Starting phenix.real_space_refine on Thu Sep 26 13:42:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jse_22451/09_2024/7jse_22451.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jse_22451/09_2024/7jse_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jse_22451/09_2024/7jse_22451.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jse_22451/09_2024/7jse_22451.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jse_22451/09_2024/7jse_22451.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jse_22451/09_2024/7jse_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-5461/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: 10.05, per 1000 atoms: 0.76 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: 4.06 Conformation dependent library (CDL) restraints added in 2.9 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: 2.12 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: 3.80 Time building geometry restraints manager: 4.55 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: 0.00 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: 3.630 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: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.400 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.310 ------------------------------------------------------------------------------- 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= 0.101 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.102 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0220 time to fit residues: 0.2915 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.113 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5978 moved from start: 0.9698 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= 0.425 Angle : 0.924 7.470 16816 Z= 0.587 Chirality : 0.046 0.102 120 Planarity : 0.005 0.013 3184 Dihedral : 13.645 175.864 3440 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 0.47 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: -0.77 (0.15), residues: 3136 helix: 1.22 (0.16), residues: 1296 sheet: -2.83 (0.20), residues: 480 loop : -1.28 (0.16), residues: 1360 *********************** 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 fitting. 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: 0.0111 time to fit residues: 0.2240 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 fitting. 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 153 optimal weight: 40.0000 chunk 85 optimal weight: 40.0000 chunk 229 optimal weight: 30.0000 chunk 187 optimal weight: 9.9990 chunk 76 optimal weight: 50.0000 chunk 276 optimal weight: 30.0000 chunk 298 optimal weight: 50.0000 chunk 246 optimal weight: 40.0000 chunk 274 optimal weight: 40.0000 chunk 94 optimal weight: 50.0000 chunk 221 optimal weight: 10.0000 overall best weight: 23.9998 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 moved from start: 1.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 13328 Z= 0.530 Angle : 0.994 8.171 16816 Z= 0.627 Chirality : 0.052 0.106 120 Planarity : 0.005 0.014 3184 Dihedral : 14.620 179.755 3440 Min Nonbonded Distance : 2.504 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: -0.81 (0.15), residues: 3136 helix: 1.18 (0.14), residues: 1200 sheet: -1.81 (0.26), residues: 384 loop : -1.62 (0.15), residues: 1552 *********************** REFINEMENT MACRO_CYCLE 3 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 fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.105 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0104 time to fit residues: 0.2475 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 40.0000 chunk 207 optimal weight: 30.0000 chunk 143 optimal weight: 30.0000 chunk 30 optimal weight: 30.0000 chunk 131 optimal weight: 20.0000 chunk 185 optimal weight: 30.0000 chunk 277 optimal weight: 20.0000 chunk 293 optimal weight: 50.0000 chunk 145 optimal weight: 8.9990 chunk 263 optimal weight: 30.0000 chunk 79 optimal weight: 30.0000 overall best weight: 21.7998 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 moved from start: 1.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13328 Z= 0.469 Angle : 0.860 5.575 16816 Z= 0.550 Chirality : 0.064 0.141 120 Planarity : 0.005 0.013 3184 Dihedral : 14.789 175.460 3440 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.12 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: -0.65 (0.15), residues: 3136 helix: 1.41 (0.15), residues: 1184 sheet: -2.29 (0.25), residues: 432 loop : -1.35 (0.15), residues: 1520 *********************** REFINEMENT MACRO_CYCLE 4 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 fitting. 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: 0.0211 time to fit residues: 0.3077 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.091 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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: 0.0036 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 244 optimal weight: 20.0000 chunk 166 optimal weight: 30.0000 chunk 4 optimal weight: 30.0000 chunk 218 optimal weight: 40.0000 chunk 121 optimal weight: 20.0000 chunk 250 optimal weight: 30.0000 chunk 203 optimal weight: 40.0000 chunk 0 optimal weight: 30.0000 chunk 150 optimal weight: 20.0000 chunk 263 optimal weight: 40.0000 chunk 74 optimal weight: 30.0000 overall best weight: 24.0000 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 1.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 13328 Z= 0.513 Angle : 0.929 6.303 16816 Z= 0.589 Chirality : 0.071 0.138 120 Planarity : 0.005 0.014 3184 Dihedral : 14.872 164.540 3440 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.78 % Favored : 86.22 % 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: -1.62 (0.15), residues: 3136 helix: 0.49 (0.15), residues: 1200 sheet: -2.76 (0.25), residues: 432 loop : -1.86 (0.15), residues: 1504 *********************** REFINEMENT MACRO_CYCLE 5 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 fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.097 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0109 time to fit residues: 0.2433 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.129 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 98 optimal weight: 40.0000 chunk 264 optimal weight: 30.0000 chunk 58 optimal weight: 30.0000 chunk 172 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 294 optimal weight: 50.0000 chunk 244 optimal weight: 20.0000 chunk 136 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 154 optimal weight: 30.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 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 : 0.006 0.044 13328 Z= 0.426 Angle : 0.788 4.720 16816 Z= 0.504 Chirality : 0.073 0.163 120 Planarity : 0.004 0.011 3184 Dihedral : 14.399 174.161 3440 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 0.76 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: -1.56 (0.15), residues: 3136 helix: 1.19 (0.16), residues: 1088 sheet: -2.73 (0.26), residues: 416 loop : -2.21 (0.15), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 6 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 fitting. 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: 0.0105 time to fit residues: 0.2377 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.100 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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: 0.0048 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 283 optimal weight: 40.0000 chunk 33 optimal weight: 30.0000 chunk 167 optimal weight: 30.0000 chunk 214 optimal weight: 30.0000 chunk 166 optimal weight: 30.0000 chunk 247 optimal weight: 30.0000 chunk 164 optimal weight: 9.9990 chunk 293 optimal weight: 50.0000 chunk 183 optimal weight: 20.0000 chunk 178 optimal weight: 40.0000 chunk 135 optimal weight: 20.0000 overall best weight: 21.9998 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 1.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 13328 Z= 0.469 Angle : 0.892 5.180 16816 Z= 0.560 Chirality : 0.082 0.169 120 Planarity : 0.004 0.013 3184 Dihedral : 14.931 176.112 3440 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.33 % Favored : 83.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 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: -1.94 (0.15), residues: 3136 helix: 0.95 (0.16), residues: 1072 sheet: -2.95 (0.24), residues: 416 loop : -2.46 (0.15), residues: 1648 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 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 fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0102 time to fit residues: 0.2294 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 30.0000 chunk 117 optimal weight: 30.0000 chunk 174 optimal weight: 50.0000 chunk 88 optimal weight: 0.0970 chunk 57 optimal weight: 40.0000 chunk 56 optimal weight: 40.0000 chunk 186 optimal weight: 0.0980 chunk 199 optimal weight: 50.0000 chunk 144 optimal weight: 20.0000 chunk 27 optimal weight: 40.0000 chunk 230 optimal weight: 20.0000 overall best weight: 14.0390 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 1.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13328 Z= 0.310 Angle : 0.667 4.069 16816 Z= 0.420 Chirality : 0.070 0.168 120 Planarity : 0.003 0.009 3184 Dihedral : 14.022 168.210 3440 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.47 (0.16), residues: 3136 helix: 1.56 (0.16), residues: 1088 sheet: -2.96 (0.26), residues: 416 loop : -2.31 (0.15), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 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 fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.110 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0090 time to fit residues: 0.1963 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.122 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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: 0.0045 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 30.0000 chunk 280 optimal weight: 9.9990 chunk 256 optimal weight: 50.0000 chunk 273 optimal weight: 40.0000 chunk 164 optimal weight: 40.0000 chunk 118 optimal weight: 40.0000 chunk 214 optimal weight: 30.0000 chunk 83 optimal weight: 50.0000 chunk 246 optimal weight: 30.0000 chunk 258 optimal weight: 20.0000 chunk 272 optimal weight: 30.0000 overall best weight: 23.9998 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 1.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13328 Z= 0.483 Angle : 0.875 5.327 16816 Z= 0.560 Chirality : 0.084 0.183 120 Planarity : 0.004 0.013 3184 Dihedral : 14.415 170.602 3440 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.35 % Favored : 82.65 % 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: -2.34 (0.15), residues: 3136 helix: 0.85 (0.16), residues: 1056 sheet: -3.44 (0.23), residues: 416 loop : -2.77 (0.14), residues: 1664 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 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 fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.100 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0102 time to fit residues: 0.2351 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.101 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 179 optimal weight: 50.0000 chunk 288 optimal weight: 30.0000 chunk 176 optimal weight: 30.0000 chunk 136 optimal weight: 40.0000 chunk 200 optimal weight: 30.0000 chunk 302 optimal weight: 30.0000 chunk 278 optimal weight: 30.0000 chunk 241 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 186 optimal weight: 20.0000 chunk 147 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 1.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 13328 Z= 0.510 Angle : 0.908 5.134 16816 Z= 0.583 Chirality : 0.089 0.198 120 Planarity : 0.004 0.014 3184 Dihedral : 14.733 166.041 3440 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.39 % Favored : 80.61 % 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: -2.70 (0.15), residues: 3136 helix: 0.47 (0.16), residues: 1056 sheet: -3.69 (0.22), residues: 416 loop : -2.91 (0.14), residues: 1664 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 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 fitting. 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: 0.0104 time to fit residues: 0.2382 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.100 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 191 optimal weight: 40.0000 chunk 256 optimal weight: 50.0000 chunk 73 optimal weight: 0.0270 chunk 222 optimal weight: 30.0000 chunk 35 optimal weight: 0.0570 chunk 67 optimal weight: 20.0000 chunk 241 optimal weight: 30.0000 chunk 101 optimal weight: 20.0000 chunk 248 optimal weight: 40.0000 chunk 30 optimal weight: 20.0000 chunk 44 optimal weight: 30.0000 overall best weight: 12.0168 ------------------------------------------------------------------------------- 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 = 0.2144 r_free = 0.2144 target = 0.022446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.1995 r_free = 0.1995 target = 0.019214 restraints weight = 20997.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2003 r_free = 0.2003 target = 0.019364 restraints weight = 16329.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2009 r_free = 0.2009 target = 0.019479 restraints weight = 13469.881| |-----------------------------------------------------------------------------| r_work (final): 0.2109 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.054044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.051211 restraints weight = 860.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.052131 restraints weight = 311.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.052715 restraints weight = 174.373| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 1.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13328 Z= 0.273 Angle : 0.648 4.028 16816 Z= 0.401 Chirality : 0.073 0.163 120 Planarity : 0.003 0.009 3184 Dihedral : 14.021 161.965 3440 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.78 % Favored : 86.22 % 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: -1.86 (0.16), residues: 3136 helix: 1.68 (0.16), residues: 1056 sheet: -3.73 (0.21), residues: 416 loop : -2.64 (0.15), residues: 1664 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2561.11 seconds wall clock time: 46 minutes 11.51 seconds (2771.51 seconds total)