Starting phenix.real_space_refine on Sun Aug 9 21:24:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qbl_18314/08_2026/8qbl_18314.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qbl_18314/08_2026/8qbl_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qbl_18314/08_2026/8qbl_18314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qbl_18314/08_2026/8qbl_18314.map" model { file = "/net/cci-nas-00/data/ceres_data/8qbl_18314/08_2026/8qbl_18314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qbl_18314/08_2026/8qbl_18314.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: 9.75, per 1000 atoms: 0.25 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: 3.22 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 6.28 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: 9.28 Time building geometry restraints manager: 4.31 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=" C1' DC L 12 " pdb=" N1 DC L 12 " ideal model delta sigma weight residual 1.468 1.524 -0.056 1.40e-02 5.10e+03 1.62e+01 bond pdb=" C1' DC B 12 " pdb=" N1 DC B 12 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.46e+01 bond pdb=" C1' DC V 12 " pdb=" N1 DC V 12 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.44e+01 bond pdb=" C1' DC Q 12 " pdb=" N1 DC Q 12 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.42e+01 bond pdb=" C1' DC J 12 " pdb=" N1 DC J 12 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.32e+01 ... (remaining 41991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 60198 2.62 - 5.23: 827 5.23 - 7.85: 81 7.85 - 10.46: 12 10.46 - 13.08: 4 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 119.70 106.62 13.08 1.20e+00 6.94e-01 1.19e+02 angle pdb=" C3' U R 72 " pdb=" O3' U R 72 " pdb=" P C R 73 " ideal model delta sigma weight residual 119.70 107.91 11.79 1.20e+00 6.94e-01 9.66e+01 angle pdb=" C3' C W 65 " pdb=" O3' C W 65 " pdb=" P A W 66 " ideal model delta sigma weight residual 119.70 108.80 10.90 1.20e+00 6.94e-01 8.25e+01 angle pdb=" C3' G M 69 " pdb=" O3' G M 69 " pdb=" P A M 70 " ideal model delta sigma weight residual 119.70 109.30 10.40 1.20e+00 6.94e-01 7.51e+01 angle pdb=" C3' U R 67 " pdb=" O3' U R 67 " pdb=" P U R 68 " ideal model delta sigma weight residual 119.70 109.69 10.01 1.20e+00 6.94e-01 6.96e+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: 6863 0.104 - 0.208: 661 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: 18.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 41.650 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.190 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: 0.000 Load rotamer database and sin/cos tables:10.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 41996 Z= 0.384 Angle : 0.741 13.077 61122 Z= 0.608 Chirality : 0.059 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 are 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/Z covalent geometry : bond 0.00491 / 0.38 (41996) covalent geometry : angle 0.74130 / 0.61 (61122) hydrogen bonds : bond 0.15924 / 10.85 ( 2215) hydrogen bonds : angle 5.64629 / 5.83 ( 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 : 1.038 Fit side-chains revert: symmetry clash 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 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: 0.7715 (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: 0.8032 (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) REVERT: T 304 TYR cc_start: 0.5188 (t80) cc_final: 0.4983 (t80) outliers start: 4 outliers final: 4 residues processed: 284 average time/residue: 0.5694 time to fit residues: 202.4613 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 : 1.026 ------------------------------------------------------------------------------- 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: 40.0000 chunk 388 optimal weight: 40.0000 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: 10.0000 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... U 21 ASN E 157 ASN F 12 GLN H 10 GLN H 198 ASN T 198 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.214722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.125738 restraints weight = 142842.449| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.90 r_work: 0.3392 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 41996 Z= 0.146 Angle : 0.555 10.497 61122 Z= 0.323 Chirality : 0.041 0.354 7568 Planarity : 0.004 0.078 4725 Dihedral : 26.134 179.227 15297 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.13 % Allowed : 19.91 % Favored : 77.96 % 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 are not related in a simple way. whole: 2.21 (0.15), residues: 3180 helix: 2.23 (0.12), residues: 1789 sheet: 1.45 (0.27), residues: 330 loop : 0.21 (0.20), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 24 TYR 0.021 0.001 TYR K 179 PHE 0.016 0.001 PHE A 10 TRP 0.006 0.001 TRP H 45 HIS 0.009 0.001 HIS H 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.15 (41996) covalent geometry : angle 0.55475 / 0.32 (61122) hydrogen bonds : bond 0.05136 / 3.57 ( 2215) hydrogen bonds : angle 4.18622 / 4.06 ( 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 210 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 1.515 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.6479 (pt0) cc_final: 0.6180 (tt0) REVERT: A 28 LYS cc_start: 0.7603 (mttp) cc_final: 0.7306 (mttt) REVERT: K 88 SER cc_start: 0.7640 (m) cc_final: 0.7194 (t) REVERT: K 223 GLU cc_start: 0.6535 (mm-30) cc_final: 0.6251 (mm-30) REVERT: U 88 SER cc_start: 0.8083 (m) cc_final: 0.7708 (p) REVERT: E 41 ASN cc_start: 0.7599 (t0) cc_final: 0.7328 (t0) REVERT: E 129 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8308 (tttm) REVERT: F 63 TYR cc_start: 0.8553 (m-10) cc_final: 0.7864 (m-10) REVERT: F 69 ASP cc_start: 0.7466 (t70) cc_final: 0.7173 (m-30) REVERT: F 118 ARG cc_start: 0.8206 (mtm-85) cc_final: 0.7971 (mtp-110) REVERT: F 241 ARG cc_start: 0.7489 (ttp-110) cc_final: 0.6787 (mmp80) REVERT: F 293 ARG cc_start: 0.7821 (mtm110) cc_final: 0.7518 (mtp-110) REVERT: F 298 ASN cc_start: 0.8132 (t0) cc_final: 0.7722 (t0) REVERT: F 301 LYS cc_start: 0.8404 (mttt) cc_final: 0.7765 (mptt) REVERT: H 201 TYR cc_start: 0.7642 (m-80) cc_final: 0.7329 (m-10) REVERT: T 155 SER cc_start: 0.8247 (OUTLIER) cc_final: 0.8018 (p) REVERT: T 261 GLN cc_start: 0.7503 (pt0) cc_final: 0.7092 (pt0) REVERT: T 285 GLU cc_start: 0.7707 (tp30) cc_final: 0.7101 (tp30) outliers start: 34 outliers final: 14 residues processed: 204 average time/residue: 0.5857 time to fit residues: 150.7653 Evaluate side-chains 159 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain K residue 288 ILE 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 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 231 GLN Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain T residue 155 SER 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: 50.0000 chunk 130 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 78 optimal weight: 40.0000 chunk 62 optimal weight: 5.9990 chunk 320 optimal weight: 2.9990 chunk 294 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 225 optimal weight: 50.0000 chunk 158 optimal weight: 0.9980 chunk 114 optimal weight: 30.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN A 296 HIS U 21 ASN E 124 GLN E 157 ASN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 ASN T 124 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.208578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.119195 restraints weight = 155588.569| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.32 r_work: 0.3237 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 41996 Z= 0.251 Angle : 0.611 8.973 61122 Z= 0.346 Chirality : 0.045 0.388 7568 Planarity : 0.005 0.070 4725 Dihedral : 26.094 178.073 15295 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.44 % Allowed : 19.66 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.15), residues: 3180 helix: 1.80 (0.12), residues: 1783 sheet: 0.86 (0.25), residues: 366 loop : 0.11 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 24 TYR 0.032 0.002 TYR A 42 PHE 0.032 0.002 PHE A 10 TRP 0.009 0.002 TRP A 78 HIS 0.008 0.002 HIS K 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.25 (41996) covalent geometry : angle 0.61118 / 0.35 (61122) hydrogen bonds : bond 0.05365 / 3.74 ( 2215) hydrogen bonds : angle 4.06301 / 3.86 ( 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 221 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 166 time to evaluate : 1.063 Fit side-chains REVERT: A 28 LYS cc_start: 0.7850 (mttp) cc_final: 0.7530 (mtpt) REVERT: A 31 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.6728 (mpp80) REVERT: K 157 ASN cc_start: 0.6527 (p0) cc_final: 0.5776 (t0) REVERT: K 223 GLU cc_start: 0.6698 (mm-30) cc_final: 0.6344 (mm-30) REVERT: U 11 ARG cc_start: 0.6983 (ptt180) cc_final: 0.6001 (ptm160) REVERT: U 21 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8333 (m110) REVERT: U 47 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7138 (mtt180) REVERT: E 41 ASN cc_start: 0.7821 (t0) cc_final: 0.7536 (t0) REVERT: E 180 MET cc_start: 0.8205 (mmm) cc_final: 0.7890 (mmm) REVERT: F 63 TYR cc_start: 0.8727 (m-10) cc_final: 0.8378 (m-10) REVERT: F 97 PHE cc_start: 0.8189 (m-80) cc_final: 0.7987 (m-80) REVERT: F 203 GLU cc_start: 0.7765 (pm20) cc_final: 0.7532 (pm20) REVERT: F 241 ARG cc_start: 0.7584 (ttp-110) cc_final: 0.6916 (tpp-160) REVERT: F 293 ARG cc_start: 0.8180 (mtm110) cc_final: 0.7897 (mtp-110) REVERT: F 301 LYS cc_start: 0.8303 (mttt) cc_final: 0.7697 (mptt) REVERT: T 155 SER cc_start: 0.8177 (OUTLIER) cc_final: 0.7948 (p) REVERT: T 261 GLN cc_start: 0.7647 (pt0) cc_final: 0.7257 (pt0) REVERT: T 285 GLU cc_start: 0.7857 (tp30) cc_final: 0.7280 (tp30) outliers start: 55 outliers final: 25 residues processed: 215 average time/residue: 0.5930 time to fit residues: 160.7529 Evaluate side-chains 174 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 262 VAL Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 202 SER Chi-restraints excluded: chain U residue 21 ASN 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 243 VAL 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 215 SER 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 216 VAL 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 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: 6.9990 chunk 147 optimal weight: 9.9990 chunk 238 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 211 optimal weight: 0.1980 chunk 290 optimal weight: 0.9990 chunk 311 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 384 optimal weight: 40.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 280 HIS E 157 ASN H 85 ASN H 291 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.210745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.121195 restraints weight = 133312.340| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.50 r_work: 0.3238 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 41996 Z= 0.134 Angle : 0.511 8.219 61122 Z= 0.299 Chirality : 0.039 0.294 7568 Planarity : 0.004 0.043 4725 Dihedral : 26.043 179.519 15293 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.51 % Allowed : 20.16 % Favored : 76.33 % 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 are not related in a simple way. whole: 1.88 (0.15), residues: 3180 helix: 2.03 (0.12), residues: 1785 sheet: 0.78 (0.25), residues: 366 loop : 0.11 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 24 TYR 0.020 0.001 TYR U 179 PHE 0.015 0.001 PHE A 10 TRP 0.008 0.001 TRP A 78 HIS 0.007 0.001 HIS H 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 (41996) covalent geometry : angle 0.51105 / 0.30 (61122) hydrogen bonds : bond 0.04320 / 3.04 ( 2215) hydrogen bonds : angle 3.79642 / 3.61 ( 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 229 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 173 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7817 (mttp) cc_final: 0.7463 (mtmm) REVERT: A 31 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7252 (mtt180) REVERT: K 157 ASN cc_start: 0.6549 (p0) cc_final: 0.5896 (t0) REVERT: K 223 GLU cc_start: 0.6589 (mm-30) cc_final: 0.6249 (mm-30) REVERT: E 41 ASN cc_start: 0.7751 (t0) cc_final: 0.7503 (t0) REVERT: E 69 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: E 129 LYS cc_start: 0.8565 (ttmp) cc_final: 0.8206 (tttm) REVERT: E 180 MET cc_start: 0.8182 (mmm) cc_final: 0.7851 (mmm) REVERT: F 63 TYR cc_start: 0.8594 (m-10) cc_final: 0.8133 (m-10) REVERT: F 97 PHE cc_start: 0.8150 (m-80) cc_final: 0.7919 (m-80) REVERT: F 118 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7908 (mtp85) REVERT: F 241 ARG cc_start: 0.7486 (ttp-110) cc_final: 0.6836 (mmp80) REVERT: F 265 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7085 (mp) REVERT: F 293 ARG cc_start: 0.8052 (mtm110) cc_final: 0.7702 (mtp-110) REVERT: F 301 LYS cc_start: 0.8231 (mttt) cc_final: 0.7638 (mptt) REVERT: T 155 SER cc_start: 0.8159 (OUTLIER) cc_final: 0.7939 (p) REVERT: T 261 GLN cc_start: 0.7604 (pt0) cc_final: 0.7197 (pt0) REVERT: T 285 GLU cc_start: 0.7735 (tp30) cc_final: 0.7142 (tp30) REVERT: T 300 ASP cc_start: 0.8358 (m-30) cc_final: 0.8069 (m-30) outliers start: 56 outliers final: 26 residues processed: 220 average time/residue: 0.5594 time to fit residues: 156.4703 Evaluate side-chains 179 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 262 VAL Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain U residue 26 MET 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 48 GLN Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 215 SER 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 265 LEU Chi-restraints excluded: chain H residue 16 HIS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain T residue 67 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 296 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 243 optimal weight: 2.9990 chunk 245 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 260 optimal weight: 0.7980 chunk 254 optimal weight: 1.9990 chunk 371 optimal weight: 30.0000 chunk 348 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 21 ASN E 42 HIS E 157 ASN F 112 ASN F 288 ASN H 112 ASN H 291 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.208266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.118042 restraints weight = 117892.360| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.36 r_work: 0.3186 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41996 Z= 0.153 Angle : 0.513 9.085 61122 Z= 0.298 Chirality : 0.039 0.294 7568 Planarity : 0.004 0.054 4725 Dihedral : 25.985 179.971 15293 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.63 % Allowed : 19.85 % 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 are not related in a simple way. whole: 1.96 (0.15), residues: 3180 helix: 2.11 (0.12), residues: 1779 sheet: 0.75 (0.25), residues: 366 loop : 0.15 (0.20), residues: 1035 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 0.022 0.001 PHE A 10 TRP 0.007 0.001 TRP A 78 HIS 0.007 0.001 HIS H 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (41996) covalent geometry : angle 0.51280 / 0.30 (61122) hydrogen bonds : bond 0.04301 / 3.02 ( 2215) hydrogen bonds : angle 3.69476 / 3.49 ( 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 209 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 151 time to evaluate : 1.181 Fit side-chains REVERT: A 28 LYS cc_start: 0.7855 (mttp) cc_final: 0.7601 (mtpt) REVERT: A 31 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7197 (mtt180) REVERT: K 157 ASN cc_start: 0.6693 (p0) cc_final: 0.6109 (t0) REVERT: K 223 GLU cc_start: 0.6510 (mm-30) cc_final: 0.6204 (mm-30) REVERT: U 157 ASN cc_start: 0.7460 (p0) cc_final: 0.7066 (t0) REVERT: E 41 ASN cc_start: 0.7817 (t0) cc_final: 0.7587 (t0) REVERT: E 46 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6956 (ttt180) REVERT: E 69 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7624 (m-30) REVERT: E 129 LYS cc_start: 0.8555 (ttmp) cc_final: 0.8234 (tttm) REVERT: E 180 MET cc_start: 0.8114 (mmm) cc_final: 0.7763 (mmm) REVERT: E 250 GLU cc_start: 0.7882 (pt0) cc_final: 0.7662 (pt0) REVERT: F 63 TYR cc_start: 0.8618 (m-10) cc_final: 0.8232 (m-10) REVERT: F 97 PHE cc_start: 0.8192 (m-80) cc_final: 0.7917 (m-80) REVERT: F 118 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7913 (mtp85) REVERT: F 241 ARG cc_start: 0.7494 (ttp-110) cc_final: 0.6807 (tpp-160) REVERT: F 265 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7127 (mp) REVERT: F 293 ARG cc_start: 0.8052 (mtm110) cc_final: 0.7788 (mtp-110) REVERT: F 301 LYS cc_start: 0.8266 (mttt) cc_final: 0.7674 (mptt) REVERT: T 14 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7656 (mm) REVERT: T 155 SER cc_start: 0.8172 (OUTLIER) cc_final: 0.7956 (p) REVERT: T 261 GLN cc_start: 0.7662 (pt0) cc_final: 0.7332 (pt0) REVERT: T 285 GLU cc_start: 0.7748 (tp30) cc_final: 0.7242 (tp30) REVERT: T 287 MET cc_start: 0.6402 (mtp) cc_final: 0.6196 (mtp) outliers start: 58 outliers final: 34 residues processed: 201 average time/residue: 0.6049 time to fit residues: 153.7046 Evaluate side-chains 181 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 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 110 ILE Chi-restraints excluded: chain U residue 26 MET 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 39 VAL Chi-restraints excluded: chain E residue 46 ARG 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 E residue 215 SER Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain F residue 148 SER 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 F residue 265 LEU Chi-restraints excluded: chain H residue 16 HIS Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain T residue 14 ILE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 67 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 127 optimal weight: 0.9990 chunk 196 optimal weight: 30.0000 chunk 336 optimal weight: 9.9990 chunk 95 optimal weight: 0.1980 chunk 287 optimal weight: 0.5980 chunk 316 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 388 optimal weight: 50.0000 chunk 341 optimal weight: 1.9990 chunk 68 optimal weight: 30.0000 chunk 164 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 157 ASN F 112 ASN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 ASN T 42 HIS T 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.204840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.121667 restraints weight = 144369.088| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.46 r_work: 0.3175 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41996 Z= 0.152 Angle : 0.506 8.664 61122 Z= 0.293 Chirality : 0.039 0.297 7568 Planarity : 0.004 0.108 4725 Dihedral : 25.970 179.680 15293 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.13 % Allowed : 20.04 % Favored : 75.83 % 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 are not related in a simple way. whole: 1.98 (0.15), residues: 3180 helix: 2.16 (0.12), residues: 1780 sheet: 0.70 (0.25), residues: 366 loop : 0.12 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 246 TYR 0.022 0.001 TYR P 155 PHE 0.016 0.001 PHE A 10 TRP 0.007 0.001 TRP A 78 HIS 0.005 0.001 HIS H 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (41996) covalent geometry : angle 0.50573 / 0.29 (61122) hydrogen bonds : bond 0.04174 / 2.94 ( 2215) hydrogen bonds : angle 3.64164 / 3.44 ( 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 221 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 155 time to evaluate : 1.071 Fit side-chains REVERT: A 28 LYS cc_start: 0.8071 (mttp) cc_final: 0.7747 (mtmt) REVERT: A 31 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7497 (mtt180) REVERT: K 157 ASN cc_start: 0.6875 (p0) cc_final: 0.6302 (t0) REVERT: K 223 GLU cc_start: 0.6687 (mm-30) cc_final: 0.6374 (mm-30) REVERT: U 47 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7143 (mtt180) REVERT: U 157 ASN cc_start: 0.7507 (p0) cc_final: 0.7183 (t0) REVERT: U 206 MET cc_start: 0.7719 (mmm) cc_final: 0.7356 (tpp) REVERT: E 41 ASN cc_start: 0.7893 (t0) cc_final: 0.7674 (t0) REVERT: E 46 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7115 (ttt180) REVERT: E 69 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: E 129 LYS cc_start: 0.8661 (ttmp) cc_final: 0.8333 (tttm) REVERT: E 180 MET cc_start: 0.8288 (mmm) cc_final: 0.7918 (mmm) REVERT: E 250 GLU cc_start: 0.8149 (pt0) cc_final: 0.7895 (pt0) REVERT: F 24 ARG cc_start: 0.8158 (mtt-85) cc_final: 0.7623 (mmt90) REVERT: F 69 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7273 (m-30) REVERT: F 97 PHE cc_start: 0.8329 (m-80) cc_final: 0.8091 (m-80) REVERT: F 118 ARG cc_start: 0.8257 (mtm-85) cc_final: 0.8007 (mtp85) REVERT: F 241 ARG cc_start: 0.7650 (ttp-110) cc_final: 0.6944 (tpp-160) REVERT: F 293 ARG cc_start: 0.8158 (mtm110) cc_final: 0.7895 (mtp-110) REVERT: F 301 LYS cc_start: 0.8337 (mttt) cc_final: 0.7740 (mptt) REVERT: T 14 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7767 (mm) REVERT: T 51 GLN cc_start: 0.7207 (mm110) cc_final: 0.6884 (mm110) REVERT: T 261 GLN cc_start: 0.7969 (pt0) cc_final: 0.7552 (pt0) REVERT: T 285 GLU cc_start: 0.7853 (tp30) cc_final: 0.7299 (tp30) REVERT: T 287 MET cc_start: 0.6902 (mtp) cc_final: 0.6701 (mtp) outliers start: 66 outliers final: 36 residues processed: 210 average time/residue: 0.5682 time to fit residues: 151.9194 Evaluate side-chains 190 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 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 110 ILE Chi-restraints excluded: chain U residue 21 ASN 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 128 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 ARG 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 E residue 215 SER Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 148 SER 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 39 VAL Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain T residue 14 ILE 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 Chi-restraints excluded: chain T residue 262 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 356 optimal weight: 20.0000 chunk 340 optimal weight: 0.7980 chunk 187 optimal weight: 10.0000 chunk 368 optimal weight: 40.0000 chunk 48 optimal weight: 10.0000 chunk 221 optimal weight: 9.9990 chunk 332 optimal weight: 0.0980 chunk 125 optimal weight: 0.0030 chunk 297 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 21 ASN E 157 ASN F 112 ASN H 11 GLN H 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.209157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.115726 restraints weight = 123446.205| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.66 r_work: 0.3250 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 41996 Z= 0.138 Angle : 0.494 10.192 61122 Z= 0.288 Chirality : 0.038 0.299 7568 Planarity : 0.004 0.052 4725 Dihedral : 25.945 179.983 15293 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.51 % Allowed : 20.73 % Favored : 75.77 % 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 are not related in a simple way. whole: 2.05 (0.15), residues: 3180 helix: 2.22 (0.12), residues: 1786 sheet: 0.70 (0.25), residues: 366 loop : 0.13 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 24 TYR 0.022 0.001 TYR A 302 PHE 0.016 0.001 PHE A 10 TRP 0.007 0.001 TRP A 78 HIS 0.005 0.001 HIS H 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (41996) covalent geometry : angle 0.49405 / 0.29 (61122) hydrogen bonds : bond 0.04048 / 2.85 ( 2215) hydrogen bonds : angle 3.55517 / 3.36 ( 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 213 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 157 time to evaluate : 1.147 Fit side-chains REVERT: A 28 LYS cc_start: 0.7952 (mttp) cc_final: 0.7711 (mtpt) REVERT: A 31 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7239 (mtt180) REVERT: K 157 ASN cc_start: 0.6821 (p0) cc_final: 0.6219 (t0) REVERT: K 223 GLU cc_start: 0.6615 (mm-30) cc_final: 0.6273 (mm-30) REVERT: U 157 ASN cc_start: 0.7357 (p0) cc_final: 0.7120 (t0) REVERT: E 41 ASN cc_start: 0.7746 (t0) cc_final: 0.7538 (t0) REVERT: E 69 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: E 129 LYS cc_start: 0.8545 (ttmp) cc_final: 0.8210 (tttp) REVERT: E 250 GLU cc_start: 0.7957 (pt0) cc_final: 0.7757 (pt0) REVERT: F 63 TYR cc_start: 0.8627 (m-10) cc_final: 0.8149 (m-10) REVERT: F 69 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7172 (m-30) REVERT: F 97 PHE cc_start: 0.8202 (m-80) cc_final: 0.7958 (m-80) REVERT: F 241 ARG cc_start: 0.7488 (ttp-110) cc_final: 0.6802 (tpp-160) REVERT: F 293 ARG cc_start: 0.8059 (mtm110) cc_final: 0.7805 (mtp-110) REVERT: F 301 LYS cc_start: 0.8195 (mttt) cc_final: 0.7629 (mptt) REVERT: T 51 GLN cc_start: 0.7097 (mm110) cc_final: 0.6790 (mm110) REVERT: T 261 GLN cc_start: 0.7810 (pt0) cc_final: 0.7441 (pt0) REVERT: T 263 THR cc_start: 0.6911 (OUTLIER) cc_final: 0.6563 (p) REVERT: T 285 GLU cc_start: 0.7788 (tp30) cc_final: 0.7193 (tp30) outliers start: 56 outliers final: 36 residues processed: 205 average time/residue: 0.5514 time to fit residues: 145.3695 Evaluate side-chains 185 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 A residue 259 LYS Chi-restraints excluded: chain K residue 89 SER 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 110 ILE 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 128 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 39 VAL 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 E residue 262 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 148 SER 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 213 LEU Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 244 VAL 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 262 VAL Chi-restraints excluded: chain T residue 263 THR 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: 20.0000 chunk 52 optimal weight: 10.0000 chunk 385 optimal weight: 40.0000 chunk 205 optimal weight: 50.0000 chunk 202 optimal weight: 30.0000 chunk 369 optimal weight: 40.0000 chunk 373 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 270 optimal weight: 2.9990 chunk 194 optimal weight: 30.0000 overall best weight: 10.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN H 11 GLN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 ASN ** T 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.198068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.102211 restraints weight = 141170.714| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.60 r_work: 0.2962 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.027 0.303 41996 Z= 1.138 Angle : 1.320 26.729 61122 Z= 0.667 Chirality : 0.087 0.659 7568 Planarity : 0.011 0.195 4725 Dihedral : 26.415 179.835 15293 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.32 % Allowed : 19.29 % Favored : 75.39 % 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 are not related in a simple way. whole: -0.84 (0.14), residues: 3180 helix: -0.32 (0.12), residues: 1752 sheet: 0.21 (0.27), residues: 336 loop : -0.97 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.004 ARG F 251 TYR 0.059 0.007 TYR A 42 PHE 0.057 0.006 PHE A 10 TRP 0.039 0.007 TRP A 78 HIS 0.021 0.005 HIS K 280 Details of bonding type rmsd/Z covalent geometry : bond 0.02650 / 1.14 (41996) covalent geometry : angle 1.31957 / 0.67 (61122) hydrogen bonds : bond 0.10346 / 7.11 ( 2215) hydrogen bonds : angle 5.43942 / 5.02 ( 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 215 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 130 time to evaluate : 1.079 Fit side-chains REVERT: A 11 ARG cc_start: 0.7448 (ptt180) cc_final: 0.6297 (ptm160) REVERT: A 28 LYS cc_start: 0.8078 (mttp) cc_final: 0.7765 (mtpt) REVERT: A 31 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7845 (mmm-85) REVERT: A 302 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.7094 (t80) REVERT: K 25 ASP cc_start: 0.7448 (m-30) cc_final: 0.7241 (m-30) REVERT: K 223 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6556 (mm-30) REVERT: P 65 ILE cc_start: 0.6366 (mm) cc_final: 0.5669 (pt) REVERT: U 11 ARG cc_start: 0.7394 (ptt180) cc_final: 0.7148 (ptp90) REVERT: U 206 MET cc_start: 0.8306 (mmm) cc_final: 0.7727 (tpp) REVERT: E 69 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7658 (m-30) REVERT: F 69 ASP cc_start: 0.7785 (m-30) cc_final: 0.7409 (m-30) REVERT: F 241 ARG cc_start: 0.7664 (ttp-110) cc_final: 0.6972 (tpp-160) REVERT: F 293 ARG cc_start: 0.8424 (mtm110) cc_final: 0.8175 (mtp-110) REVERT: F 301 LYS cc_start: 0.8309 (mttt) cc_final: 0.7717 (mptt) REVERT: H 72 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7505 (mp) REVERT: H 201 TYR cc_start: 0.7612 (m-80) cc_final: 0.7386 (m-10) REVERT: T 46 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6037 (ttm-80) REVERT: T 285 GLU cc_start: 0.7965 (tp30) cc_final: 0.7484 (tp30) REVERT: T 294 LYS cc_start: 0.7677 (mttt) cc_final: 0.7474 (mtpt) outliers start: 85 outliers final: 48 residues processed: 204 average time/residue: 0.5717 time to fit residues: 148.1634 Evaluate side-chains 170 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 117 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 27 SER 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 302 TYR 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 214 ASP Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 255 ILE Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 202 SER Chi-restraints excluded: chain U residue 9 THR 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 128 THR Chi-restraints excluded: chain U residue 243 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 39 VAL 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 E residue 215 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain H residue 35 CYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain T residue 14 ILE Chi-restraints excluded: chain T residue 46 ARG 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: 50.0000 chunk 43 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 112 optimal weight: 50.0000 chunk 101 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 218 optimal weight: 30.0000 chunk 325 optimal weight: 0.7980 chunk 249 optimal weight: 0.7980 chunk 225 optimal weight: 50.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 112 ASN E 157 ASN F 112 ASN H 11 GLN H 249 ASN H 288 ASN H 291 ASN ** T 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.205494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.113419 restraints weight = 144323.391| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.43 r_work: 0.3123 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 41996 Z= 0.199 Angle : 0.601 12.210 61122 Z= 0.340 Chirality : 0.042 0.311 7568 Planarity : 0.005 0.085 4725 Dihedral : 26.268 178.737 15293 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.32 % Allowed : 21.29 % Favored : 75.39 % 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 are not related in a simple way. whole: 0.58 (0.15), residues: 3180 helix: 1.01 (0.12), residues: 1756 sheet: 0.13 (0.26), residues: 366 loop : -0.44 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 24 TYR 0.023 0.002 TYR A 302 PHE 0.026 0.002 PHE A 10 TRP 0.011 0.002 TRP U 78 HIS 0.007 0.001 HIS H 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 (41996) covalent geometry : angle 0.60113 / 0.34 (61122) hydrogen bonds : bond 0.05063 / 3.56 ( 2215) hydrogen bonds : angle 4.19792 / 3.93 ( 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 200 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 147 time to evaluate : 1.040 Fit side-chains REVERT: A 28 LYS cc_start: 0.7917 (mttp) cc_final: 0.7612 (mtmt) REVERT: A 31 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7462 (mtt180) REVERT: G 285 GLU cc_start: 0.6081 (tp30) cc_final: 0.5644 (tm-30) REVERT: K 223 GLU cc_start: 0.6675 (mm-30) cc_final: 0.6394 (mm-30) REVERT: P 65 ILE cc_start: 0.6208 (mm) cc_final: 0.5684 (pt) REVERT: U 11 ARG cc_start: 0.6946 (ptt180) cc_final: 0.5770 (ptm160) REVERT: U 47 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7102 (mtt180) REVERT: E 48 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.6417 (mp10) REVERT: E 69 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7602 (m-30) REVERT: F 65 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: F 241 ARG cc_start: 0.7586 (ttp-110) cc_final: 0.6952 (tpp-160) REVERT: F 293 ARG cc_start: 0.8197 (mtm110) cc_final: 0.7926 (mtp-110) REVERT: F 301 LYS cc_start: 0.8319 (mttt) cc_final: 0.7733 (mptt) REVERT: T 285 GLU cc_start: 0.7752 (tp30) cc_final: 0.7253 (tp30) outliers start: 53 outliers final: 30 residues processed: 188 average time/residue: 0.5374 time to fit residues: 127.9129 Evaluate side-chains 170 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 27 SER 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 262 VAL Chi-restraints excluded: chain K residue 89 SER 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 47 ARG Chi-restraints excluded: chain U residue 53 VAL 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 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 69 ASP Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 244 VAL 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 352 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 chunk 355 optimal weight: 40.0000 chunk 386 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 4 optimal weight: 0.2980 chunk 212 optimal weight: 10.0000 chunk 239 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 371 optimal weight: 30.0000 chunk 238 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 112 ASN E 157 ASN F 112 ASN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN H 288 ASN ** T 47 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 = 0.4727 r_free = 0.4727 target = 0.206050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.114199 restraints weight = 148191.713| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.64 r_work: 0.3135 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 41996 Z= 0.201 Angle : 0.567 12.003 61122 Z= 0.320 Chirality : 0.041 0.321 7568 Planarity : 0.004 0.070 4725 Dihedral : 26.136 179.968 15293 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.63 % Allowed : 21.98 % Favored : 75.39 % 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 are not related in a simple way. whole: 1.12 (0.15), residues: 3180 helix: 1.52 (0.12), residues: 1776 sheet: 0.19 (0.25), residues: 366 loop : -0.29 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 24 TYR 0.020 0.002 TYR A 302 PHE 0.025 0.002 PHE A 10 TRP 0.009 0.001 TRP A 78 HIS 0.006 0.001 HIS F 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (41996) covalent geometry : angle 0.56724 / 0.32 (61122) hydrogen bonds : bond 0.04656 / 3.26 ( 2215) hydrogen bonds : angle 3.92887 / 3.65 ( 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 185 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 1.043 Fit side-chains REVERT: A 28 LYS cc_start: 0.7948 (mttp) cc_final: 0.7731 (mtpt) REVERT: A 31 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7368 (mtt180) REVERT: G 285 GLU cc_start: 0.6099 (tp30) cc_final: 0.5649 (tm-30) REVERT: K 223 GLU cc_start: 0.6712 (mm-30) cc_final: 0.6446 (mm-30) REVERT: U 11 ARG cc_start: 0.6950 (ptt180) cc_final: 0.5809 (ptm160) REVERT: U 206 MET cc_start: 0.7631 (mmm) cc_final: 0.7213 (tpp) REVERT: E 69 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: F 65 GLU cc_start: 0.8479 (pm20) cc_final: 0.7975 (mp0) REVERT: F 69 ASP cc_start: 0.7208 (m-30) cc_final: 0.6861 (m-30) REVERT: F 97 PHE cc_start: 0.8087 (m-80) cc_final: 0.7855 (m-80) REVERT: F 241 ARG cc_start: 0.7567 (ttp-110) cc_final: 0.6901 (tpm170) REVERT: F 293 ARG cc_start: 0.8183 (mtm110) cc_final: 0.7906 (mtp-110) REVERT: F 301 LYS cc_start: 0.8317 (mttt) cc_final: 0.7724 (mptt) REVERT: T 285 GLU cc_start: 0.7763 (tp30) cc_final: 0.7271 (tp30) outliers start: 42 outliers final: 31 residues processed: 179 average time/residue: 0.5796 time to fit residues: 131.3120 Evaluate side-chains 168 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 27 SER 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 262 VAL Chi-restraints excluded: chain G residue 283 ARG Chi-restraints excluded: chain K residue 89 SER 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 53 VAL 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 E residue 34 LEU Chi-restraints excluded: chain E residue 39 VAL 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 257 THR Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 244 VAL 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: 0.9980 chunk 261 optimal weight: 0.8980 chunk 333 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 306 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 329 optimal weight: 0.8980 chunk 285 optimal weight: 0.3980 chunk 80 optimal weight: 0.6980 chunk 177 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 112 ASN E 157 ASN F 112 ASN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN H 288 ASN T 112 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.207750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.118977 restraints weight = 148155.817| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.53 r_work: 0.3190 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41996 Z= 0.138 Angle : 0.518 11.682 61122 Z= 0.298 Chirality : 0.039 0.303 7568 Planarity : 0.004 0.059 4725 Dihedral : 26.064 178.856 15293 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.07 % Allowed : 22.86 % Favored : 75.08 % 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 are not related in a simple way. whole: 1.54 (0.15), residues: 3180 helix: 1.85 (0.12), residues: 1776 sheet: 0.32 (0.25), residues: 366 loop : -0.07 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 24 TYR 0.022 0.001 TYR A 302 PHE 0.018 0.001 PHE H 289 TRP 0.011 0.001 TRP U 78 HIS 0.007 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (41996) covalent geometry : angle 0.51771 / 0.30 (61122) hydrogen bonds : bond 0.04150 / 2.91 ( 2215) hydrogen bonds : angle 3.72801 / 3.45 ( 5674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25847.11 seconds wall clock time: 436 minutes 58.07 seconds (26218.07 seconds total)