Starting phenix.real_space_refine on Wed Jun 11 21:35:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jse_22451/06_2025/7jse_22451.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jse_22451/06_2025/7jse_22451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jse_22451/06_2025/7jse_22451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jse_22451/06_2025/7jse_22451.map" model { file = "/net/cci-nas-00/data/ceres_data/7jse_22451/06_2025/7jse_22451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jse_22451/06_2025/7jse_22451.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} 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: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} 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: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} 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: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} 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: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} 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: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} 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: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} 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: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} 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: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} 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: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} 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: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} 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: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} 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: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} 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: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} 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: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} 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: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} 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: 10.85, per 1000 atoms: 0.82 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: 4.12 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.07 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: 3.90 Time building geometry restraints manager: 4.72 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=" C ASN F 139 " pdb=" O ASN F 139 " ideal model delta sigma weight residual 1.227 1.236 -0.008 7.80e-03 1.64e+04 1.14e+00 bond pdb=" C3' DT Q 7 " pdb=" O3' DT Q 7 " ideal model delta sigma weight residual 1.422 1.449 -0.027 3.00e-02 1.11e+03 8.22e-01 bond pdb=" C3' DT W 7 " pdb=" O3' DT W 7 " ideal model delta sigma weight residual 1.422 1.449 -0.027 3.00e-02 1.11e+03 8.16e-01 bond pdb=" N GLY O 85 " pdb=" CA GLY O 85 " ideal model delta sigma weight residual 1.444 1.451 -0.008 9.10e-03 1.21e+04 6.94e-01 bond pdb=" N SER O 87 " pdb=" CA SER O 87 " ideal model delta sigma weight residual 1.468 1.458 0.010 1.24e-02 6.50e+03 6.62e-01 ... (remaining 13323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.75: 16163 0.75 - 1.50: 374 1.50 - 2.25: 182 2.25 - 3.00: 70 3.00 - 3.76: 27 Bond angle restraints: 16816 Sorted by residual: angle pdb=" C GLN K 50 " pdb=" N ALA K 51 " pdb=" CA ALA K 51 " ideal model delta sigma weight residual 120.09 122.78 -2.69 1.25e+00 6.40e-01 4.63e+00 angle pdb=" C GLN N 50 " pdb=" N ALA N 51 " pdb=" CA ALA N 51 " ideal model delta sigma weight residual 120.09 122.77 -2.68 1.25e+00 6.40e-01 4.61e+00 angle pdb=" C GLN P 50 " pdb=" N ALA P 51 " pdb=" CA ALA P 51 " ideal model delta sigma weight residual 120.09 122.75 -2.66 1.25e+00 6.40e-01 4.55e+00 angle pdb=" C GLN O 50 " pdb=" N ALA O 51 " pdb=" CA ALA O 51 " ideal model delta sigma weight residual 120.09 122.74 -2.65 1.25e+00 6.40e-01 4.49e+00 angle pdb=" C GLN J 50 " pdb=" N ALA J 51 " pdb=" CA ALA J 51 " ideal model delta sigma weight residual 120.09 122.74 -2.65 1.25e+00 6.40e-01 4.48e+00 ... (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: 0.000 - 0.020: 100 0.020 - 0.041: 17 0.041 - 0.061: 1 0.061 - 0.081: 0 0.081 - 0.102: 2 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 2.35 -2.45 -0.10 2.00e-01 2.50e+01 2.58e-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 2.35 -2.44 -0.09 2.00e-01 2.50e+01 2.06e-01 chirality pdb=" P DT U 8 " pdb=" OP1 DT U 8 " pdb=" OP2 DT U 8 " pdb=" O5' DT U 8 " both_signs ideal model delta sigma weight residual True 2.35 -2.40 -0.06 2.00e-01 2.50e+01 8.75e-02 ... (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: 0.10 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: 4.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 37.270 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4958 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 : 0.001 0.027 13328 Z= 0.095 Angle : 0.381 3.756 16816 Z= 0.240 Chirality : 0.019 0.102 120 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 hydrogen bonds : bond 0.12880 ( 1006) hydrogen bonds : angle 5.89636 ( 2940) covalent geometry : bond 0.00134 (13328) covalent geometry : angle 0.38090 (16816) *********************** 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 : 0.099 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0235 time to fit residues: 0.3088 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 : 0.105 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0043 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 : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 50.0000 chunk 230 optimal weight: 20.0000 chunk 127 optimal weight: 40.0000 chunk 78 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 123 optimal weight: 50.0000 chunk 238 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 144 optimal weight: 30.0000 chunk 177 optimal weight: 30.0000 chunk 276 optimal weight: 20.0000 overall best weight: 17.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2262 r_free = 0.2262 target = 0.025450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2024 r_free = 0.2024 target = 0.019199 restraints weight = 14906.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2028 r_free = 0.2028 target = 0.019285 restraints weight = 13628.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2032 r_free = 0.2032 target = 0.019351 restraints weight = 12671.015| |-----------------------------------------------------------------------------| r_work (final): 0.2044 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.050215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.042105 restraints weight = 761.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.042730 restraints weight = 528.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.043238 restraints weight = 424.792| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5476 moved from start: 0.9678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 13328 Z= 0.386 Angle : 0.926 7.714 16816 Z= 0.593 Chirality : 0.045 0.098 120 Planarity : 0.005 0.013 3184 Dihedral : 13.647 175.866 3440 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 0.71 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 3136 helix: 1.22 (0.16), residues: 1296 sheet: -2.85 (0.20), residues: 480 loop : -1.23 (0.16), residues: 1360 Details of bonding type rmsd hydrogen bonds : bond 0.05383 ( 1006) hydrogen bonds : angle 5.93336 ( 2940) covalent geometry : bond 0.00558 (13328) covalent geometry : angle 0.92637 (16816) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 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 : 0.098 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0102 time to fit residues: 0.2346 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 : 0.107 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0044 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 : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 13 optimal weight: 40.0000 chunk 68 optimal weight: 30.0000 chunk 198 optimal weight: 50.0000 chunk 20 optimal weight: 20.0000 chunk 18 optimal weight: 40.0000 chunk 295 optimal weight: 30.0000 chunk 128 optimal weight: 40.0000 chunk 271 optimal weight: 20.0000 chunk 65 optimal weight: 50.0000 chunk 132 optimal weight: 40.0000 chunk 108 optimal weight: 40.0000 overall best weight: 28.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.031057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2260 r_free = 0.2260 target = 0.024144 restraints weight = 10608.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2280 r_free = 0.2280 target = 0.024626 restraints weight = 7966.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2294 r_free = 0.2294 target = 0.024968 restraints weight = 6381.812| |-----------------------------------------------------------------------------| r_work (final): 0.2100 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.061571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.056327 restraints weight = 1120.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.057868 restraints weight = 515.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.059004 restraints weight = 335.265| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 1.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 13328 Z= 0.564 Angle : 1.099 9.434 16816 Z= 0.696 Chirality : 0.059 0.118 120 Planarity : 0.006 0.016 3184 Dihedral : 14.909 178.424 3440 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 3136 helix: 1.01 (0.15), residues: 1168 sheet: -1.88 (0.26), residues: 384 loop : -1.57 (0.16), residues: 1584 Details of bonding type rmsd hydrogen bonds : bond 0.06148 ( 1006) hydrogen bonds : angle 7.10862 ( 2940) covalent geometry : bond 0.00821 (13328) covalent geometry : angle 1.09919 (16816) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 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 : 0.106 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0108 time to fit residues: 0.2534 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 : 0.104 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0044 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 : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 20 optimal weight: 30.0000 chunk 173 optimal weight: 30.0000 chunk 158 optimal weight: 30.0000 chunk 261 optimal weight: 30.0000 chunk 178 optimal weight: 30.0000 chunk 147 optimal weight: 20.0000 chunk 237 optimal weight: 40.0000 chunk 105 optimal weight: 20.0000 chunk 169 optimal weight: 30.0000 chunk 215 optimal weight: 30.0000 chunk 302 optimal weight: 30.0000 overall best weight: 26.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.031822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2275 r_free = 0.2275 target = 0.024723 restraints weight = 10476.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2296 r_free = 0.2296 target = 0.025185 restraints weight = 7899.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.025522 restraints weight = 6370.216| |-----------------------------------------------------------------------------| r_work (final): 0.2112 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.059649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.053978 restraints weight = 1116.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.055047 restraints weight = 537.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.056159 restraints weight = 403.035| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 1.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 13328 Z= 0.509 Angle : 0.987 6.510 16816 Z= 0.632 Chirality : 0.073 0.179 120 Planarity : 0.005 0.014 3184 Dihedral : 15.054 171.103 3440 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.64 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 : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 3136 helix: 0.99 (0.15), residues: 1168 sheet: -2.48 (0.25), residues: 432 loop : -1.38 (0.16), residues: 1536 Details of bonding type rmsd hydrogen bonds : bond 0.05350 ( 1006) hydrogen bonds : angle 6.68276 ( 2940) covalent geometry : bond 0.00730 (13328) covalent geometry : angle 0.98722 (16816) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 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 : 0.092 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0098 time to fit residues: 0.2224 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 : 0.111 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0044 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 : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 37 optimal weight: 20.0000 chunk 94 optimal weight: 50.0000 chunk 191 optimal weight: 40.0000 chunk 115 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 chunk 116 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 180 optimal weight: 50.0000 chunk 170 optimal weight: 50.0000 chunk 111 optimal weight: 20.0000 chunk 129 optimal weight: 0.0970 overall best weight: 16.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2267 r_free = 0.2267 target = 0.025165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2045 r_free = 0.2045 target = 0.019837 restraints weight = 17017.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2052 r_free = 0.2052 target = 0.019968 restraints weight = 14612.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2058 r_free = 0.2058 target = 0.020089 restraints weight = 12942.121| |-----------------------------------------------------------------------------| r_work (final): 0.2102 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.062752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.055867 restraints weight = 764.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.057159 restraints weight = 527.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.058035 restraints weight = 398.363| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4543 moved from start: 1.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13328 Z= 0.317 Angle : 0.687 4.246 16816 Z= 0.436 Chirality : 0.063 0.124 120 Planarity : 0.003 0.011 3184 Dihedral : 14.359 176.086 3440 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3136 helix: 1.90 (0.16), residues: 1056 sheet: -2.39 (0.26), residues: 432 loop : -1.88 (0.15), residues: 1648 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 1006) hydrogen bonds : angle 5.71549 ( 2940) covalent geometry : bond 0.00460 (13328) covalent geometry : angle 0.68738 (16816) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 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 : 0.099 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0105 time to fit residues: 0.2430 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 : 0.097 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0039 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 : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 164 optimal weight: 40.0000 chunk 46 optimal weight: 50.0000 chunk 50 optimal weight: 9.9990 chunk 8 optimal weight: 50.0000 chunk 34 optimal weight: 0.0980 chunk 188 optimal weight: 30.0000 chunk 193 optimal weight: 5.9990 chunk 160 optimal weight: 50.0000 chunk 239 optimal weight: 20.0000 chunk 166 optimal weight: 8.9990 chunk 77 optimal weight: 50.0000 overall best weight: 9.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.030609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2266 r_free = 0.2266 target = 0.024094 restraints weight = 10886.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2285 r_free = 0.2285 target = 0.024533 restraints weight = 7957.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2299 r_free = 0.2299 target = 0.024861 restraints weight = 6342.457| |-----------------------------------------------------------------------------| r_work (final): 0.2151 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.060802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.052641 restraints weight = 812.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.053778 restraints weight = 588.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.054700 restraints weight = 476.967| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 1.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13328 Z= 0.196 Angle : 0.527 3.577 16816 Z= 0.329 Chirality : 0.058 0.139 120 Planarity : 0.002 0.007 3184 Dihedral : 13.767 175.073 3440 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 3136 helix: 2.92 (0.16), residues: 1056 sheet: -2.38 (0.25), residues: 432 loop : -1.47 (0.15), residues: 1648 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 1006) hydrogen bonds : angle 4.95793 ( 2940) covalent geometry : bond 0.00295 (13328) covalent geometry : angle 0.52744 (16816) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 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 : 0.108 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0110 time to fit residues: 0.2561 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 : 0.102 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0044 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 : 0.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 261 optimal weight: 40.0000 chunk 229 optimal weight: 40.0000 chunk 246 optimal weight: 20.0000 chunk 138 optimal weight: 30.0000 chunk 289 optimal weight: 40.0000 chunk 185 optimal weight: 30.0000 chunk 84 optimal weight: 50.0000 chunk 100 optimal weight: 20.0000 chunk 113 optimal weight: 30.0000 chunk 39 optimal weight: 30.0000 chunk 195 optimal weight: 30.0000 overall best weight: 26.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2261 r_free = 0.2261 target = 0.025155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2107 r_free = 0.2107 target = 0.021304 restraints weight = 19699.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2112 r_free = 0.2112 target = 0.021406 restraints weight = 17152.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2115 r_free = 0.2115 target = 0.021494 restraints weight = 15258.822| |-----------------------------------------------------------------------------| r_work (final): 0.2199 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.066126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.059394 restraints weight = 811.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.061196 restraints weight = 412.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.062343 restraints weight = 251.881| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4783 moved from start: 1.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 13328 Z= 0.495 Angle : 0.928 6.858 16816 Z= 0.597 Chirality : 0.083 0.171 120 Planarity : 0.005 0.014 3184 Dihedral : 14.854 174.179 3440 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.15), residues: 3136 helix: 1.03 (0.15), residues: 1168 sheet: -2.93 (0.24), residues: 432 loop : -1.86 (0.15), residues: 1536 Details of bonding type rmsd hydrogen bonds : bond 0.05765 ( 1006) hydrogen bonds : angle 6.86203 ( 2940) covalent geometry : bond 0.00731 (13328) covalent geometry : angle 0.92754 (16816) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 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 : 0.104 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0100 time to fit residues: 0.2307 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 : 0.106 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0044 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 : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 185 optimal weight: 30.0000 chunk 277 optimal weight: 20.0000 chunk 215 optimal weight: 30.0000 chunk 211 optimal weight: 30.0000 chunk 280 optimal weight: 30.0000 chunk 218 optimal weight: 40.0000 chunk 165 optimal weight: 40.0000 chunk 263 optimal weight: 40.0000 chunk 279 optimal weight: 30.0000 chunk 281 optimal weight: 0.0010 chunk 68 optimal weight: 30.0000 overall best weight: 22.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2148 r_free = 0.2148 target = 0.022442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2004 r_free = 0.2004 target = 0.019059 restraints weight = 19838.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2012 r_free = 0.2012 target = 0.019220 restraints weight = 15303.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2018 r_free = 0.2018 target = 0.019336 restraints weight = 12477.813| |-----------------------------------------------------------------------------| r_work (final): 0.2342 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.055349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.052292 restraints weight = 956.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.053451 restraints weight = 310.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.054146 restraints weight = 162.924| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 1.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13328 Z= 0.409 Angle : 0.794 4.528 16816 Z= 0.510 Chirality : 0.076 0.195 120 Planarity : 0.004 0.012 3184 Dihedral : 14.172 168.506 3440 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 1.88 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.15), residues: 3136 helix: 1.32 (0.16), residues: 1072 sheet: -2.91 (0.25), residues: 416 loop : -2.34 (0.15), residues: 1648 Details of bonding type rmsd hydrogen bonds : bond 0.04851 ( 1006) hydrogen bonds : angle 6.45800 ( 2940) covalent geometry : bond 0.00587 (13328) covalent geometry : angle 0.79426 (16816) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 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 : 0.091 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0096 time to fit residues: 0.2207 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 : 0.092 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0042 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 : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 109 optimal weight: 8.9990 chunk 187 optimal weight: 7.9990 chunk 201 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 123 optimal weight: 50.0000 chunk 177 optimal weight: 30.0000 chunk 152 optimal weight: 40.0000 chunk 285 optimal weight: 30.0000 chunk 220 optimal weight: 20.0000 chunk 26 optimal weight: 50.0000 chunk 208 optimal weight: 30.0000 overall best weight: 13.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2167 r_free = 0.2167 target = 0.022596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2014 r_free = 0.2014 target = 0.019228 restraints weight = 20252.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2023 r_free = 0.2023 target = 0.019395 restraints weight = 15340.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2030 r_free = 0.2030 target = 0.019521 restraints weight = 12433.518| |-----------------------------------------------------------------------------| r_work (final): 0.2349 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.055869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.052768 restraints weight = 909.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.053890 restraints weight = 368.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.054502 restraints weight = 209.748| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 1.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13328 Z= 0.266 Angle : 0.636 3.944 16816 Z= 0.399 Chirality : 0.068 0.156 120 Planarity : 0.003 0.009 3184 Dihedral : 13.940 170.911 3440 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.27 % Favored : 86.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.16), residues: 3136 helix: 2.10 (0.16), residues: 1056 sheet: -3.08 (0.23), residues: 416 loop : -2.10 (0.15), residues: 1664 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 1006) hydrogen bonds : angle 5.78069 ( 2940) covalent geometry : bond 0.00394 (13328) covalent geometry : angle 0.63641 (16816) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 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 : 0.091 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0099 time to fit residues: 0.2353 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 : 0.105 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0043 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 : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 118 optimal weight: 30.0000 chunk 134 optimal weight: 30.0000 chunk 150 optimal weight: 8.9990 chunk 245 optimal weight: 30.0000 chunk 144 optimal weight: 20.0000 chunk 153 optimal weight: 40.0000 chunk 8 optimal weight: 50.0000 chunk 110 optimal weight: 0.0570 chunk 249 optimal weight: 30.0000 chunk 93 optimal weight: 30.0000 chunk 267 optimal weight: 30.0000 overall best weight: 17.8112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2151 r_free = 0.2151 target = 0.022408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2004 r_free = 0.2004 target = 0.019089 restraints weight = 20243.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2013 r_free = 0.2013 target = 0.019261 restraints weight = 15272.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2019 r_free = 0.2019 target = 0.019397 restraints weight = 12352.996| |-----------------------------------------------------------------------------| r_work (final): 0.2342 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.052947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.048763 restraints weight = 1027.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.049940 restraints weight = 412.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.050641 restraints weight = 248.030| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 1.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13328 Z= 0.339 Angle : 0.728 4.482 16816 Z= 0.460 Chirality : 0.074 0.170 120 Planarity : 0.003 0.010 3184 Dihedral : 14.126 168.834 3440 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.82 % Favored : 84.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.15), residues: 3136 helix: 1.72 (0.16), residues: 1072 sheet: -3.48 (0.21), residues: 416 loop : -2.36 (0.14), residues: 1648 Details of bonding type rmsd hydrogen bonds : bond 0.04644 ( 1006) hydrogen bonds : angle 6.16403 ( 2940) covalent geometry : bond 0.00494 (13328) covalent geometry : angle 0.72775 (16816) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 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 : 0.095 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0098 time to fit residues: 0.2204 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 : 0.096 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0037 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 : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 233 optimal weight: 30.0000 chunk 22 optimal weight: 20.0000 chunk 181 optimal weight: 20.0000 chunk 264 optimal weight: 20.0000 chunk 20 optimal weight: 30.0000 chunk 160 optimal weight: 50.0000 chunk 166 optimal weight: 30.0000 chunk 247 optimal weight: 40.0000 chunk 186 optimal weight: 0.0670 chunk 239 optimal weight: 20.0000 chunk 34 optimal weight: 0.0270 overall best weight: 12.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2154 r_free = 0.2154 target = 0.022335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2007 r_free = 0.2007 target = 0.019077 restraints weight = 20681.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2015 r_free = 0.2015 target = 0.019225 restraints weight = 15746.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2023 r_free = 0.2023 target = 0.019365 restraints weight = 12797.577| |-----------------------------------------------------------------------------| r_work (final): 0.2328 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.051866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.047406 restraints weight = 910.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.048501 restraints weight = 430.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.049163 restraints weight = 278.780| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 1.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13328 Z= 0.246 Angle : 0.591 3.701 16816 Z= 0.371 Chirality : 0.067 0.163 120 Planarity : 0.002 0.008 3184 Dihedral : 13.775 164.364 3440 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 0.94 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.16), residues: 3136 helix: 2.35 (0.16), residues: 1056 sheet: -3.37 (0.22), residues: 416 loop : -2.03 (0.15), residues: 1664 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 1006) hydrogen bonds : angle 5.62857 ( 2940) covalent geometry : bond 0.00358 (13328) covalent geometry : angle 0.59137 (16816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3135.22 seconds wall clock time: 54 minutes 38.59 seconds (3278.59 seconds total)