ptm160) cc_final: 0.8170 (ptt180) REVERT: K 111 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7095 (mm-30) REVERT: L 36 ILE cc_start: 0.8718 (mp) cc_final: 0.8386 (mp) REVERT: M 114 ASP cc_start: 0.8177 (p0) cc_final: 0.7882 (p0) REVERT: O 117 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7432 (mmp80) REVERT: P 195 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8692 (ttmt) REVERT: S 182 GLN cc_start: 0.8344 (tm-30) cc_final: 0.8064 (tm-30) REVERT: V 117 MET cc_start: 0.8078 (mtp) cc_final: 0.7864 (mtp) REVERT: b 110 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7084 (mtm) outliers start: 108 outliers final: 73 residues processed: 875 average time/residue: 1.7302 time to fit residues: 1832.6816 Evaluate side-chains 866 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 790 time to evaluate : 5.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 25 MET Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 117 ARG Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 168 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 229 VAL Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 35 THR Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain V residue 87 MET Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain X residue 130 MET Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 98 MET Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 110 MET Chi-restraints excluded: chain b residue 169 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 534 optimal weight: 0.9980 chunk 563 optimal weight: 7.9990 chunk 513 optimal weight: 0.2980 chunk 547 optimal weight: 0.9990 chunk 329 optimal weight: 7.9990 chunk 238 optimal weight: 0.8980 chunk 430 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 495 optimal weight: 4.9990 chunk 518 optimal weight: 5.9990 chunk 545 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN D 122 ASN E 118 ASN G 97 ASN H 107 GLN H 155 GLN I 92 GLN K 27 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN M 108 ASN M 159 GLN N 47 ASN P 95 GLN Q 198 ASN S 13 ASN S 114 GLN ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 225 ASN T 86 ASN V 188 GLN X 156 ASN X 168 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 30 GLN Z 39 ASN a 159 GLN b 108 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 46428 Z= 0.159 Angle : 0.502 9.665 63026 Z= 0.264 Chirality : 0.042 0.277 7364 Planarity : 0.004 0.041 8010 Dihedral : 7.660 171.712 6984 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.36 % Rotamer: Outliers : 1.96 % Allowed : 20.92 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.34 (0.11), residues: 6142 helix: 2.43 (0.11), residues: 2288 sheet: 0.56 (0.13), residues: 1518 loop : -0.41 (0.13), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 56 HIS 0.007 0.001 HIS U 201 PHE 0.017 0.001 PHE B 172 TYR 0.020 0.001 TYR b 83 ARG 0.010 0.000 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 832 time to evaluate : 5.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 20 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7127 (mtp180) REVERT: E 204 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8107 (tp-100) REVERT: J 60 GLN cc_start: 0.8499 (mt0) cc_final: 0.8286 (mt0) REVERT: M 114 ASP cc_start: 0.8165 (p0) cc_final: 0.7842 (p0) REVERT: N 64 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8411 (ttpp) REVERT: O 117 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7403 (mmp80) REVERT: P 50 LYS cc_start: 0.8377 (mtmt) cc_final: 0.8103 (mtmt) REVERT: S 182 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7784 (tp40) REVERT: V 117 MET cc_start: 0.8050 (mtp) cc_final: 0.7845 (mtp) outliers start: 84 outliers final: 66 residues processed: 893 average time/residue: 1.7700 time to fit residues: 1912.1700 Evaluate side-chains 873 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 804 time to evaluate : 5.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 25 MET Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 64 LYS Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 117 ARG Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 168 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 35 THR Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain Z residue 54 SER Chi-restraints excluded: chain Z residue 155 ASP Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 359 optimal weight: 0.7980 chunk 579 optimal weight: 6.9990 chunk 353 optimal weight: 1.9990 chunk 274 optimal weight: 6.9990 chunk 402 optimal weight: 8.9990 chunk 607 optimal weight: 4.9990 chunk 559 optimal weight: 7.9990 chunk 483 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 373 optimal weight: 0.0870 chunk 296 optimal weight: 7.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN D 122 ASN E 118 ASN F 86 ASN G 97 ASN G 180 GLN H 107 GLN H 155 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN M 80 ASN M 159 GLN N 47 ASN P 95 GLN R 146 GLN S 13 ASN S 114 GLN ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 225 ASN T 86 ASN T 121 GLN U 180 GLN V 188 GLN X 156 ASN X 168 GLN Y 55 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 30 GLN Z 39 ASN a 146 GLN a 159 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 46428 Z= 0.243 Angle : 0.526 11.881 63026 Z= 0.275 Chirality : 0.043 0.274 7364 Planarity : 0.004 0.039 8010 Dihedral : 7.603 171.603 6981 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.25 % Rotamer: Outliers : 1.94 % Allowed : 21.17 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.37 (0.11), residues: 6142 helix: 2.44 (0.11), residues: 2286 sheet: 0.58 (0.13), residues: 1518 loop : -0.39 (0.13), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 56 HIS 0.004 0.001 HIS T 65 PHE 0.033 0.001 PHE P 172 TYR 0.020 0.001 TYR R 153 ARG 0.008 0.000 ARG P 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 810 time to evaluate : 5.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 157 LYS cc_start: 0.8948 (mttt) cc_final: 0.8705 (mttt) REVERT: E 20 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7134 (mtp180) REVERT: E 204 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8110 (tp-100) REVERT: E 221 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8354 (mm-40) REVERT: J 60 GLN cc_start: 0.8535 (mt0) cc_final: 0.8324 (mt0) REVERT: M 114 ASP cc_start: 0.8182 (p0) cc_final: 0.7870 (p0) REVERT: N 64 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8414 (ttpp) REVERT: O 117 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7434 (mmp80) REVERT: S 182 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7811 (tp40) REVERT: V 117 MET cc_start: 0.8072 (mtp) cc_final: 0.7844 (mtp) outliers start: 83 outliers final: 69 residues processed: 869 average time/residue: 1.7740 time to fit residues: 1868.0952 Evaluate side-chains 870 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 798 time to evaluate : 5.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 25 MET Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 64 LYS Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 117 ARG Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 168 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain S residue 32 LYS Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 35 THR Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain W residue 87 MET Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain Z residue 155 ASP Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 384 optimal weight: 5.9990 chunk 515 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 446 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 484 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 497 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 ASN E 118 ASN F 86 ASN G 97 ASN H 107 GLN H 155 GLN J 17 ASN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN M 80 ASN M 159 GLN N 47 ASN P 95 GLN Q 69 ASN Q 198 ASN S 13 ASN S 114 GLN ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 225 ASN T 86 ASN U 180 GLN V 188 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 30 GLN Z 39 ASN a 159 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.071157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.060455 restraints weight = 86989.525| |-----------------------------------------------------------------------------| r_work (start): 0.2578 rms_B_bonded: 2.07 r_work: 0.2465 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2350 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 46428 Z= 0.403 Angle : 0.582 11.102 63026 Z= 0.304 Chirality : 0.045 0.283 7364 Planarity : 0.004 0.050 8010 Dihedral : 7.753 170.401 6981 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.00 % Rotamer: Outliers : 2.06 % Allowed : 21.22 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.27 (0.11), residues: 6142 helix: 2.36 (0.11), residues: 2270 sheet: 0.55 (0.13), residues: 1532 loop : -0.45 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 100 HIS 0.005 0.001 HIS J 187 PHE 0.021 0.001 PHE X 68 TYR 0.024 0.001 TYR R 153 ARG 0.011 0.001 ARG H 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24533.06 seconds wall clock time: 432 minutes 39.54 seconds (25959.54 seconds total)