Starting phenix.real_space_refine on Tue Aug 26 16:14:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qbm_18315/08_2025/8qbm_18315.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qbm_18315/08_2025/8qbm_18315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qbm_18315/08_2025/8qbm_18315.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qbm_18315/08_2025/8qbm_18315.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qbm_18315/08_2025/8qbm_18315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qbm_18315/08_2025/8qbm_18315.map" } resolution = 3.09 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 880 5.49 5 Mg 3 5.21 5 S 48 5.16 5 C 21863 2.51 5 N 7230 2.21 5 O 9540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39564 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 2337 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 309, 2327 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 84 Conformer: "B" Number of residues, atoms: 309, 2327 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 84 bond proxies already assigned to first conformer: 2360 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': 8, 'rna3p_pur': 23, 'rna3p_pyr': 25} Link IDs: {'rna2p': 13, 'rna3p': 47} 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: "E" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2227 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 6, 'TRANS': 295} Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 9, 'ASN:plan1': 2, 'GLN:plan1': 3, 'ARG:plan': 6, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 132 Chain: "F" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2109 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 6, 'TRANS': 295} Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 421 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 16, 'GLU:plan': 10, 'ARG:plan': 11, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLN:plan1': 6, 'PHE:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 206 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: "H" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2038 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 6, 'TRANS': 295} Unresolved non-hydrogen bonds: 426 Unresolved non-hydrogen angles: 508 Unresolved non-hydrogen dihedrals: 356 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 19, 'GLU:plan': 13, 'GLN:plan1': 8, 'ARG:plan': 13, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 255 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: 2301 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 309, 2291 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 5, 'TYR:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 109 Conformer: "B" Number of residues, atoms: 309, 2291 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 5, 'TYR:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 109 bond proxies already assigned to first conformer: 2323 Chain: "M" 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: "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': 6, 'rna2p_pyr': 8, 'rna3p_pur': 22, 'rna3p_pyr': 25} Link IDs: {'rna2p': 14, 'rna3p': 46} Chain breaks: 2 Chain: "P" Number of atoms: 1881 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 309, 1876 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 618 Unresolved non-hydrogen angles: 765 Unresolved non-hydrogen dihedrals: 510 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLU:plan': 14, 'TYR:plan': 7, 'ASN:plan1': 8, 'PHE:plan': 5, 'ARG:plan': 17, 'HIS:plan': 4, 'ASP:plan': 10, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 310 Conformer: "B" Number of residues, atoms: 309, 1876 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 618 Unresolved non-hydrogen angles: 765 Unresolved non-hydrogen dihedrals: 510 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLU:plan': 14, 'TYR:plan': 7, 'ASN:plan1': 8, 'PHE:plan': 5, 'ARG:plan': 17, 'HIS:plan': 4, 'ASP:plan': 10, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 310 bond proxies already assigned to first conformer: 1903 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: "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: "T" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2213 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 6, 'TRANS': 295} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 291 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 9, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 6, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 141 Chain: "U" Number of atoms: 2267 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 309, 2257 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 12, 'ARG:plan': 6, 'ASP:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 117 Conformer: "B" Number of residues, atoms: 309, 2257 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 12, 'ARG:plan': 6, 'ASP:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 117 bond proxies already assigned to first conformer: 2290 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: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 309, 1529 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 275} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 999 Unresolved non-hydrogen angles: 1263 Unresolved non-hydrogen dihedrals: 844 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': 9, 'GLN:plan1': 8, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 501 Conformer: "B" Number of residues, atoms: 309, 1529 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 275} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 999 Unresolved non-hydrogen angles: 1263 Unresolved non-hydrogen dihedrals: 844 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': 9, 'GLN:plan1': 8, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 501 bond proxies already assigned to first conformer: 1522 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': 8, 'rna3p_pur': 23, 'rna3p_pyr': 25} Link IDs: {'rna2p': 13, 'rna3p': 47} 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: "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: "L" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 890 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 1 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: "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: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 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} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AHIS A 24 " occ=0.49 ... (18 atoms not shown) pdb=" NE2BHIS A 24 " occ=0.51 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: 12.61, per 1000 atoms: 0.32 Number of scatterers: 39564 At special positions: 0 Unit cell: (137.28, 187.2, 351.936, 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 48 16.00 P 880 15.00 Mg 3 11.99 O 9540 8.00 N 7230 7.00 C 21863 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.64 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 715.3 nanoseconds 6360 Ramachandran restraints generated. 3180 Oldfield, 0 Emsley, 3180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6044 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 29 sheets defined 64.3% alpha, 8.7% beta 298 base pairs and 527 stacking pairs defined. Time for finding SS restraints: 6.60 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 3.590A pdb=" N LEU A 7 " --> pdb=" O SER A 3 " (cutoff:3.500A) 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 101 through 107 removed outlier: 3.644A pdb=" N ASN A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) 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 123 through 127 Processing helix chain 'A' and resid 128 through 139 removed outlier: 3.974A 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: 4.517A pdb=" N SER A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 220 removed outlier: 3.550A 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 'E' and resid 6 through 18 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 67 through 75 removed outlier: 3.620A pdb=" N LEU E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) 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: 3.630A pdb=" N ARG E 118 " --> pdb=" O GLU E 114 " (cutoff:3.500A) removed outlier: 3.966A 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 229 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 291 Processing helix chain 'F' and resid 6 through 18 removed outlier: 3.532A 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 removed outlier: 4.472A pdb=" N PHE F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 119 removed outlier: 3.712A pdb=" N ARG F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) removed outlier: 4.063A 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: 3.893A pdb=" N LYS F 227 " --> pdb=" O GLU F 223 " (cutoff:3.500A) removed outlier: 3.675A 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 removed outlier: 3.525A pdb=" N SER F 272 " --> pdb=" O SER F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 291 removed outlier: 3.546A pdb=" N PHE F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) 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 276 through 291 removed outlier: 3.530A pdb=" N GLU G 285 " --> pdb=" O ARG G 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 18 Processing helix chain 'H' and resid 44 through 56 removed outlier: 3.553A pdb=" N PHE H 56 " --> pdb=" O PHE H 52 " (cutoff:3.500A) 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 removed outlier: 3.902A pdb=" N PHE H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 118 removed outlier: 3.587A pdb=" N ARG H 118 " --> pdb=" O GLU H 114 " (cutoff:3.500A) 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: 3.735A pdb=" N LYS H 227 " --> pdb=" O GLU H 223 " (cutoff:3.500A) removed outlier: 3.709A 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: 3.558A pdb=" N LEU H 279 " --> pdb=" O ASP H 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: 4.008A 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 128 through 140 removed outlier: 3.817A pdb=" N VAL I 132 " --> pdb=" O THR I 128 " (cutoff:3.500A) removed outlier: 3.676A 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: 4.128A pdb=" N SER I 187 " --> pdb=" O GLY I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 220 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: 3.524A pdb=" N HIS I 296 " --> pdb=" O ASP I 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 15 removed outlier: 3.670A pdb=" N LEU K 15 " --> pdb=" O ARG K 11 " (cutoff:3.500A) 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 removed outlier: 3.504A pdb=" N LEU K 127 " --> pdb=" O PHE K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 139 removed outlier: 3.752A 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: 4.708A pdb=" N SER K 187 " --> pdb=" O GLY K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 220 Processing helix chain 'K' and resid 221 through 224 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 16 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 47 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: 4.085A 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: 4.315A pdb=" N SER P 187 " --> pdb=" O GLY P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 205 through 220 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 'T' and resid 6 through 18 Processing helix chain 'T' and resid 44 through 55 Processing helix chain 'T' and resid 67 through 75 removed outlier: 3.737A pdb=" N LEU T 71 " --> pdb=" O LEU T 67 " (cutoff:3.500A) 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: 3.859A 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: 3.834A 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 291 removed outlier: 3.613A pdb=" N LEU T 279 " --> pdb=" O ASP T 275 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 15 removed outlier: 3.524A pdb=" N ASN U 14 " --> pdb=" O PHE U 10 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU U 15 " --> pdb=" O ARG U 11 " (cutoff:3.500A) 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 101 through 107 removed outlier: 3.732A pdb=" N ASN U 105 " --> pdb=" O SER U 101 " (cutoff:3.500A) 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 123 through 127 Processing helix chain 'U' and resid 128 through 140 removed outlier: 3.966A pdb=" N VAL U 132 " --> pdb=" O THR U 128 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY U 140 " --> pdb=" O PHE U 136 " (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 188 removed outlier: 4.563A pdb=" N SER U 187 " --> pdb=" O GLY U 183 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG U 188 " --> pdb=" O TYR U 184 " (cutoff:3.500A) Processing helix chain 'U' and resid 205 through 220 Processing helix chain 'U' and resid 221 through 224 Processing helix chain 'U' and resid 228 through 232 removed outlier: 3.597A pdb=" N THR U 232 " --> pdb=" O SER U 229 " (cutoff:3.500A) Processing helix chain 'U' and resid 256 through 272 Processing helix chain 'U' and resid 277 through 292 Processing helix chain 'U' and resid 292 through 311 Processing helix chain 'Z' and resid 4 through 16 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: 3.815A 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 Processing helix chain 'Z' and resid 128 through 140 removed outlier: 3.730A pdb=" N VAL Z 132 " --> pdb=" O THR Z 128 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY Z 140 " --> pdb=" O PHE Z 136 " (cutoff:3.500A) Processing helix chain 'Z' and resid 142 through 154 Processing helix chain 'Z' and resid 165 through 174 Processing helix chain 'Z' and resid 174 through 188 removed outlier: 4.277A pdb=" N SER Z 187 " --> pdb=" O GLY Z 183 " (cutoff:3.500A) removed outlier: 3.890A 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: 3.573A pdb=" N THR Z 301 " --> pdb=" O ARG Z 297 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 54 removed outlier: 3.528A pdb=" N GLN A 67 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA4, first strand: chain 'E' and resid 59 through 62 removed outlier: 6.061A pdb=" N ILE E 94 " --> pdb=" O ILE E 121 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ILE E 123 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU E 96 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASP E 125 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU E 152 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N CYS E 122 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N CYS E 154 " --> pdb=" O CYS E 122 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLN E 124 " --> pdb=" O CYS E 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 253 through 255 Processing sheet with id=AA6, first strand: chain 'F' and resid 59 through 62 removed outlier: 6.143A pdb=" N THR F 31 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE F 95 " --> pdb=" O THR F 31 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N PHE F 33 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N LEU F 152 " --> pdb=" O LEU F 120 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N CYS F 122 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N CYS F 154 " --> pdb=" O CYS F 122 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN F 124 " --> pdb=" O CYS F 154 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 253 through 255 Processing sheet with id=AA8, first strand: chain 'G' and resid 253 through 255 Processing sheet with id=AA9, first strand: chain 'H' and resid 59 through 62 removed outlier: 6.079A pdb=" N ILE H 94 " --> pdb=" O ILE H 121 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE H 123 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU H 96 " --> pdb=" O ILE H 123 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ASP H 125 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N LEU H 152 " --> pdb=" O LEU H 120 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N CYS H 122 " --> pdb=" O LEU H 152 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N CYS H 154 " --> pdb=" O CYS H 122 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLN H 124 " --> pdb=" O CYS H 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 253 through 255 Processing sheet with id=AB2, first strand: chain 'I' and resid 48 through 54 removed outlier: 3.569A pdb=" N ARG I 63 " --> pdb=" O VAL I 53 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 191 through 195 Processing sheet with id=AB4, first strand: chain 'I' and resid 120 through 121 removed outlier: 4.383A pdb=" N VAL I 226 " --> pdb=" O GLU I 121 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 242 through 243 Processing sheet with id=AB6, first strand: chain 'K' and resid 48 through 54 removed outlier: 3.567A pdb=" N GLN K 67 " --> pdb=" O ARG K 49 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG K 63 " --> pdb=" O VAL K 53 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 93 through 94 Processing sheet with id=AB8, first strand: chain 'K' and resid 191 through 192 removed outlier: 3.567A pdb=" N ILE K 118 " --> pdb=" O LEU K 199 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 242 through 243 Processing sheet with id=AC1, first strand: chain 'P' and resid 51 through 54 Processing sheet with id=AC2, first strand: chain 'P' and resid 191 through 195 Processing sheet with id=AC3, first strand: chain 'P' and resid 242 through 243 Processing sheet with id=AC4, first strand: chain 'T' and resid 59 through 62 removed outlier: 5.863A pdb=" N ILE T 94 " --> pdb=" O ILE T 121 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE T 123 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU T 96 " --> pdb=" O ILE T 123 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ASP T 125 " --> pdb=" O LEU T 96 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU T 152 " --> pdb=" O LEU T 120 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N CYS T 122 " --> pdb=" O LEU T 152 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N CYS T 154 " --> pdb=" O CYS T 122 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLN T 124 " --> pdb=" O CYS T 154 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'T' and resid 253 through 255 Processing sheet with id=AC6, first strand: chain 'U' and resid 48 through 54 Processing sheet with id=AC7, first strand: chain 'U' and resid 191 through 195 Processing sheet with id=AC8, first strand: chain 'U' and resid 242 through 243 Processing sheet with id=AC9, first strand: chain 'Z' and resid 48 through 54 removed outlier: 3.596A pdb=" N ARG Z 63 " --> pdb=" O VAL Z 53 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 191 through 195 Processing sheet with id=AD2, first strand: chain 'Z' and resid 242 through 243 1465 hydrogen bonds defined for protein. 4212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 764 hydrogen bonds 1468 hydrogen bond angles 0 basepair planarities 298 basepair parallelities 527 stacking parallelities Total time for adding SS restraints: 10.12 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5060 1.32 - 1.45: 15892 1.45 - 1.57: 19338 1.57 - 1.70: 1728 1.70 - 1.82: 64 Bond restraints: 42082 Sorted by residual: bond pdb=" CD GLU E 106 " pdb=" OE2 GLU E 106 " ideal model delta sigma weight residual 1.249 1.342 -0.093 1.90e-02 2.77e+03 2.40e+01 bond pdb=" CD GLU T 106 " pdb=" OE2 GLU T 106 " ideal model delta sigma weight residual 1.249 1.342 -0.093 1.90e-02 2.77e+03 2.37e+01 bond pdb=" CD GLU H 106 " pdb=" OE2 GLU H 106 " ideal model delta sigma weight residual 1.249 1.341 -0.092 1.90e-02 2.77e+03 2.36e+01 bond pdb=" CD GLU F 106 " pdb=" OE2 GLU F 106 " ideal model delta sigma weight residual 1.249 1.336 -0.087 1.90e-02 2.77e+03 2.10e+01 bond pdb=" N LYS U 231 " pdb=" CA LYS U 231 " ideal model delta sigma weight residual 1.456 1.498 -0.043 1.32e-02 5.74e+03 1.06e+01 ... (remaining 42077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 61114 4.29 - 8.58: 149 8.58 - 12.87: 27 12.87 - 17.16: 2 17.16 - 21.45: 1 Bond angle restraints: 61293 Sorted by residual: angle pdb=" O GLU E 106 " pdb=" C GLU E 106 " pdb=" N LEU E 107 " ideal model delta sigma weight residual 122.15 100.70 21.45 1.14e+00 7.69e-01 3.54e+02 angle pdb=" O GLU H 106 " pdb=" C GLU H 106 " pdb=" N LEU H 107 " ideal model delta sigma weight residual 122.43 109.89 12.54 1.34e+00 5.57e-01 8.76e+01 angle pdb=" O GLU F 106 " pdb=" C GLU F 106 " pdb=" N LEU F 107 " ideal model delta sigma weight residual 122.43 109.50 12.93 1.46e+00 4.69e-01 7.84e+01 angle pdb=" C3' C C 65 " pdb=" O3' C C 65 " pdb=" P A C 66 " ideal model delta sigma weight residual 120.20 107.08 13.12 1.50e+00 4.44e-01 7.65e+01 angle pdb=" CA GLU F 106 " pdb=" C GLU F 106 " pdb=" O GLU F 106 " ideal model delta sigma weight residual 119.11 108.31 10.80 1.28e+00 6.10e-01 7.12e+01 ... (remaining 61288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 21572 35.88 - 71.76: 2906 71.76 - 107.64: 184 107.64 - 143.52: 2 143.52 - 179.40: 43 Dihedral angle restraints: 24707 sinusoidal: 15388 harmonic: 9319 Sorted by residual: 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 200.00 20.60 179.40 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 -160.00 14.41 -174.41 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U C 74 " pdb=" C1' U C 74 " pdb=" N1 U C 74 " pdb=" C2 U C 74 " ideal model delta sinusoidal sigma weight residual 200.00 34.14 165.86 1 1.50e+01 4.44e-03 8.40e+01 ... (remaining 24704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 7347 0.108 - 0.215: 209 0.215 - 0.323: 5 0.323 - 0.430: 30 0.430 - 0.538: 12 Chirality restraints: 7603 Sorted by residual: chirality pdb=" P DA B 79 " pdb=" OP1 DA B 79 " pdb=" OP2 DA B 79 " pdb=" O5' DA B 79 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.54 2.00e-01 2.50e+01 7.23e+00 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 -2.92 -0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" P G b 69 " pdb=" OP1 G b 69 " pdb=" OP2 G b 69 " pdb=" O5' G b 69 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 5.98e+00 ... (remaining 7600 not shown) Planarity restraints: 4716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 106 " -0.100 2.00e-02 2.50e+03 1.77e-01 3.14e+02 pdb=" C GLU E 106 " 0.307 2.00e-02 2.50e+03 pdb=" O GLU E 106 " -0.107 2.00e-02 2.50e+03 pdb=" N LEU E 107 " -0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 106 " 0.087 2.00e-02 2.50e+03 1.64e-01 2.69e+02 pdb=" C GLU F 106 " -0.284 2.00e-02 2.50e+03 pdb=" O GLU F 106 " 0.095 2.00e-02 2.50e+03 pdb=" N LEU F 107 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 106 " 0.076 2.00e-02 2.50e+03 1.43e-01 2.03e+02 pdb=" C GLU H 106 " -0.247 2.00e-02 2.50e+03 pdb=" O GLU H 106 " 0.088 2.00e-02 2.50e+03 pdb=" N LEU H 107 " 0.083 2.00e-02 2.50e+03 ... (remaining 4713 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 286 2.56 - 3.15: 30907 3.15 - 3.73: 71854 3.73 - 4.32: 93492 4.32 - 4.90: 138917 Nonbonded interactions: 335456 Sorted by model distance: nonbonded pdb=" O GLY H 36 " pdb=" O3D AR6 H 401 " model vdw 1.975 3.040 nonbonded pdb=" O GLY E 36 " pdb=" O3D AR6 E 401 " model vdw 2.003 3.040 nonbonded pdb=" O2' C C 55 " pdb=" OP2 G C 56 " model vdw 2.039 3.040 nonbonded pdb=" O2' C W 55 " pdb=" OP2 G W 56 " model vdw 2.100 3.040 nonbonded pdb=" O2' C R 55 " pdb=" OP2 G R 56 " model vdw 2.132 3.040 ... (remaining 335451 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 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 '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 223 and (name N or name \ CA or name C or name O or name CB )) or resid 224 through 311)) } ncs_group { reference = chain 'B' selection = chain 'J' selection = chain 'Q' selection = chain 'V' } ncs_group { reference = chain 'C' selection = chain 'M' selection = chain 'O' selection = chain 'R' selection = chain 'W' selection = chain 'b' } 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 23 or (resid 24 and (name \ N or name CA or name C or name O or name CB )) or (resid 25 through 29 and (nam \ e N or name CA or name C or name O or name CB )) or resid 30 through 38 or (resi \ d 39 through 43 and (name N or name CA or name C or name O or name CB )) or resi \ d 44 through 48 or (resid 49 and (name N or name CA or name C or name O or name \ CB )) or resid 50 or (resid 51 through 52 and (name N or name CA or name C or na \ me O or name CB )) or resid 53 through 54 or (resid 55 through 58 and (name N or \ name CA or name C or name O or name CB )) or resid 59 through 68 or (resid 69 t \ hrough 70 and (name N or name CA or name C or name O or name CB )) or resid 71 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 83 or (resid 84 and (name N or name CA or name C or name O \ or name CB )) or resid 85 through 96 or (resid 97 and (name N or name CA or nam \ e C or name O or name CB )) or resid 98 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 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 184 or (resid 185 and (name \ N or name CA or name C or name O or name CB )) or resid 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 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) o \ r 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 na \ me 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 (resi \ d 245 through 246 and (name N or name CA or name C or name O or name CB )) or re \ sid 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 nam \ e CA or name C or name O or name CB )) or resid 259 through 260 or (resid 261 an \ d (name N or name CA or name C or name O or name CB )) or resid 262 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 401)) 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 40 or (resid 41 through 4 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 44 through 7 \ 8 or (resid 79 and (name N or name CA or name C or name O or name CB )) or resid \ 80 or (resid 81 and (name N or name CA or name C or name O or name CB )) or res \ id 82 through 117 or (resid 118 and (name N or name CA or name C or name O or na \ me CB )) or resid 119 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 155 or (resid 156 thro \ ugh 182 and (name N or name CA or name C or name O or name CB )) or resid 183 th \ rough 191 or (resid 192 through 196 and (name N or name CA or name C or name O o \ r name CB )) or resid 197 through 202 or (resid 203 and (name N or name CA or na \ me 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 resi \ d 224 through 225 or (resid 226 and (name N or name CA or name C or name O or na \ me CB )) or resid 227 through 244 or (resid 245 through 246 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 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 name \ O or name CB )) or resid 262 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 resi \ d 282 through 284 or (resid 285 and (name N or name CA or name C or name O or na \ me 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 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 name CA or name C or name O or name CB )) \ or resid 303 through 401)) 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 \ 48 or (resid 49 and (name N or name CA or name C or name O or name CB )) or resi \ d 50 or (resid 51 through 52 and (name N or name CA or name C or name O or name \ CB )) or resid 53 through 83 or (resid 84 and (name N or name CA or name C or na \ me O or name CB )) or resid 85 through 96 or (resid 97 and (name N or name CA or \ name C or name O or name CB )) or resid 98 through 121 or (resid 122 and (name \ N or name CA or name C or name O or name CB )) or resid 123 or (resid 124 throug \ h 127 and (name N or name CA or name C or name O or name CB )) or resid 128 thro \ ugh 132 or (resid 133 and (name N or name CA or name C or name O or name CB )) o \ r 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 and (name N or \ name CA or name C or name O or name CB )) or resid 146 through 158 or (resid 15 \ 9 through 182 and (name N or name CA or name C or name O or name CB )) or resid \ 183 through 401)) 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 23 or (resid 24 and (name \ N or name CA or name C or name O or name CB )) or (resid 25 through 29 and (nam \ e N or name CA or name C or name O or name CB )) or resid 30 through 38 or (resi \ d 39 through 43 and (name N or name CA or name C or name O or name CB )) or resi \ d 44 through 48 or (resid 49 and (name N or name CA or name C or name O or name \ CB )) or resid 50 or (resid 51 through 52 and (name N or name CA or name C or na \ me O or name CB )) or resid 53 through 54 or (resid 55 through 58 and (name N or \ name CA or name C or name O or name CB )) or resid 59 through 68 or (resid 69 t \ hrough 70 and (name N or name CA or name C or name O or name CB )) or resid 71 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 83 or (resid 84 and (name N or name CA or name C or name O \ or name CB )) or resid 85 through 96 or (resid 97 and (name N or name CA or nam \ e C or name O or name CB )) or resid 98 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 through \ 124 or (resid 125 through 127 and (name N or name CA or name C or name O or name \ CB )) or resid 128 or (resid 129 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 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 18 \ 7 through 196 and (name N or name CA or name C or name O or name CB )) or resid \ 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 o \ r 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 223 an \ d (name N or name CA or name C or name O or name CB )) or resid 224 through 244 \ or (resid 245 through 246 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 na \ me 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 (resi \ d 261 and (name N or name CA or name C or name O or name CB )) or resid 262 thro \ ugh 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 nam \ e CA or name C or name O or name CB )) or resid 282 through 284 or (resid 285 an \ d (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 293 through 294 and (name N or name CA or name C or na \ me O or name CB )) or resid 295 through 297 or (resid 298 through 302 and (name \ N or name CA or name C or name O or name CB )) or resid 303 through 401)) } ncs_group { reference = (chain 'L' and (resid 1 through 19 or resid 66 through 85)) selection = chain 'a' } 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=0.49 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: 16.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.950 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 47.000 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.170 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 42086 Z= 0.223 Angle : 0.679 21.451 61293 Z= 0.402 Chirality : 0.050 0.538 7603 Planarity : 0.006 0.177 4716 Dihedral : 25.642 179.399 18663 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.38 % Allowed : 23.04 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.16), residues: 3180 helix: 2.11 (0.13), residues: 1756 sheet: 1.12 (0.28), residues: 360 loop : -0.22 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 246 TYR 0.018 0.001 TYR E 176 PHE 0.032 0.001 PHE E 56 TRP 0.006 0.001 TRP U 78 HIS 0.005 0.001 HIS K 280 Details of bonding type rmsd covalent geometry : bond 0.00418 (42082) covalent geometry : angle 0.67859 (61293) hydrogen bonds : bond 0.16290 ( 2229) hydrogen bonds : angle 6.00277 ( 5680) Misc. bond : bond 0.05398 ( 4) *********************** 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 186 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 180 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.8327 (m) cc_final: 0.7942 (m) REVERT: F 128 PHE cc_start: 0.8537 (m-10) cc_final: 0.8268 (m-10) REVERT: F 137 TYR cc_start: 0.6783 (m-80) cc_final: 0.6138 (m-80) REVERT: H 137 TYR cc_start: 0.6661 (m-80) cc_final: 0.6359 (m-10) REVERT: P 287 PHE cc_start: 0.8382 (t80) cc_final: 0.8163 (t80) REVERT: T 304 TYR cc_start: 0.5098 (t80) cc_final: 0.4487 (t80) outliers start: 6 outliers final: 4 residues processed: 184 average time/residue: 0.2854 time to fit residues: 84.2502 Evaluate side-chains 148 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain Z residue 198 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 291 ASN T 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.224243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.183577 restraints weight = 138009.693| |-----------------------------------------------------------------------------| r_work (start): 0.4444 rms_B_bonded: 3.69 r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4445 r_free = 0.4445 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4445 r_free = 0.4445 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.102 42086 Z= 0.376 Angle : 0.697 9.461 61293 Z= 0.369 Chirality : 0.044 0.290 7603 Planarity : 0.006 0.123 4716 Dihedral : 26.385 179.977 15402 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.39 % Allowed : 19.86 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.15), residues: 3180 helix: 1.38 (0.12), residues: 1767 sheet: 0.54 (0.27), residues: 366 loop : -0.40 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 298 TYR 0.025 0.003 TYR A 42 PHE 0.036 0.002 PHE A 10 TRP 0.011 0.002 TRP T 45 HIS 0.007 0.001 HIS K 280 Details of bonding type rmsd covalent geometry : bond 0.00883 (42082) covalent geometry : angle 0.69739 (61293) hydrogen bonds : bond 0.05436 ( 2229) hydrogen bonds : angle 4.36823 ( 5680) Misc. bond : bond 0.00177 ( 4) *********************** 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 229 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 160 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7645 (tptt) REVERT: A 227 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7396 (mt) REVERT: E 261 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8077 (pt0) REVERT: F 265 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8581 (tt) REVERT: K 26 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7216 (ttt) outliers start: 69 outliers final: 45 residues processed: 213 average time/residue: 0.2647 time to fit residues: 91.7760 Evaluate side-chains 192 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain E residue 6 THR 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 192 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 292 ARG Chi-restraints excluded: chain K residue 26 MET Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 150 THR Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 257 THR Chi-restraints excluded: chain T residue 262 VAL Chi-restraints excluded: chain T residue 296 THR Chi-restraints excluded: chain U residue 45 ASP Chi-restraints excluded: chain U residue 92 PHE Chi-restraints excluded: chain U residue 107 THR Chi-restraints excluded: chain U residue 110 ILE Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain Z residue 198 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 80 optimal weight: 0.8980 chunk 307 optimal weight: 0.7980 chunk 343 optimal weight: 30.0000 chunk 269 optimal weight: 0.3980 chunk 116 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 266 optimal weight: 1.9990 chunk 128 optimal weight: 0.0570 chunk 196 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 ASN E 113 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.227712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.191417 restraints weight = 124683.872| |-----------------------------------------------------------------------------| r_work (start): 0.4584 rms_B_bonded: 3.84 r_work: 0.4047 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4043 r_free = 0.4043 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4043 r_free = 0.4043 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 42086 Z= 0.139 Angle : 0.529 11.096 61293 Z= 0.284 Chirality : 0.035 0.211 7603 Planarity : 0.004 0.058 4716 Dihedral : 26.149 178.374 15398 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.55 % Allowed : 21.77 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.15), residues: 3180 helix: 1.96 (0.12), residues: 1783 sheet: 0.55 (0.26), residues: 366 loop : -0.22 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 11 TYR 0.013 0.001 TYR K 260 PHE 0.022 0.001 PHE T 52 TRP 0.010 0.001 TRP U 78 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00303 (42082) covalent geometry : angle 0.52864 (61293) hydrogen bonds : bond 0.04000 ( 2229) hydrogen bonds : angle 3.63773 ( 5680) Misc. bond : bond 0.00028 ( 4) *********************** 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 223 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 113 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8653 (t0) REVERT: E 123 ILE cc_start: 0.8301 (mp) cc_final: 0.8079 (mp) REVERT: F 137 TYR cc_start: 0.7378 (m-80) cc_final: 0.7084 (m-80) REVERT: P 117 ASN cc_start: 0.6807 (t0) cc_final: 0.5734 (m110) REVERT: T 52 PHE cc_start: 0.8168 (t80) cc_final: 0.7930 (t80) outliers start: 40 outliers final: 20 residues processed: 213 average time/residue: 0.2550 time to fit residues: 89.3401 Evaluate side-chains 182 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain K residue 292 ASP Chi-restraints excluded: chain T residue 192 VAL Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 227 ILE Chi-restraints excluded: chain Z residue 198 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 105 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 258 optimal weight: 0.9980 chunk 247 optimal weight: 7.9990 chunk 289 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 177 optimal weight: 0.0870 chunk 296 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 chunk 285 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 ASN E 249 ASN F 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.227668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.191262 restraints weight = 172425.248| |-----------------------------------------------------------------------------| r_work (start): 0.4583 rms_B_bonded: 3.84 r_work: 0.4087 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4109 r_free = 0.4109 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4109 r_free = 0.4109 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 42086 Z= 0.140 Angle : 0.514 9.414 61293 Z= 0.276 Chirality : 0.034 0.213 7603 Planarity : 0.003 0.049 4716 Dihedral : 26.020 179.905 15397 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.86 % Allowed : 22.47 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.15), residues: 3180 helix: 2.15 (0.12), residues: 1787 sheet: 0.50 (0.26), residues: 366 loop : -0.15 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 11 TYR 0.020 0.001 TYR P 192 PHE 0.017 0.001 PHE A 10 TRP 0.007 0.001 TRP A 78 HIS 0.014 0.001 HIS H 47 Details of bonding type rmsd covalent geometry : bond 0.00312 (42082) covalent geometry : angle 0.51447 (61293) hydrogen bonds : bond 0.03804 ( 2229) hydrogen bonds : angle 3.45621 ( 5680) Misc. bond : bond 0.00029 ( 4) *********************** 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 222 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 123 ILE cc_start: 0.8258 (mp) cc_final: 0.8042 (mp) REVERT: G 287 MET cc_start: 0.6585 (mtp) cc_final: 0.6367 (ttm) REVERT: P 117 ASN cc_start: 0.6884 (t0) cc_final: 0.5848 (m110) REVERT: T 52 PHE cc_start: 0.8120 (t80) cc_final: 0.7899 (t80) outliers start: 45 outliers final: 29 residues processed: 211 average time/residue: 0.2623 time to fit residues: 91.1893 Evaluate side-chains 192 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain K residue 292 ASP Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 202 SER Chi-restraints excluded: chain T residue 35 CYS Chi-restraints excluded: chain T residue 192 VAL Chi-restraints excluded: chain T residue 250 GLU Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 227 ILE Chi-restraints excluded: chain U residue 246 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 270 optimal weight: 1.9990 chunk 281 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 14 optimal weight: 0.0980 chunk 157 optimal weight: 50.0000 chunk 356 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4943 r_free = 0.4943 target = 0.230805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.187717 restraints weight = 159190.810| |-----------------------------------------------------------------------------| r_work (start): 0.4464 rms_B_bonded: 3.70 r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4465 r_free = 0.4465 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4465 r_free = 0.4465 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 42086 Z= 0.205 Angle : 0.548 9.195 61293 Z= 0.293 Chirality : 0.036 0.214 7603 Planarity : 0.004 0.063 4716 Dihedral : 26.062 179.665 15395 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.12 % Allowed : 22.66 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.15), residues: 3180 helix: 2.02 (0.12), residues: 1775 sheet: 0.38 (0.26), residues: 366 loop : -0.12 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 11 TYR 0.019 0.002 TYR A 260 PHE 0.030 0.001 PHE A 10 TRP 0.006 0.001 TRP T 45 HIS 0.004 0.001 HIS U 280 Details of bonding type rmsd covalent geometry : bond 0.00476 (42082) covalent geometry : angle 0.54782 (61293) hydrogen bonds : bond 0.04062 ( 2229) hydrogen bonds : angle 3.59344 ( 5680) Misc. bond : bond 0.00067 ( 4) *********************** 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 213 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.7892 (ttmm) cc_final: 0.7561 (tptt) REVERT: E 123 ILE cc_start: 0.7949 (mp) cc_final: 0.7748 (mp) REVERT: F 265 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8393 (tt) REVERT: K 299 LEU cc_start: 0.7805 (mt) cc_final: 0.7605 (tt) REVERT: P 117 ASN cc_start: 0.6646 (t0) cc_final: 0.5891 (m110) outliers start: 49 outliers final: 36 residues processed: 200 average time/residue: 0.2569 time to fit residues: 84.9986 Evaluate side-chains 195 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 292 ASP Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 202 SER Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 35 CYS Chi-restraints excluded: chain T residue 192 VAL Chi-restraints excluded: chain T residue 250 GLU Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 92 PHE Chi-restraints excluded: chain U residue 110 ILE Chi-restraints excluded: chain U residue 227 ILE Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain Z residue 198 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 353 optimal weight: 30.0000 chunk 107 optimal weight: 3.9990 chunk 319 optimal weight: 20.0000 chunk 202 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 341 optimal weight: 1.9990 chunk 272 optimal weight: 0.6980 chunk 276 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 ASN E 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.226574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.186708 restraints weight = 114133.760| |-----------------------------------------------------------------------------| r_work (start): 0.4512 rms_B_bonded: 3.65 r_work (final): 0.4512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4512 r_free = 0.4512 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4512 r_free = 0.4512 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 42086 Z= 0.189 Angle : 0.536 9.643 61293 Z= 0.287 Chirality : 0.036 0.213 7603 Planarity : 0.004 0.050 4716 Dihedral : 26.052 179.996 15395 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.88 % Allowed : 22.22 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.15), residues: 3180 helix: 2.05 (0.12), residues: 1775 sheet: 0.29 (0.26), residues: 366 loop : -0.12 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 11 TYR 0.021 0.002 TYR P 192 PHE 0.022 0.001 PHE A 10 TRP 0.007 0.001 TRP T 45 HIS 0.005 0.001 HIS H 47 Details of bonding type rmsd covalent geometry : bond 0.00439 (42082) covalent geometry : angle 0.53622 (61293) hydrogen bonds : bond 0.03912 ( 2229) hydrogen bonds : angle 3.52852 ( 5680) Misc. bond : bond 0.00062 ( 4) *********************** 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 223 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 162 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.7851 (ttmm) cc_final: 0.7573 (tptt) REVERT: E 261 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8098 (pt0) REVERT: F 265 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8331 (tt) REVERT: H 51 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7153 (mp10) REVERT: P 117 ASN cc_start: 0.6700 (t0) cc_final: 0.6025 (m110) REVERT: U 31 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7833 (mtt90) outliers start: 61 outliers final: 41 residues processed: 209 average time/residue: 0.2557 time to fit residues: 88.2866 Evaluate side-chains 201 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 292 ASP Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain T residue 35 CYS Chi-restraints excluded: chain T residue 192 VAL Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 31 ARG Chi-restraints excluded: chain U residue 45 ASP Chi-restraints excluded: chain U residue 92 PHE Chi-restraints excluded: chain U residue 110 ILE Chi-restraints excluded: chain U residue 227 ILE Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain Z residue 198 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 1 optimal weight: 0.0970 chunk 374 optimal weight: 7.9990 chunk 294 optimal weight: 0.0980 chunk 32 optimal weight: 6.9990 chunk 292 optimal weight: 0.2980 chunk 190 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 381 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 386 optimal weight: 10.0000 chunk 145 optimal weight: 40.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.226773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.190144 restraints weight = 149130.798| |-----------------------------------------------------------------------------| r_work (start): 0.4569 rms_B_bonded: 3.86 r_work: 0.3976 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3983 r_free = 0.3983 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3983 r_free = 0.3983 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 42086 Z= 0.157 Angle : 0.520 9.229 61293 Z= 0.278 Chirality : 0.035 0.210 7603 Planarity : 0.003 0.050 4716 Dihedral : 26.015 179.176 15395 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.44 % Allowed : 22.53 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.15), residues: 3180 helix: 2.16 (0.12), residues: 1782 sheet: 0.31 (0.26), residues: 366 loop : -0.09 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 298 TYR 0.021 0.001 TYR P 192 PHE 0.026 0.001 PHE T 52 TRP 0.009 0.001 TRP A 78 HIS 0.004 0.001 HIS U 280 Details of bonding type rmsd covalent geometry : bond 0.00361 (42082) covalent geometry : angle 0.52017 (61293) hydrogen bonds : bond 0.03747 ( 2229) hydrogen bonds : angle 3.41841 ( 5680) Misc. bond : bond 0.00055 ( 4) *********************** 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 223 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 169 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 265 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8466 (tt) REVERT: H 51 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7248 (mp10) REVERT: K 198 ASP cc_start: 0.8306 (t70) cc_final: 0.8074 (t0) REVERT: P 117 ASN cc_start: 0.6828 (t0) cc_final: 0.5735 (m110) REVERT: U 31 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8165 (mtt90) outliers start: 54 outliers final: 43 residues processed: 209 average time/residue: 0.2409 time to fit residues: 84.0870 Evaluate side-chains 209 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 292 ASP Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 35 CYS Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 192 VAL Chi-restraints excluded: chain T residue 296 THR Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 31 ARG Chi-restraints excluded: chain U residue 45 ASP Chi-restraints excluded: chain U residue 92 PHE Chi-restraints excluded: chain U residue 227 ILE Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain Z residue 198 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 203 optimal weight: 20.0000 chunk 391 optimal weight: 20.0000 chunk 255 optimal weight: 1.9990 chunk 342 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 281 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 189 optimal weight: 0.1980 chunk 266 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.227594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.188379 restraints weight = 123353.013| |-----------------------------------------------------------------------------| r_work (start): 0.4503 rms_B_bonded: 3.72 r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4503 r_free = 0.4503 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4503 r_free = 0.4503 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 42086 Z= 0.142 Angle : 0.510 10.187 61293 Z= 0.273 Chirality : 0.034 0.208 7603 Planarity : 0.003 0.048 4716 Dihedral : 25.983 178.794 15395 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.06 % Allowed : 22.98 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.15), residues: 3180 helix: 2.23 (0.12), residues: 1792 sheet: 0.35 (0.26), residues: 366 loop : -0.14 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 118 TYR 0.022 0.001 TYR P 192 PHE 0.028 0.001 PHE T 52 TRP 0.009 0.001 TRP A 78 HIS 0.005 0.001 HIS U 280 Details of bonding type rmsd covalent geometry : bond 0.00320 (42082) covalent geometry : angle 0.51013 (61293) hydrogen bonds : bond 0.03660 ( 2229) hydrogen bonds : angle 3.35690 ( 5680) Misc. bond : bond 0.00055 ( 4) *********************** 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 212 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 164 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 261 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.8031 (pt0) REVERT: F 265 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8245 (tt) REVERT: H 51 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7203 (mp10) REVERT: P 117 ASN cc_start: 0.6658 (t0) cc_final: 0.6062 (m110) REVERT: U 31 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7800 (mtt90) outliers start: 48 outliers final: 40 residues processed: 202 average time/residue: 0.2528 time to fit residues: 84.7576 Evaluate side-chains 201 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 292 ASP Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 35 CYS Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 192 VAL Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 31 ARG Chi-restraints excluded: chain U residue 45 ASP Chi-restraints excluded: chain U residue 92 PHE Chi-restraints excluded: chain U residue 110 ILE Chi-restraints excluded: chain U residue 227 ILE Chi-restraints excluded: chain U residue 246 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 22 optimal weight: 0.9990 chunk 191 optimal weight: 10.0000 chunk 331 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 229 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 159 optimal weight: 8.9990 chunk 300 optimal weight: 0.9980 chunk 298 optimal weight: 0.9990 chunk 241 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 ASN ** H 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.225219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.190412 restraints weight = 124179.658| |-----------------------------------------------------------------------------| r_work (start): 0.4473 rms_B_bonded: 3.22 r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4472 r_free = 0.4472 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4472 r_free = 0.4472 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 42086 Z= 0.159 Angle : 0.516 9.109 61293 Z= 0.276 Chirality : 0.034 0.207 7603 Planarity : 0.003 0.050 4716 Dihedral : 25.981 179.189 15395 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.18 % Allowed : 22.98 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.15), residues: 3180 helix: 2.23 (0.12), residues: 1786 sheet: 0.40 (0.26), residues: 366 loop : -0.09 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 118 TYR 0.020 0.001 TYR T 137 PHE 0.028 0.001 PHE T 52 TRP 0.007 0.001 TRP A 78 HIS 0.004 0.001 HIS U 280 Details of bonding type rmsd covalent geometry : bond 0.00364 (42082) covalent geometry : angle 0.51630 (61293) hydrogen bonds : bond 0.03739 ( 2229) hydrogen bonds : angle 3.38710 ( 5680) Misc. bond : bond 0.00059 ( 4) *********************** 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 207 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 157 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 261 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7778 (pt0) REVERT: F 265 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8262 (tt) REVERT: H 51 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7172 (mp10) REVERT: P 117 ASN cc_start: 0.6631 (t0) cc_final: 0.6075 (m110) REVERT: U 31 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7709 (mtt90) outliers start: 50 outliers final: 40 residues processed: 199 average time/residue: 0.2388 time to fit residues: 79.9830 Evaluate side-chains 198 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 35 CYS Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 192 VAL Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 31 ARG Chi-restraints excluded: chain U residue 45 ASP Chi-restraints excluded: chain U residue 92 PHE Chi-restraints excluded: chain U residue 110 ILE Chi-restraints excluded: chain U residue 227 ILE Chi-restraints excluded: chain U residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 347 optimal weight: 40.0000 chunk 199 optimal weight: 30.0000 chunk 204 optimal weight: 10.0000 chunk 220 optimal weight: 0.3980 chunk 257 optimal weight: 3.9990 chunk 302 optimal weight: 0.0000 chunk 12 optimal weight: 0.5980 chunk 186 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 254 optimal weight: 0.0570 chunk 190 optimal weight: 0.6980 overall best weight: 0.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 ASN H 198 ASN U 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.227161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.185889 restraints weight = 145396.626| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 3.58 r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4450 r_free = 0.4450 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4450 r_free = 0.4450 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 42086 Z= 0.117 Angle : 0.494 9.160 61293 Z= 0.265 Chirality : 0.033 0.204 7603 Planarity : 0.003 0.047 4716 Dihedral : 25.918 179.988 15395 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.61 % Allowed : 23.62 % Favored : 73.77 % 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 aren not related in a simple way. whole: 2.09 (0.15), residues: 3180 helix: 2.40 (0.12), residues: 1798 sheet: 0.48 (0.26), residues: 366 loop : -0.08 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 246 TYR 0.019 0.001 TYR P 192 PHE 0.034 0.001 PHE P 287 TRP 0.013 0.001 TRP A 78 HIS 0.005 0.001 HIS U 280 Details of bonding type rmsd covalent geometry : bond 0.00251 (42082) covalent geometry : angle 0.49401 (61293) hydrogen bonds : bond 0.03504 ( 2229) hydrogen bonds : angle 3.23857 ( 5680) Misc. bond : bond 0.00030 ( 4) ********************** 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 214 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 123 ILE cc_start: 0.7896 (mp) cc_final: 0.7651 (mp) REVERT: F 45 TRP cc_start: 0.7171 (m100) cc_final: 0.6959 (m-10) REVERT: F 293 ARG cc_start: 0.7369 (mtm180) cc_final: 0.7109 (mtm180) REVERT: H 51 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7129 (mp10) REVERT: H 198 ASN cc_start: 0.7929 (OUTLIER) cc_final: 0.7724 (m-40) REVERT: K 62 MET cc_start: 0.3918 (mmm) cc_final: 0.3553 (mmm) REVERT: P 102 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.7959 (mt) REVERT: P 117 ASN cc_start: 0.6723 (t0) cc_final: 0.6104 (m110) outliers start: 41 outliers final: 28 residues processed: 205 average time/residue: 0.2368 time to fit residues: 82.3215 Evaluate side-chains 189 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 35 CYS Chi-restraints excluded: chain T residue 192 VAL Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 37 optimal weight: 1.9990 chunk 373 optimal weight: 10.0000 chunk 316 optimal weight: 30.0000 chunk 90 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 299 optimal weight: 0.5980 chunk 244 optimal weight: 20.0000 chunk 295 optimal weight: 0.4980 chunk 313 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.226905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.185388 restraints weight = 145677.096| |-----------------------------------------------------------------------------| r_work (start): 0.4452 rms_B_bonded: 3.64 r_work (final): 0.4452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4452 r_free = 0.4452 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4452 r_free = 0.4452 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.158 42086 Z= 0.145 Angle : 0.594 59.199 61293 Z= 0.336 Chirality : 0.034 0.204 7603 Planarity : 0.003 0.047 4716 Dihedral : 25.918 179.998 15395 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.36 % Allowed : 23.93 % Favored : 73.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.15), residues: 3180 helix: 2.39 (0.12), residues: 1798 sheet: 0.49 (0.27), residues: 366 loop : -0.09 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 246 TYR 0.028 0.001 TYR H 269 PHE 0.029 0.001 PHE P 287 TRP 0.012 0.001 TRP A 78 HIS 0.005 0.001 HIS U 280 Details of bonding type rmsd covalent geometry : bond 0.00313 (42082) covalent geometry : angle 0.59354 (61293) hydrogen bonds : bond 0.03527 ( 2229) hydrogen bonds : angle 3.23650 ( 5680) Misc. bond : bond 0.00053 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10409.76 seconds wall clock time: 179 minutes 8.86 seconds (10748.86 seconds total)