Starting phenix.real_space_refine on Sat Sep 12 02:54:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jse_22451/09_2026/7jse_22451.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jse_22451/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7jse_22451/09_2026/7jse_22451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jse_22451/09_2026/7jse_22451.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jse_22451/09_2026/7jse_22451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jse_22451/09_2026/7jse_22451.map" } 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-2.2.1-6174/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: 4.09, per 1000 atoms: 0.31 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: 1.24 Conformation dependent library (CDL) restraints added in 999.7 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: 0.45 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: 2.10 Time building geometry restraints manager: 1.63 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: 15891 0.75 - 1.50: 525 1.50 - 2.25: 229 2.25 - 3.00: 143 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: 0.05 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: 4.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.360 Find NCS groups from input model: 0.670 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.680 ------------------------------------------------------------------------------- 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 : 0.438 3.756 16816 Z= 0.366 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 0.43832 / 0.37 (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 : 0.040 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0077 time to fit residues: 0.1114 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 : 0.032 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: 0.0015 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 = 0.2288 r_free = 0.2288 target = 0.025928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2040 r_free = 0.2040 target = 0.019338 restraints weight = 14913.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2044 r_free = 0.2044 target = 0.019411 restraints weight = 13914.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2047 r_free = 0.2047 target = 0.019466 restraints weight = 13063.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2047 r_free = 0.2047 target = 0.019466 restraints weight = 12584.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2047 r_free = 0.2047 target = 0.019466 restraints weight = 12584.744| |-----------------------------------------------------------------------------| r_work (final): 0.2039 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.052456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.044927 restraints weight = 644.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.045391 restraints weight = 483.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.045794 restraints weight = 398.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.046099 restraints weight = 349.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.046254 restraints weight = 316.626| |-----------------------------------------------------------------------------| r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5404 moved from start: 0.8946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 13328 Z= 0.312 Angle : 0.811 8.033 16816 Z= 0.513 Chirality : 0.040 0.116 120 Planarity : 0.004 0.011 3184 Dihedral : 13.440 175.755 3440 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.63 % Favored : 92.86 % 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: -1.02 (0.15), residues: 3136 helix: 1.23 (0.16), residues: 1280 sheet: -3.23 (0.17), residues: 560 loop : -1.35 (0.16), residues: 1296 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.31 (13328) covalent geometry : angle 0.81088 / 0.51 (16816) hydrogen bonds : bond 0.04863 / 3.81 ( 1006) hydrogen bonds : angle 5.68186 / 4.42 ( 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 : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0042 time to fit residues: 0.0843 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 : 0.023 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: 0.0014 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: 30.0000 chunk 278 optimal weight: 9.9990 chunk 207 optimal weight: 20.0000 chunk 143 optimal weight: 30.0000 chunk 11 optimal weight: 30.0000 chunk 61 optimal weight: 30.0000 chunk 138 optimal weight: 20.0000 chunk 20 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 131 optimal weight: 20.0000 overall best weight: 19.9998 ------------------------------------------------------------------------------- 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 = 0.2232 r_free = 0.2232 target = 0.024920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2018 r_free = 0.2018 target = 0.019266 restraints weight = 15961.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2025 r_free = 0.2025 target = 0.019387 restraints weight = 13945.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2029 r_free = 0.2029 target = 0.019479 restraints weight = 12553.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2033 r_free = 0.2033 target = 0.019552 restraints weight = 11602.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2036 r_free = 0.2036 target = 0.019613 restraints weight = 10865.128| |-----------------------------------------------------------------------------| r_work (final): 0.2056 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.048762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.043599 restraints weight = 1015.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.044211 restraints weight = 639.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.044566 restraints weight = 491.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.044935 restraints weight = 410.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.045189 restraints weight = 355.423| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5687 moved from start: 1.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 13328 Z= 0.404 Angle : 0.865 6.879 16816 Z= 0.549 Chirality : 0.042 0.106 120 Planarity : 0.004 0.013 3184 Dihedral : 13.905 178.727 3440 Min Nonbonded Distance : 2.539 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: -0.25 (0.15), residues: 3136 helix: 1.83 (0.16), residues: 1200 sheet: -1.64 (0.26), residues: 384 loop : -1.43 (0.15), residues: 1552 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.40 (13328) covalent geometry : angle 0.86457 / 0.55 (16816) hydrogen bonds : bond 0.05025 / 3.96 ( 1006) hydrogen bonds : angle 5.86900 / 4.58 ( 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 : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0047 time to fit residues: 0.0907 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: 0.0011 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 50.0000 chunk 22 optimal weight: 20.0000 chunk 211 optimal weight: 40.0000 chunk 31 optimal weight: 10.0000 chunk 159 optimal weight: 40.0000 chunk 199 optimal weight: 50.0000 chunk 26 optimal weight: 50.0000 chunk 86 optimal weight: 30.0000 chunk 183 optimal weight: 0.9990 chunk 39 optimal weight: 40.0000 chunk 209 optimal weight: 30.0000 overall best weight: 18.1998 ------------------------------------------------------------------------------- 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 = 0.2520 r_free = 0.2520 target = 0.030734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2245 r_free = 0.2245 target = 0.023894 restraints weight = 10793.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2265 r_free = 0.2265 target = 0.024346 restraints weight = 8191.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2281 r_free = 0.2281 target = 0.024707 restraints weight = 6606.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2291 r_free = 0.2291 target = 0.024940 restraints weight = 5579.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2297 r_free = 0.2297 target = 0.025069 restraints weight = 4924.162| |-----------------------------------------------------------------------------| r_work (final): 0.2111 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.065089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.059826 restraints weight = 1037.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.061277 restraints weight = 569.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.062417 restraints weight = 387.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.063998 restraints weight = 285.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.064391 restraints weight = 144.337| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 1.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 13328 Z= 0.381 Angle : 0.804 6.041 16816 Z= 0.511 Chirality : 0.052 0.133 120 Planarity : 0.004 0.014 3184 Dihedral : 14.140 173.796 3440 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % 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: -0.06 (0.15), residues: 3136 helix: 1.95 (0.15), residues: 1184 sheet: -2.16 (0.25), residues: 432 loop : -1.00 (0.16), residues: 1520 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.38 (13328) covalent geometry : angle 0.80382 / 0.51 (16816) hydrogen bonds : bond 0.04485 / 3.54 ( 1006) hydrogen bonds : angle 5.68111 / 4.42 ( 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 : 0.035 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0042 time to fit residues: 0.0787 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 : 0.032 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 : 0.001 ------------------------------------------------------------------------------- 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: 40.0000 chunk 53 optimal weight: 20.0000 chunk 266 optimal weight: 40.0000 chunk 38 optimal weight: 40.0000 chunk 300 optimal weight: 20.0000 chunk 65 optimal weight: 40.0000 chunk 248 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 chunk 114 optimal weight: 30.0000 chunk 177 optimal weight: 30.0000 chunk 49 optimal weight: 20.0000 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 = 0.2548 r_free = 0.2548 target = 0.031415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2266 r_free = 0.2266 target = 0.024382 restraints weight = 11137.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2288 r_free = 0.2288 target = 0.024885 restraints weight = 8220.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2305 r_free = 0.2305 target = 0.025266 restraints weight = 6488.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2316 r_free = 0.2316 target = 0.025532 restraints weight = 5421.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2324 r_free = 0.2324 target = 0.025741 restraints weight = 4715.018| |-----------------------------------------------------------------------------| r_work (final): 0.2137 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.061792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.056009 restraints weight = 1066.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.057538 restraints weight = 597.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.058767 restraints weight = 427.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.059671 restraints weight = 293.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.060323 restraints weight = 204.716| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 1.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.017 13328 Z= 0.416 Angle : 0.864 6.395 16816 Z= 0.548 Chirality : 0.099 0.332 120 Planarity : 0.004 0.012 3184 Dihedral : 14.770 176.324 3440 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.70 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: -0.52 (0.15), residues: 3136 helix: 1.53 (0.15), residues: 1184 sheet: -2.23 (0.25), residues: 432 loop : -1.28 (0.15), residues: 1520 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.42 (13328) covalent geometry : angle 0.86388 / 0.55 (16816) hydrogen bonds : bond 0.05165 / 4.08 ( 1006) hydrogen bonds : angle 6.44712 / 5.02 ( 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 : 0.037 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0047 time to fit residues: 0.0926 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: 0.0019 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 77 optimal weight: 50.0000 chunk 17 optimal weight: 0.5980 chunk 156 optimal weight: 40.0000 chunk 227 optimal weight: 50.0000 chunk 264 optimal weight: 20.0000 chunk 294 optimal weight: 50.0000 chunk 212 optimal weight: 40.0000 chunk 107 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 104 optimal weight: 50.0000 chunk 200 optimal weight: 20.0000 overall best weight: 16.1196 ------------------------------------------------------------------------------- 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 = 0.2522 r_free = 0.2522 target = 0.030362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2248 r_free = 0.2248 target = 0.023734 restraints weight = 10926.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2268 r_free = 0.2268 target = 0.024181 restraints weight = 8325.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2282 r_free = 0.2282 target = 0.024509 restraints weight = 6736.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2293 r_free = 0.2293 target = 0.024750 restraints weight = 5727.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2300 r_free = 0.2300 target = 0.024927 restraints weight = 5059.988| |-----------------------------------------------------------------------------| r_work (final): 0.2122 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.060394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.052948 restraints weight = 939.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054156 restraints weight = 628.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.055101 restraints weight = 502.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.057828 restraints weight = 419.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.058559 restraints weight = 209.141| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 1.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 13328 Z= 0.309 Angle : 0.701 5.688 16816 Z= 0.438 Chirality : 0.110 0.367 120 Planarity : 0.003 0.010 3184 Dihedral : 14.261 173.809 3440 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % 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: -0.56 (0.15), residues: 3136 helix: 2.20 (0.16), residues: 1072 sheet: -2.44 (0.25), residues: 432 loop : -1.61 (0.15), residues: 1632 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.31 (13328) covalent geometry : angle 0.70100 / 0.44 (16816) hydrogen bonds : bond 0.04346 / 3.43 ( 1006) hydrogen bonds : angle 5.79450 / 4.51 ( 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 : 0.035 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0046 time to fit residues: 0.0889 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 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 : 0.001 ------------------------------------------------------------------------------- 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: 20.0000 chunk 195 optimal weight: 30.0000 chunk 227 optimal weight: 50.0000 chunk 109 optimal weight: 10.0000 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: 40.0000 chunk 94 optimal weight: 40.0000 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 = 0.2261 r_free = 0.2261 target = 0.025125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2111 r_free = 0.2111 target = 0.021325 restraints weight = 19799.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2115 r_free = 0.2115 target = 0.021420 restraints weight = 17344.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2119 r_free = 0.2119 target = 0.021508 restraints weight = 15572.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2123 r_free = 0.2123 target = 0.021574 restraints weight = 14241.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2124 r_free = 0.2124 target = 0.021612 restraints weight = 13376.130| |-----------------------------------------------------------------------------| r_work (final): 0.2207 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.064232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.056984 restraints weight = 801.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.058351 restraints weight = 449.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.059297 restraints weight = 313.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.060095 restraints weight = 234.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.060681 restraints weight = 184.965| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4788 moved from start: 1.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.024 13328 Z= 0.412 Angle : 0.882 6.029 16816 Z= 0.557 Chirality : 0.097 0.272 120 Planarity : 0.004 0.012 3184 Dihedral : 14.734 168.934 3440 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 1.70 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 : 0.54 % 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: -1.02 (0.15), residues: 3136 helix: 1.35 (0.16), residues: 1168 sheet: -2.55 (0.26), residues: 432 loop : -1.76 (0.15), residues: 1536 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.41 (13328) covalent geometry : angle 0.88183 / 0.56 (16816) hydrogen bonds : bond 0.05275 / 4.17 ( 1006) hydrogen bonds : angle 6.65509 / 5.17 ( 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 : 0.046 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0031 time to fit residues: 0.0699 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 : 0.020 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 150 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 chunk 55 optimal weight: 0.5980 chunk 183 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 99 optimal weight: 40.0000 chunk 174 optimal weight: 40.0000 chunk 119 optimal weight: 30.0000 chunk 123 optimal weight: 50.0000 chunk 102 optimal weight: 40.0000 overall best weight: 16.1196 ------------------------------------------------------------------------------- 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 = 0.2162 r_free = 0.2162 target = 0.022533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2019 r_free = 0.2019 target = 0.019199 restraints weight = 20173.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2026 r_free = 0.2026 target = 0.019350 restraints weight = 15708.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2033 r_free = 0.2033 target = 0.019463 restraints weight = 12954.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2037 r_free = 0.2037 target = 0.019549 restraints weight = 11162.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2041 r_free = 0.2041 target = 0.019621 restraints weight = 9916.357| |-----------------------------------------------------------------------------| r_work (final): 0.2333 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.057356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.054059 restraints weight = 905.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.055460 restraints weight = 292.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.056318 restraints weight = 141.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.056690 restraints weight = 73.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.056953 restraints weight = 40.325| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 1.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 13328 Z= 0.316 Angle : 0.709 5.690 16816 Z= 0.444 Chirality : 0.108 0.362 120 Planarity : 0.003 0.010 3184 Dihedral : 14.239 178.275 3440 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % 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: -0.93 (0.16), residues: 3136 helix: 1.85 (0.16), residues: 1088 sheet: -2.62 (0.26), residues: 432 loop : -1.85 (0.15), residues: 1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.32 (13328) covalent geometry : angle 0.70855 / 0.44 (16816) hydrogen bonds : bond 0.04595 / 3.63 ( 1006) hydrogen bonds : angle 6.07710 / 4.73 ( 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 : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0047 time to fit residues: 0.0908 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: 0.0017 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: 20.0000 chunk 108 optimal weight: 40.0000 chunk 289 optimal weight: 40.0000 chunk 26 optimal weight: 40.0000 chunk 55 optimal weight: 30.0000 chunk 135 optimal weight: 20.0000 chunk 221 optimal weight: 4.9990 chunk 51 optimal weight: 40.0000 chunk 19 optimal weight: 40.0000 chunk 167 optimal weight: 0.0030 overall best weight: 15.0004 ------------------------------------------------------------------------------- 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 = 0.2460 r_free = 0.2460 target = 0.028673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2252 r_free = 0.2252 target = 0.023967 restraints weight = 11684.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2273 r_free = 0.2273 target = 0.024406 restraints weight = 8321.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2288 r_free = 0.2288 target = 0.024723 restraints weight = 6431.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2298 r_free = 0.2298 target = 0.024926 restraints weight = 5268.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2307 r_free = 0.2307 target = 0.025114 restraints weight = 4564.969| |-----------------------------------------------------------------------------| r_work (final): 0.2116 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.066988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.059133 restraints weight = 694.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.060222 restraints weight = 442.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.061119 restraints weight = 338.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.061851 restraints weight = 268.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.062488 restraints weight = 222.441| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 1.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 13328 Z= 0.299 Angle : 0.709 5.592 16816 Z= 0.439 Chirality : 0.103 0.339 120 Planarity : 0.003 0.010 3184 Dihedral : 14.138 172.777 3440 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 1.06 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 : 0.00 % 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: -0.82 (0.15), residues: 3136 helix: 2.25 (0.16), residues: 1072 sheet: -2.66 (0.24), residues: 432 loop : -1.96 (0.15), residues: 1632 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.30 (13328) covalent geometry : angle 0.70887 / 0.44 (16816) hydrogen bonds : bond 0.04465 / 3.53 ( 1006) hydrogen bonds : angle 5.88722 / 4.58 ( 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 : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0048 time to fit residues: 0.0900 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 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=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: 50.0000 chunk 286 optimal weight: 30.0000 chunk 144 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 chunk 106 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- 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 = 0.022481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2003 r_free = 0.2003 target = 0.019146 restraints weight = 20101.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2012 r_free = 0.2012 target = 0.019307 restraints weight = 15312.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2019 r_free = 0.2019 target = 0.019445 restraints weight = 12436.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2024 r_free = 0.2024 target = 0.019538 restraints weight = 10577.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2027 r_free = 0.2027 target = 0.019610 restraints weight = 9063.416| |-----------------------------------------------------------------------------| r_work (final): 0.2101 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.052501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.047757 restraints weight = 934.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.049062 restraints weight = 378.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.049815 restraints weight = 226.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.050400 restraints weight = 159.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.050790 restraints weight = 118.884| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 1.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.019 13328 Z= 0.390 Angle : 0.808 5.863 16816 Z= 0.512 Chirality : 0.102 0.319 120 Planarity : 0.004 0.011 3184 Dihedral : 14.577 174.227 3440 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % 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: -1.25 (0.15), residues: 3136 helix: 1.94 (0.16), residues: 1056 sheet: -3.07 (0.23), residues: 432 loop : -2.16 (0.14), residues: 1648 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.39 (13328) covalent geometry : angle 0.80763 / 0.51 (16816) hydrogen bonds : bond 0.05085 / 4.02 ( 1006) hydrogen bonds : angle 6.46294 / 5.02 ( 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 : 0.038 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0049 time to fit residues: 0.0947 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 : 0.001 ------------------------------------------------------------------------------- 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: 0.0000 chunk 148 optimal weight: 20.0000 chunk 3 optimal weight: 40.0000 chunk 179 optimal weight: 40.0000 chunk 138 optimal weight: 30.0000 chunk 46 optimal weight: 50.0000 chunk 7 optimal weight: 30.0000 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: 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 = 0.2165 r_free = 0.2165 target = 0.022420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2013 r_free = 0.2013 target = 0.019109 restraints weight = 20909.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2022 r_free = 0.2022 target = 0.019275 restraints weight = 16276.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2028 r_free = 0.2028 target = 0.019398 restraints weight = 13438.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 14)----------------| | r_work = 0.2033 r_free = 0.2033 target = 0.019497 restraints weight = 11492.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2036 r_free = 0.2036 target = 0.019568 restraints weight = 9915.712| |-----------------------------------------------------------------------------| r_work (final): 0.2079 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.051740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 18)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.048106 restraints weight = 956.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.049052 restraints weight = 398.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.049680 restraints weight = 245.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.050121 restraints weight = 172.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.050438 restraints weight = 129.159| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5801 moved from start: 1.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 13328 Z= 0.309 Angle : 0.704 6.269 16816 Z= 0.439 Chirality : 0.108 0.360 120 Planarity : 0.003 0.011 3184 Dihedral : 14.509 169.991 3440 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.12 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 : 0.00 % 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: -1.21 (0.15), residues: 3136 helix: 2.04 (0.16), residues: 1072 sheet: -3.08 (0.23), residues: 432 loop : -2.23 (0.15), residues: 1632 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.31 (13328) covalent geometry : angle 0.70417 / 0.44 (16816) hydrogen bonds : bond 0.04609 / 3.64 ( 1006) hydrogen bonds : angle 6.06166 / 4.72 ( 2940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1411.78 seconds wall clock time: 24 minutes 52.02 seconds (1492.02 seconds total)