Starting phenix.real_space_refine on Tue Aug 26 16:10:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qbl_18314/08_2025/8qbl_18314.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qbl_18314/08_2025/8qbl_18314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qbl_18314/08_2025/8qbl_18314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qbl_18314/08_2025/8qbl_18314.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qbl_18314/08_2025/8qbl_18314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qbl_18314/08_2025/8qbl_18314.map" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 871 5.49 5 Mg 5 5.21 5 S 49 5.16 5 C 21857 2.51 5 N 7217 2.21 5 O 9497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39496 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 309, 2332 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 78 Conformer: "B" Number of residues, atoms: 309, 2332 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 78 bond proxies already assigned to first conformer: 2365 Chain: "C" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1293 Classifications: {'RNA': 61} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 23, 'rna3p_pyr': 26} Link IDs: {'rna2p': 12, 'rna3p': 48} Chain breaks: 2 Chain: "D" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 8, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "G" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 695 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 448 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 4, 'GLN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 6, 'TYR:plan': 4, 'ARG:plan': 10, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 195 Chain: "I" Number of atoms: 1531 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 309, 1526 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 276} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1002 Unresolved non-hydrogen angles: 1267 Unresolved non-hydrogen dihedrals: 846 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLU:plan': 14, 'TYR:plan': 14, 'ASN:plan1': 14, 'PHE:plan': 13, 'ARG:plan': 22, 'HIS:plan': 8, 'ASP:plan': 10, 'GLN:plan1': 8, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 504 Conformer: "B" Number of residues, atoms: 309, 1526 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 276} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1002 Unresolved non-hydrogen angles: 1267 Unresolved non-hydrogen dihedrals: 846 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLU:plan': 14, 'TYR:plan': 14, 'ASN:plan1': 14, 'PHE:plan': 13, 'ARG:plan': 22, 'HIS:plan': 8, 'ASP:plan': 10, 'GLN:plan1': 8, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 504 bond proxies already assigned to first conformer: 1519 Chain: "K" Number of atoms: 2296 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 309, 2286 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 6, 'TYR:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 114 Conformer: "B" Number of residues, atoms: 309, 2286 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 6, 'TYR:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 114 bond proxies already assigned to first conformer: 2318 Chain: "L" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 767 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain breaks: 1 Chain: "M" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1231 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 22, 'rna3p_pyr': 24} Link IDs: {'rna2p': 12, 'rna3p': 45} Chain breaks: 2 Chain: "N" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 8, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "O" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1293 Classifications: {'RNA': 61} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 23, 'rna3p_pyr': 25} Link IDs: {'rna2p': 13, 'rna3p': 47} Chain breaks: 2 Chain: "P" Number of atoms: 1896 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 309, 1891 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 747 Unresolved non-hydrogen dihedrals: 498 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLU:plan': 14, 'TYR:plan': 7, 'ASN:plan1': 7, 'PHE:plan': 5, 'HIS:plan': 4, 'ASP:plan': 10, 'ARG:plan': 15, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 297 Conformer: "B" Number of residues, atoms: 309, 1891 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 747 Unresolved non-hydrogen dihedrals: 498 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLU:plan': 14, 'TYR:plan': 7, 'ASN:plan1': 7, 'PHE:plan': 5, 'HIS:plan': 4, 'ASP:plan': 10, 'ARG:plan': 15, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 297 bond proxies already assigned to first conformer: 1918 Chain: "S" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 8, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "U" Number of atoms: 2270 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 309, 2260 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 6, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 110 Conformer: "B" Number of residues, atoms: 309, 2260 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 6, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 110 bond proxies already assigned to first conformer: 2293 Chain: "W" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1293 Classifications: {'RNA': 61} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 23, 'rna3p_pyr': 25} Link IDs: {'rna2p': 13, 'rna3p': 47} Chain breaks: 2 Chain: "X" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 8, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "Y" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 8, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "Z" Number of atoms: 1531 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 309, 1526 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 276} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1002 Unresolved non-hydrogen angles: 1267 Unresolved non-hydrogen dihedrals: 846 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLU:plan': 14, 'TYR:plan': 14, 'ASN:plan1': 14, 'PHE:plan': 13, 'ARG:plan': 22, 'HIS:plan': 8, 'ASP:plan': 10, 'GLN:plan1': 8, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 504 Conformer: "B" Number of residues, atoms: 309, 1526 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 276} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1002 Unresolved non-hydrogen angles: 1267 Unresolved non-hydrogen dihedrals: 846 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLU:plan': 14, 'TYR:plan': 14, 'ASN:plan1': 14, 'PHE:plan': 13, 'ARG:plan': 22, 'HIS:plan': 8, 'ASP:plan': 10, 'GLN:plan1': 8, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 504 bond proxies already assigned to first conformer: 1519 Chain: "b" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1293 Classifications: {'RNA': 61} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 23, 'rna3p_pyr': 26} Link IDs: {'rna2p': 12, 'rna3p': 48} Chain breaks: 2 Chain: "c" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 8, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "E" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2240 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 6, 'TRANS': 295} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 9, 'ASN:plan1': 2, 'GLN:plan1': 2, 'ARG:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 123 Chain: "F" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2177 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 6, 'TRANS': 295} Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 7, 'ASN:plan1': 3, 'GLN:plan1': 5, 'PHE:plan': 1, 'ARG:plan': 8, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 155 Chain: "H" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2035 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 6, 'TRANS': 295} Unresolved non-hydrogen bonds: 424 Unresolved non-hydrogen angles: 504 Unresolved non-hydrogen dihedrals: 354 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 18, 'GLU:plan': 13, 'GLN:plan1': 9, 'ARG:plan': 14, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 255 Chain: "T" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2235 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 6, 'TRANS': 295} Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 8, 'ASN:plan1': 3, 'GLN:plan1': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 121 Chain: "B" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1752 Classifications: {'DNA': 85} Link IDs: {'rna3p': 84} Chain: "J" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1752 Classifications: {'DNA': 85} Link IDs: {'rna3p': 84} Chain: "Q" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1752 Classifications: {'DNA': 85} Link IDs: {'rna3p': 84} Chain: "R" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1293 Classifications: {'RNA': 61} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 23, 'rna3p_pyr': 25} Link IDs: {'rna2p': 13, 'rna3p': 47} Chain breaks: 2 Chain: "V" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1752 Classifications: {'DNA': 85} Link IDs: {'rna3p': 84} Chain: "a" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'NAD:plan-2': 1, 'NAD:plan-4': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'NAD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'NAD:plan-2': 2, 'NAD:plan-4': 2} Unresolved non-hydrogen planarities: 22 Chain: "T" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'NAD:plan-2': 1, 'NAD:plan-4': 1} Unresolved non-hydrogen planarities: 11 Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AHIS A 24 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 24 " occ=0.50 residue: pdb=" N AHIS I 24 " occ=0.50 ... (8 atoms not shown) pdb=" CB BHIS I 24 " occ=0.50 residue: pdb=" N AHIS K 24 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS K 24 " occ=0.50 residue: pdb=" N AHIS P 24 " occ=0.50 ... (8 atoms not shown) pdb=" CB BHIS P 24 " occ=0.50 residue: pdb=" N AHIS U 24 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS U 24 " occ=0.50 residue: pdb=" N AHIS Z 24 " occ=0.50 ... (8 atoms not shown) pdb=" CB BHIS Z 24 " occ=0.50 Time building chain proxies: 11.25, per 1000 atoms: 0.28 Number of scatterers: 39496 At special positions: 0 Unit cell: (138.944, 185.536, 346.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 49 16.00 P 871 15.00 Mg 5 11.99 O 9497 8.00 N 7217 7.00 C 21857 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 - 3.00 Amino acid : True - 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: 3.36 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6044 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 28 sheets defined 65.0% alpha, 8.9% beta 289 base pairs and 523 stacking pairs defined. Time for finding SS restraints: 5.23 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 33 through 43 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 69 through 83 Processing helix chain 'A' and resid 84 through 87 Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 128 through 140 removed outlier: 3.937A pdb=" N VAL A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 154 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 174 through 187 removed outlier: 4.415A pdb=" N SER A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 220 removed outlier: 3.592A pdb=" N VAL A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 224 Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 256 through 272 Processing helix chain 'A' and resid 277 through 292 Processing helix chain 'A' and resid 293 through 311 Processing helix chain 'G' and resid 6 through 19 Processing helix chain 'G' and resid 205 through 213 Processing helix chain 'G' and resid 217 through 230 Processing helix chain 'G' and resid 232 through 250 Processing helix chain 'G' and resid 263 through 274 Processing helix chain 'G' and resid 275 through 291 removed outlier: 3.652A pdb=" N LEU G 279 " --> pdb=" O ASP G 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 16 Processing helix chain 'I' and resid 22 through 31 Processing helix chain 'I' and resid 33 through 43 Processing helix chain 'I' and resid 44 through 46 No H-bonds generated for 'chain 'I' and resid 44 through 46' Processing helix chain 'I' and resid 69 through 83 Processing helix chain 'I' and resid 84 through 87 Processing helix chain 'I' and resid 101 through 107 removed outlier: 3.893A pdb=" N ASN I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 110 No H-bonds generated for 'chain 'I' and resid 108 through 110' Processing helix chain 'I' and resid 122 through 127 removed outlier: 3.597A pdb=" N LEU I 127 " --> pdb=" O PHE I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 140 removed outlier: 3.759A pdb=" N VAL I 132 " --> pdb=" O THR I 128 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY I 140 " --> pdb=" O PHE I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 154 Processing helix chain 'I' and resid 165 through 174 Processing helix chain 'I' and resid 174 through 187 removed outlier: 4.106A pdb=" N SER I 187 " --> pdb=" O GLY I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 220 removed outlier: 3.540A pdb=" N VAL I 209 " --> pdb=" O SER I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 224 Processing helix chain 'I' and resid 229 through 232 Processing helix chain 'I' and resid 256 through 272 Processing helix chain 'I' and resid 277 through 292 Processing helix chain 'I' and resid 292 through 311 removed outlier: 3.542A pdb=" N HIS I 296 " --> pdb=" O ASP I 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 15 Processing helix chain 'K' and resid 22 through 31 Processing helix chain 'K' and resid 33 through 43 Processing helix chain 'K' and resid 44 through 46 No H-bonds generated for 'chain 'K' and resid 44 through 46' Processing helix chain 'K' and resid 69 through 83 Processing helix chain 'K' and resid 84 through 87 Processing helix chain 'K' and resid 102 through 107 Processing helix chain 'K' and resid 108 through 110 No H-bonds generated for 'chain 'K' and resid 108 through 110' Processing helix chain 'K' and resid 122 through 127 Processing helix chain 'K' and resid 128 through 140 removed outlier: 3.937A pdb=" N VAL K 132 " --> pdb=" O THR K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 154 Processing helix chain 'K' and resid 165 through 174 Processing helix chain 'K' and resid 174 through 187 removed outlier: 4.414A pdb=" N SER K 187 " --> pdb=" O GLY K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 220 removed outlier: 3.592A pdb=" N VAL K 209 " --> pdb=" O SER K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 224 Processing helix chain 'K' and resid 228 through 232 Processing helix chain 'K' and resid 256 through 272 Processing helix chain 'K' and resid 277 through 292 Processing helix chain 'K' and resid 293 through 311 Processing helix chain 'P' and resid 4 through 15 Processing helix chain 'P' and resid 22 through 31 Processing helix chain 'P' and resid 33 through 43 Processing helix chain 'P' and resid 44 through 46 No H-bonds generated for 'chain 'P' and resid 44 through 46' Processing helix chain 'P' and resid 69 through 83 Processing helix chain 'P' and resid 84 through 87 Processing helix chain 'P' and resid 102 through 107 Processing helix chain 'P' and resid 108 through 110 No H-bonds generated for 'chain 'P' and resid 108 through 110' Processing helix chain 'P' and resid 122 through 127 Processing helix chain 'P' and resid 128 through 140 removed outlier: 3.938A pdb=" N VAL P 132 " --> pdb=" O THR P 128 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 154 Processing helix chain 'P' and resid 165 through 174 Processing helix chain 'P' and resid 174 through 187 removed outlier: 4.415A pdb=" N SER P 187 " --> pdb=" O GLY P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 205 through 220 removed outlier: 3.592A pdb=" N VAL P 209 " --> pdb=" O SER P 205 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 224 Processing helix chain 'P' and resid 228 through 232 Processing helix chain 'P' and resid 256 through 272 Processing helix chain 'P' and resid 277 through 292 Processing helix chain 'P' and resid 293 through 311 Processing helix chain 'U' and resid 4 through 15 Processing helix chain 'U' and resid 22 through 31 Processing helix chain 'U' and resid 33 through 43 Processing helix chain 'U' and resid 44 through 46 No H-bonds generated for 'chain 'U' and resid 44 through 46' Processing helix chain 'U' and resid 69 through 83 Processing helix chain 'U' and resid 84 through 87 Processing helix chain 'U' and resid 102 through 107 Processing helix chain 'U' and resid 108 through 110 No H-bonds generated for 'chain 'U' and resid 108 through 110' Processing helix chain 'U' and resid 122 through 127 Processing helix chain 'U' and resid 128 through 140 removed outlier: 3.937A pdb=" N VAL U 132 " --> pdb=" O THR U 128 " (cutoff:3.500A) Processing helix chain 'U' and resid 142 through 154 Processing helix chain 'U' and resid 165 through 174 Processing helix chain 'U' and resid 174 through 187 removed outlier: 4.415A pdb=" N SER U 187 " --> pdb=" O GLY U 183 " (cutoff:3.500A) Processing helix chain 'U' and resid 205 through 220 removed outlier: 3.593A pdb=" N VAL U 209 " --> pdb=" O SER U 205 " (cutoff:3.500A) Processing helix chain 'U' and resid 221 through 224 Processing helix chain 'U' and resid 228 through 232 Processing helix chain 'U' and resid 256 through 272 Processing helix chain 'U' and resid 277 through 292 Processing helix chain 'U' and resid 293 through 311 Processing helix chain 'Z' and resid 4 through 16 removed outlier: 3.659A pdb=" N LEU Z 15 " --> pdb=" O ARG Z 11 " (cutoff:3.500A) Processing helix chain 'Z' and resid 22 through 31 Processing helix chain 'Z' and resid 33 through 43 Processing helix chain 'Z' and resid 44 through 46 No H-bonds generated for 'chain 'Z' and resid 44 through 46' Processing helix chain 'Z' and resid 69 through 83 Processing helix chain 'Z' and resid 84 through 87 Processing helix chain 'Z' and resid 101 through 107 removed outlier: 3.816A pdb=" N ASN Z 105 " --> pdb=" O SER Z 101 " (cutoff:3.500A) Processing helix chain 'Z' and resid 108 through 110 No H-bonds generated for 'chain 'Z' and resid 108 through 110' Processing helix chain 'Z' and resid 122 through 127 removed outlier: 3.617A pdb=" N LEU Z 127 " --> pdb=" O PHE Z 123 " (cutoff:3.500A) Processing helix chain 'Z' and resid 128 through 140 removed outlier: 3.757A pdb=" N VAL Z 132 " --> pdb=" O THR Z 128 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY Z 140 " --> pdb=" O PHE Z 136 " (cutoff:3.500A) Processing helix chain 'Z' and resid 142 through 153 Processing helix chain 'Z' and resid 165 through 174 Processing helix chain 'Z' and resid 174 through 188 removed outlier: 4.131A pdb=" N SER Z 187 " --> pdb=" O GLY Z 183 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG Z 188 " --> pdb=" O TYR Z 184 " (cutoff:3.500A) Processing helix chain 'Z' and resid 205 through 220 Processing helix chain 'Z' and resid 221 through 224 Processing helix chain 'Z' and resid 228 through 232 Processing helix chain 'Z' and resid 256 through 272 Processing helix chain 'Z' and resid 277 through 292 Processing helix chain 'Z' and resid 292 through 311 removed outlier: 3.660A pdb=" N THR Z 301 " --> pdb=" O ARG Z 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 19 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 68 through 75 Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 100 through 113 Processing helix chain 'E' and resid 113 through 119 removed outlier: 3.946A pdb=" N LYS E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 133 through 138 Processing helix chain 'E' and resid 138 through 147 Processing helix chain 'E' and resid 155 through 164 Processing helix chain 'E' and resid 166 through 171 Processing helix chain 'E' and resid 173 through 190 Processing helix chain 'E' and resid 198 through 201 Processing helix chain 'E' and resid 202 through 213 Proline residue: E 208 - end of helix Processing helix chain 'E' and resid 217 through 230 removed outlier: 3.629A pdb=" N LYS E 230 " --> pdb=" O PHE E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 250 Processing helix chain 'E' and resid 263 through 274 Processing helix chain 'E' and resid 275 through 292 removed outlier: 3.646A pdb=" N LEU E 279 " --> pdb=" O ASP E 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 18 removed outlier: 3.509A pdb=" N HIS F 16 " --> pdb=" O GLN F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 55 Processing helix chain 'F' and resid 67 through 75 Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 100 through 112 Processing helix chain 'F' and resid 113 through 119 removed outlier: 3.979A pdb=" N LYS F 119 " --> pdb=" O ASN F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 133 through 138 Processing helix chain 'F' and resid 138 through 147 Processing helix chain 'F' and resid 155 through 164 Processing helix chain 'F' and resid 166 through 171 Processing helix chain 'F' and resid 173 through 190 Processing helix chain 'F' and resid 198 through 201 Processing helix chain 'F' and resid 202 through 213 Proline residue: F 208 - end of helix Processing helix chain 'F' and resid 217 through 230 removed outlier: 3.542A pdb=" N LYS F 227 " --> pdb=" O GLU F 223 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS F 230 " --> pdb=" O PHE F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 250 Processing helix chain 'F' and resid 263 through 274 Processing helix chain 'F' and resid 276 through 292 Processing helix chain 'H' and resid 6 through 18 Processing helix chain 'H' and resid 44 through 55 Processing helix chain 'H' and resid 67 through 75 Processing helix chain 'H' and resid 79 through 91 Processing helix chain 'H' and resid 100 through 113 Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'H' and resid 127 through 129 No H-bonds generated for 'chain 'H' and resid 127 through 129' Processing helix chain 'H' and resid 133 through 138 Processing helix chain 'H' and resid 138 through 147 Processing helix chain 'H' and resid 155 through 164 Processing helix chain 'H' and resid 166 through 171 Processing helix chain 'H' and resid 173 through 190 Processing helix chain 'H' and resid 198 through 201 Processing helix chain 'H' and resid 202 through 213 Proline residue: H 208 - end of helix Processing helix chain 'H' and resid 217 through 230 removed outlier: 3.680A pdb=" N LYS H 227 " --> pdb=" O GLU H 223 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS H 230 " --> pdb=" O PHE H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 250 Processing helix chain 'H' and resid 263 through 274 Processing helix chain 'H' and resid 275 through 292 removed outlier: 3.657A pdb=" N LEU H 279 " --> pdb=" O ASP H 275 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 19 Processing helix chain 'T' and resid 44 through 55 Processing helix chain 'T' and resid 68 through 75 Processing helix chain 'T' and resid 79 through 91 Processing helix chain 'T' and resid 100 through 113 Processing helix chain 'T' and resid 113 through 119 removed outlier: 3.947A pdb=" N LYS T 119 " --> pdb=" O ASN T 115 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 129 No H-bonds generated for 'chain 'T' and resid 127 through 129' Processing helix chain 'T' and resid 133 through 138 Processing helix chain 'T' and resid 138 through 147 Processing helix chain 'T' and resid 155 through 164 Processing helix chain 'T' and resid 166 through 171 Processing helix chain 'T' and resid 173 through 190 Processing helix chain 'T' and resid 198 through 201 Processing helix chain 'T' and resid 202 through 213 Proline residue: T 208 - end of helix Processing helix chain 'T' and resid 217 through 230 removed outlier: 3.629A pdb=" N LYS T 230 " --> pdb=" O PHE T 226 " (cutoff:3.500A) Processing helix chain 'T' and resid 232 through 250 Processing helix chain 'T' and resid 263 through 274 Processing helix chain 'T' and resid 275 through 292 removed outlier: 3.646A pdb=" N LEU T 279 " --> pdb=" O ASP T 275 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 195 Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA4, first strand: chain 'G' and resid 253 through 255 Processing sheet with id=AA5, first strand: chain 'I' and resid 48 through 54 removed outlier: 3.535A pdb=" N ARG I 63 " --> pdb=" O VAL I 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 191 through 195 Processing sheet with id=AA7, first strand: chain 'I' and resid 120 through 121 removed outlier: 4.395A pdb=" N VAL I 226 " --> pdb=" O GLU I 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 242 through 243 Processing sheet with id=AA9, first strand: chain 'K' and resid 48 through 54 Processing sheet with id=AB1, first strand: chain 'K' and resid 191 through 195 Processing sheet with id=AB2, first strand: chain 'K' and resid 242 through 243 Processing sheet with id=AB3, first strand: chain 'P' and resid 48 through 54 Processing sheet with id=AB4, first strand: chain 'P' and resid 191 through 195 Processing sheet with id=AB5, first strand: chain 'P' and resid 242 through 243 Processing sheet with id=AB6, first strand: chain 'U' and resid 48 through 54 Processing sheet with id=AB7, first strand: chain 'U' and resid 191 through 195 Processing sheet with id=AB8, first strand: chain 'U' and resid 242 through 243 Processing sheet with id=AB9, first strand: chain 'Z' and resid 48 through 54 removed outlier: 3.605A pdb=" N ARG Z 63 " --> pdb=" O VAL Z 53 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Z' and resid 93 through 94 Processing sheet with id=AC2, first strand: chain 'Z' and resid 242 through 243 Processing sheet with id=AC3, first strand: chain 'E' and resid 59 through 62 removed outlier: 6.270A pdb=" N THR E 31 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE E 95 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N PHE E 33 " --> pdb=" O ILE E 95 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE E 94 " --> pdb=" O ILE E 121 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE E 123 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU E 96 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ASP E 125 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N LEU E 152 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N CYS E 122 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N CYS E 154 " --> pdb=" O CYS E 122 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLN E 124 " --> pdb=" O CYS E 154 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 253 through 255 Processing sheet with id=AC5, first strand: chain 'F' and resid 59 through 62 removed outlier: 6.211A pdb=" N THR F 31 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE F 95 " --> pdb=" O THR F 31 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N PHE F 33 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE F 94 " --> pdb=" O ILE F 121 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE F 123 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU F 96 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ASP F 125 " --> pdb=" O LEU F 96 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N LEU F 152 " --> pdb=" O LEU F 120 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N CYS F 122 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N CYS F 154 " --> pdb=" O CYS F 122 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLN F 124 " --> pdb=" O CYS F 154 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 253 through 255 Processing sheet with id=AC7, first strand: chain 'H' and resid 59 through 62 removed outlier: 6.254A pdb=" N THR H 31 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE H 95 " --> pdb=" O THR H 31 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N PHE H 33 " --> pdb=" O ILE H 95 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE H 94 " --> pdb=" O ILE H 121 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE H 123 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU H 96 " --> pdb=" O ILE H 123 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASP H 125 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LEU H 152 " --> pdb=" O LEU H 120 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS H 122 " --> pdb=" O LEU H 152 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N CYS H 154 " --> pdb=" O CYS H 122 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLN H 124 " --> pdb=" O CYS H 154 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 253 through 255 Processing sheet with id=AC9, first strand: chain 'T' and resid 59 through 62 removed outlier: 6.270A pdb=" N THR T 31 " --> pdb=" O VAL T 93 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE T 95 " --> pdb=" O THR T 31 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N PHE T 33 " --> pdb=" O ILE T 95 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE T 94 " --> pdb=" O ILE T 121 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE T 123 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU T 96 " --> pdb=" O ILE T 123 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ASP T 125 " --> pdb=" O LEU T 96 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N LEU T 152 " --> pdb=" O LEU T 120 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N CYS T 122 " --> pdb=" O LEU T 152 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N CYS T 154 " --> pdb=" O CYS T 122 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLN T 124 " --> pdb=" O CYS T 154 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'T' and resid 253 through 255 1475 hydrogen bonds defined for protein. 4254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 740 hydrogen bonds 1420 hydrogen bond angles 0 basepair planarities 289 basepair parallelities 523 stacking parallelities Total time for adding SS restraints: 7.98 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6675 1.33 - 1.45: 14353 1.45 - 1.57: 19193 1.57 - 1.69: 1709 1.69 - 1.81: 66 Bond restraints: 41996 Sorted by residual: bond pdb=" O3' C M 65 " pdb=" P A M 66 " ideal model delta sigma weight residual 1.607 1.563 0.044 1.50e-02 4.44e+03 8.45e+00 bond pdb=" O3 NAD F 402 " pdb=" PA NAD F 402 " ideal model delta sigma weight residual 1.653 1.599 0.054 2.00e-02 2.50e+03 7.24e+00 bond pdb=" O3 NAD E 401 " pdb=" PA NAD E 401 " ideal model delta sigma weight residual 1.653 1.600 0.053 2.00e-02 2.50e+03 7.12e+00 bond pdb=" O3 NAD T 401 " pdb=" PA NAD T 401 " ideal model delta sigma weight residual 1.653 1.600 0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" O3 NAD F 401 " pdb=" PA NAD F 401 " ideal model delta sigma weight residual 1.653 1.600 0.053 2.00e-02 2.50e+03 6.90e+00 ... (remaining 41991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 60670 2.72 - 5.43: 365 5.43 - 8.15: 71 8.15 - 10.86: 11 10.86 - 13.58: 5 Bond angle restraints: 61122 Sorted by residual: angle pdb=" C3' C R 65 " pdb=" O3' C R 65 " pdb=" P A R 66 " ideal model delta sigma weight residual 120.20 106.62 13.58 1.50e+00 4.44e-01 8.19e+01 angle pdb=" C3' U R 72 " pdb=" O3' U R 72 " pdb=" P C R 73 " ideal model delta sigma weight residual 120.20 107.91 12.29 1.50e+00 4.44e-01 6.72e+01 angle pdb=" C3' C W 65 " pdb=" O3' C W 65 " pdb=" P A W 66 " ideal model delta sigma weight residual 120.20 108.80 11.40 1.50e+00 4.44e-01 5.78e+01 angle pdb=" O ALA F 106 " pdb=" C ALA F 106 " pdb=" N LEU F 107 " ideal model delta sigma weight residual 122.12 114.40 7.72 1.06e+00 8.90e-01 5.30e+01 angle pdb=" C3' G M 69 " pdb=" O3' G M 69 " pdb=" P A M 70 " ideal model delta sigma weight residual 120.20 109.30 10.90 1.50e+00 4.44e-01 5.28e+01 ... (remaining 61117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 21685 35.89 - 71.78: 2762 71.78 - 107.67: 187 107.67 - 143.56: 3 143.56 - 179.45: 39 Dihedral angle restraints: 24676 sinusoidal: 15357 harmonic: 9319 Sorted by residual: dihedral pdb=" O4' U b 67 " pdb=" C1' U b 67 " pdb=" N1 U b 67 " pdb=" C2 U b 67 " ideal model delta sinusoidal sigma weight residual 200.00 20.55 179.45 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U b 74 " pdb=" C1' U b 74 " pdb=" N1 U b 74 " pdb=" C2 U b 74 " ideal model delta sinusoidal sigma weight residual -160.00 17.83 -177.83 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U O 74 " pdb=" C1' U O 74 " pdb=" N1 U O 74 " pdb=" C2 U O 74 " ideal model delta sinusoidal sigma weight residual 200.00 22.83 177.17 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 24673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 7321 0.104 - 0.208: 203 0.208 - 0.313: 11 0.313 - 0.417: 16 0.417 - 0.521: 17 Chirality restraints: 7568 Sorted by residual: chirality pdb=" P G W 69 " pdb=" OP1 G W 69 " pdb=" OP2 G W 69 " pdb=" O5' G W 69 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.79e+00 chirality pdb=" P G C 69 " pdb=" OP1 G C 69 " pdb=" OP2 G C 69 " pdb=" O5' G C 69 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" P A C 66 " pdb=" OP1 A C 66 " pdb=" OP2 A C 66 " pdb=" O5' A C 66 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.49e+00 ... (remaining 7565 not shown) Planarity restraints: 4725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 106 " -0.048 2.00e-02 2.50e+03 9.11e-02 8.30e+01 pdb=" C ALA F 106 " 0.158 2.00e-02 2.50e+03 pdb=" O ALA F 106 " -0.058 2.00e-02 2.50e+03 pdb=" N LEU F 107 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 106 " -0.043 2.00e-02 2.50e+03 8.57e-02 7.34e+01 pdb=" C ALA E 106 " 0.148 2.00e-02 2.50e+03 pdb=" O ALA E 106 " -0.054 2.00e-02 2.50e+03 pdb=" N LEU E 107 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 106 " 0.044 2.00e-02 2.50e+03 8.39e-02 7.03e+01 pdb=" C ALA H 106 " -0.145 2.00e-02 2.50e+03 pdb=" O ALA H 106 " 0.054 2.00e-02 2.50e+03 pdb=" N LEU H 107 " 0.047 2.00e-02 2.50e+03 ... (remaining 4722 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 194 2.50 - 3.10: 27541 3.10 - 3.70: 70001 3.70 - 4.30: 96601 4.30 - 4.90: 142405 Nonbonded interactions: 336742 Sorted by model distance: nonbonded pdb=" OD1 ASP U 197 " pdb=" O3' DG V 85 " model vdw 1.899 3.040 nonbonded pdb=" OD2 ASP E 69 " pdb=" O3D NAD T 401 " model vdw 1.900 3.040 nonbonded pdb=" OD2 ASP T 69 " pdb=" O3D NAD E 401 " model vdw 1.900 3.040 nonbonded pdb=" NH1 ARG U 31 " pdb=" O TYR F 211 " model vdw 2.067 3.120 nonbonded pdb=" OP1 C C 73 " pdb=" NH2 ARG E 292 " model vdw 2.097 3.120 ... (remaining 336737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 3 through 15 and (name N or name CA or name C or name O o \ r name CB )) or resid 16 or (resid 17 through 23 and (name N or name CA or name \ C or name O or name CB )) or (resid 25 through 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 or (resid 58 through 76 and (name N or na \ me CA or name C or name O or name CB )) or resid 77 or (resid 78 through 94 and \ (name N or name CA or name C or name O or name CB )) or resid 95 or (resid 96 th \ rough 110 and (name N or name CA or name C or name O or name CB )) or (resid 111 \ through 133 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 34 or (resid 135 through 139 and (name N or name CA or name C or name O or name \ CB )) or resid 140 or (resid 141 through 161 and (name N or name CA or name C or \ name O or name CB )) or (resid 162 through 182 and (name N or name CA or name C \ or name O or name CB )) or resid 183 or (resid 184 through 185 and (name N or n \ ame CA or name C or name O or name CB )) or resid 186 or (resid 187 through 188 \ and (name N or name CA or name C or name O or name CB )) or resid 189 or (resid \ 190 through 223 and (name N or name CA or name C or name O or name CB )) or resi \ d 224 or (resid 225 through 235 and (name N or name CA or name C or name O or na \ me CB )) or resid 236 or (resid 237 through 244 and (name N or name CA or name C \ or name O or name CB )) or resid 245 or (resid 246 through 253 and (name N or n \ ame CA or name C or name O or name CB )) or resid 254 or (resid 255 and (name N \ or name CA or name C or name O or name CB )) or resid 256 or (resid 257 through \ 272 and (name N or name CA or name C or name O or name CB )) or (resid 273 throu \ gh 282 and (name N or name CA or name C or name O or name CB )) or resid 283 or \ (resid 284 through 310 and (name N or name CA or name C or name O or name CB )) \ or resid 311)) selection = (chain 'I' and (resid 3 through 23 or resid 25 through 311)) selection = (chain 'K' and ((resid 3 through 15 and (name N or name CA or name C or name O o \ r name CB )) or resid 16 or (resid 17 through 23 and (name N or name CA or name \ C or name O or name CB )) or (resid 25 through 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 or (resid 58 through 76 and (name N or na \ me CA or name C or name O or name CB )) or resid 77 or (resid 78 through 94 and \ (name N or name CA or name C or name O or name CB )) or resid 95 or (resid 96 th \ rough 110 and (name N or name CA or name C or name O or name CB )) or (resid 111 \ through 133 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 34 or (resid 135 through 139 and (name N or name CA or name C or name O or name \ CB )) or resid 140 or (resid 141 through 161 and (name N or name CA or name C or \ name O or name CB )) or (resid 162 through 182 and (name N or name CA or name C \ or name O or name CB )) or resid 183 or (resid 184 through 185 and (name N or n \ ame CA or name C or name O or name CB )) or resid 186 or (resid 187 through 188 \ and (name N or name CA or name C or name O or name CB )) or resid 189 or (resid \ 190 through 223 and (name N or name CA or name C or name O or name CB )) or resi \ d 224 or (resid 225 through 235 and (name N or name CA or name C or name O or na \ me CB )) or resid 236 or (resid 237 through 244 and (name N or name CA or name C \ or name O or name CB )) or resid 245 or (resid 246 through 253 and (name N or n \ ame CA or name C or name O or name CB )) or resid 254 or (resid 255 and (name N \ or name CA or name C or name O or name CB )) or (resid 256 through 272 and (name \ N or name CA or name C or name O or name CB )) or (resid 273 through 282 and (n \ ame N or name CA or name C or name O or name CB )) or resid 283 or (resid 284 th \ rough 310 and (name N or name CA or name C or name O or name CB )) or resid 311) \ ) selection = (chain 'P' and ((resid 3 through 15 and (name N or name CA or name C or name O o \ r name CB )) or (resid 16 through 23 and (name N or name CA or name C or name O \ or name CB )) or (resid 25 through 56 and (name N or name CA or name C or name O \ or name CB )) or resid 57 or (resid 58 through 76 and (name N or name CA or nam \ e C or name O or name CB )) or resid 77 or (resid 78 through 94 and (name N or n \ ame CA or name C or name O or name CB )) or resid 95 or (resid 96 through 110 an \ d (name N or name CA or name C or name O or name CB )) or (resid 111 through 133 \ and (name N or name CA or name C or name O or name CB )) or resid 134 or (resid \ 135 through 139 and (name N or name CA or name C or name O or name CB )) or res \ id 140 or (resid 141 through 161 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 162 through 182 and (name N or name CA or name C or name O o \ r name CB )) or (resid 183 through 223 and (name N or name CA or name C or name \ O or name CB )) or (resid 224 through 244 and (name N or name CA or name C or na \ me O or name CB )) or (resid 245 through 253 and (name N or name CA or name C or \ name O or name CB )) or (resid 254 through 282 and (name N or name CA or name C \ or name O or name CB )) or resid 283 or (resid 284 through 310 and (name N or n \ ame CA or name C or name O or name CB )) or resid 311)) selection = (chain 'U' and ((resid 3 through 15 and (name N or name CA or name C or name O o \ r name CB )) or resid 16 or (resid 17 through 23 and (name N or name CA or name \ C or name O or name CB )) or (resid 25 through 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 or (resid 58 through 76 and (name N or na \ me CA or name C or name O or name CB )) or resid 77 or (resid 78 through 94 and \ (name N or name CA or name C or name O or name CB )) or resid 95 or (resid 96 th \ rough 110 and (name N or name CA or name C or name O or name CB )) or (resid 111 \ through 133 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 34 or (resid 135 through 139 and (name N or name CA or name C or name O or name \ CB )) or resid 140 or (resid 141 through 161 and (name N or name CA or name C or \ name O or name CB )) or (resid 162 through 182 and (name N or name CA or name C \ or name O or name CB )) or resid 183 or (resid 184 through 185 and (name N or n \ ame CA or name C or name O or name CB )) or resid 186 or (resid 187 through 188 \ and (name N or name CA or name C or name O or name CB )) or resid 189 or (resid \ 190 through 223 and (name N or name CA or name C or name O or name CB )) or resi \ d 224 or (resid 225 through 235 and (name N or name CA or name C or name O or na \ me CB )) or resid 236 or (resid 237 through 244 and (name N or name CA or name C \ or name O or name CB )) or resid 245 or (resid 246 through 253 and (name N or n \ ame CA or name C or name O or name CB )) or resid 254 or (resid 255 and (name N \ or name CA or name C or name O or name CB )) or (resid 256 through 272 and (name \ N or name CA or name C or name O or name CB )) or (resid 273 through 282 and (n \ ame N or name CA or name C or name O or name CB )) or resid 283 or (resid 284 th \ rough 310 and (name N or name CA or name C or name O or name CB )) or resid 311) \ ) selection = (chain 'Z' and (resid 3 through 23 or resid 25 through 311)) } ncs_group { reference = chain 'B' selection = chain 'J' selection = (chain 'Q' and resid 1 through 85) selection = chain 'V' } ncs_group { reference = (chain 'C' and resid 2 through 79) selection = chain 'M' selection = (chain 'O' and resid 2 through 79) selection = (chain 'R' and resid 2 through 79) selection = (chain 'W' and resid 2 through 79) selection = (chain 'b' and resid 2 through 79) } ncs_group { reference = chain 'D' selection = chain 'N' selection = chain 'S' selection = chain 'X' selection = chain 'Y' selection = chain 'c' } ncs_group { reference = (chain 'E' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 or (resid 6 through 9 and (name N or name CA or name C or \ name O or name CB )) or resid 10 through 11 or (resid 12 and (name N or name CA \ or name C or name O or name CB )) or resid 13 through 18 or (resid 19 through 2 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 21 through 2 \ 3 or (resid 24 and (name N or name CA or name C or name O or name CB )) or (resi \ d 25 through 29 and (name N or name CA or name C or name O or name CB )) or resi \ d 30 through 38 or (resid 39 through 43 and (name N or name CA or name C or name \ O or name CB )) or resid 44 through 47 or (resid 48 and (name N or name CA or n \ ame C or name O or name CB )) or resid 49 through 50 or (resid 51 and (name N or \ name CA or name C or name O or name CB )) or resid 52 through 54 or (resid 55 t \ hrough 58 and (name N or name CA or name C or name O or name CB )) or resid 59 t \ hrough 76 or (resid 77 and (name N or name CA or name C or name O or name CB )) \ or resid 78 or (resid 79 and (name N or name CA or name C or name O or name CB ) \ ) or resid 80 through 98 or (resid 99 through 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 117 or (resid 118 and (name N or \ name CA or name C or name O or name CB )) or resid 119 through 121 or (resid 12 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 123 or (resi \ d 124 through 127 and (name N or name CA or name C or name O or name CB )) or re \ sid 128 or (resid 129 through 133 and (name N or name CA or name C or name O or \ name CB )) or resid 134 through 140 or (resid 141 and (name N or name CA or name \ C or name O or name CB )) or resid 142 through 143 or (resid 144 through 145 an \ d (name N or name CA or name C or name O or name CB )) or resid 146 through 147 \ or (resid 148 through 150 and (name N or name CA or name C or name O or name CB \ )) or resid 151 through 152 or (resid 153 and (name N or name CA or name C or na \ me O or name CB )) or resid 154 or (resid 155 through 182 and (name N or name CA \ or name C or name O or name CB )) or resid 183 through 186 or (resid 187 throug \ h 196 and (name N or name CA or name C or name O or name CB )) or resid 197 thro \ ugh 214 or (resid 215 and (name N or name CA or name C or name O or name CB )) o \ r resid 216 or (resid 217 and (name N or name CA or name C or name O or name CB \ )) or resid 218 through 221 or (resid 222 through 223 and (name N or name CA or \ name C or name O or name CB )) or resid 224 through 244 or (resid 245 through 24 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 247 through \ 249 or (resid 250 and (name N or name CA or name C or name O or name CB )) or re \ sid 251 through 253 or (resid 254 through 258 and (name N or name CA or name C o \ r name O or name CB )) or resid 259 through 260 or (resid 261 and (name N or nam \ e CA or name C or name O or name CB )) or resid 262 through 270 or (resid 271 an \ d (name N or name CA or name C or name O or name CB )) or resid 272 through 274 \ or (resid 275 through 277 and (name N or name CA or name C or name O or name CB \ )) or resid 278 through 279 or (resid 280 through 281 and (name N or name CA or \ name C or name O or name CB )) or resid 282 through 284 or (resid 285 and (name \ N or name CA or name C or name O or name CB )) or resid 286 through 289 or (resi \ d 290 and (name N or name CA or name C or name O or name CB )) or resid 291 thro \ ugh 292 or (resid 293 through 294 and (name N or name CA or name C or name O or \ name CB )) or resid 295 through 297 or (resid 298 through 302 and (name N or nam \ e CA or name C or name O or name CB )) or resid 303 through 304)) selection = (chain 'F' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 or (resid 6 through 9 and (name N or name CA or name C or \ name O or name CB )) or resid 10 through 11 or (resid 12 and (name N or name CA \ or name C or name O or name CB )) or resid 13 through 18 or (resid 19 through 2 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 21 through 2 \ 3 or (resid 24 and (name N or name CA or name C or name O or name CB )) or resid \ 25 through 40 or (resid 41 through 43 and (name N or name CA or name C or name \ O or name CB )) or resid 44 through 64 or (resid 65 through 66 and (name N or na \ me CA or name C or name O or name CB )) or resid 67 through 78 or (resid 79 and \ (name N or name CA or name C or name O or name CB )) or resid 80 through 117 or \ (resid 118 and (name N or name CA or name C or name O or name CB )) or resid 119 \ through 123 or (resid 124 through 127 and (name N or name CA or name C or name \ O or name CB )) or resid 128 through 147 or (resid 148 through 150 and (name N o \ r name CA or name C or name O or name CB )) or resid 151 through 155 or (resid 1 \ 56 through 182 and (name N or name CA or name C or name O or name CB )) or resid \ 183 through 191 or (resid 192 through 196 and (name N or name CA or name C or n \ ame O or name CB )) or resid 197 through 202 or (resid 203 and (name N or name C \ A or name C or name O or name CB )) or resid 204 through 216 or (resid 217 and ( \ name N or name CA or name C or name O or name CB )) or resid 218 through 221 or \ (resid 222 through 223 and (name N or name CA or name C or name O or name CB )) \ or resid 224 through 225 or (resid 226 and (name N or name CA or name C or name \ O or name CB )) or resid 227 through 236 or (resid 237 and (name N or name CA or \ name C or name O or name CB )) or resid 238 through 240 or (resid 241 and (name \ N or name CA or name C or name O or name CB )) or resid 242 through 244 or (res \ id 245 through 246 and (name N or name CA or name C or name O or name CB )) or r \ esid 247 through 249 or (resid 250 and (name N or name CA or name C or name O or \ name CB )) or resid 251 through 253 or (resid 254 through 258 and (name N or na \ me CA or name C or name O or name CB )) or resid 259 through 260 or (resid 261 a \ nd (name N or name CA or name C or name O or name CB )) or resid 262 through 270 \ or (resid 271 and (name N or name CA or name C or name O or name CB )) or resid \ 272 through 274 or (resid 275 through 277 and (name N or name CA or name C or n \ ame O or name CB )) or resid 278 through 279 or (resid 280 through 281 and (name \ N or name CA or name C or name O or name CB )) or resid 282 through 284 or (res \ id 285 and (name N or name CA or name C or name O or name CB )) or resid 286 thr \ ough 289 or (resid 290 and (name N or name CA or name C or name O or name CB )) \ or resid 291 through 292 or (resid 293 through 294 and (name N or name CA or nam \ e C or name O or name CB )) or resid 295 through 297 or (resid 298 through 302 a \ nd (name N or name CA or name C or name O or name CB )) or resid 303 through 304 \ )) selection = (chain 'H' and (resid 3 through 27 or (resid 28 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 30 through 38 or (resid 39 through \ 43 and (name N or name CA or name C or name O or name CB )) or resid 44 through \ 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) or resi \ d 52 through 121 or (resid 122 and (name N or name CA or name C or name O or nam \ e CB )) or resid 123 through 132 or (resid 133 and (name N or name CA or name C \ or name O or name CB )) or resid 134 through 140 or (resid 141 and (name N or na \ me CA or name C or name O or name CB )) or resid 142 through 143 or (resid 144 t \ hrough 145 and (name N or name CA or name C or name O or name CB )) or resid 146 \ through 158 or (resid 159 through 182 and (name N or name CA or name C or name \ O or name CB )) or resid 183 through 225 or (resid 226 and (name N or name CA or \ name C or name O or name CB )) or resid 227 through 304)) selection = (chain 'T' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 or (resid 6 through 9 and (name N or name CA or name C or \ name O or name CB )) or resid 10 through 11 or (resid 12 and (name N or name CA \ or name C or name O or name CB )) or resid 13 through 18 or (resid 19 through 2 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 21 through 2 \ 3 or (resid 24 and (name N or name CA or name C or name O or name CB )) or (resi \ d 25 through 29 and (name N or name CA or name C or name O or name CB )) or resi \ d 30 through 38 or (resid 39 through 43 and (name N or name CA or name C or name \ O or name CB )) or resid 44 through 47 or (resid 48 and (name N or name CA or n \ ame C or name O or name CB )) or resid 49 through 50 or (resid 51 and (name N or \ name CA or name C or name O or name CB )) or resid 52 through 54 or (resid 55 t \ hrough 58 and (name N or name CA or name C or name O or name CB )) or resid 59 t \ hrough 76 or (resid 77 and (name N or name CA or name C or name O or name CB )) \ or resid 78 or (resid 79 and (name N or name CA or name C or name O or name CB ) \ ) or resid 80 through 98 or (resid 99 through 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 117 or (resid 118 and (name N or \ name CA or name C or name O or name CB )) or resid 119 through 121 or (resid 12 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 123 or (resi \ d 124 through 127 and (name N or name CA or name C or name O or name CB )) or re \ sid 128 through 129 or (resid 130 through 133 and (name N or name CA or name C o \ r name O or name CB )) or resid 134 through 140 or (resid 141 and (name N or nam \ e CA or name C or name O or name CB )) or resid 142 through 143 or (resid 144 th \ rough 145 and (name N or name CA or name C or name O or name CB )) or resid 146 \ through 147 or (resid 148 through 150 and (name N or name CA or name C or name O \ or name CB )) or resid 151 through 152 or (resid 153 and (name N or name CA or \ name C or name O or name CB )) or resid 154 or (resid 155 through 182 and (name \ N or name CA or name C or name O or name CB )) or resid 183 through 186 or (resi \ d 187 through 196 and (name N or name CA or name C or name O or name CB )) or re \ sid 197 through 202 or (resid 203 and (name N or name CA or name C or name O or \ name CB )) or resid 204 through 214 or (resid 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 or (resid 217 and (name N or name CA or \ name C or name O or name CB )) or resid 218 through 221 or (resid 222 through 22 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 224 through \ 225 or (resid 226 and (name N or name CA or name C or name O or name CB )) or re \ sid 227 through 236 or (resid 237 and (name N or name CA or name C or name O or \ name CB )) or resid 238 through 244 or (resid 245 through 246 and (name N or nam \ e CA or name C or name O or name CB )) or resid 247 through 249 or (resid 250 an \ d (name N or name CA or name C or name O or name CB )) or resid 251 through 253 \ or (resid 254 through 258 and (name N or name CA or name C or name O or name CB \ )) or resid 259 through 260 or (resid 261 and (name N or name CA or name C or na \ me O or name CB )) or resid 262 through 270 or (resid 271 and (name N or name CA \ or name C or name O or name CB )) or resid 272 through 274 or (resid 275 throug \ h 277 and (name N or name CA or name C or name O or name CB )) or resid 278 thro \ ugh 279 or (resid 280 through 281 and (name N or name CA or name C or name O or \ name CB )) or resid 282 through 284 or (resid 285 and (name N or name CA or name \ C or name O or name CB )) or resid 286 through 289 or (resid 290 and (name N or \ name CA or name C or name O or name CB )) or resid 291 through 292 or (resid 29 \ 3 through 294 and (name N or name CA or name C or name O or name CB )) or resid \ 295 through 297 or (resid 298 through 302 and (name N or name CA or name C or na \ me O or name CB )) or resid 303 through 304)) } ncs_group { reference = chain 'L' selection = (chain 'a' and (resid 1 through 18 or resid 67 through 101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 21.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 39.350 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.150 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:8.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 : 0.004 0.054 41996 Z= 0.191 Angle : 0.611 13.577 61122 Z= 0.354 Chirality : 0.048 0.521 7568 Planarity : 0.004 0.091 4725 Dihedral : 25.322 179.455 18632 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.25 % Allowed : 15.72 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.16), residues: 3180 helix: 2.57 (0.13), residues: 1774 sheet: 1.49 (0.27), residues: 360 loop : 0.42 (0.20), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG T 246 TYR 0.015 0.001 TYR K 179 PHE 0.011 0.001 PHE A 215 TRP 0.002 0.001 TRP T 45 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00394 (41996) covalent geometry : angle 0.61136 (61122) hydrogen bonds : bond 0.15924 ( 2215) hydrogen bonds : angle 5.64629 ( 5674) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 281 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.6578 (pt0) cc_final: 0.6130 (pt0) REVERT: A 28 LYS cc_start: 0.7980 (mttp) cc_final: 0.7701 (mttt) REVERT: K 25 ASP cc_start: 0.7773 (m-30) cc_final: 0.7569 (m-30) REVERT: K 88 SER cc_start: 0.7909 (m) cc_final: 0.7561 (t) REVERT: K 223 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6831 (mm-30) REVERT: P 102 ILE cc_start: 0.7710 (pt) cc_final: 0.7190 (mt) REVERT: P 247 VAL cc_start: 0.8201 (t) cc_final: 0.7938 (m) REVERT: U 11 ARG cc_start: 0.7451 (ptt180) cc_final: 0.6783 (ptm160) REVERT: U 88 SER cc_start: 0.8236 (m) cc_final: 0.7946 (p) REVERT: E 129 LYS cc_start: 0.8888 (ttmt) cc_final: 0.8588 (tttm) REVERT: E 155 SER cc_start: 0.8044 (p) cc_final: 0.7779 (t) REVERT: F 241 ARG cc_start: 0.7810 (ttp-110) cc_final: 0.7194 (mmp80) REVERT: F 293 ARG cc_start: 0.7949 (mtm110) cc_final: 0.7584 (mtp-110) REVERT: F 298 ASN cc_start: 0.8209 (t0) cc_final: 0.7838 (t0) REVERT: F 301 LYS cc_start: 0.8734 (mttt) cc_final: 0.8031 (mptt) REVERT: H 82 SER cc_start: 0.8367 (t) cc_final: 0.8015 (p) REVERT: H 201 TYR cc_start: 0.8228 (m-80) cc_final: 0.7958 (m-80) REVERT: T 261 GLN cc_start: 0.7640 (pt0) cc_final: 0.7144 (pt0) REVERT: T 285 GLU cc_start: 0.8147 (tp30) cc_final: 0.7791 (tp30) outliers start: 4 outliers final: 4 residues processed: 284 average time/residue: 0.6272 time to fit residues: 221.5683 Evaluate side-chains 158 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 154 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain T residue 213 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 30.0000 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.0050 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.6980 overall best weight: 0.4372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS U 21 ASN E 157 ASN F 12 GLN H 10 GLN H 291 ASN T 198 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.213840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.125101 restraints weight = 142195.118| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.84 r_work: 0.3397 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 41996 Z= 0.143 Angle : 0.544 10.533 61122 Z= 0.291 Chirality : 0.035 0.253 7568 Planarity : 0.004 0.062 4725 Dihedral : 26.001 177.509 15297 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.32 % Allowed : 19.35 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.15), residues: 3180 helix: 2.29 (0.12), residues: 1797 sheet: 1.46 (0.27), residues: 330 loop : 0.30 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 24 TYR 0.019 0.001 TYR U 179 PHE 0.018 0.001 PHE A 10 TRP 0.004 0.001 TRP F 45 HIS 0.004 0.001 HIS K 280 Details of bonding type rmsd covalent geometry : bond 0.00301 (41996) covalent geometry : angle 0.54448 (61122) hydrogen bonds : bond 0.04298 ( 2215) hydrogen bonds : angle 3.99898 ( 5674) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 1.188 Fit side-chains REVERT: A 5 GLU cc_start: 0.6442 (pt0) cc_final: 0.6143 (tt0) REVERT: A 28 LYS cc_start: 0.7783 (mttp) cc_final: 0.7333 (mtmm) REVERT: K 88 SER cc_start: 0.7753 (m) cc_final: 0.7299 (t) REVERT: K 156 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7483 (mtpp) REVERT: K 223 GLU cc_start: 0.6648 (mm-30) cc_final: 0.6290 (mm-30) REVERT: U 88 SER cc_start: 0.8118 (m) cc_final: 0.7690 (p) REVERT: U 157 ASN cc_start: 0.7100 (p0) cc_final: 0.6665 (t0) REVERT: E 41 ASN cc_start: 0.7669 (t0) cc_final: 0.7424 (t0) REVERT: E 129 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8297 (tttm) REVERT: F 24 ARG cc_start: 0.7870 (mmt90) cc_final: 0.7620 (mmt90) REVERT: F 63 TYR cc_start: 0.8521 (m-10) cc_final: 0.7950 (m-10) REVERT: F 69 ASP cc_start: 0.7427 (t0) cc_final: 0.7157 (m-30) REVERT: F 97 PHE cc_start: 0.8274 (m-80) cc_final: 0.8013 (m-80) REVERT: F 118 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7927 (mtp-110) REVERT: F 241 ARG cc_start: 0.7432 (ttp-110) cc_final: 0.6743 (mmp80) REVERT: F 293 ARG cc_start: 0.7851 (mtm110) cc_final: 0.7399 (mtp-110) REVERT: F 298 ASN cc_start: 0.8158 (t0) cc_final: 0.7777 (t0) REVERT: F 301 LYS cc_start: 0.8390 (mttt) cc_final: 0.7748 (mptt) REVERT: H 201 TYR cc_start: 0.7626 (m-80) cc_final: 0.7384 (m-10) REVERT: T 261 GLN cc_start: 0.7561 (pt0) cc_final: 0.7171 (pt0) REVERT: T 285 GLU cc_start: 0.7715 (tp30) cc_final: 0.7203 (tp30) outliers start: 37 outliers final: 16 residues processed: 221 average time/residue: 0.6263 time to fit residues: 173.9031 Evaluate side-chains 171 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain K residue 156 LYS Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 288 ILE Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain U residue 21 ASN Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain T residue 213 LEU Chi-restraints excluded: chain T residue 215 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 76 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 320 optimal weight: 0.0670 chunk 294 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 225 optimal weight: 30.0000 chunk 158 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 280 HIS E 157 ASN H 291 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.211745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.125644 restraints weight = 157654.240| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.57 r_work: 0.3268 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41996 Z= 0.151 Angle : 0.523 11.896 61122 Z= 0.280 Chirality : 0.035 0.227 7568 Planarity : 0.004 0.064 4725 Dihedral : 25.859 176.740 15295 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.26 % Allowed : 19.10 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.15), residues: 3180 helix: 2.27 (0.12), residues: 1797 sheet: 1.06 (0.25), residues: 354 loop : 0.30 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 298 TYR 0.019 0.001 TYR U 179 PHE 0.019 0.001 PHE A 10 TRP 0.005 0.001 TRP A 78 HIS 0.004 0.001 HIS K 280 Details of bonding type rmsd covalent geometry : bond 0.00336 (41996) covalent geometry : angle 0.52301 (61122) hydrogen bonds : bond 0.04000 ( 2215) hydrogen bonds : angle 3.69122 ( 5674) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 1.187 Fit side-chains REVERT: A 5 GLU cc_start: 0.6387 (pt0) cc_final: 0.6167 (tt0) REVERT: A 28 LYS cc_start: 0.7776 (mttp) cc_final: 0.7419 (mtmm) REVERT: A 262 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7418 (mt-10) REVERT: K 156 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7327 (mtpp) REVERT: K 223 GLU cc_start: 0.6708 (mm-30) cc_final: 0.6393 (mm-30) REVERT: P 194 ARG cc_start: 0.7671 (ttp80) cc_final: 0.7213 (ttp-110) REVERT: U 31 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7720 (tpp80) REVERT: U 47 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.6946 (mtt180) REVERT: E 41 ASN cc_start: 0.7716 (t0) cc_final: 0.7509 (t0) REVERT: E 129 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8304 (tttp) REVERT: E 180 MET cc_start: 0.8126 (mmm) cc_final: 0.7764 (mmm) REVERT: F 24 ARG cc_start: 0.7773 (mmt90) cc_final: 0.7465 (mmt90) REVERT: F 63 TYR cc_start: 0.8563 (m-10) cc_final: 0.8009 (m-10) REVERT: F 69 ASP cc_start: 0.7461 (t70) cc_final: 0.7225 (m-30) REVERT: F 97 PHE cc_start: 0.8243 (m-80) cc_final: 0.7960 (m-80) REVERT: F 241 ARG cc_start: 0.7468 (ttp-110) cc_final: 0.6832 (mmp80) REVERT: F 293 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7833 (mtp-110) REVERT: F 301 LYS cc_start: 0.8250 (mttt) cc_final: 0.7654 (mptt) REVERT: T 32 ILE cc_start: 0.8039 (mt) cc_final: 0.7645 (mp) REVERT: T 261 GLN cc_start: 0.7769 (pt0) cc_final: 0.7365 (pt0) REVERT: T 285 GLU cc_start: 0.7766 (tp30) cc_final: 0.7188 (tp30) outliers start: 52 outliers final: 22 residues processed: 225 average time/residue: 0.6731 time to fit residues: 188.4657 Evaluate side-chains 179 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 156 LYS Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 247 VAL Chi-restraints excluded: chain U residue 26 MET Chi-restraints excluded: chain U residue 31 ARG Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 128 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain H residue 16 HIS Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain T residue 67 LEU Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 192 VAL Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain T residue 213 LEU Chi-restraints excluded: chain T residue 215 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 165 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 238 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 211 optimal weight: 0.2980 chunk 290 optimal weight: 7.9990 chunk 311 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 384 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN U 21 ASN E 124 GLN E 157 ASN H 112 ASN H 291 ASN T 291 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.210585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.122853 restraints weight = 133399.504| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.84 r_work: 0.3255 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 41996 Z= 0.157 Angle : 0.520 8.516 61122 Z= 0.278 Chirality : 0.035 0.228 7568 Planarity : 0.004 0.045 4725 Dihedral : 25.773 175.698 15293 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.69 % Allowed : 19.60 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.15), residues: 3180 helix: 2.34 (0.12), residues: 1781 sheet: 0.89 (0.25), residues: 366 loop : 0.21 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 246 TYR 0.021 0.001 TYR P 155 PHE 0.025 0.001 PHE H 289 TRP 0.006 0.001 TRP A 78 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00353 (41996) covalent geometry : angle 0.52047 (61122) hydrogen bonds : bond 0.03824 ( 2215) hydrogen bonds : angle 3.59384 ( 5674) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 167 time to evaluate : 0.731 Fit side-chains REVERT: A 28 LYS cc_start: 0.7928 (mttp) cc_final: 0.7643 (mtpt) REVERT: A 239 SER cc_start: 0.8262 (t) cc_final: 0.7664 (m) REVERT: K 156 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7355 (mtpp) REVERT: K 157 ASN cc_start: 0.6608 (p0) cc_final: 0.6036 (t0) REVERT: K 223 GLU cc_start: 0.6763 (mm-30) cc_final: 0.6485 (mm-30) REVERT: U 47 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.6840 (mtt180) REVERT: E 41 ASN cc_start: 0.7770 (t0) cc_final: 0.7569 (t0) REVERT: E 69 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: E 129 LYS cc_start: 0.8685 (ttmt) cc_final: 0.8295 (tttm) REVERT: E 180 MET cc_start: 0.8182 (mmm) cc_final: 0.7808 (mmm) REVERT: F 24 ARG cc_start: 0.7635 (mmt90) cc_final: 0.7266 (mmt90) REVERT: F 63 TYR cc_start: 0.8634 (m-10) cc_final: 0.8095 (m-10) REVERT: F 97 PHE cc_start: 0.8247 (m-80) cc_final: 0.7950 (m-80) REVERT: F 241 ARG cc_start: 0.7497 (ttp-110) cc_final: 0.6813 (tpp-160) REVERT: F 293 ARG cc_start: 0.7988 (mtm110) cc_final: 0.7688 (mtp-110) REVERT: F 301 LYS cc_start: 0.8262 (mttt) cc_final: 0.7668 (mptt) REVERT: H 204 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6417 (mtm180) REVERT: T 261 GLN cc_start: 0.7745 (pt0) cc_final: 0.7312 (pt0) REVERT: T 285 GLU cc_start: 0.7755 (tp30) cc_final: 0.7309 (tp30) outliers start: 59 outliers final: 27 residues processed: 217 average time/residue: 0.5773 time to fit residues: 155.9770 Evaluate side-chains 175 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 156 LYS Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 202 SER Chi-restraints excluded: chain U residue 26 MET Chi-restraints excluded: chain U residue 31 ARG Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 128 THR Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 255 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain H residue 16 HIS Chi-restraints excluded: chain H residue 204 ARG Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain T residue 67 LEU Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 192 VAL Chi-restraints excluded: chain T residue 213 LEU Chi-restraints excluded: chain T residue 215 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 296 optimal weight: 0.8980 chunk 91 optimal weight: 0.0050 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 243 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 371 optimal weight: 8.9990 chunk 348 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN F 112 ASN H 112 ASN H 291 ASN T 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.210796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.123976 restraints weight = 119347.534| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.64 r_work: 0.3283 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41996 Z= 0.134 Angle : 0.503 9.985 61122 Z= 0.268 Chirality : 0.034 0.207 7568 Planarity : 0.003 0.044 4725 Dihedral : 25.714 175.171 15293 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.44 % Allowed : 20.04 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.15), residues: 3180 helix: 2.40 (0.12), residues: 1789 sheet: 0.98 (0.26), residues: 354 loop : 0.18 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 246 TYR 0.020 0.001 TYR A 302 PHE 0.019 0.001 PHE H 289 TRP 0.005 0.001 TRP A 78 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00297 (41996) covalent geometry : angle 0.50263 (61122) hydrogen bonds : bond 0.03650 ( 2215) hydrogen bonds : angle 3.48448 ( 5674) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 162 time to evaluate : 0.962 Fit side-chains REVERT: A 28 LYS cc_start: 0.7934 (mttp) cc_final: 0.7670 (mtpt) REVERT: A 239 SER cc_start: 0.8237 (t) cc_final: 0.7604 (m) REVERT: K 157 ASN cc_start: 0.6684 (p0) cc_final: 0.6155 (t0) REVERT: K 223 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6487 (mm-30) REVERT: K 225 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8844 (mp) REVERT: U 31 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7722 (tpp80) REVERT: U 47 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.6917 (mtt180) REVERT: E 41 ASN cc_start: 0.7792 (t0) cc_final: 0.7541 (t0) REVERT: E 69 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7709 (m-30) REVERT: E 129 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8251 (tttp) REVERT: E 180 MET cc_start: 0.8158 (mmm) cc_final: 0.7761 (mmm) REVERT: F 24 ARG cc_start: 0.7627 (mmt90) cc_final: 0.7220 (mmt90) REVERT: F 63 TYR cc_start: 0.8582 (m-10) cc_final: 0.8051 (m-10) REVERT: F 69 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.6997 (m-30) REVERT: F 97 PHE cc_start: 0.8235 (m-80) cc_final: 0.7969 (m-80) REVERT: F 241 ARG cc_start: 0.7479 (ttp-110) cc_final: 0.6763 (mmp80) REVERT: F 293 ARG cc_start: 0.7945 (mtm110) cc_final: 0.7625 (mtp-110) REVERT: F 301 LYS cc_start: 0.8255 (mttt) cc_final: 0.7675 (mptt) REVERT: H 204 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.6440 (mtm180) REVERT: T 51 GLN cc_start: 0.7173 (mm110) cc_final: 0.6886 (mm110) REVERT: T 261 GLN cc_start: 0.7719 (pt0) cc_final: 0.7392 (pt0) REVERT: T 285 GLU cc_start: 0.7702 (tp30) cc_final: 0.7185 (tp30) outliers start: 55 outliers final: 27 residues processed: 205 average time/residue: 0.5975 time to fit residues: 153.7739 Evaluate side-chains 181 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 225 LEU Chi-restraints excluded: chain K residue 255 ILE Chi-restraints excluded: chain P residue 202 SER Chi-restraints excluded: chain U residue 26 MET Chi-restraints excluded: chain U residue 31 ARG Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 128 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain H residue 16 HIS Chi-restraints excluded: chain H residue 204 ARG Chi-restraints excluded: chain T residue 19 LYS Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 67 LEU Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 192 VAL Chi-restraints excluded: chain T residue 213 LEU Chi-restraints excluded: chain T residue 215 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 127 optimal weight: 0.7980 chunk 196 optimal weight: 8.9990 chunk 336 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 287 optimal weight: 0.5980 chunk 316 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 388 optimal weight: 20.0000 chunk 341 optimal weight: 0.0470 chunk 68 optimal weight: 30.0000 chunk 164 optimal weight: 0.0050 overall best weight: 0.4892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN E 157 ASN F 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.211255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.121402 restraints weight = 145763.159| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.70 r_work: 0.3264 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41996 Z= 0.129 Angle : 0.502 11.437 61122 Z= 0.267 Chirality : 0.034 0.210 7568 Planarity : 0.003 0.043 4725 Dihedral : 25.662 175.000 15293 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.76 % Allowed : 20.35 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.15), residues: 3180 helix: 2.49 (0.12), residues: 1783 sheet: 1.00 (0.26), residues: 354 loop : 0.11 (0.20), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 24 TYR 0.022 0.001 TYR A 302 PHE 0.018 0.001 PHE H 289 TRP 0.004 0.001 TRP A 78 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00282 (41996) covalent geometry : angle 0.50232 (61122) hydrogen bonds : bond 0.03571 ( 2215) hydrogen bonds : angle 3.42031 ( 5674) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 162 time to evaluate : 0.704 Fit side-chains REVERT: A 28 LYS cc_start: 0.7929 (mttp) cc_final: 0.7674 (mtpt) REVERT: A 239 SER cc_start: 0.8200 (t) cc_final: 0.7560 (m) REVERT: K 156 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7331 (mtpp) REVERT: K 157 ASN cc_start: 0.6734 (p0) cc_final: 0.6280 (t0) REVERT: K 223 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6489 (mm-30) REVERT: K 225 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8813 (mp) REVERT: U 47 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6920 (mtt180) REVERT: E 41 ASN cc_start: 0.7793 (t0) cc_final: 0.7501 (t0) REVERT: E 129 LYS cc_start: 0.8654 (ttmt) cc_final: 0.8410 (ttmm) REVERT: E 180 MET cc_start: 0.8138 (mmm) cc_final: 0.7811 (mmm) REVERT: F 24 ARG cc_start: 0.7599 (mmt90) cc_final: 0.7178 (mmt90) REVERT: F 63 TYR cc_start: 0.8542 (m-10) cc_final: 0.7958 (m-10) REVERT: F 65 GLU cc_start: 0.8555 (pm20) cc_final: 0.8062 (mp0) REVERT: F 69 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6990 (m-30) REVERT: F 241 ARG cc_start: 0.7447 (ttp-110) cc_final: 0.6739 (mmp80) REVERT: F 293 ARG cc_start: 0.7935 (mtm110) cc_final: 0.7616 (mtp-110) REVERT: F 301 LYS cc_start: 0.8214 (mttt) cc_final: 0.7632 (mptt) REVERT: H 204 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6460 (mtm180) REVERT: T 51 GLN cc_start: 0.7159 (mm110) cc_final: 0.6859 (mm110) REVERT: T 261 GLN cc_start: 0.7674 (pt0) cc_final: 0.7376 (pt0) REVERT: T 263 THR cc_start: 0.6819 (OUTLIER) cc_final: 0.6524 (p) REVERT: T 285 GLU cc_start: 0.7745 (tp30) cc_final: 0.7288 (tp30) outliers start: 60 outliers final: 29 residues processed: 211 average time/residue: 0.5693 time to fit residues: 149.6123 Evaluate side-chains 178 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 156 LYS Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 225 LEU Chi-restraints excluded: chain K residue 255 ILE Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain U residue 26 MET Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain H residue 204 ARG Chi-restraints excluded: chain T residue 19 LYS Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 67 LEU Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 192 VAL Chi-restraints excluded: chain T residue 213 LEU Chi-restraints excluded: chain T residue 215 SER Chi-restraints excluded: chain T residue 263 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 356 optimal weight: 4.9990 chunk 340 optimal weight: 0.0980 chunk 187 optimal weight: 7.9990 chunk 368 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 221 optimal weight: 8.9990 chunk 332 optimal weight: 5.9990 chunk 125 optimal weight: 0.3980 chunk 297 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN F 112 ASN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 ASN T 124 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.205720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.109927 restraints weight = 121529.811| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.61 r_work: 0.3161 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 41996 Z= 0.322 Angle : 0.625 11.996 61122 Z= 0.328 Chirality : 0.041 0.273 7568 Planarity : 0.005 0.106 4725 Dihedral : 25.846 174.265 15293 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.76 % Allowed : 20.73 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.15), residues: 3180 helix: 1.94 (0.12), residues: 1784 sheet: 0.75 (0.26), residues: 366 loop : -0.00 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 251 TYR 0.027 0.002 TYR A 42 PHE 0.035 0.002 PHE U 10 TRP 0.012 0.002 TRP A 78 HIS 0.006 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00755 (41996) covalent geometry : angle 0.62547 (61122) hydrogen bonds : bond 0.04827 ( 2215) hydrogen bonds : angle 3.88888 ( 5674) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 143 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7133 (ptt180) cc_final: 0.6229 (ptm160) REVERT: A 28 LYS cc_start: 0.8047 (mttp) cc_final: 0.7695 (mtmt) REVERT: A 31 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.6595 (mtp85) REVERT: A 239 SER cc_start: 0.8361 (t) cc_final: 0.7641 (m) REVERT: K 157 ASN cc_start: 0.6793 (p0) cc_final: 0.6450 (t0) REVERT: K 225 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8918 (mp) REVERT: P 65 ILE cc_start: 0.6205 (mm) cc_final: 0.5823 (pt) REVERT: U 47 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7112 (mtt180) REVERT: E 129 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8456 (ttmm) REVERT: F 69 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7140 (m-30) REVERT: F 241 ARG cc_start: 0.7630 (ttp-110) cc_final: 0.6961 (tpp-160) REVERT: F 293 ARG cc_start: 0.8258 (mtm110) cc_final: 0.7950 (mtp-110) REVERT: F 301 LYS cc_start: 0.8212 (mttt) cc_final: 0.7631 (mptt) REVERT: T 261 GLN cc_start: 0.7774 (pt0) cc_final: 0.7440 (pt0) REVERT: T 285 GLU cc_start: 0.7796 (tp30) cc_final: 0.7230 (tp30) outliers start: 60 outliers final: 35 residues processed: 197 average time/residue: 0.6569 time to fit residues: 160.5574 Evaluate side-chains 173 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 225 LEU Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 255 ILE Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 202 SER Chi-restraints excluded: chain U residue 26 MET Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 281 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain T residue 19 LYS Chi-restraints excluded: chain T residue 67 LEU Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 155 SER Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 192 VAL Chi-restraints excluded: chain T residue 213 LEU Chi-restraints excluded: chain T residue 215 SER Chi-restraints excluded: chain T residue 262 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 61 optimal weight: 50.0000 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 385 optimal weight: 10.0000 chunk 205 optimal weight: 50.0000 chunk 202 optimal weight: 30.0000 chunk 369 optimal weight: 10.0000 chunk 373 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 270 optimal weight: 0.8980 chunk 194 optimal weight: 40.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 157 ASN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 ASN ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.202007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.110493 restraints weight = 142610.647| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 4.19 r_work: 0.3013 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.127 41996 Z= 0.540 Angle : 0.783 12.409 61122 Z= 0.409 Chirality : 0.051 0.272 7568 Planarity : 0.007 0.140 4725 Dihedral : 26.213 175.874 15293 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.63 % Allowed : 21.04 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.15), residues: 3180 helix: 1.08 (0.12), residues: 1752 sheet: 0.35 (0.26), residues: 366 loop : -0.46 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 251 TYR 0.035 0.003 TYR A 42 PHE 0.042 0.003 PHE A 10 TRP 0.014 0.003 TRP A 78 HIS 0.010 0.002 HIS U 137 Details of bonding type rmsd covalent geometry : bond 0.01263 (41996) covalent geometry : angle 0.78253 (61122) hydrogen bonds : bond 0.06516 ( 2215) hydrogen bonds : angle 4.45843 ( 5674) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 147 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7233 (ptt180) cc_final: 0.6218 (ptm160) REVERT: A 28 LYS cc_start: 0.7981 (mttp) cc_final: 0.7621 (mtmt) REVERT: A 31 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7788 (mmm-85) REVERT: A 288 ILE cc_start: 0.7114 (OUTLIER) cc_final: 0.6665 (mp) REVERT: G 285 GLU cc_start: 0.6166 (tp30) cc_final: 0.5771 (tm-30) REVERT: K 157 ASN cc_start: 0.7078 (p0) cc_final: 0.6733 (t0) REVERT: P 65 ILE cc_start: 0.6227 (mm) cc_final: 0.5668 (pt) REVERT: U 47 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7140 (mtt180) REVERT: E 48 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6397 (mp10) REVERT: F 241 ARG cc_start: 0.7656 (ttp-110) cc_final: 0.6990 (tpp-160) REVERT: F 293 ARG cc_start: 0.8303 (mtm110) cc_final: 0.8049 (mtp-110) REVERT: F 301 LYS cc_start: 0.8360 (mttt) cc_final: 0.7772 (mptt) REVERT: T 285 GLU cc_start: 0.7844 (tp30) cc_final: 0.7244 (tp30) REVERT: T 298 ASN cc_start: 0.6756 (m-40) cc_final: 0.5690 (p0) outliers start: 58 outliers final: 39 residues processed: 198 average time/residue: 0.6470 time to fit residues: 161.0453 Evaluate side-chains 183 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 255 ILE Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 202 SER Chi-restraints excluded: chain U residue 26 MET Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 128 THR Chi-restraints excluded: chain U residue 255 ILE Chi-restraints excluded: chain U residue 281 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain T residue 19 LYS Chi-restraints excluded: chain T residue 67 LEU Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 155 SER Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 213 LEU Chi-restraints excluded: chain T residue 215 SER Chi-restraints excluded: chain T residue 262 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 121 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 218 optimal weight: 20.0000 chunk 325 optimal weight: 0.5980 chunk 249 optimal weight: 0.0010 chunk 225 optimal weight: 30.0000 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 157 ASN F 112 ASN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.205809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.117136 restraints weight = 144287.057| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.88 r_work: 0.3184 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 41996 Z= 0.211 Angle : 0.576 10.757 61122 Z= 0.306 Chirality : 0.037 0.249 7568 Planarity : 0.004 0.053 4725 Dihedral : 26.041 177.062 15293 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.07 % Allowed : 21.67 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.15), residues: 3180 helix: 1.57 (0.12), residues: 1776 sheet: 0.49 (0.26), residues: 360 loop : -0.26 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 24 TYR 0.021 0.002 TYR A 302 PHE 0.025 0.002 PHE U 10 TRP 0.016 0.002 TRP E 45 HIS 0.020 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00487 (41996) covalent geometry : angle 0.57575 (61122) hydrogen bonds : bond 0.04311 ( 2215) hydrogen bonds : angle 3.91419 ( 5674) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 146 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.6859 (ptt180) cc_final: 0.5953 (ptm160) REVERT: A 28 LYS cc_start: 0.7933 (mttp) cc_final: 0.7682 (mtpt) REVERT: G 285 GLU cc_start: 0.6237 (tp30) cc_final: 0.5917 (tp30) REVERT: K 157 ASN cc_start: 0.7003 (p0) cc_final: 0.6676 (t0) REVERT: P 65 ILE cc_start: 0.6199 (mm) cc_final: 0.5743 (pt) REVERT: F 69 ASP cc_start: 0.7334 (m-30) cc_final: 0.7030 (m-30) REVERT: F 241 ARG cc_start: 0.7575 (ttp-110) cc_final: 0.6888 (tpm170) REVERT: F 293 ARG cc_start: 0.8134 (mtm110) cc_final: 0.7889 (mtp-110) REVERT: F 301 LYS cc_start: 0.8290 (mttt) cc_final: 0.7695 (mptt) REVERT: H 28 ILE cc_start: 0.8190 (mt) cc_final: 0.7952 (mp) REVERT: T 263 THR cc_start: 0.7049 (OUTLIER) cc_final: 0.6637 (p) REVERT: T 285 GLU cc_start: 0.7845 (tp30) cc_final: 0.7240 (tp30) outliers start: 49 outliers final: 36 residues processed: 184 average time/residue: 0.6725 time to fit residues: 154.8649 Evaluate side-chains 170 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 255 ILE Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 202 SER Chi-restraints excluded: chain U residue 26 MET Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 281 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain T residue 19 LYS Chi-restraints excluded: chain T residue 67 LEU Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 213 LEU Chi-restraints excluded: chain T residue 215 SER Chi-restraints excluded: chain T residue 262 VAL Chi-restraints excluded: chain T residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 352 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 355 optimal weight: 10.0000 chunk 386 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 212 optimal weight: 7.9990 chunk 239 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 371 optimal weight: 8.9990 chunk 238 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS B ** E 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN F 112 ASN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN H 249 ASN ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.205367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.115945 restraints weight = 145814.483| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.86 r_work: 0.3113 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 41996 Z= 0.242 Angle : 0.585 11.919 61122 Z= 0.310 Chirality : 0.038 0.238 7568 Planarity : 0.004 0.054 4725 Dihedral : 25.962 178.015 15293 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.57 % Allowed : 22.60 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.15), residues: 3180 helix: 1.69 (0.12), residues: 1776 sheet: 0.50 (0.26), residues: 360 loop : -0.25 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 24 TYR 0.022 0.002 TYR A 302 PHE 0.028 0.002 PHE A 10 TRP 0.010 0.001 TRP A 78 HIS 0.006 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00566 (41996) covalent geometry : angle 0.58538 (61122) hydrogen bonds : bond 0.04483 ( 2215) hydrogen bonds : angle 3.84785 ( 5674) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.6838 (ptt180) cc_final: 0.5962 (ptm160) REVERT: A 28 LYS cc_start: 0.7948 (mttp) cc_final: 0.7602 (mtmt) REVERT: A 239 SER cc_start: 0.8536 (t) cc_final: 0.7712 (p) REVERT: G 285 GLU cc_start: 0.6192 (tp30) cc_final: 0.5872 (tp30) REVERT: K 157 ASN cc_start: 0.6897 (p0) cc_final: 0.6607 (t0) REVERT: P 65 ILE cc_start: 0.6156 (mm) cc_final: 0.5781 (pt) REVERT: U 206 MET cc_start: 0.7978 (mmm) cc_final: 0.7740 (tpt) REVERT: F 69 ASP cc_start: 0.7337 (m-30) cc_final: 0.7029 (m-30) REVERT: F 241 ARG cc_start: 0.7491 (ttp-110) cc_final: 0.6839 (tpm170) REVERT: F 293 ARG cc_start: 0.8104 (mtm110) cc_final: 0.7840 (mtp-110) REVERT: F 301 LYS cc_start: 0.8348 (mttt) cc_final: 0.7767 (mptt) REVERT: H 28 ILE cc_start: 0.8176 (mt) cc_final: 0.7937 (mp) REVERT: T 285 GLU cc_start: 0.7815 (tp30) cc_final: 0.7217 (tp30) outliers start: 41 outliers final: 35 residues processed: 176 average time/residue: 0.6444 time to fit residues: 143.2146 Evaluate side-chains 173 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 255 ILE Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 202 SER Chi-restraints excluded: chain U residue 26 MET Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 281 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain T residue 19 LYS Chi-restraints excluded: chain T residue 67 LEU Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 213 LEU Chi-restraints excluded: chain T residue 215 SER Chi-restraints excluded: chain T residue 262 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 307 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 chunk 333 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 306 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 329 optimal weight: 1.9990 chunk 285 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 chunk 177 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 113 ASN ** E 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN F 112 ASN H 51 GLN H 85 ASN H 112 ASN ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.207794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.119058 restraints weight = 136728.730| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.67 r_work: 0.3182 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 41996 Z= 0.145 Angle : 0.526 11.586 61122 Z= 0.279 Chirality : 0.035 0.228 7568 Planarity : 0.004 0.051 4725 Dihedral : 25.863 178.594 15293 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.07 % Allowed : 23.04 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.15), residues: 3180 helix: 2.01 (0.12), residues: 1776 sheet: 0.60 (0.26), residues: 360 loop : -0.10 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 24 TYR 0.021 0.001 TYR A 302 PHE 0.016 0.001 PHE H 289 TRP 0.008 0.001 TRP A 78 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00323 (41996) covalent geometry : angle 0.52555 (61122) hydrogen bonds : bond 0.03750 ( 2215) hydrogen bonds : angle 3.60935 ( 5674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28254.22 seconds wall clock time: 477 minutes 55.92 seconds (28675.92 seconds total)