Starting phenix.real_space_refine on Fri Jul 3 09:06:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jp9_36472/07_2026/8jp9_36472.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jp9_36472/07_2026/8jp9_36472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jp9_36472/07_2026/8jp9_36472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jp9_36472/07_2026/8jp9_36472.map" model { file = "/net/cci-nas-00/data/ceres_data/8jp9_36472/07_2026/8jp9_36472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jp9_36472/07_2026/8jp9_36472.cif" } resolution = 3.37 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= 0.012 sd= 0.113 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: 6 Type Number sf(0) Gaussians Ca 16 9.91 5 Zn 4 6.06 5 S 36 5.16 5 C 8466 2.51 5 N 2346 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13500 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2619 Classifications: {'peptide': 326} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 309} Chain: "B" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2517 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 297} Chain breaks: 1 Chain: "C" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "D" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "E" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2619 Classifications: {'peptide': 326} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 309} Chain: "F" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2517 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 297} Chain breaks: 1 Chain: "G" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "H" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 2.22, per 1000 atoms: 0.16 Number of scatterers: 13500 At special positions: 0 Unit cell: (120.516, 116.532, 128.484, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Ca 16 19.99 S 36 16.00 O 2632 8.00 N 2346 7.00 C 8466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS E 190 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS F 190 " - pdb=" SG CYS F 230 " 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: 0.80 Conformation dependent library (CDL) restraints added in 379.8 milliseconds 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 16 sheets defined 32.7% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.646A pdb=" N ASP A 181 " --> pdb=" O HIS A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.728A pdb=" N LYS A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 309 removed outlier: 4.095A pdb=" N LYS A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 362 removed outlier: 3.799A pdb=" N ASN A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 51 Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.816A pdb=" N ASP B 181 " --> pdb=" O HIS B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 309 removed outlier: 3.714A pdb=" N LYS B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 361 removed outlier: 3.589A pdb=" N ARG B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.512A pdb=" N ILE C 52 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 81 removed outlier: 3.508A pdb=" N ASP C 81 " --> pdb=" O PHE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 98 Processing helix chain 'C' and resid 113 through 129 Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 68 through 81 Processing helix chain 'D' and resid 89 through 98 Processing helix chain 'D' and resid 113 through 128 Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'E' and resid 48 through 51 Processing helix chain 'E' and resid 177 through 181 removed outlier: 3.556A pdb=" N ASN E 180 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP E 181 " --> pdb=" O HIS E 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 177 through 181' Processing helix chain 'E' and resid 282 through 309 removed outlier: 4.102A pdb=" N LYS E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS E 302 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU E 306 " --> pdb=" O LYS E 302 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE E 307 " --> pdb=" O LYS E 303 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 362 removed outlier: 3.818A pdb=" N ASN E 339 " --> pdb=" O PHE E 335 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG E 340 " --> pdb=" O GLU E 336 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE E 341 " --> pdb=" O GLY E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 51 Processing helix chain 'F' and resid 177 through 181 removed outlier: 3.577A pdb=" N ASN F 180 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP F 181 " --> pdb=" O HIS F 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 177 through 181' Processing helix chain 'F' and resid 282 through 309 removed outlier: 3.709A pdb=" N LYS F 286 " --> pdb=" O SER F 282 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU F 306 " --> pdb=" O LYS F 302 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE F 307 " --> pdb=" O LYS F 303 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 361 removed outlier: 3.581A pdb=" N ARG F 361 " --> pdb=" O ASP F 357 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 47 Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.514A pdb=" N ILE G 52 " --> pdb=" O ASP G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 81 Processing helix chain 'G' and resid 89 through 98 removed outlier: 3.553A pdb=" N THR G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 129 Processing helix chain 'G' and resid 137 through 142 Processing helix chain 'H' and resid 42 through 47 Processing helix chain 'H' and resid 48 through 57 Processing helix chain 'H' and resid 68 through 81 Processing helix chain 'H' and resid 89 through 98 Processing helix chain 'H' and resid 113 through 128 Processing helix chain 'H' and resid 137 through 142 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.946A pdb=" N HIS A 257 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 46 removed outlier: 5.593A pdb=" N HIS A 257 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N THR A 113 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL A 259 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG A 111 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE A 216 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE A 229 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 71 removed outlier: 5.855A pdb=" N PHE A 244 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 71 removed outlier: 5.855A pdb=" N PHE A 244 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 249 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY A 122 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 123 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL A 147 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA A 188 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 43 through 46 removed outlier: 6.927A pdb=" N HIS B 257 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 53 removed outlier: 5.558A pdb=" N HIS B 257 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N THR B 113 " --> pdb=" O HIS B 257 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL B 259 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ARG B 111 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ILE B 216 " --> pdb=" O PHE B 229 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N PHE B 229 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 67 through 71 removed outlier: 5.855A pdb=" N PHE B 244 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 67 through 71 removed outlier: 5.855A pdb=" N PHE B 244 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 249 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY B 122 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 123 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA B 188 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 43 through 46 removed outlier: 7.037A pdb=" N HIS E 257 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 43 through 46 removed outlier: 5.588A pdb=" N HIS E 257 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N THR E 113 " --> pdb=" O HIS E 257 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL E 259 " --> pdb=" O ARG E 111 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG E 111 " --> pdb=" O VAL E 259 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER E 261 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE E 216 " --> pdb=" O PHE E 229 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N PHE E 229 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.814A pdb=" N PHE E 244 " --> pdb=" O THR E 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.814A pdb=" N PHE E 244 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA E 249 " --> pdb=" O GLY E 122 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY E 122 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU E 123 " --> pdb=" O PHE E 151 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA E 188 " --> pdb=" O ILE E 167 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 43 through 46 removed outlier: 7.030A pdb=" N HIS F 257 " --> pdb=" O VAL F 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 43 through 46 removed outlier: 5.547A pdb=" N HIS F 257 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR F 113 " --> pdb=" O HIS F 257 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL F 259 " --> pdb=" O ARG F 111 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG F 111 " --> pdb=" O VAL F 259 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE F 216 " --> pdb=" O PHE F 229 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE F 229 " --> pdb=" O ILE F 216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 67 through 71 removed outlier: 5.771A pdb=" N PHE F 244 " --> pdb=" O THR F 95 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 67 through 71 removed outlier: 5.771A pdb=" N PHE F 244 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA F 249 " --> pdb=" O GLY F 122 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY F 122 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU F 123 " --> pdb=" O PHE F 151 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA F 188 " --> pdb=" O ILE F 167 " (cutoff:3.500A) 653 hydrogen bonds defined for protein. 1836 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: 1.77 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4624 1.34 - 1.46: 2940 1.46 - 1.58: 6166 1.58 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 13794 Sorted by residual: bond pdb=" N LEU H 72 " pdb=" CA LEU H 72 " ideal model delta sigma weight residual 1.459 1.486 -0.028 1.28e-02 6.10e+03 4.68e+00 bond pdb=" N LEU D 72 " pdb=" CA LEU D 72 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.52e+00 bond pdb=" N VAL A 58 " pdb=" CA VAL A 58 " ideal model delta sigma weight residual 1.459 1.446 0.013 1.25e-02 6.40e+03 1.04e+00 bond pdb=" CA LEU H 72 " pdb=" C LEU H 72 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.35e-02 5.49e+03 6.87e-01 bond pdb=" CB PHE A 52 " pdb=" CG PHE A 52 " ideal model delta sigma weight residual 1.502 1.521 -0.019 2.30e-02 1.89e+03 6.82e-01 ... (remaining 13789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 18328 1.68 - 3.36: 278 3.36 - 5.04: 19 5.04 - 6.72: 3 6.72 - 8.40: 2 Bond angle restraints: 18630 Sorted by residual: angle pdb=" N LEU D 72 " pdb=" CA LEU D 72 " pdb=" C LEU D 72 " ideal model delta sigma weight residual 111.28 108.52 2.76 1.09e+00 8.42e-01 6.39e+00 angle pdb=" CA LEU D 72 " pdb=" C LEU D 72 " pdb=" O LEU D 72 " ideal model delta sigma weight residual 120.55 117.94 2.61 1.06e+00 8.90e-01 6.07e+00 angle pdb=" CA LEU G 117 " pdb=" CB LEU G 117 " pdb=" CG LEU G 117 " ideal model delta sigma weight residual 116.30 124.70 -8.40 3.50e+00 8.16e-02 5.76e+00 angle pdb=" CA LEU C 117 " pdb=" CB LEU C 117 " pdb=" CG LEU C 117 " ideal model delta sigma weight residual 116.30 124.61 -8.31 3.50e+00 8.16e-02 5.63e+00 angle pdb=" CA GLN B 173 " pdb=" CB GLN B 173 " pdb=" CG GLN B 173 " ideal model delta sigma weight residual 114.10 118.42 -4.32 2.00e+00 2.50e-01 4.67e+00 ... (remaining 18625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 7033 15.26 - 30.52: 847 30.52 - 45.78: 238 45.78 - 61.03: 80 61.03 - 76.29: 50 Dihedral angle restraints: 8248 sinusoidal: 3432 harmonic: 4816 Sorted by residual: dihedral pdb=" CA TRP B 126 " pdb=" C TRP B 126 " pdb=" N TYR B 127 " pdb=" CA TYR B 127 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CB CYS F 190 " pdb=" SG CYS F 190 " pdb=" SG CYS F 230 " pdb=" CB CYS F 230 " ideal model delta sinusoidal sigma weight residual -86.00 -118.21 32.21 1 1.00e+01 1.00e-02 1.48e+01 dihedral pdb=" CB CYS B 190 " pdb=" SG CYS B 190 " pdb=" SG CYS B 230 " pdb=" CB CYS B 230 " ideal model delta sinusoidal sigma weight residual -86.00 -117.56 31.56 1 1.00e+01 1.00e-02 1.42e+01 ... (remaining 8245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1059 0.029 - 0.059: 547 0.059 - 0.088: 172 0.088 - 0.117: 107 0.117 - 0.147: 31 Chirality restraints: 1916 Sorted by residual: chirality pdb=" CA VAL A 93 " pdb=" N VAL A 93 " pdb=" C VAL A 93 " pdb=" CB VAL A 93 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA VAL F 93 " pdb=" N VAL F 93 " pdb=" C VAL F 93 " pdb=" CB VAL F 93 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE B 238 " pdb=" N ILE B 238 " pdb=" C ILE B 238 " pdb=" CB ILE B 238 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1913 not shown) Planarity restraints: 2510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 54 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO E 55 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 55 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 55 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 128 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C ALA A 128 " 0.024 2.00e-02 2.50e+03 pdb=" O ALA A 128 " -0.009 2.00e-02 2.50e+03 pdb=" N GLU A 129 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 68 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.59e+00 pdb=" N PRO H 69 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO H 69 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 69 " -0.018 5.00e-02 4.00e+02 ... (remaining 2507 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 37 2.31 - 2.96: 5957 2.96 - 3.61: 19536 3.61 - 4.25: 31040 4.25 - 4.90: 52691 Nonbonded interactions: 109261 Sorted by model distance: nonbonded pdb=" OD1 ASP B 155 " pdb=" OD1 ASN B 162 " model vdw 1.666 3.040 nonbonded pdb=" OD1 ASP F 155 " pdb=" OD1 ASN F 162 " model vdw 1.714 3.040 nonbonded pdb=" OD1 ASP A 155 " pdb=" OD1 ASN A 162 " model vdw 1.732 3.040 nonbonded pdb=" OD1 ASP E 155 " pdb=" OD1 ASN E 162 " model vdw 1.741 3.040 nonbonded pdb=" NE2 HIS G 99 " pdb="ZN ZN G 703 " model vdw 1.995 2.310 ... (remaining 109256 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 42 through 312 or resid 324 through 365 or resid 601 throu \ gh 602)) selection = chain 'B' selection = (chain 'E' and (resid 42 through 312 or resid 324 through 365 or resid 601 throu \ gh 602)) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 individual isotropic 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.170 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 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 0.029 13798 Z= 0.145 Angle : 0.508 8.403 18638 Z= 0.280 Chirality : 0.044 0.147 1916 Planarity : 0.004 0.037 2510 Dihedral : 16.109 76.292 5140 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.14 % Allowed : 10.65 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.23 (0.20), residues: 1650 helix: 1.18 (0.23), residues: 490 sheet: 0.17 (0.28), residues: 362 loop : -1.17 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 45 TYR 0.013 0.001 TYR H 76 PHE 0.015 0.001 PHE B 52 TRP 0.017 0.002 TRP E 126 HIS 0.006 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (13794) covalent geometry : angle 0.50674 / 0.28 (18630) SS BOND : bond 0.00129 / 0.08 ( 4) SS BOND : angle 1.60901 / 0.82 ( 8) hydrogen bonds : bond 0.13244 / 8.83 ( 605) hydrogen bonds : angle 5.41680 / 3.79 ( 1836) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 339 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8479 (mptt) cc_final: 0.7395 (tptt) REVERT: A 297 GLN cc_start: 0.9044 (mt0) cc_final: 0.8263 (mt0) REVERT: B 295 HIS cc_start: 0.8988 (t70) cc_final: 0.8784 (t70) REVERT: B 340 ARG cc_start: 0.7883 (mtm-85) cc_final: 0.7669 (mtp85) REVERT: C 48 ASP cc_start: 0.8511 (t0) cc_final: 0.8035 (t0) REVERT: C 71 GLU cc_start: 0.8821 (tp30) cc_final: 0.8476 (tp30) REVERT: C 132 ASN cc_start: 0.9064 (t0) cc_final: 0.8694 (t0) REVERT: D 72 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8577 (pp) REVERT: D 89 ASP cc_start: 0.8349 (p0) cc_final: 0.7988 (p0) REVERT: D 115 ASP cc_start: 0.8289 (m-30) cc_final: 0.7304 (m-30) REVERT: D 127 ASP cc_start: 0.8473 (m-30) cc_final: 0.8160 (m-30) REVERT: E 48 TYR cc_start: 0.8530 (p90) cc_final: 0.8316 (p90) REVERT: E 85 SER cc_start: 0.8828 (t) cc_final: 0.8496 (t) REVERT: E 118 ILE cc_start: 0.8402 (mm) cc_final: 0.7855 (mm) REVERT: E 137 VAL cc_start: 0.7941 (t) cc_final: 0.7538 (p) REVERT: E 207 TYR cc_start: 0.7641 (t80) cc_final: 0.7378 (t80) REVERT: E 330 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7243 (pt0) REVERT: E 351 GLN cc_start: 0.7902 (tt0) cc_final: 0.7639 (tm-30) REVERT: F 215 MET cc_start: 0.8741 (mtp) cc_final: 0.8383 (mtm) REVERT: G 48 ASP cc_start: 0.8729 (t0) cc_final: 0.8202 (m-30) REVERT: G 138 TYR cc_start: 0.8572 (t80) cc_final: 0.8205 (t80) REVERT: H 53 MET cc_start: 0.9149 (mmm) cc_final: 0.8905 (mmt) REVERT: H 75 HIS cc_start: 0.8561 (m-70) cc_final: 0.8249 (m-70) REVERT: H 77 PHE cc_start: 0.8262 (t80) cc_final: 0.8044 (t80) outliers start: 2 outliers final: 0 residues processed: 341 average time/residue: 0.1129 time to fit residues: 54.2067 Evaluate side-chains 230 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 GLN A 156 ASN A 162 ASN A 351 GLN B 162 ASN B 175 HIS B 178 HIS B 191 GLN B 196 ASN B 241 GLN B 333 GLN B 342 HIS C 49 GLN C 80 HIS D 70 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN E 175 HIS E 298 GLN E 351 GLN F 156 ASN F 162 ASN F 241 GLN F 333 GLN G 70 GLN G 80 HIS ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.164795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.109063 restraints weight = 19764.735| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.95 r_work: 0.3154 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13798 Z= 0.163 Angle : 0.559 9.800 18638 Z= 0.298 Chirality : 0.045 0.142 1916 Planarity : 0.003 0.031 2510 Dihedral : 4.148 24.752 1790 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.49 % Allowed : 13.49 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.09 (0.20), residues: 1650 helix: 1.56 (0.24), residues: 490 sheet: 0.14 (0.28), residues: 348 loop : -1.19 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 117 TYR 0.030 0.002 TYR B 208 PHE 0.020 0.002 PHE A 296 TRP 0.016 0.001 TRP E 126 HIS 0.017 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (13794) covalent geometry : angle 0.55834 / 0.30 (18630) SS BOND : bond 0.00242 / 0.13 ( 4) SS BOND : angle 1.66299 / 0.92 ( 8) hydrogen bonds : bond 0.03784 / 2.51 ( 605) hydrogen bonds : angle 4.36855 / 3.06 ( 1836) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8588 (mptt) cc_final: 0.7472 (tptt) REVERT: A 192 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8634 (mmt-90) REVERT: A 226 ASP cc_start: 0.8486 (t70) cc_final: 0.7564 (t0) REVERT: A 297 GLN cc_start: 0.8711 (mt0) cc_final: 0.8454 (mt0) REVERT: B 289 TYR cc_start: 0.9009 (m-80) cc_final: 0.8754 (m-10) REVERT: B 355 ILE cc_start: 0.7803 (tt) cc_final: 0.7572 (tt) REVERT: C 70 GLN cc_start: 0.9190 (pp30) cc_final: 0.8524 (pp30) REVERT: C 75 HIS cc_start: 0.8895 (OUTLIER) cc_final: 0.8514 (t-90) REVERT: C 132 ASN cc_start: 0.9077 (t0) cc_final: 0.8645 (t0) REVERT: D 89 ASP cc_start: 0.8062 (p0) cc_final: 0.7762 (p0) REVERT: D 129 ASP cc_start: 0.7084 (t0) cc_final: 0.6360 (t0) REVERT: E 48 TYR cc_start: 0.8682 (p90) cc_final: 0.8415 (p90) REVERT: E 118 ILE cc_start: 0.8438 (mm) cc_final: 0.8038 (mm) REVERT: E 137 VAL cc_start: 0.8152 (t) cc_final: 0.7804 (p) REVERT: F 215 MET cc_start: 0.8666 (mtp) cc_final: 0.8346 (mtm) REVERT: G 48 ASP cc_start: 0.8667 (t0) cc_final: 0.8228 (m-30) REVERT: G 49 GLN cc_start: 0.8954 (pp30) cc_final: 0.8734 (pp30) REVERT: G 52 ILE cc_start: 0.9333 (tp) cc_final: 0.8932 (tt) REVERT: G 73 GLN cc_start: 0.8254 (pp30) cc_final: 0.8005 (pp30) REVERT: G 135 TYR cc_start: 0.8125 (m-80) cc_final: 0.7864 (m-80) REVERT: G 140 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7395 (tt0) REVERT: H 75 HIS cc_start: 0.9117 (m-70) cc_final: 0.8413 (m-70) REVERT: H 117 LEU cc_start: 0.8203 (tp) cc_final: 0.7947 (tp) REVERT: H 126 ARG cc_start: 0.8587 (ttp-110) cc_final: 0.8179 (ptp-110) REVERT: H 132 ASN cc_start: 0.7583 (t0) cc_final: 0.7221 (t0) outliers start: 36 outliers final: 20 residues processed: 285 average time/residue: 0.1034 time to fit residues: 42.3006 Evaluate side-chains 252 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 67 MET Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 101 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 152 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN B 162 ASN B 191 GLN C 86 ASN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 HIS F 191 GLN G 70 GLN G 80 HIS G 86 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.158326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.097553 restraints weight = 19871.343| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.16 r_work: 0.2969 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13798 Z= 0.169 Angle : 0.559 9.036 18638 Z= 0.295 Chirality : 0.045 0.155 1916 Planarity : 0.004 0.074 2510 Dihedral : 4.235 22.018 1788 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.04 % Allowed : 14.25 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.19 (0.20), residues: 1650 helix: 1.42 (0.24), residues: 502 sheet: -0.01 (0.28), residues: 348 loop : -1.21 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 126 TYR 0.025 0.002 TYR B 208 PHE 0.024 0.002 PHE H 77 TRP 0.016 0.001 TRP E 126 HIS 0.013 0.001 HIS G 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (13794) covalent geometry : angle 0.55805 / 0.29 (18630) SS BOND : bond 0.00381 / 0.19 ( 4) SS BOND : angle 1.79661 / 0.92 ( 8) hydrogen bonds : bond 0.03722 / 2.41 ( 605) hydrogen bonds : angle 4.28211 / 3.00 ( 1836) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 245 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8666 (mptt) cc_final: 0.7463 (tptt) REVERT: A 226 ASP cc_start: 0.8527 (t70) cc_final: 0.7557 (t0) REVERT: A 297 GLN cc_start: 0.8794 (mt0) cc_final: 0.8578 (mt0) REVERT: B 289 TYR cc_start: 0.9089 (m-80) cc_final: 0.8857 (m-10) REVERT: B 355 ILE cc_start: 0.7679 (tt) cc_final: 0.7443 (tt) REVERT: C 71 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8737 (mp0) REVERT: C 75 HIS cc_start: 0.8938 (OUTLIER) cc_final: 0.8543 (t-90) REVERT: C 132 ASN cc_start: 0.9108 (t0) cc_final: 0.8682 (t0) REVERT: D 67 MET cc_start: 0.8578 (mmp) cc_final: 0.7225 (ttm) REVERT: D 71 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9193 (mp0) REVERT: D 89 ASP cc_start: 0.8097 (p0) cc_final: 0.7535 (p0) REVERT: D 92 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7927 (mt-10) REVERT: D 129 ASP cc_start: 0.7305 (t0) cc_final: 0.7036 (t0) REVERT: E 48 TYR cc_start: 0.8755 (p90) cc_final: 0.8504 (p90) REVERT: E 118 ILE cc_start: 0.8467 (mm) cc_final: 0.8166 (mm) REVERT: E 137 VAL cc_start: 0.7920 (t) cc_final: 0.7619 (p) REVERT: E 207 TYR cc_start: 0.8070 (t80) cc_final: 0.7774 (t80) REVERT: E 354 MET cc_start: 0.8280 (tpp) cc_final: 0.8050 (ttm) REVERT: F 191 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8621 (tp40) REVERT: F 215 MET cc_start: 0.8801 (mtp) cc_final: 0.8450 (mtm) REVERT: G 48 ASP cc_start: 0.8736 (t0) cc_final: 0.8241 (m-30) REVERT: G 49 GLN cc_start: 0.9044 (pp30) cc_final: 0.8690 (pp30) REVERT: G 71 GLU cc_start: 0.9118 (tt0) cc_final: 0.8490 (tm-30) REVERT: G 73 GLN cc_start: 0.8502 (pp30) cc_final: 0.8194 (pp30) REVERT: G 140 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7224 (mt-10) REVERT: H 75 HIS cc_start: 0.9151 (m-70) cc_final: 0.8456 (m-70) REVERT: H 112 MET cc_start: 0.8665 (tpp) cc_final: 0.8287 (tpp) REVERT: H 116 GLU cc_start: 0.8744 (mp0) cc_final: 0.8491 (mp0) REVERT: H 132 ASN cc_start: 0.7826 (t0) cc_final: 0.7149 (t0) outliers start: 44 outliers final: 26 residues processed: 273 average time/residue: 0.1077 time to fit residues: 42.8735 Evaluate side-chains 254 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 191 GLN Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 101 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 71 optimal weight: 0.3980 chunk 68 optimal weight: 0.9990 chunk 162 optimal weight: 50.0000 chunk 69 optimal weight: 30.0000 chunk 135 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.0670 chunk 5 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 191 GLN C 49 GLN C 86 ASN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN E 175 HIS E 257 HIS G 70 GLN G 86 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.161887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.100339 restraints weight = 19863.077| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.86 r_work: 0.3045 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13798 Z= 0.107 Angle : 0.533 8.910 18638 Z= 0.281 Chirality : 0.043 0.159 1916 Planarity : 0.003 0.052 2510 Dihedral : 4.109 21.208 1788 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.21 % Allowed : 16.53 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.13 (0.20), residues: 1650 helix: 1.41 (0.23), residues: 502 sheet: 0.34 (0.30), residues: 308 loop : -1.22 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 117 TYR 0.023 0.001 TYR B 208 PHE 0.028 0.001 PHE H 77 TRP 0.011 0.001 TRP E 126 HIS 0.007 0.001 HIS G 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (13794) covalent geometry : angle 0.53186 / 0.28 (18630) SS BOND : bond 0.00265 / 0.15 ( 4) SS BOND : angle 1.58832 / 0.86 ( 8) hydrogen bonds : bond 0.03279 / 2.13 ( 605) hydrogen bonds : angle 4.06397 / 2.84 ( 1836) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8623 (mptt) cc_final: 0.7411 (tptt) REVERT: A 226 ASP cc_start: 0.8444 (t70) cc_final: 0.7477 (t0) REVERT: A 350 ARG cc_start: 0.7654 (mtm-85) cc_final: 0.7309 (mtm-85) REVERT: B 215 MET cc_start: 0.8857 (mtp) cc_final: 0.8543 (mtp) REVERT: C 62 LYS cc_start: 0.8777 (tptt) cc_final: 0.8545 (tptt) REVERT: C 70 GLN cc_start: 0.9109 (pm20) cc_final: 0.8811 (pm20) REVERT: C 71 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8792 (mp0) REVERT: C 75 HIS cc_start: 0.8796 (OUTLIER) cc_final: 0.8496 (t-90) REVERT: C 132 ASN cc_start: 0.9102 (t0) cc_final: 0.8670 (t0) REVERT: D 53 MET cc_start: 0.9466 (mmp) cc_final: 0.9126 (mmm) REVERT: D 68 SER cc_start: 0.9549 (t) cc_final: 0.9295 (t) REVERT: D 89 ASP cc_start: 0.8023 (p0) cc_final: 0.7602 (p0) REVERT: D 92 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7694 (mt-10) REVERT: D 112 MET cc_start: 0.8714 (tmm) cc_final: 0.8455 (tmm) REVERT: D 115 ASP cc_start: 0.8130 (m-30) cc_final: 0.7692 (m-30) REVERT: D 127 ASP cc_start: 0.8793 (m-30) cc_final: 0.8427 (m-30) REVERT: D 129 ASP cc_start: 0.7152 (t0) cc_final: 0.6836 (t0) REVERT: D 137 ASP cc_start: 0.8418 (t0) cc_final: 0.6951 (p0) REVERT: E 48 TYR cc_start: 0.8676 (p90) cc_final: 0.8390 (p90) REVERT: E 118 ILE cc_start: 0.8467 (mm) cc_final: 0.8185 (mm) REVERT: E 137 VAL cc_start: 0.7863 (t) cc_final: 0.7592 (p) REVERT: E 207 TYR cc_start: 0.8004 (t80) cc_final: 0.7777 (t80) REVERT: E 354 MET cc_start: 0.8281 (tpp) cc_final: 0.8066 (ttm) REVERT: F 215 MET cc_start: 0.8731 (mtp) cc_final: 0.8392 (mtm) REVERT: G 53 MET cc_start: 0.9015 (mmt) cc_final: 0.8715 (mmm) REVERT: G 71 GLU cc_start: 0.9109 (tt0) cc_final: 0.8493 (tm-30) REVERT: G 132 ASN cc_start: 0.8640 (t0) cc_final: 0.7549 (t0) REVERT: H 75 HIS cc_start: 0.9106 (m-70) cc_final: 0.8400 (m-70) REVERT: H 86 ASN cc_start: 0.8885 (t0) cc_final: 0.7805 (t0) REVERT: H 132 ASN cc_start: 0.7870 (t0) cc_final: 0.7454 (t0) REVERT: H 135 TYR cc_start: 0.8352 (m-10) cc_final: 0.8064 (m-10) outliers start: 32 outliers final: 20 residues processed: 268 average time/residue: 0.1076 time to fit residues: 42.5554 Evaluate side-chains 257 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 101 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 40 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 165 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 GLN B 191 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 HIS G 70 GLN G 86 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.159857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.099084 restraints weight = 19898.604| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.15 r_work: 0.2990 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13798 Z= 0.149 Angle : 0.555 8.911 18638 Z= 0.293 Chirality : 0.045 0.266 1916 Planarity : 0.003 0.049 2510 Dihedral : 4.127 22.034 1788 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.90 % Allowed : 16.87 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.13 (0.20), residues: 1650 helix: 1.37 (0.23), residues: 498 sheet: 0.17 (0.28), residues: 344 loop : -1.15 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 126 TYR 0.030 0.001 TYR G 138 PHE 0.028 0.001 PHE H 77 TRP 0.012 0.001 TRP E 126 HIS 0.006 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (13794) covalent geometry : angle 0.55372 / 0.29 (18630) SS BOND : bond 0.00414 / 0.26 ( 4) SS BOND : angle 1.65123 / 0.88 ( 8) hydrogen bonds : bond 0.03499 / 2.24 ( 605) hydrogen bonds : angle 4.17932 / 2.92 ( 1836) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 240 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8645 (mptt) cc_final: 0.7394 (tptt) REVERT: B 215 MET cc_start: 0.8915 (mtp) cc_final: 0.8644 (mtp) REVERT: B 306 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8295 (pm20) REVERT: C 62 LYS cc_start: 0.8962 (tptt) cc_final: 0.8760 (tptt) REVERT: C 70 GLN cc_start: 0.9098 (pm20) cc_final: 0.8677 (pm20) REVERT: C 71 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8895 (mp0) REVERT: C 75 HIS cc_start: 0.8783 (OUTLIER) cc_final: 0.8470 (t-90) REVERT: C 126 ARG cc_start: 0.8847 (ttp80) cc_final: 0.8617 (ttp80) REVERT: C 132 ASN cc_start: 0.9126 (t0) cc_final: 0.8697 (t0) REVERT: D 53 MET cc_start: 0.9573 (mmp) cc_final: 0.9186 (mmm) REVERT: D 71 GLU cc_start: 0.9079 (mp0) cc_final: 0.8850 (mp0) REVERT: D 89 ASP cc_start: 0.8081 (p0) cc_final: 0.7697 (p0) REVERT: D 112 MET cc_start: 0.8638 (tmm) cc_final: 0.8218 (tmm) REVERT: D 115 ASP cc_start: 0.8039 (m-30) cc_final: 0.7818 (m-30) REVERT: D 127 ASP cc_start: 0.8794 (m-30) cc_final: 0.8467 (m-30) REVERT: D 129 ASP cc_start: 0.7367 (t0) cc_final: 0.7151 (t0) REVERT: D 137 ASP cc_start: 0.8477 (t0) cc_final: 0.7039 (p0) REVERT: E 48 TYR cc_start: 0.8739 (p90) cc_final: 0.8469 (p90) REVERT: E 118 ILE cc_start: 0.8460 (mm) cc_final: 0.8211 (mm) REVERT: E 137 VAL cc_start: 0.7920 (t) cc_final: 0.7639 (p) REVERT: E 207 TYR cc_start: 0.8086 (t80) cc_final: 0.7804 (t80) REVERT: E 354 MET cc_start: 0.8269 (tpp) cc_final: 0.8049 (ttm) REVERT: F 215 MET cc_start: 0.8808 (mtp) cc_final: 0.8457 (mtm) REVERT: G 71 GLU cc_start: 0.9161 (tt0) cc_final: 0.8546 (tm-30) REVERT: G 132 ASN cc_start: 0.8696 (t0) cc_final: 0.7603 (t0) REVERT: H 75 HIS cc_start: 0.9129 (m-70) cc_final: 0.8413 (m-70) REVERT: H 86 ASN cc_start: 0.8837 (t0) cc_final: 0.7961 (t0) REVERT: H 126 ARG cc_start: 0.8820 (ttp-110) cc_final: 0.8499 (ptp-110) REVERT: H 132 ASN cc_start: 0.7941 (t0) cc_final: 0.7224 (t0) outliers start: 42 outliers final: 32 residues processed: 266 average time/residue: 0.1093 time to fit residues: 42.6926 Evaluate side-chains 265 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 101 HIS Chi-restraints excluded: chain H residue 113 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 139 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 162 optimal weight: 50.0000 chunk 10 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 191 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 HIS F 79 GLN G 70 GLN G 86 ASN H 55 HIS H 80 HIS H 101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.159495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.096252 restraints weight = 19552.130| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.25 r_work: 0.2950 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13798 Z= 0.176 Angle : 0.576 9.587 18638 Z= 0.306 Chirality : 0.046 0.165 1916 Planarity : 0.004 0.050 2510 Dihedral : 4.238 22.807 1788 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.53 % Allowed : 17.36 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.22 (0.20), residues: 1650 helix: 1.25 (0.23), residues: 502 sheet: 0.06 (0.28), residues: 344 loop : -1.15 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 350 TYR 0.031 0.002 TYR G 138 PHE 0.029 0.002 PHE H 77 TRP 0.014 0.001 TRP E 126 HIS 0.005 0.001 HIS D 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (13794) covalent geometry : angle 0.57544 / 0.31 (18630) SS BOND : bond 0.00186 / 0.10 ( 4) SS BOND : angle 1.66860 / 0.90 ( 8) hydrogen bonds : bond 0.03597 / 2.27 ( 605) hydrogen bonds : angle 4.27886 / 3.00 ( 1836) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 233 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8656 (mptt) cc_final: 0.7407 (tptt) REVERT: B 306 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8271 (pm20) REVERT: C 48 ASP cc_start: 0.8256 (t0) cc_final: 0.7919 (t70) REVERT: C 62 LYS cc_start: 0.9095 (tptt) cc_final: 0.8885 (tptt) REVERT: C 70 GLN cc_start: 0.9089 (pm20) cc_final: 0.8562 (pm20) REVERT: C 71 GLU cc_start: 0.9247 (mt-10) cc_final: 0.9042 (mp0) REVERT: C 75 HIS cc_start: 0.8781 (OUTLIER) cc_final: 0.8470 (t-90) REVERT: C 126 ARG cc_start: 0.8870 (ttp80) cc_final: 0.8665 (ttp80) REVERT: C 132 ASN cc_start: 0.9153 (t0) cc_final: 0.8735 (t0) REVERT: D 53 MET cc_start: 0.9601 (mmp) cc_final: 0.9216 (mmp) REVERT: D 89 ASP cc_start: 0.8287 (p0) cc_final: 0.8045 (p0) REVERT: D 112 MET cc_start: 0.8626 (tmm) cc_final: 0.8243 (tmm) REVERT: D 115 ASP cc_start: 0.8197 (m-30) cc_final: 0.7901 (m-30) REVERT: D 127 ASP cc_start: 0.8888 (m-30) cc_final: 0.8573 (m-30) REVERT: D 129 ASP cc_start: 0.7548 (t0) cc_final: 0.7207 (t70) REVERT: E 48 TYR cc_start: 0.8778 (p90) cc_final: 0.8533 (p90) REVERT: E 137 VAL cc_start: 0.8000 (t) cc_final: 0.7706 (p) REVERT: E 207 TYR cc_start: 0.8089 (t80) cc_final: 0.7802 (t80) REVERT: E 354 MET cc_start: 0.8247 (tpp) cc_final: 0.8022 (ttm) REVERT: F 215 MET cc_start: 0.8873 (mtp) cc_final: 0.8519 (mtm) REVERT: G 71 GLU cc_start: 0.9177 (tt0) cc_final: 0.8606 (tm-30) REVERT: G 86 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8232 (t0) REVERT: G 112 MET cc_start: 0.8457 (tmm) cc_final: 0.8156 (tmm) REVERT: G 132 ASN cc_start: 0.8789 (t0) cc_final: 0.7710 (t0) REVERT: G 140 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7075 (mt-10) REVERT: H 75 HIS cc_start: 0.9123 (m-70) cc_final: 0.8334 (m-70) REVERT: H 86 ASN cc_start: 0.8937 (t0) cc_final: 0.8111 (t0) REVERT: H 126 ARG cc_start: 0.8904 (ttp-110) cc_final: 0.8567 (ptp-110) REVERT: H 132 ASN cc_start: 0.8018 (t0) cc_final: 0.7338 (t0) outliers start: 51 outliers final: 38 residues processed: 264 average time/residue: 0.1048 time to fit residues: 40.7949 Evaluate side-chains 260 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 80 HIS Chi-restraints excluded: chain H residue 101 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 150 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 152 optimal weight: 0.0370 chunk 58 optimal weight: 7.9990 chunk 4 optimal weight: 0.2980 chunk 144 optimal weight: 0.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 HIS A 297 GLN B 191 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN G 49 GLN G 86 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 HIS ** H 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.160913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.098357 restraints weight = 19383.633| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.92 r_work: 0.3015 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13798 Z= 0.116 Angle : 0.569 10.537 18638 Z= 0.301 Chirality : 0.045 0.213 1916 Planarity : 0.003 0.043 2510 Dihedral : 4.156 22.436 1788 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.11 % Allowed : 18.46 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.19 (0.20), residues: 1650 helix: 1.15 (0.23), residues: 512 sheet: 0.18 (0.29), residues: 344 loop : -1.12 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 126 TYR 0.027 0.001 TYR C 138 PHE 0.027 0.001 PHE H 77 TRP 0.012 0.001 TRP E 126 HIS 0.012 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (13794) covalent geometry : angle 0.56814 / 0.30 (18630) SS BOND : bond 0.00233 / 0.12 ( 4) SS BOND : angle 1.58781 / 0.87 ( 8) hydrogen bonds : bond 0.03407 / 2.15 ( 605) hydrogen bonds : angle 4.19070 / 2.94 ( 1836) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 235 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8617 (mptt) cc_final: 0.7380 (tptt) REVERT: B 306 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8207 (pm20) REVERT: C 48 ASP cc_start: 0.8211 (t0) cc_final: 0.7859 (t70) REVERT: C 70 GLN cc_start: 0.9078 (pm20) cc_final: 0.8557 (pm20) REVERT: C 75 HIS cc_start: 0.8725 (OUTLIER) cc_final: 0.8405 (t-90) REVERT: C 132 ASN cc_start: 0.9138 (t0) cc_final: 0.8711 (t0) REVERT: D 53 MET cc_start: 0.9590 (mmp) cc_final: 0.9231 (mmp) REVERT: D 70 GLN cc_start: 0.9013 (pm20) cc_final: 0.8810 (pm20) REVERT: D 112 MET cc_start: 0.8519 (tmm) cc_final: 0.8135 (tmm) REVERT: D 115 ASP cc_start: 0.8118 (m-30) cc_final: 0.7857 (m-30) REVERT: D 127 ASP cc_start: 0.8827 (m-30) cc_final: 0.8492 (m-30) REVERT: D 137 ASP cc_start: 0.8467 (t0) cc_final: 0.7107 (p0) REVERT: E 48 TYR cc_start: 0.8705 (p90) cc_final: 0.8414 (p90) REVERT: E 207 TYR cc_start: 0.7991 (t80) cc_final: 0.7749 (t80) REVERT: E 291 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8768 (pm20) REVERT: E 354 MET cc_start: 0.8227 (tpp) cc_final: 0.8005 (ttm) REVERT: F 215 MET cc_start: 0.8795 (mtp) cc_final: 0.8451 (mtm) REVERT: G 71 GLU cc_start: 0.9090 (tt0) cc_final: 0.8617 (tm-30) REVERT: G 112 MET cc_start: 0.8467 (tmm) cc_final: 0.8157 (tmm) REVERT: G 132 ASN cc_start: 0.8762 (t0) cc_final: 0.7678 (t0) REVERT: G 140 GLU cc_start: 0.7807 (mt-10) cc_final: 0.6721 (mt-10) REVERT: H 75 HIS cc_start: 0.9037 (m-70) cc_final: 0.8314 (m-70) REVERT: H 85 ASN cc_start: 0.8865 (p0) cc_final: 0.8454 (p0) REVERT: H 86 ASN cc_start: 0.8971 (t0) cc_final: 0.8383 (t0) REVERT: H 126 ARG cc_start: 0.8894 (ttp-110) cc_final: 0.8593 (ptp-110) REVERT: H 132 ASN cc_start: 0.7972 (t0) cc_final: 0.7292 (t0) outliers start: 45 outliers final: 34 residues processed: 262 average time/residue: 0.1088 time to fit residues: 41.8024 Evaluate side-chains 262 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 225 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 80 HIS Chi-restraints excluded: chain H residue 101 HIS Chi-restraints excluded: chain H residue 113 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 191 GLN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN H 73 GLN H 80 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.158773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.095965 restraints weight = 19309.070| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.90 r_work: 0.2969 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13798 Z= 0.197 Angle : 0.615 10.348 18638 Z= 0.327 Chirality : 0.047 0.163 1916 Planarity : 0.004 0.045 2510 Dihedral : 4.300 23.425 1788 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.04 % Allowed : 19.85 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.34 (0.20), residues: 1650 helix: 0.98 (0.23), residues: 514 sheet: -0.01 (0.29), residues: 348 loop : -1.12 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 126 TYR 0.022 0.002 TYR B 208 PHE 0.024 0.002 PHE H 77 TRP 0.014 0.001 TRP E 126 HIS 0.016 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (13794) covalent geometry : angle 0.61421 / 0.33 (18630) SS BOND : bond 0.00194 / 0.11 ( 4) SS BOND : angle 1.93312 / 0.97 ( 8) hydrogen bonds : bond 0.03728 / 2.34 ( 605) hydrogen bonds : angle 4.40470 / 3.10 ( 1836) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 221 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8663 (mptt) cc_final: 0.7393 (tptt) REVERT: A 297 GLN cc_start: 0.8651 (mp10) cc_final: 0.8387 (mp10) REVERT: B 207 TYR cc_start: 0.9380 (t80) cc_final: 0.8932 (t80) REVERT: B 289 TYR cc_start: 0.8946 (m-10) cc_final: 0.8722 (m-10) REVERT: C 48 ASP cc_start: 0.8266 (t0) cc_final: 0.7906 (t70) REVERT: C 62 LYS cc_start: 0.8769 (tptt) cc_final: 0.8485 (tptt) REVERT: C 75 HIS cc_start: 0.8822 (OUTLIER) cc_final: 0.8402 (t-90) REVERT: C 86 ASN cc_start: 0.8753 (m110) cc_final: 0.8525 (t0) REVERT: C 132 ASN cc_start: 0.9157 (t0) cc_final: 0.8752 (t0) REVERT: D 53 MET cc_start: 0.9609 (mmp) cc_final: 0.9265 (mmp) REVERT: D 112 MET cc_start: 0.8554 (tmm) cc_final: 0.8097 (tmm) REVERT: E 48 TYR cc_start: 0.8755 (p90) cc_final: 0.8523 (p90) REVERT: E 207 TYR cc_start: 0.8055 (t80) cc_final: 0.7797 (t80) REVERT: E 354 MET cc_start: 0.8260 (tpp) cc_final: 0.8024 (ttm) REVERT: F 215 MET cc_start: 0.8795 (mtp) cc_final: 0.8429 (mtm) REVERT: G 71 GLU cc_start: 0.9088 (tt0) cc_final: 0.8585 (tm-30) REVERT: G 86 ASN cc_start: 0.8409 (m-40) cc_final: 0.8145 (t0) REVERT: G 112 MET cc_start: 0.8534 (tmm) cc_final: 0.8214 (tmm) REVERT: G 132 ASN cc_start: 0.8821 (t0) cc_final: 0.7808 (t0) REVERT: H 75 HIS cc_start: 0.8994 (m-70) cc_final: 0.8316 (m-70) REVERT: H 86 ASN cc_start: 0.9039 (t0) cc_final: 0.8347 (t0) REVERT: H 126 ARG cc_start: 0.8917 (ttp-110) cc_final: 0.8616 (ptp-110) REVERT: H 132 ASN cc_start: 0.8022 (t0) cc_final: 0.7305 (t0) outliers start: 44 outliers final: 40 residues processed: 246 average time/residue: 0.1082 time to fit residues: 38.7190 Evaluate side-chains 253 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 212 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain E residue 362 TYR Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 80 HIS Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 101 HIS Chi-restraints excluded: chain H residue 113 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 52 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 GLN B 191 GLN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 HIS H 73 GLN H 80 HIS ** H 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.159454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.098283 restraints weight = 19877.282| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.83 r_work: 0.3021 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13798 Z= 0.123 Angle : 0.604 11.813 18638 Z= 0.317 Chirality : 0.045 0.169 1916 Planarity : 0.004 0.070 2510 Dihedral : 4.206 22.920 1788 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.90 % Allowed : 20.26 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.24 (0.20), residues: 1650 helix: 1.01 (0.23), residues: 512 sheet: 0.15 (0.29), residues: 344 loop : -1.06 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 126 TYR 0.021 0.001 TYR B 208 PHE 0.024 0.001 PHE H 77 TRP 0.013 0.001 TRP F 126 HIS 0.019 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (13794) covalent geometry : angle 0.60287 / 0.32 (18630) SS BOND : bond 0.00218 / 0.12 ( 4) SS BOND : angle 1.80445 / 0.91 ( 8) hydrogen bonds : bond 0.03423 / 2.14 ( 605) hydrogen bonds : angle 4.24657 / 2.98 ( 1836) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 225 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8657 (mptt) cc_final: 0.7429 (tptt) REVERT: B 207 TYR cc_start: 0.9360 (t80) cc_final: 0.8906 (t80) REVERT: B 215 MET cc_start: 0.8888 (mtp) cc_final: 0.8618 (mtp) REVERT: C 48 ASP cc_start: 0.8218 (t0) cc_final: 0.7856 (t70) REVERT: C 75 HIS cc_start: 0.8752 (OUTLIER) cc_final: 0.8331 (t-90) REVERT: C 86 ASN cc_start: 0.8847 (m110) cc_final: 0.8580 (t0) REVERT: C 93 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8220 (mm) REVERT: C 132 ASN cc_start: 0.9139 (t0) cc_final: 0.8736 (t0) REVERT: D 53 MET cc_start: 0.9614 (mmp) cc_final: 0.9282 (mmp) REVERT: D 70 GLN cc_start: 0.9000 (pm20) cc_final: 0.8798 (pm20) REVERT: D 112 MET cc_start: 0.8590 (tmm) cc_final: 0.8150 (tmm) REVERT: D 115 ASP cc_start: 0.8132 (m-30) cc_final: 0.7868 (m-30) REVERT: D 132 ASN cc_start: 0.8830 (t0) cc_final: 0.8552 (t0) REVERT: E 48 TYR cc_start: 0.8702 (p90) cc_final: 0.8427 (p90) REVERT: E 352 LEU cc_start: 0.8015 (tp) cc_final: 0.7597 (tt) REVERT: F 215 MET cc_start: 0.8749 (mtp) cc_final: 0.8422 (mtm) REVERT: G 62 LYS cc_start: 0.8276 (tptt) cc_final: 0.7917 (mtmm) REVERT: G 71 GLU cc_start: 0.9076 (tt0) cc_final: 0.8746 (pt0) REVERT: G 112 MET cc_start: 0.8465 (tmm) cc_final: 0.8158 (tmm) REVERT: G 132 ASN cc_start: 0.8804 (t0) cc_final: 0.7745 (t0) REVERT: G 140 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6250 (mt-10) REVERT: H 75 HIS cc_start: 0.8979 (m-70) cc_final: 0.8303 (m-70) REVERT: H 86 ASN cc_start: 0.9088 (t0) cc_final: 0.8328 (t0) REVERT: H 126 ARG cc_start: 0.8881 (ttp-110) cc_final: 0.8596 (ptp-110) REVERT: H 132 ASN cc_start: 0.7970 (t0) cc_final: 0.7436 (t0) outliers start: 42 outliers final: 36 residues processed: 251 average time/residue: 0.1165 time to fit residues: 42.6473 Evaluate side-chains 257 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 219 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain E residue 362 TYR Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 80 HIS Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 101 HIS Chi-restraints excluded: chain H residue 113 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 59 optimal weight: 0.0470 chunk 29 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 GLN B 191 GLN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.157899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.096835 restraints weight = 19954.062| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.82 r_work: 0.2992 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13798 Z= 0.178 Angle : 0.647 12.559 18638 Z= 0.340 Chirality : 0.046 0.166 1916 Planarity : 0.004 0.057 2510 Dihedral : 4.263 23.205 1788 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.70 % Allowed : 20.54 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.33 (0.20), residues: 1650 helix: 0.93 (0.23), residues: 510 sheet: 0.05 (0.29), residues: 348 loop : -1.09 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 360 TYR 0.024 0.002 TYR G 76 PHE 0.027 0.002 PHE H 77 TRP 0.013 0.001 TRP E 126 HIS 0.008 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (13794) covalent geometry : angle 0.64628 / 0.34 (18630) SS BOND : bond 0.00191 / 0.10 ( 4) SS BOND : angle 1.88190 / 0.95 ( 8) hydrogen bonds : bond 0.03681 / 2.30 ( 605) hydrogen bonds : angle 4.33903 / 3.04 ( 1836) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8674 (mptt) cc_final: 0.7436 (tptt) REVERT: B 207 TYR cc_start: 0.9412 (t80) cc_final: 0.8930 (t80) REVERT: B 289 TYR cc_start: 0.8976 (m-10) cc_final: 0.8748 (m-10) REVERT: C 48 ASP cc_start: 0.8233 (t0) cc_final: 0.7879 (t70) REVERT: C 75 HIS cc_start: 0.8742 (OUTLIER) cc_final: 0.8348 (t-90) REVERT: C 86 ASN cc_start: 0.8825 (m110) cc_final: 0.8569 (t0) REVERT: C 93 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8244 (mm) REVERT: C 132 ASN cc_start: 0.9149 (t0) cc_final: 0.8755 (t0) REVERT: D 53 MET cc_start: 0.9592 (mmp) cc_final: 0.9269 (mmp) REVERT: D 112 MET cc_start: 0.8600 (tmm) cc_final: 0.8153 (tmm) REVERT: D 115 ASP cc_start: 0.8175 (m-30) cc_final: 0.7949 (m-30) REVERT: D 132 ASN cc_start: 0.8885 (t0) cc_final: 0.8624 (t0) REVERT: E 48 TYR cc_start: 0.8723 (p90) cc_final: 0.8473 (p90) REVERT: E 192 ARG cc_start: 0.8244 (ttm110) cc_final: 0.7889 (mmt180) REVERT: F 215 MET cc_start: 0.8705 (mtp) cc_final: 0.8380 (mtm) REVERT: G 112 MET cc_start: 0.8480 (tmm) cc_final: 0.8153 (tmm) REVERT: G 132 ASN cc_start: 0.8836 (t0) cc_final: 0.7811 (t0) REVERT: H 75 HIS cc_start: 0.8988 (m-70) cc_final: 0.8308 (m-70) REVERT: H 126 ARG cc_start: 0.8885 (ttp-110) cc_final: 0.8594 (ptp-110) REVERT: H 132 ASN cc_start: 0.7993 (t0) cc_final: 0.7500 (t0) outliers start: 39 outliers final: 33 residues processed: 241 average time/residue: 0.1171 time to fit residues: 41.2743 Evaluate side-chains 250 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain E residue 362 TYR Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 80 HIS Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 101 HIS Chi-restraints excluded: chain H residue 113 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 20 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 0.0060 chunk 67 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 71 optimal weight: 0.0470 chunk 164 optimal weight: 2.9990 overall best weight: 1.1898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 GLN B 191 GLN C 49 GLN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 HIS ** E 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN H 55 HIS H 73 GLN H 80 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.159262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.099000 restraints weight = 19993.254| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.06 r_work: 0.3001 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13798 Z= 0.137 Angle : 0.642 12.055 18638 Z= 0.336 Chirality : 0.045 0.196 1916 Planarity : 0.004 0.054 2510 Dihedral : 4.210 23.010 1788 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.63 % Allowed : 20.75 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.24 (0.20), residues: 1650 helix: 0.99 (0.23), residues: 508 sheet: 0.15 (0.29), residues: 344 loop : -1.05 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 360 TYR 0.027 0.001 TYR E 207 PHE 0.027 0.001 PHE H 77 TRP 0.012 0.001 TRP E 126 HIS 0.006 0.001 HIS D 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (13794) covalent geometry : angle 0.64153 / 0.34 (18630) SS BOND : bond 0.00214 / 0.11 ( 4) SS BOND : angle 1.80997 / 0.92 ( 8) hydrogen bonds : bond 0.03496 / 2.19 ( 605) hydrogen bonds : angle 4.27090 / 3.00 ( 1836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3174.44 seconds wall clock time: 55 minutes 2.22 seconds (3302.22 seconds total)