Starting phenix.real_space_refine on Fri Jul 3 08:56:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jse_22451/07_2026/7jse_22451.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jse_22451/07_2026/7jse_22451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jse_22451/07_2026/7jse_22451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jse_22451/07_2026/7jse_22451.map" model { file = "/net/cci-nas-00/data/ceres_data/7jse_22451/07_2026/7jse_22451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jse_22451/07_2026/7jse_22451.cif" } resolution = 4.6 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= 0.013 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians P 24 5.49 5 C 6656 2.51 5 N 3232 2.21 5 O 3376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13288 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'PHE:plan': 9, 'TYR:plan': 6, 'GLU:plan': 18, 'ASP:plan': 8, 'HIS:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 6, 'GLN:plan1': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 427 Chain: "B" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'PHE:plan': 9, 'TYR:plan': 6, 'GLU:plan': 18, 'ASP:plan': 8, 'HIS:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 6, 'GLN:plan1': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 427 Chain: "C" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'PHE:plan': 9, 'TYR:plan': 6, 'GLU:plan': 18, 'ASP:plan': 8, 'HIS:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 6, 'GLN:plan1': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 427 Chain: "D" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'PHE:plan': 9, 'TYR:plan': 6, 'GLU:plan': 18, 'ASP:plan': 8, 'HIS:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 6, 'GLN:plan1': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 427 Chain: "E" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'PHE:plan': 9, 'TYR:plan': 6, 'GLU:plan': 18, 'ASP:plan': 8, 'HIS:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 6, 'GLN:plan1': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 427 Chain: "F" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'PHE:plan': 9, 'TYR:plan': 6, 'GLU:plan': 18, 'ASP:plan': 8, 'HIS:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 6, 'GLN:plan1': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 427 Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'PHE:plan': 9, 'TYR:plan': 6, 'GLU:plan': 18, 'ASP:plan': 8, 'HIS:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 6, 'GLN:plan1': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 427 Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'PHE:plan': 9, 'TYR:plan': 6, 'GLU:plan': 18, 'ASP:plan': 8, 'HIS:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 6, 'GLN:plan1': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 427 Chain: "I" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'PHE:plan': 9, 'TYR:plan': 6, 'GLU:plan': 18, 'ASP:plan': 8, 'HIS:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 6, 'GLN:plan1': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 427 Chain: "J" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'PHE:plan': 9, 'TYR:plan': 6, 'GLU:plan': 18, 'ASP:plan': 8, 'HIS:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 6, 'GLN:plan1': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 427 Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'PHE:plan': 9, 'TYR:plan': 6, 'GLU:plan': 18, 'ASP:plan': 8, 'HIS:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 6, 'GLN:plan1': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 427 Chain: "L" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'PHE:plan': 9, 'TYR:plan': 6, 'GLU:plan': 18, 'ASP:plan': 8, 'HIS:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 6, 'GLN:plan1': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 427 Chain: "M" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'PHE:plan': 9, 'TYR:plan': 6, 'GLU:plan': 18, 'ASP:plan': 8, 'HIS:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 6, 'GLN:plan1': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 427 Chain: "N" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'PHE:plan': 9, 'TYR:plan': 6, 'GLU:plan': 18, 'ASP:plan': 8, 'HIS:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 6, 'GLN:plan1': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 427 Chain: "O" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'PHE:plan': 9, 'TYR:plan': 6, 'GLU:plan': 18, 'ASP:plan': 8, 'HIS:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 6, 'GLN:plan1': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 427 Chain: "P" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'PHE:plan': 9, 'TYR:plan': 6, 'GLU:plan': 18, 'ASP:plan': 8, 'HIS:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 6, 'GLN:plan1': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 427 Chain: "Q" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Classifications: {'DNA': 4} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 3} Chain: "R" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Classifications: {'DNA': 4} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 3} Chain: "S" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Classifications: {'DNA': 4} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 3} Chain: "T" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Classifications: {'DNA': 4} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 3} Chain: "U" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Classifications: {'DNA': 4} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 3} Chain: "V" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Classifications: {'DNA': 4} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 3} Chain: "W" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Classifications: {'DNA': 4} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 3} Chain: "X" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Classifications: {'DNA': 4} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 3} Time building chain proxies: 3.27, per 1000 atoms: 0.25 Number of scatterers: 13288 At special positions: 0 Unit cell: (164.135, 160.011, 130.318, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 24 15.00 O 3376 8.00 N 3232 7.00 C 6656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 642.0 milliseconds 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 32 sheets defined 36.9% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 removed outlier: 4.424A pdb=" N VAL A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 72 removed outlier: 3.540A pdb=" N LYS A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 120 Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 181 through 197 removed outlier: 3.548A pdb=" N ARG A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 removed outlier: 4.175A pdb=" N VAL B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 72 removed outlier: 3.515A pdb=" N LYS B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 120 Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.548A pdb=" N ARG B 185 " --> pdb=" O ASN B 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 32 removed outlier: 4.160A pdb=" N VAL C 27 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 72 Processing helix chain 'C' and resid 104 through 120 Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.548A pdb=" N ARG C 185 " --> pdb=" O ASN C 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 32 removed outlier: 4.203A pdb=" N VAL D 27 " --> pdb=" O SER D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 72 removed outlier: 3.512A pdb=" N LYS D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 120 Processing helix chain 'D' and resid 152 through 157 Processing helix chain 'D' and resid 181 through 197 removed outlier: 3.544A pdb=" N ARG D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 32 removed outlier: 4.353A pdb=" N VAL E 27 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 72 Processing helix chain 'E' and resid 104 through 120 Processing helix chain 'E' and resid 152 through 157 Processing helix chain 'E' and resid 181 through 197 removed outlier: 3.547A pdb=" N ARG E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 32 removed outlier: 4.166A pdb=" N VAL F 27 " --> pdb=" O SER F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 72 Processing helix chain 'F' and resid 104 through 120 Processing helix chain 'F' and resid 152 through 157 Processing helix chain 'F' and resid 181 through 197 removed outlier: 3.546A pdb=" N ARG F 185 " --> pdb=" O ASN F 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 32 removed outlier: 4.422A pdb=" N VAL G 27 " --> pdb=" O SER G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 72 removed outlier: 3.531A pdb=" N LYS G 58 " --> pdb=" O THR G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 120 Processing helix chain 'G' and resid 152 through 157 Processing helix chain 'G' and resid 181 through 197 removed outlier: 3.548A pdb=" N ARG G 185 " --> pdb=" O ASN G 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 32 removed outlier: 4.207A pdb=" N VAL H 27 " --> pdb=" O SER H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 72 removed outlier: 3.505A pdb=" N LYS H 58 " --> pdb=" O THR H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 120 Processing helix chain 'H' and resid 152 through 157 Processing helix chain 'H' and resid 181 through 197 removed outlier: 3.544A pdb=" N ARG H 185 " --> pdb=" O ASN H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 32 removed outlier: 3.986A pdb=" N VAL I 27 " --> pdb=" O SER I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 72 Processing helix chain 'I' and resid 104 through 120 Processing helix chain 'I' and resid 152 through 157 Processing helix chain 'I' and resid 181 through 197 removed outlier: 3.543A pdb=" N ARG I 185 " --> pdb=" O ASN I 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 32 removed outlier: 3.995A pdb=" N VAL J 27 " --> pdb=" O SER J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 72 Processing helix chain 'J' and resid 104 through 120 Processing helix chain 'J' and resid 152 through 157 Processing helix chain 'J' and resid 181 through 197 removed outlier: 3.545A pdb=" N ARG J 185 " --> pdb=" O ASN J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 32 removed outlier: 3.981A pdb=" N VAL K 27 " --> pdb=" O SER K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 72 Processing helix chain 'K' and resid 104 through 120 Processing helix chain 'K' and resid 152 through 157 Processing helix chain 'K' and resid 181 through 197 removed outlier: 3.545A pdb=" N ARG K 185 " --> pdb=" O ASN K 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 32 removed outlier: 3.828A pdb=" N VAL L 27 " --> pdb=" O SER L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 72 Processing helix chain 'L' and resid 104 through 120 Processing helix chain 'L' and resid 152 through 157 Processing helix chain 'L' and resid 181 through 197 removed outlier: 3.545A pdb=" N ARG L 185 " --> pdb=" O ASN L 181 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 32 removed outlier: 3.992A pdb=" N VAL M 27 " --> pdb=" O SER M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 72 Processing helix chain 'M' and resid 104 through 120 Processing helix chain 'M' and resid 152 through 157 Processing helix chain 'M' and resid 181 through 197 removed outlier: 3.546A pdb=" N ARG M 185 " --> pdb=" O ASN M 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 32 removed outlier: 3.818A pdb=" N VAL N 27 " --> pdb=" O SER N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 72 Processing helix chain 'N' and resid 104 through 120 Processing helix chain 'N' and resid 152 through 157 Processing helix chain 'N' and resid 181 through 197 removed outlier: 3.547A pdb=" N ARG N 185 " --> pdb=" O ASN N 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 32 removed outlier: 3.983A pdb=" N VAL O 27 " --> pdb=" O SER O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 72 Processing helix chain 'O' and resid 104 through 120 Processing helix chain 'O' and resid 152 through 157 Processing helix chain 'O' and resid 181 through 197 removed outlier: 3.544A pdb=" N ARG O 185 " --> pdb=" O ASN O 181 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 32 removed outlier: 3.989A pdb=" N VAL P 27 " --> pdb=" O SER P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 72 Processing helix chain 'P' and resid 104 through 120 Processing helix chain 'P' and resid 152 through 157 Processing helix chain 'P' and resid 181 through 197 removed outlier: 3.546A pdb=" N ARG P 185 " --> pdb=" O ASN P 181 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 3.631A pdb=" N VAL A 95 " --> pdb=" O TYR A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 132 through 134 removed outlier: 4.320A pdb=" N ALA A 133 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL A 8 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 89 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP A 167 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 95 through 96 removed outlier: 3.577A pdb=" N VAL B 95 " --> pdb=" O TYR B 5 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 132 through 134 removed outlier: 4.309A pdb=" N ALA B 133 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 8 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE B 89 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP B 167 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.579A pdb=" N VAL C 95 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 132 through 134 removed outlier: 4.313A pdb=" N ALA C 133 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C 8 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE C 89 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TRP C 167 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 95 through 96 removed outlier: 3.602A pdb=" N VAL D 95 " --> pdb=" O TYR D 5 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 132 through 134 removed outlier: 4.315A pdb=" N ALA D 133 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL D 8 " --> pdb=" O ALA D 133 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE D 89 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP D 167 " --> pdb=" O PHE D 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.648A pdb=" N VAL E 95 " --> pdb=" O TYR E 5 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 132 through 134 removed outlier: 4.316A pdb=" N ALA E 133 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL E 8 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE E 89 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP E 167 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.638A pdb=" N VAL F 95 " --> pdb=" O TYR F 5 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 132 through 134 removed outlier: 4.319A pdb=" N ALA F 133 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL F 8 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE F 89 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP F 167 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 4 through 5 removed outlier: 3.656A pdb=" N VAL G 95 " --> pdb=" O TYR G 5 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 132 through 134 removed outlier: 4.290A pdb=" N ALA G 133 " --> pdb=" O VAL G 8 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL G 8 " --> pdb=" O ALA G 133 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE G 89 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TRP G 167 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.632A pdb=" N VAL H 95 " --> pdb=" O TYR H 5 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 132 through 134 removed outlier: 4.320A pdb=" N ALA H 133 " --> pdb=" O VAL H 8 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL H 8 " --> pdb=" O ALA H 133 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE H 89 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TRP H 167 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 94 through 96 removed outlier: 3.601A pdb=" N VAL I 95 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 132 through 134 removed outlier: 4.328A pdb=" N ALA I 133 " --> pdb=" O VAL I 8 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL I 8 " --> pdb=" O ALA I 133 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE I 89 " --> pdb=" O VAL I 11 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TRP I 167 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 95 through 96 removed outlier: 3.641A pdb=" N VAL J 95 " --> pdb=" O TYR J 5 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 132 through 134 removed outlier: 4.332A pdb=" N ALA J 133 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL J 8 " --> pdb=" O ALA J 133 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE J 89 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TRP J 167 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 94 through 96 removed outlier: 3.606A pdb=" N VAL K 95 " --> pdb=" O TYR K 5 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 132 through 134 removed outlier: 4.324A pdb=" N ALA K 133 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL K 8 " --> pdb=" O ALA K 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE K 89 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP K 167 " --> pdb=" O PHE K 82 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 95 through 96 removed outlier: 3.622A pdb=" N VAL L 95 " --> pdb=" O TYR L 5 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 132 through 134 removed outlier: 4.337A pdb=" N ALA L 133 " --> pdb=" O VAL L 8 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL L 8 " --> pdb=" O ALA L 133 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE L 89 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP L 167 " --> pdb=" O PHE L 82 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 94 through 96 removed outlier: 3.632A pdb=" N VAL M 95 " --> pdb=" O TYR M 5 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 132 through 134 removed outlier: 4.333A pdb=" N ALA M 133 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL M 8 " --> pdb=" O ALA M 133 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE M 89 " --> pdb=" O VAL M 11 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP M 167 " --> pdb=" O PHE M 82 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.667A pdb=" N VAL N 95 " --> pdb=" O TYR N 5 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 132 through 134 removed outlier: 4.324A pdb=" N ALA N 133 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL N 8 " --> pdb=" O ALA N 133 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE N 89 " --> pdb=" O VAL N 11 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP N 167 " --> pdb=" O PHE N 82 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 94 through 96 removed outlier: 3.657A pdb=" N VAL O 95 " --> pdb=" O TYR O 5 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 132 through 134 removed outlier: 4.326A pdb=" N ALA O 133 " --> pdb=" O VAL O 8 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL O 8 " --> pdb=" O ALA O 133 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE O 89 " --> pdb=" O VAL O 11 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS O 90 " --> pdb=" O GLU O 83 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP O 167 " --> pdb=" O PHE O 82 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 94 through 96 removed outlier: 3.627A pdb=" N VAL P 95 " --> pdb=" O TYR P 5 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 132 through 134 removed outlier: 4.325A pdb=" N ALA P 133 " --> pdb=" O VAL P 8 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL P 8 " --> pdb=" O ALA P 133 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE P 89 " --> pdb=" O VAL P 11 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP P 167 " --> pdb=" O PHE P 82 " (cutoff:3.500A) 1006 hydrogen bonds defined for protein. 2940 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.30: 3232 1.30 - 1.38: 3233 1.38 - 1.45: 682 1.45 - 1.53: 6132 1.53 - 1.61: 49 Bond restraints: 13328 Sorted by residual: bond pdb=" C1' DT U 9 " pdb=" N1 DT U 9 " ideal model delta sigma weight residual 1.468 1.500 -0.032 1.40e-02 5.10e+03 5.15e+00 bond pdb=" C1' DT X 9 " pdb=" N1 DT X 9 " ideal model delta sigma weight residual 1.468 1.499 -0.031 1.40e-02 5.10e+03 5.05e+00 bond pdb=" C1' DT W 9 " pdb=" N1 DT W 9 " ideal model delta sigma weight residual 1.468 1.499 -0.031 1.40e-02 5.10e+03 4.97e+00 bond pdb=" C1' DT Q 9 " pdb=" N1 DT Q 9 " ideal model delta sigma weight residual 1.468 1.499 -0.031 1.40e-02 5.10e+03 4.95e+00 bond pdb=" C1' DT R 9 " pdb=" N1 DT R 9 " ideal model delta sigma weight residual 1.468 1.499 -0.031 1.40e-02 5.10e+03 4.90e+00 ... (remaining 13323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.75: 15893 0.75 - 1.50: 523 1.50 - 2.25: 232 2.25 - 3.00: 140 3.00 - 3.76: 28 Bond angle restraints: 16816 Sorted by residual: angle pdb=" N3 DT U 8 " pdb=" C4 DT U 8 " pdb=" O4 DT U 8 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT V 6 " pdb=" C4 DT V 6 " pdb=" O4 DT V 6 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT R 6 " pdb=" C4 DT R 6 " pdb=" O4 DT R 6 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT S 8 " pdb=" C4 DT S 8 " pdb=" O4 DT S 8 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT X 7 " pdb=" C4 DT X 7 " pdb=" O4 DT X 7 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 ... (remaining 16811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 3355 35.55 - 71.11: 77 71.11 - 106.66: 6 106.66 - 142.21: 0 142.21 - 177.77: 2 Dihedral angle restraints: 3440 sinusoidal: 288 harmonic: 3152 Sorted by residual: dihedral pdb=" C4' DT W 7 " pdb=" C3' DT W 7 " pdb=" O3' DT W 7 " pdb=" P DT W 8 " ideal model delta sinusoidal sigma weight residual 220.00 42.23 177.77 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT Q 7 " pdb=" C3' DT Q 7 " pdb=" O3' DT Q 7 " pdb=" P DT Q 8 " ideal model delta sinusoidal sigma weight residual 220.00 43.53 176.47 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT U 7 " pdb=" C3' DT U 7 " pdb=" O3' DT U 7 " pdb=" P DT U 8 " ideal model delta sinusoidal sigma weight residual 220.00 147.58 72.42 1 3.50e+01 8.16e-04 5.47e+00 ... (remaining 3437 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.023: 38 0.023 - 0.045: 47 0.045 - 0.068: 9 0.068 - 0.090: 22 0.090 - 0.112: 4 Chirality restraints: 120 Sorted by residual: chirality pdb=" P DT Q 8 " pdb=" OP1 DT Q 8 " pdb=" OP2 DT Q 8 " pdb=" O5' DT Q 8 " both_signs ideal model delta sigma weight residual True 2.34 -2.45 -0.11 2.00e-01 2.50e+01 3.13e-01 chirality pdb=" P DT W 8 " pdb=" OP1 DT W 8 " pdb=" OP2 DT W 8 " pdb=" O5' DT W 8 " both_signs ideal model delta sigma weight residual True 2.34 -2.44 -0.10 2.00e-01 2.50e+01 2.55e-01 chirality pdb=" C3' DT W 7 " pdb=" C4' DT W 7 " pdb=" O3' DT W 7 " pdb=" C2' DT W 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.63 -0.10 2.00e-01 2.50e+01 2.46e-01 ... (remaining 117 not shown) Planarity restraints: 3184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 55 " 0.003 2.00e-02 2.50e+03 5.91e-03 3.49e-01 pdb=" C VAL A 55 " -0.010 2.00e-02 2.50e+03 pdb=" O VAL A 55 " 0.004 2.00e-02 2.50e+03 pdb=" N ALA A 56 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 55 " -0.003 2.00e-02 2.50e+03 5.78e-03 3.34e-01 pdb=" C VAL C 55 " 0.010 2.00e-02 2.50e+03 pdb=" O VAL C 55 " -0.004 2.00e-02 2.50e+03 pdb=" N ALA C 56 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 55 " -0.003 2.00e-02 2.50e+03 5.77e-03 3.33e-01 pdb=" C VAL L 55 " 0.010 2.00e-02 2.50e+03 pdb=" O VAL L 55 " -0.004 2.00e-02 2.50e+03 pdb=" N ALA L 56 " -0.003 2.00e-02 2.50e+03 ... (remaining 3181 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 6225 2.92 - 3.42: 8329 3.42 - 3.91: 16139 3.91 - 4.40: 12957 4.40 - 4.90: 24162 Nonbonded interactions: 67812 Sorted by model distance: nonbonded pdb=" N LYS O 84 " pdb=" O GLU O 164 " model vdw 2.425 3.120 nonbonded pdb=" N LYS G 84 " pdb=" O GLU G 164 " model vdw 2.489 3.120 nonbonded pdb=" N LYS J 84 " pdb=" O GLU J 164 " model vdw 2.490 3.120 nonbonded pdb=" N LYS N 84 " pdb=" O GLU N 164 " model vdw 2.494 3.120 nonbonded pdb=" N LYS H 84 " pdb=" O GLU H 164 " model vdw 2.498 3.120 ... (remaining 67807 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } pdb_interpretation.ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.560 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5036 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 : 0.002 0.032 13328 Z= 0.172 Angle : 0.437 3.756 16816 Z= 0.365 Chirality : 0.045 0.112 120 Planarity : 0.001 0.006 3184 Dihedral : 10.507 177.766 3440 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.35 % Favored : 88.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.14), residues: 3136 helix: -0.12 (0.15), residues: 1248 sheet: -2.34 (0.23), residues: 496 loop : -3.19 (0.12), residues: 1392 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.17 (13328) covalent geometry : angle 0.43734 / 0.36 (16816) hydrogen bonds : bond 0.12880 / 10.15 ( 1006) hydrogen bonds : angle 5.89636 / 4.63 ( 2940) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.035 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0082 time to fit residues: 0.1137 Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.037 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 40.0000 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 50.0000 overall best weight: 13.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2269 r_free = 0.2269 target = 0.025598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2032 r_free = 0.2032 target = 0.019109 restraints weight = 14715.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2035 r_free = 0.2035 target = 0.019171 restraints weight = 13727.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2037 r_free = 0.2037 target = 0.019215 restraints weight = 13031.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2037 r_free = 0.2037 target = 0.019215 restraints weight = 12477.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2037 r_free = 0.2037 target = 0.019215 restraints weight = 12477.759| |-----------------------------------------------------------------------------| r_work (final): 0.2038 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.052065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.044605 restraints weight = 624.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.045054 restraints weight = 451.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.045460 restraints weight = 380.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.045720 restraints weight = 327.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.045914 restraints weight = 297.242| |-----------------------------------------------------------------------------| r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5367 moved from start: 0.8483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 13328 Z= 0.305 Angle : 0.817 7.337 16816 Z= 0.515 Chirality : 0.041 0.120 120 Planarity : 0.004 0.012 3184 Dihedral : 13.337 177.175 3440 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.12 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.15), residues: 3136 helix: 1.17 (0.16), residues: 1280 sheet: -3.28 (0.18), residues: 560 loop : -1.39 (0.16), residues: 1296 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.30 (13328) covalent geometry : angle 0.81674 / 0.51 (16816) hydrogen bonds : bond 0.04796 / 3.77 ( 1006) hydrogen bonds : angle 5.37620 / 4.17 ( 2940) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.037 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0047 time to fit residues: 0.0931 Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.037 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 254 optimal weight: 30.0000 chunk 118 optimal weight: 20.0000 chunk 278 optimal weight: 10.0000 chunk 207 optimal weight: 30.0000 chunk 143 optimal weight: 20.0000 chunk 11 optimal weight: 30.0000 chunk 61 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 chunk 20 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 131 optimal weight: 30.0000 overall best weight: 18.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2234 r_free = 0.2234 target = 0.024869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2015 r_free = 0.2015 target = 0.019166 restraints weight = 16160.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2021 r_free = 0.2021 target = 0.019283 restraints weight = 14191.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2026 r_free = 0.2026 target = 0.019383 restraints weight = 12723.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2026 r_free = 0.2026 target = 0.019383 restraints weight = 11766.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2026 r_free = 0.2026 target = 0.019383 restraints weight = 11766.225| |-----------------------------------------------------------------------------| r_work (final): 0.2079 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.048923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.043817 restraints weight = 1013.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.044419 restraints weight = 638.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.044816 restraints weight = 491.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.045095 restraints weight = 415.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.045373 restraints weight = 368.585| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5466 moved from start: 1.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 13328 Z= 0.377 Angle : 0.854 6.443 16816 Z= 0.538 Chirality : 0.038 0.082 120 Planarity : 0.005 0.016 3184 Dihedral : 13.823 178.186 3440 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.15), residues: 3136 helix: 1.93 (0.15), residues: 1168 sheet: -1.98 (0.25), residues: 384 loop : -1.23 (0.16), residues: 1584 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.38 (13328) covalent geometry : angle 0.85423 / 0.54 (16816) hydrogen bonds : bond 0.05105 / 4.03 ( 1006) hydrogen bonds : angle 5.84547 / 4.55 ( 2940) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.035 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0047 time to fit residues: 0.0918 Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.033 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 40.0000 chunk 22 optimal weight: 40.0000 chunk 211 optimal weight: 30.0000 chunk 31 optimal weight: 20.0000 chunk 159 optimal weight: 30.0000 chunk 199 optimal weight: 50.0000 chunk 26 optimal weight: 50.0000 chunk 86 optimal weight: 30.0000 chunk 183 optimal weight: 30.0000 chunk 39 optimal weight: 40.0000 chunk 209 optimal weight: 30.0000 overall best weight: 28.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.031480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2274 r_free = 0.2274 target = 0.024568 restraints weight = 10928.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2295 r_free = 0.2295 target = 0.025035 restraints weight = 8317.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2310 r_free = 0.2310 target = 0.025363 restraints weight = 6761.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2320 r_free = 0.2320 target = 0.025613 restraints weight = 5746.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2322 r_free = 0.2322 target = 0.025641 restraints weight = 5068.831| |-----------------------------------------------------------------------------| r_work (final): 0.2116 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.059759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.054474 restraints weight = 1049.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.056129 restraints weight = 527.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.057343 restraints weight = 330.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.058411 restraints weight = 227.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.059124 restraints weight = 154.577| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 1.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.028 13328 Z= 0.542 Angle : 1.082 8.522 16816 Z= 0.694 Chirality : 0.056 0.120 120 Planarity : 0.006 0.016 3184 Dihedral : 15.103 177.656 3440 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 3136 helix: 0.88 (0.15), residues: 1184 sheet: -2.66 (0.24), residues: 432 loop : -1.34 (0.16), residues: 1520 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.54 (13328) covalent geometry : angle 1.08168 / 0.69 (16816) hydrogen bonds : bond 0.05992 / 4.72 ( 1006) hydrogen bonds : angle 7.07225 / 5.51 ( 2940) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.036 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0034 time to fit residues: 0.0717 Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.035 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 292 optimal weight: 50.0000 chunk 53 optimal weight: 9.9990 chunk 266 optimal weight: 40.0000 chunk 38 optimal weight: 40.0000 chunk 300 optimal weight: 20.0000 chunk 65 optimal weight: 50.0000 chunk 248 optimal weight: 40.0000 chunk 17 optimal weight: 30.0000 chunk 114 optimal weight: 30.0000 chunk 177 optimal weight: 30.0000 chunk 49 optimal weight: 20.0000 overall best weight: 21.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2268 r_free = 0.2268 target = 0.025491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2096 r_free = 0.2096 target = 0.021241 restraints weight = 20715.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2101 r_free = 0.2101 target = 0.021343 restraints weight = 17831.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 13)----------------| | r_work = 0.2105 r_free = 0.2105 target = 0.021431 restraints weight = 15894.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2109 r_free = 0.2109 target = 0.021501 restraints weight = 14511.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2112 r_free = 0.2112 target = 0.021577 restraints weight = 13395.885| |-----------------------------------------------------------------------------| r_work (final): 0.2424 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.062590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.055229 restraints weight = 886.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.056871 restraints weight = 551.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.058192 restraints weight = 411.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.059869 restraints weight = 307.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.061053 restraints weight = 205.762| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 1.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.019 13328 Z= 0.412 Angle : 0.850 5.416 16816 Z= 0.536 Chirality : 0.101 0.319 120 Planarity : 0.004 0.013 3184 Dihedral : 14.695 169.445 3440 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.15), residues: 3136 helix: 0.94 (0.15), residues: 1184 sheet: -3.02 (0.24), residues: 432 loop : -1.41 (0.15), residues: 1520 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.41 (13328) covalent geometry : angle 0.84966 / 0.54 (16816) hydrogen bonds : bond 0.05122 / 4.04 ( 1006) hydrogen bonds : angle 6.50578 / 5.06 ( 2940) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.026 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0049 time to fit residues: 0.1060 Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.022 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 77 optimal weight: 40.0000 chunk 17 optimal weight: 20.0000 chunk 156 optimal weight: 50.0000 chunk 227 optimal weight: 50.0000 chunk 264 optimal weight: 20.0000 chunk 294 optimal weight: 50.0000 chunk 212 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 104 optimal weight: 50.0000 chunk 200 optimal weight: 30.0000 overall best weight: 22.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2259 r_free = 0.2259 target = 0.025111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2104 r_free = 0.2104 target = 0.021248 restraints weight = 19326.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2108 r_free = 0.2108 target = 0.021352 restraints weight = 16622.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2112 r_free = 0.2112 target = 0.021443 restraints weight = 14758.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2115 r_free = 0.2115 target = 0.021502 restraints weight = 13535.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2118 r_free = 0.2118 target = 0.021566 restraints weight = 12693.821| |-----------------------------------------------------------------------------| r_work (final): 0.2418 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.065752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.058795 restraints weight = 876.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.060148 restraints weight = 474.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.061121 restraints weight = 332.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.062031 restraints weight = 247.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.062716 restraints weight = 183.956| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 1.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.022 13328 Z= 0.439 Angle : 0.923 5.630 16816 Z= 0.584 Chirality : 0.104 0.320 120 Planarity : 0.004 0.014 3184 Dihedral : 14.880 178.175 3440 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.15), residues: 3136 helix: 0.84 (0.15), residues: 1184 sheet: -3.19 (0.24), residues: 432 loop : -1.72 (0.15), residues: 1520 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.44 (13328) covalent geometry : angle 0.92262 / 0.58 (16816) hydrogen bonds : bond 0.05363 / 4.24 ( 1006) hydrogen bonds : angle 6.83694 / 5.30 ( 2940) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0045 time to fit residues: 0.0922 Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.022 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 219 optimal weight: 30.0000 chunk 195 optimal weight: 30.0000 chunk 227 optimal weight: 40.0000 chunk 109 optimal weight: 30.0000 chunk 129 optimal weight: 20.0000 chunk 32 optimal weight: 40.0000 chunk 81 optimal weight: 30.0000 chunk 291 optimal weight: 30.0000 chunk 1 optimal weight: 30.0000 chunk 154 optimal weight: 30.0000 chunk 94 optimal weight: 40.0000 overall best weight: 28.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2244 r_free = 0.2244 target = 0.024761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2091 r_free = 0.2091 target = 0.020960 restraints weight = 21164.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 14)----------------| | r_work = 0.2097 r_free = 0.2097 target = 0.021084 restraints weight = 18138.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2102 r_free = 0.2102 target = 0.021184 restraints weight = 15758.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2105 r_free = 0.2105 target = 0.021258 restraints weight = 14205.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2107 r_free = 0.2107 target = 0.021300 restraints weight = 13304.027| |-----------------------------------------------------------------------------| r_work (final): 0.2248 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.057301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.054268 restraints weight = 971.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.055244 restraints weight = 360.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.055871 restraints weight = 204.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.056273 restraints weight = 132.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.056412 restraints weight = 90.667| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5468 moved from start: 1.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.028 13328 Z= 0.519 Angle : 1.035 6.782 16816 Z= 0.659 Chirality : 0.103 0.246 120 Planarity : 0.005 0.016 3184 Dihedral : 15.552 179.682 3440 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.33 % Favored : 83.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.15), residues: 3136 helix: 0.31 (0.15), residues: 1072 sheet: -3.50 (0.23), residues: 416 loop : -2.20 (0.16), residues: 1648 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.52 (13328) covalent geometry : angle 1.03485 / 0.66 (16816) hydrogen bonds : bond 0.06139 / 4.85 ( 1006) hydrogen bonds : angle 7.74159 / 6.02 ( 2940) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0030 time to fit residues: 0.0576 Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.034 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 150 optimal weight: 30.0000 chunk 29 optimal weight: 30.0000 chunk 135 optimal weight: 20.0000 chunk 55 optimal weight: 40.0000 chunk 183 optimal weight: 30.0000 chunk 145 optimal weight: 20.0000 chunk 99 optimal weight: 40.0000 chunk 174 optimal weight: 40.0000 chunk 119 optimal weight: 20.0000 chunk 123 optimal weight: 50.0000 chunk 102 optimal weight: 40.0000 overall best weight: 24.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2146 r_free = 0.2146 target = 0.022487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.1991 r_free = 0.1991 target = 0.018920 restraints weight = 19789.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.1998 r_free = 0.1998 target = 0.019074 restraints weight = 15707.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2003 r_free = 0.2003 target = 0.019189 restraints weight = 13090.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2007 r_free = 0.2007 target = 0.019280 restraints weight = 11305.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2010 r_free = 0.2010 target = 0.019342 restraints weight = 10117.126| |-----------------------------------------------------------------------------| r_work (final): 0.2336 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.052088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.048760 restraints weight = 1048.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.049733 restraints weight = 369.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.050305 restraints weight = 214.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.050768 restraints weight = 146.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.051000 restraints weight = 103.687| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 1.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.022 13328 Z= 0.445 Angle : 0.894 6.344 16816 Z= 0.570 Chirality : 0.104 0.321 120 Planarity : 0.004 0.014 3184 Dihedral : 14.766 169.924 3440 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.31 % Favored : 84.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.15), residues: 3136 helix: 0.57 (0.15), residues: 1072 sheet: -3.68 (0.23), residues: 416 loop : -2.40 (0.15), residues: 1648 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.44 (13328) covalent geometry : angle 0.89415 / 0.57 (16816) hydrogen bonds : bond 0.05591 / 4.41 ( 1006) hydrogen bonds : angle 7.16684 / 5.57 ( 2940) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.038 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0050 time to fit residues: 0.0988 Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.035 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 255 optimal weight: 50.0000 chunk 296 optimal weight: 30.0000 chunk 108 optimal weight: 40.0000 chunk 289 optimal weight: 40.0000 chunk 26 optimal weight: 50.0000 chunk 55 optimal weight: 30.0000 chunk 135 optimal weight: 20.0000 chunk 221 optimal weight: 7.9990 chunk 51 optimal weight: 30.0000 chunk 19 optimal weight: 40.0000 chunk 167 optimal weight: 30.0000 overall best weight: 23.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2146 r_free = 0.2146 target = 0.022488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.1991 r_free = 0.1991 target = 0.018980 restraints weight = 20436.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.1999 r_free = 0.1999 target = 0.019131 restraints weight = 16117.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2004 r_free = 0.2004 target = 0.019245 restraints weight = 13394.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2008 r_free = 0.2008 target = 0.019323 restraints weight = 11613.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2011 r_free = 0.2011 target = 0.019389 restraints weight = 10476.646| |-----------------------------------------------------------------------------| r_work (final): 0.2331 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.054977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.051735 restraints weight = 800.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.052740 restraints weight = 356.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.053340 restraints weight = 211.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.053810 restraints weight = 150.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.054154 restraints weight = 104.474| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 1.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.021 13328 Z= 0.435 Angle : 0.876 5.821 16816 Z= 0.561 Chirality : 0.101 0.271 120 Planarity : 0.004 0.014 3184 Dihedral : 14.969 169.425 3440 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.15), residues: 3136 helix: 0.28 (0.15), residues: 1168 sheet: -3.67 (0.23), residues: 416 loop : -2.55 (0.15), residues: 1552 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.44 (13328) covalent geometry : angle 0.87643 / 0.56 (16816) hydrogen bonds : bond 0.05667 / 4.48 ( 1006) hydrogen bonds : angle 7.33625 / 5.70 ( 2940) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.046 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0034 time to fit residues: 0.0815 Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.035 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 122 optimal weight: 50.0000 chunk 67 optimal weight: 20.0000 chunk 191 optimal weight: 40.0000 chunk 192 optimal weight: 20.0000 chunk 198 optimal weight: 40.0000 chunk 286 optimal weight: 30.0000 chunk 144 optimal weight: 20.0000 chunk 96 optimal weight: 50.0000 chunk 106 optimal weight: 20.0000 chunk 35 optimal weight: 0.0000 chunk 93 optimal weight: 40.0000 overall best weight: 16.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2148 r_free = 0.2148 target = 0.022554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.1998 r_free = 0.1998 target = 0.019133 restraints weight = 19518.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2005 r_free = 0.2005 target = 0.019288 restraints weight = 15593.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2010 r_free = 0.2010 target = 0.019394 restraints weight = 12575.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2013 r_free = 0.2013 target = 0.019462 restraints weight = 11053.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2016 r_free = 0.2016 target = 0.019512 restraints weight = 10111.934| |-----------------------------------------------------------------------------| r_work (final): 0.2312 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.053345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.048783 restraints weight = 865.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.050054 restraints weight = 453.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.050847 restraints weight = 295.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.051404 restraints weight = 211.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.051770 restraints weight = 161.743| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 1.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.013 13328 Z= 0.308 Angle : 0.714 6.351 16816 Z= 0.449 Chirality : 0.105 0.330 120 Planarity : 0.003 0.011 3184 Dihedral : 14.529 165.383 3440 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.16), residues: 3136 helix: 1.22 (0.16), residues: 1152 sheet: -3.73 (0.22), residues: 416 loop : -2.28 (0.16), residues: 1568 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.31 (13328) covalent geometry : angle 0.71405 / 0.45 (16816) hydrogen bonds : bond 0.04689 / 3.71 ( 1006) hydrogen bonds : angle 6.47987 / 5.03 ( 2940) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0030 time to fit residues: 0.0560 Evaluate side-chains 5 residues out of total 178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.026 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 155 optimal weight: 30.0000 chunk 148 optimal weight: 8.9990 chunk 3 optimal weight: 40.0000 chunk 179 optimal weight: 50.0000 chunk 138 optimal weight: 20.0000 chunk 46 optimal weight: 50.0000 chunk 7 optimal weight: 50.0000 chunk 12 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 76 optimal weight: 40.0000 overall best weight: 17.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2149 r_free = 0.2149 target = 0.022498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2000 r_free = 0.2000 target = 0.019088 restraints weight = 20714.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2007 r_free = 0.2007 target = 0.019238 restraints weight = 16207.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2013 r_free = 0.2013 target = 0.019375 restraints weight = 13410.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2017 r_free = 0.2017 target = 0.019469 restraints weight = 11120.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2020 r_free = 0.2020 target = 0.019539 restraints weight = 9916.145| |-----------------------------------------------------------------------------| r_work (final): 0.2341 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.053960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.050999 restraints weight = 856.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.052032 restraints weight = 402.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.052536 restraints weight = 260.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.053023 restraints weight = 176.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.053340 restraints weight = 114.379| |-----------------------------------------------------------------------------| r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 1.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.014 13328 Z= 0.340 Angle : 0.742 6.289 16816 Z= 0.472 Chirality : 0.102 0.311 120 Planarity : 0.003 0.011 3184 Dihedral : 14.506 165.081 3440 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.80 % Favored : 85.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.16), residues: 3136 helix: 1.33 (0.16), residues: 1152 sheet: -3.67 (0.23), residues: 416 loop : -2.38 (0.16), residues: 1568 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.34 (13328) covalent geometry : angle 0.74177 / 0.47 (16816) hydrogen bonds : bond 0.04878 / 3.86 ( 1006) hydrogen bonds : angle 6.66030 / 5.18 ( 2940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1281.59 seconds wall clock time: 22 minutes 35.54 seconds (1355.54 seconds total)