Starting phenix.real_space_refine on Wed Mar 4 20:15:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsv_32768/03_2026/7wsv_32768.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsv_32768/03_2026/7wsv_32768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wsv_32768/03_2026/7wsv_32768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsv_32768/03_2026/7wsv_32768.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wsv_32768/03_2026/7wsv_32768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsv_32768/03_2026/7wsv_32768.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 S 77 5.16 5 C 10934 2.51 5 N 2555 2.21 5 O 2877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16443 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2349 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2349 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2349 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2349 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2349 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2349 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2349 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 3.50, per 1000 atoms: 0.21 Number of scatterers: 16443 At special positions: 0 Unit cell: (109.648, 109.648, 123.2, 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) S 77 16.00 O 2877 8.00 N 2555 7.00 C 10934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.04 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.04 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.04 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.04 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.04 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.04 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.04 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 713.0 milliseconds 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3990 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 7 sheets defined 69.6% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 33 through 61 Proline residue: A 46 - end of helix removed outlier: 3.817A pdb=" N SER A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE A 60 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 100 through 129 Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 158 removed outlier: 3.673A pdb=" N ALA A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.794A pdb=" N ASN A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 236 removed outlier: 4.061A pdb=" N LYS A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.011A pdb=" N ARG A 254 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 255 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 296 Proline residue: A 289 - end of helix removed outlier: 3.665A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 338 removed outlier: 3.824A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'B' and resid 33 through 61 Proline residue: B 46 - end of helix removed outlier: 3.816A pdb=" N SER B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE B 60 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 Processing helix chain 'B' and resid 100 through 129 Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 158 removed outlier: 3.672A pdb=" N ALA B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS B 158 " --> pdb=" O ILE B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.794A pdb=" N ASN B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 236 removed outlier: 4.060A pdb=" N LYS B 212 " --> pdb=" O ASN B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 4.011A pdb=" N ARG B 254 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN B 255 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 296 Proline residue: B 289 - end of helix removed outlier: 3.666A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 338 removed outlier: 3.824A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 356 Processing helix chain 'C' and resid 33 through 61 Proline residue: C 46 - end of helix removed outlier: 3.817A pdb=" N SER C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE C 60 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 100 through 129 Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 158 removed outlier: 3.672A pdb=" N ALA C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.794A pdb=" N ASN C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 236 removed outlier: 4.061A pdb=" N LYS C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 4.011A pdb=" N ARG C 254 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN C 255 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 296 Proline residue: C 289 - end of helix removed outlier: 3.666A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 338 removed outlier: 3.825A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 356 Processing helix chain 'D' and resid 33 through 61 Proline residue: D 46 - end of helix removed outlier: 3.816A pdb=" N SER D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 87 Processing helix chain 'D' and resid 100 through 129 Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 158 removed outlier: 3.672A pdb=" N ALA D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS D 158 " --> pdb=" O ILE D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.793A pdb=" N ASN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 236 removed outlier: 4.061A pdb=" N LYS D 212 " --> pdb=" O ASN D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 4.011A pdb=" N ARG D 254 " --> pdb=" O GLY D 251 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN D 255 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 296 Proline residue: D 289 - end of helix removed outlier: 3.666A pdb=" N PHE D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 338 removed outlier: 3.825A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 356 Processing helix chain 'E' and resid 33 through 61 Proline residue: E 46 - end of helix removed outlier: 3.816A pdb=" N SER E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE E 60 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 87 Processing helix chain 'E' and resid 100 through 129 Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 158 removed outlier: 3.673A pdb=" N ALA E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS E 158 " --> pdb=" O ILE E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.793A pdb=" N ASN E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER E 206 " --> pdb=" O THR E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 236 removed outlier: 4.060A pdb=" N LYS E 212 " --> pdb=" O ASN E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 255 removed outlier: 4.011A pdb=" N ARG E 254 " --> pdb=" O GLY E 251 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN E 255 " --> pdb=" O ILE E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 296 Proline residue: E 289 - end of helix removed outlier: 3.666A pdb=" N PHE E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 338 removed outlier: 3.824A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 356 Processing helix chain 'F' and resid 33 through 61 Proline residue: F 46 - end of helix removed outlier: 3.816A pdb=" N SER F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 87 Processing helix chain 'F' and resid 100 through 129 Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 158 removed outlier: 3.672A pdb=" N ALA F 157 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS F 158 " --> pdb=" O ILE F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.795A pdb=" N ASN F 205 " --> pdb=" O LYS F 201 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER F 206 " --> pdb=" O THR F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 236 removed outlier: 4.060A pdb=" N LYS F 212 " --> pdb=" O ASN F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 255 removed outlier: 4.011A pdb=" N ARG F 254 " --> pdb=" O GLY F 251 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN F 255 " --> pdb=" O ILE F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 296 Proline residue: F 289 - end of helix removed outlier: 3.665A pdb=" N PHE F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 338 removed outlier: 3.825A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 356 Processing helix chain 'G' and resid 33 through 61 Proline residue: G 46 - end of helix removed outlier: 3.817A pdb=" N SER G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE G 60 " --> pdb=" O GLN G 56 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 87 Processing helix chain 'G' and resid 100 through 129 Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 158 removed outlier: 3.673A pdb=" N ALA G 157 " --> pdb=" O ALA G 153 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS G 158 " --> pdb=" O ILE G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.794A pdb=" N ASN G 205 " --> pdb=" O LYS G 201 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER G 206 " --> pdb=" O THR G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 236 removed outlier: 4.060A pdb=" N LYS G 212 " --> pdb=" O ASN G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 255 removed outlier: 4.011A pdb=" N ARG G 254 " --> pdb=" O GLY G 251 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN G 255 " --> pdb=" O ILE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 296 Proline residue: G 289 - end of helix removed outlier: 3.666A pdb=" N PHE G 296 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 338 removed outlier: 3.825A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 356 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 3.591A pdb=" N PHE A 244 " --> pdb=" O CYS A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 removed outlier: 3.591A pdb=" N PHE B 244 " --> pdb=" O CYS B 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 removed outlier: 3.592A pdb=" N PHE C 244 " --> pdb=" O CYS C 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 removed outlier: 3.592A pdb=" N PHE D 244 " --> pdb=" O CYS D 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 removed outlier: 3.592A pdb=" N PHE E 244 " --> pdb=" O CYS E 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 removed outlier: 3.591A pdb=" N PHE F 244 " --> pdb=" O CYS F 265 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 removed outlier: 3.591A pdb=" N PHE G 244 " --> pdb=" O CYS G 265 " (cutoff:3.500A) 1022 hydrogen bonds defined for protein. 3024 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4897 1.35 - 1.47: 4119 1.47 - 1.59: 7700 1.59 - 1.71: 0 1.71 - 1.83: 91 Bond restraints: 16807 Sorted by residual: bond pdb=" CD GLU C 144 " pdb=" OE1 GLU C 144 " ideal model delta sigma weight residual 1.249 1.230 0.019 1.90e-02 2.77e+03 9.71e-01 bond pdb=" CA LEU C 318 " pdb=" CB LEU C 318 " ideal model delta sigma weight residual 1.527 1.552 -0.024 2.48e-02 1.63e+03 9.66e-01 bond pdb=" CA LEU G 318 " pdb=" CB LEU G 318 " ideal model delta sigma weight residual 1.527 1.551 -0.024 2.48e-02 1.63e+03 9.24e-01 bond pdb=" CA LEU E 318 " pdb=" CB LEU E 318 " ideal model delta sigma weight residual 1.527 1.551 -0.024 2.48e-02 1.63e+03 9.14e-01 bond pdb=" CA LEU F 318 " pdb=" CB LEU F 318 " ideal model delta sigma weight residual 1.527 1.551 -0.024 2.48e-02 1.63e+03 9.13e-01 ... (remaining 16802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 21942 1.57 - 3.15: 644 3.15 - 4.72: 96 4.72 - 6.30: 89 6.30 - 7.87: 28 Bond angle restraints: 22799 Sorted by residual: angle pdb=" CA LYS C 307 " pdb=" CB LYS C 307 " pdb=" CG LYS C 307 " ideal model delta sigma weight residual 114.10 120.96 -6.86 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CA LYS D 307 " pdb=" CB LYS D 307 " pdb=" CG LYS D 307 " ideal model delta sigma weight residual 114.10 120.95 -6.85 2.00e+00 2.50e-01 1.17e+01 angle pdb=" CA LYS A 307 " pdb=" CB LYS A 307 " pdb=" CG LYS A 307 " ideal model delta sigma weight residual 114.10 120.95 -6.85 2.00e+00 2.50e-01 1.17e+01 angle pdb=" CA LYS F 307 " pdb=" CB LYS F 307 " pdb=" CG LYS F 307 " ideal model delta sigma weight residual 114.10 120.94 -6.84 2.00e+00 2.50e-01 1.17e+01 angle pdb=" CA LYS G 307 " pdb=" CB LYS G 307 " pdb=" CG LYS G 307 " ideal model delta sigma weight residual 114.10 120.94 -6.84 2.00e+00 2.50e-01 1.17e+01 ... (remaining 22794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.29: 8912 14.29 - 28.59: 755 28.59 - 42.88: 350 42.88 - 57.18: 70 57.18 - 71.47: 14 Dihedral angle restraints: 10101 sinusoidal: 3976 harmonic: 6125 Sorted by residual: dihedral pdb=" CA ALA G 269 " pdb=" C ALA G 269 " pdb=" N VAL G 270 " pdb=" CA VAL G 270 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ALA B 269 " pdb=" C ALA B 269 " pdb=" N VAL B 270 " pdb=" CA VAL B 270 " ideal model delta harmonic sigma weight residual -180.00 -159.45 -20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA ALA E 269 " pdb=" C ALA E 269 " pdb=" N VAL E 270 " pdb=" CA VAL E 270 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 10098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1687 0.032 - 0.064: 649 0.064 - 0.095: 277 0.095 - 0.127: 82 0.127 - 0.159: 21 Chirality restraints: 2716 Sorted by residual: chirality pdb=" CA GLU G 144 " pdb=" N GLU G 144 " pdb=" C GLU G 144 " pdb=" CB GLU G 144 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA GLU D 144 " pdb=" N GLU D 144 " pdb=" C GLU D 144 " pdb=" CB GLU D 144 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA GLU C 144 " pdb=" N GLU C 144 " pdb=" C GLU C 144 " pdb=" CB GLU C 144 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 ... (remaining 2713 not shown) Planarity restraints: 2751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 123 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO A 124 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 123 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO D 124 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 124 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 124 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 123 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO G 124 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO G 124 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 124 " -0.022 5.00e-02 4.00e+02 ... (remaining 2748 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3923 2.79 - 3.32: 16765 3.32 - 3.85: 27275 3.85 - 4.37: 27251 4.37 - 4.90: 48664 Nonbonded interactions: 123878 Sorted by model distance: nonbonded pdb=" OD2 ASP F 138 " pdb=" OH TYR F 331 " model vdw 2.263 3.040 nonbonded pdb=" OD2 ASP G 138 " pdb=" OH TYR G 331 " model vdw 2.263 3.040 nonbonded pdb=" OD2 ASP C 138 " pdb=" OH TYR C 331 " model vdw 2.264 3.040 nonbonded pdb=" OD2 ASP D 138 " pdb=" OH TYR D 331 " model vdw 2.264 3.040 nonbonded pdb=" OD2 ASP A 138 " pdb=" OH TYR A 331 " model vdw 2.264 3.040 ... (remaining 123873 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: 0.04 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' } Set up NCS constraints Number of NCS constrained groups: 1 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' } 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: 0.200 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.880 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.003 0.047 16821 Z= 0.142 Angle : 0.740 7.869 22827 Z= 0.366 Chirality : 0.042 0.159 2716 Planarity : 0.004 0.038 2751 Dihedral : 13.526 71.473 6069 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.20), residues: 2009 helix: 1.66 (0.14), residues: 1407 sheet: -2.55 (0.45), residues: 84 loop : -2.37 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 152 TYR 0.019 0.001 TYR C 345 PHE 0.010 0.001 PHE F 273 TRP 0.011 0.002 TRP F 127 HIS 0.001 0.000 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00305 (16807) covalent geometry : angle 0.73907 (22799) SS BOND : bond 0.00337 ( 14) SS BOND : angle 1.16558 ( 28) hydrogen bonds : bond 0.06682 ( 1022) hydrogen bonds : angle 3.76853 ( 3024) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8485 (t80) cc_final: 0.7691 (t80) REVERT: A 140 LYS cc_start: 0.7065 (mmtt) cc_final: 0.6749 (mmtt) REVERT: A 143 MET cc_start: 0.8314 (ppp) cc_final: 0.7553 (ppp) REVERT: A 307 LYS cc_start: 0.8804 (tptp) cc_final: 0.8591 (tptp) REVERT: A 327 ASP cc_start: 0.7442 (m-30) cc_final: 0.7135 (m-30) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.0459 time to fit residues: 6.5661 Evaluate side-chains 101 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* 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 = 0.3876 r_free = 0.3876 target = 0.168024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.136822 restraints weight = 3967.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140778 restraints weight = 2615.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.143846 restraints weight = 1910.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.145998 restraints weight = 1493.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.147580 restraints weight = 1234.086| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16821 Z= 0.123 Angle : 0.601 6.908 22827 Z= 0.294 Chirality : 0.039 0.121 2716 Planarity : 0.004 0.035 2751 Dihedral : 3.565 17.296 2184 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.38 % Allowed : 4.15 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.19), residues: 2009 helix: 2.26 (0.14), residues: 1365 sheet: -2.71 (0.44), residues: 84 loop : -2.69 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 75 TYR 0.010 0.001 TYR B 345 PHE 0.014 0.001 PHE A 273 TRP 0.007 0.001 TRP G 127 HIS 0.001 0.000 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00284 (16807) covalent geometry : angle 0.60094 (22799) SS BOND : bond 0.00316 ( 14) SS BOND : angle 0.71113 ( 28) hydrogen bonds : bond 0.02867 ( 1022) hydrogen bonds : angle 3.44028 ( 3024) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8429 (t80) cc_final: 0.7722 (t80) REVERT: A 143 MET cc_start: 0.8311 (ppp) cc_final: 0.7892 (ppp) REVERT: A 339 ILE cc_start: 0.9005 (tt) cc_final: 0.8664 (tt) REVERT: A 345 TYR cc_start: 0.8057 (t80) cc_final: 0.7772 (t80) outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.0482 time to fit residues: 7.5654 Evaluate side-chains 102 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 182 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 177 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 158 optimal weight: 20.0000 chunk 197 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.161900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.130003 restraints weight = 3963.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.134034 restraints weight = 2588.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.136793 restraints weight = 1868.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.138781 restraints weight = 1472.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.140324 restraints weight = 1231.663| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16821 Z= 0.147 Angle : 0.639 6.802 22827 Z= 0.317 Chirality : 0.039 0.124 2716 Planarity : 0.003 0.033 2751 Dihedral : 3.598 16.596 2184 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 2009 helix: 2.36 (0.14), residues: 1372 sheet: -2.75 (0.47), residues: 84 loop : -2.58 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 75 TYR 0.013 0.001 TYR E 111 PHE 0.012 0.001 PHE F 72 TRP 0.006 0.001 TRP A 74 HIS 0.000 0.000 HIS C 106 Details of bonding type rmsd covalent geometry : bond 0.00335 (16807) covalent geometry : angle 0.63865 (22799) SS BOND : bond 0.00413 ( 14) SS BOND : angle 0.82641 ( 28) hydrogen bonds : bond 0.03210 ( 1022) hydrogen bonds : angle 3.45537 ( 3024) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: A 39 THR cc_start: 0.9408 (p) cc_final: 0.9172 (t) REVERT: A 56 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8245 (tm-30) REVERT: A 74 TRP cc_start: 0.7855 (t60) cc_final: 0.7608 (t60) REVERT: A 121 TYR cc_start: 0.8505 (t80) cc_final: 0.7858 (t80) REVERT: A 143 MET cc_start: 0.8367 (ppp) cc_final: 0.8027 (ppp) REVERT: A 220 THR cc_start: 0.9571 (m) cc_final: 0.9361 (m) REVERT: A 284 TYR cc_start: 0.9056 (m-80) cc_final: 0.8757 (m-80) REVERT: A 339 ILE cc_start: 0.9135 (tt) cc_final: 0.8849 (tt) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.0501 time to fit residues: 8.0596 Evaluate side-chains 109 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 111 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 92 optimal weight: 0.8980 chunk 192 optimal weight: 0.8980 chunk 57 optimal weight: 0.0060 chunk 30 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 157 optimal weight: 9.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.168118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.138591 restraints weight = 3923.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.142226 restraints weight = 2561.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144906 restraints weight = 1858.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.146873 restraints weight = 1463.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.148134 restraints weight = 1216.932| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16821 Z= 0.121 Angle : 0.668 7.663 22827 Z= 0.321 Chirality : 0.040 0.132 2716 Planarity : 0.004 0.034 2751 Dihedral : 3.788 19.303 2184 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.20), residues: 2009 helix: 2.27 (0.14), residues: 1372 sheet: -2.57 (0.50), residues: 84 loop : -2.51 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 254 TYR 0.013 0.001 TYR E 345 PHE 0.010 0.001 PHE G 334 TRP 0.009 0.001 TRP D 74 HIS 0.001 0.001 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00271 (16807) covalent geometry : angle 0.66267 (22799) SS BOND : bond 0.00285 ( 14) SS BOND : angle 2.43960 ( 28) hydrogen bonds : bond 0.02989 ( 1022) hydrogen bonds : angle 3.48702 ( 3024) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.086 Fit side-chains REVERT: A 39 THR cc_start: 0.9405 (p) cc_final: 0.9145 (t) REVERT: A 74 TRP cc_start: 0.7689 (t60) cc_final: 0.7313 (t60) REVERT: A 121 TYR cc_start: 0.8492 (t80) cc_final: 0.7825 (t80) REVERT: A 305 VAL cc_start: 0.7325 (t) cc_final: 0.7075 (t) REVERT: A 307 LYS cc_start: 0.8711 (tptp) cc_final: 0.8452 (tptp) REVERT: A 339 ILE cc_start: 0.9207 (tt) cc_final: 0.8913 (tt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0435 time to fit residues: 7.0565 Evaluate side-chains 109 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 0.1980 chunk 12 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.163623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.132441 restraints weight = 3965.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.136429 restraints weight = 2557.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.139120 restraints weight = 1844.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.141114 restraints weight = 1455.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.141966 restraints weight = 1228.241| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16821 Z= 0.153 Angle : 0.675 7.213 22827 Z= 0.334 Chirality : 0.041 0.152 2716 Planarity : 0.004 0.033 2751 Dihedral : 3.834 17.956 2184 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.20), residues: 2009 helix: 2.31 (0.14), residues: 1372 sheet: -1.18 (0.73), residues: 49 loop : -2.30 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 254 TYR 0.014 0.001 TYR F 111 PHE 0.008 0.001 PHE A 273 TRP 0.004 0.001 TRP D 74 HIS 0.000 0.000 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00359 (16807) covalent geometry : angle 0.67031 (22799) SS BOND : bond 0.00523 ( 14) SS BOND : angle 2.29608 ( 28) hydrogen bonds : bond 0.03355 ( 1022) hydrogen bonds : angle 3.56640 ( 3024) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.091 Fit side-chains REVERT: A 39 THR cc_start: 0.9397 (p) cc_final: 0.9140 (t) REVERT: A 56 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8290 (tp40) REVERT: A 74 TRP cc_start: 0.8001 (t60) cc_final: 0.7664 (t60) REVERT: A 121 TYR cc_start: 0.8516 (t80) cc_final: 0.7934 (t80) REVERT: A 220 THR cc_start: 0.9606 (m) cc_final: 0.9392 (m) REVERT: A 284 TYR cc_start: 0.9178 (m-80) cc_final: 0.8944 (m-80) REVERT: A 305 VAL cc_start: 0.7442 (t) cc_final: 0.6300 (t) REVERT: A 327 ASP cc_start: 0.7322 (m-30) cc_final: 0.7057 (m-30) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.0469 time to fit residues: 7.0776 Evaluate side-chains 108 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 116 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 168 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 chunk 187 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.162856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.132038 restraints weight = 4013.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.136130 restraints weight = 2556.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.138989 restraints weight = 1827.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.140905 restraints weight = 1426.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.141743 restraints weight = 1197.377| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16821 Z= 0.140 Angle : 0.684 6.816 22827 Z= 0.336 Chirality : 0.041 0.151 2716 Planarity : 0.004 0.033 2751 Dihedral : 3.887 19.240 2184 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.20), residues: 2009 helix: 2.30 (0.14), residues: 1372 sheet: -1.09 (0.73), residues: 49 loop : -2.25 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 29 TYR 0.013 0.001 TYR A 111 PHE 0.008 0.001 PHE C 273 TRP 0.003 0.001 TRP D 74 HIS 0.000 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00329 (16807) covalent geometry : angle 0.68108 (22799) SS BOND : bond 0.00604 ( 14) SS BOND : angle 1.98818 ( 28) hydrogen bonds : bond 0.03261 ( 1022) hydrogen bonds : angle 3.56031 ( 3024) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 39 THR cc_start: 0.9434 (p) cc_final: 0.9142 (t) REVERT: A 74 TRP cc_start: 0.8032 (t60) cc_final: 0.7733 (t60) REVERT: A 121 TYR cc_start: 0.8558 (t80) cc_final: 0.7939 (t80) REVERT: A 143 MET cc_start: 0.8695 (ptm) cc_final: 0.7137 (ppp) REVERT: A 144 GLU cc_start: 0.7713 (mp0) cc_final: 0.6993 (mp0) REVERT: A 220 THR cc_start: 0.9637 (m) cc_final: 0.9436 (m) REVERT: A 254 ARG cc_start: 0.8385 (mmm160) cc_final: 0.7960 (tpp80) REVERT: A 284 TYR cc_start: 0.9158 (m-80) cc_final: 0.8920 (m-80) REVERT: A 305 VAL cc_start: 0.7493 (t) cc_final: 0.6470 (t) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.0419 time to fit residues: 6.3731 Evaluate side-chains 107 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 25 optimal weight: 9.9990 chunk 182 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.162634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.132052 restraints weight = 4014.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.135959 restraints weight = 2561.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.138726 restraints weight = 1833.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140592 restraints weight = 1431.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.141294 restraints weight = 1198.104| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16821 Z= 0.159 Angle : 0.710 8.079 22827 Z= 0.343 Chirality : 0.042 0.135 2716 Planarity : 0.005 0.058 2751 Dihedral : 3.997 18.026 2184 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.20), residues: 2009 helix: 2.33 (0.14), residues: 1365 sheet: -1.06 (0.72), residues: 49 loop : -2.18 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 254 TYR 0.012 0.001 TYR D 111 PHE 0.013 0.001 PHE A 129 TRP 0.003 0.001 TRP C 85 HIS 0.001 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00377 (16807) covalent geometry : angle 0.70654 (22799) SS BOND : bond 0.00393 ( 14) SS BOND : angle 2.02145 ( 28) hydrogen bonds : bond 0.03471 ( 1022) hydrogen bonds : angle 3.61415 ( 3024) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: A 39 THR cc_start: 0.9425 (p) cc_final: 0.9127 (t) REVERT: A 56 GLN cc_start: 0.8569 (tp40) cc_final: 0.8358 (tp40) REVERT: A 74 TRP cc_start: 0.8047 (t60) cc_final: 0.7776 (t60) REVERT: A 121 TYR cc_start: 0.8614 (t80) cc_final: 0.7998 (t80) REVERT: A 140 LYS cc_start: 0.6595 (mtpp) cc_final: 0.5517 (mmtm) REVERT: A 143 MET cc_start: 0.8684 (ptm) cc_final: 0.7535 (ppp) REVERT: A 254 ARG cc_start: 0.8506 (mmm160) cc_final: 0.8193 (tpp80) REVERT: A 284 TYR cc_start: 0.9233 (m-80) cc_final: 0.8946 (m-80) REVERT: A 305 VAL cc_start: 0.7449 (t) cc_final: 0.6285 (t) REVERT: A 339 ILE cc_start: 0.9176 (tt) cc_final: 0.8940 (tt) REVERT: A 349 LYS cc_start: 0.8984 (mttm) cc_final: 0.8771 (mmtt) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0455 time to fit residues: 6.7886 Evaluate side-chains 106 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 198 optimal weight: 8.9990 chunk 125 optimal weight: 0.0770 chunk 88 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.159689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.129642 restraints weight = 3987.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.133551 restraints weight = 2551.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.136111 restraints weight = 1818.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.138014 restraints weight = 1418.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.139231 restraints weight = 1174.704| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16821 Z= 0.172 Angle : 0.730 7.388 22827 Z= 0.357 Chirality : 0.042 0.154 2716 Planarity : 0.005 0.050 2751 Dihedral : 4.143 17.867 2184 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.20), residues: 2009 helix: 2.12 (0.14), residues: 1365 sheet: -1.07 (0.69), residues: 49 loop : -2.15 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 254 TYR 0.013 0.001 TYR F 111 PHE 0.011 0.001 PHE D 129 TRP 0.003 0.001 TRP C 85 HIS 0.001 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00404 (16807) covalent geometry : angle 0.72660 (22799) SS BOND : bond 0.00439 ( 14) SS BOND : angle 2.02039 ( 28) hydrogen bonds : bond 0.03583 ( 1022) hydrogen bonds : angle 3.86678 ( 3024) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: A 39 THR cc_start: 0.9448 (p) cc_final: 0.9104 (t) REVERT: A 56 GLN cc_start: 0.8613 (tp40) cc_final: 0.8120 (tp40) REVERT: A 76 GLN cc_start: 0.8326 (mt0) cc_final: 0.8018 (mt0) REVERT: A 121 TYR cc_start: 0.8573 (t80) cc_final: 0.8039 (t80) REVERT: A 143 MET cc_start: 0.8739 (ptm) cc_final: 0.8163 (ppp) REVERT: A 254 ARG cc_start: 0.8575 (mmm160) cc_final: 0.8221 (tpp80) REVERT: A 305 VAL cc_start: 0.7544 (t) cc_final: 0.6293 (t) REVERT: A 339 ILE cc_start: 0.9226 (tt) cc_final: 0.8971 (tt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0465 time to fit residues: 6.8806 Evaluate side-chains 104 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 176 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 161 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 152 optimal weight: 0.0670 chunk 12 optimal weight: 6.9990 chunk 197 optimal weight: 0.0050 chunk 9 optimal weight: 0.2980 chunk 114 optimal weight: 8.9990 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.166760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135827 restraints weight = 3990.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140034 restraints weight = 2529.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.142907 restraints weight = 1800.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.144727 restraints weight = 1396.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.146163 restraints weight = 1165.523| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16821 Z= 0.127 Angle : 0.713 7.825 22827 Z= 0.337 Chirality : 0.042 0.150 2716 Planarity : 0.004 0.034 2751 Dihedral : 4.116 22.926 2184 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.20), residues: 2009 helix: 2.22 (0.14), residues: 1365 sheet: -2.61 (0.48), residues: 84 loop : -2.25 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 29 TYR 0.009 0.001 TYR B 331 PHE 0.010 0.001 PHE E 129 TRP 0.023 0.002 TRP C 74 HIS 0.003 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00281 (16807) covalent geometry : angle 0.71013 (22799) SS BOND : bond 0.00161 ( 14) SS BOND : angle 1.85165 ( 28) hydrogen bonds : bond 0.03108 ( 1022) hydrogen bonds : angle 3.72269 ( 3024) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 39 THR cc_start: 0.9386 (p) cc_final: 0.9100 (t) REVERT: A 56 GLN cc_start: 0.8605 (tp40) cc_final: 0.8098 (tp40) REVERT: A 121 TYR cc_start: 0.8610 (t80) cc_final: 0.7929 (t80) REVERT: A 143 MET cc_start: 0.8725 (ptm) cc_final: 0.7780 (ppp) REVERT: A 254 ARG cc_start: 0.8603 (mmm160) cc_final: 0.8198 (tpp80) REVERT: A 305 VAL cc_start: 0.7406 (t) cc_final: 0.6544 (t) REVERT: A 339 ILE cc_start: 0.9082 (tt) cc_final: 0.8857 (tt) REVERT: A 349 LYS cc_start: 0.9009 (mttm) cc_final: 0.8633 (mmtm) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.0473 time to fit residues: 7.1569 Evaluate side-chains 111 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 198 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 187 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.160232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.129793 restraints weight = 3989.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.133649 restraints weight = 2543.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.136368 restraints weight = 1823.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.138287 restraints weight = 1422.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.139526 restraints weight = 1182.290| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16821 Z= 0.176 Angle : 0.756 7.238 22827 Z= 0.367 Chirality : 0.044 0.167 2716 Planarity : 0.005 0.046 2751 Dihedral : 4.135 19.978 2184 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.20), residues: 2009 helix: 2.17 (0.14), residues: 1365 sheet: -2.89 (0.46), residues: 84 loop : -2.18 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 29 TYR 0.016 0.001 TYR A 111 PHE 0.017 0.001 PHE E 116 TRP 0.021 0.002 TRP F 74 HIS 0.001 0.000 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00418 (16807) covalent geometry : angle 0.75280 (22799) SS BOND : bond 0.00446 ( 14) SS BOND : angle 2.00902 ( 28) hydrogen bonds : bond 0.03575 ( 1022) hydrogen bonds : angle 3.87587 ( 3024) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8634 (tp40) cc_final: 0.8123 (tp40) REVERT: A 76 GLN cc_start: 0.8243 (mt0) cc_final: 0.7941 (mt0) REVERT: A 121 TYR cc_start: 0.8627 (t80) cc_final: 0.8026 (t80) REVERT: A 143 MET cc_start: 0.8724 (ptm) cc_final: 0.7754 (ppp) REVERT: A 220 THR cc_start: 0.9561 (m) cc_final: 0.9356 (m) REVERT: A 280 ASN cc_start: 0.9169 (t0) cc_final: 0.8517 (t0) REVERT: A 284 TYR cc_start: 0.9216 (m-80) cc_final: 0.8673 (m-80) REVERT: A 305 VAL cc_start: 0.7650 (t) cc_final: 0.6669 (t) REVERT: A 332 ASN cc_start: 0.9188 (m110) cc_final: 0.8852 (m110) REVERT: A 339 ILE cc_start: 0.9155 (tt) cc_final: 0.8921 (tt) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0426 time to fit residues: 6.4347 Evaluate side-chains 106 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 56 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 37 optimal weight: 0.0980 chunk 128 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.156138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.126203 restraints weight = 3861.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.130126 restraints weight = 2393.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.132899 restraints weight = 1685.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.134887 restraints weight = 1292.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.136146 restraints weight = 1060.438| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16821 Z= 0.151 Angle : 0.748 7.126 22827 Z= 0.360 Chirality : 0.043 0.162 2716 Planarity : 0.006 0.075 2751 Dihedral : 4.156 21.650 2184 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.20), residues: 2009 helix: 2.26 (0.14), residues: 1365 sheet: -3.31 (0.42), residues: 84 loop : -2.08 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 254 TYR 0.013 0.001 TYR F 111 PHE 0.015 0.001 PHE A 235 TRP 0.024 0.002 TRP A 74 HIS 0.000 0.000 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00364 (16807) covalent geometry : angle 0.74533 (22799) SS BOND : bond 0.00392 ( 14) SS BOND : angle 1.84841 ( 28) hydrogen bonds : bond 0.03485 ( 1022) hydrogen bonds : angle 3.77004 ( 3024) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1089.28 seconds wall clock time: 20 minutes 10.05 seconds (1210.05 seconds total)