Starting phenix.real_space_refine on Sat Aug 23 16:24:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jp9_36472/08_2025/8jp9_36472.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jp9_36472/08_2025/8jp9_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jp9_36472/08_2025/8jp9_36472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jp9_36472/08_2025/8jp9_36472.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jp9_36472/08_2025/8jp9_36472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jp9_36472/08_2025/8jp9_36472.map" } 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-2.0-5787/lib/python3.9/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, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.67, per 1000 atoms: 0.20 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: 0.82 Conformation dependent library (CDL) restraints added in 479.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.49 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: 1.93 Time building geometry restraints manager: 1.13 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.160 Find NCS groups from input model: 0.250 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 aren 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 covalent geometry : bond 0.00310 (13794) covalent geometry : angle 0.50674 (18630) SS BOND : bond 0.00129 ( 4) SS BOND : angle 1.60901 ( 8) hydrogen bonds : bond 0.13244 ( 605) hydrogen bonds : angle 5.41680 ( 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 : 0.348 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: 0.8036 (t0) REVERT: C 71 GLU cc_start: 0.8821 (tp30) cc_final: 0.8475 (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: 0.8576 (pp) REVERT: D 89 ASP cc_start: 0.8350 (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: 0.1206 time to fit residues: 57.0963 Evaluate side-chains 231 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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: 7.9990 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... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 351 GLN 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 43 HIS E 175 HIS E 298 GLN E 351 GLN F 191 GLN 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.164574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109469 restraints weight = 19908.504| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.89 r_work: 0.3143 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2087 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= 0.166 Angle : 0.560 9.301 18638 Z= 0.298 Chirality : 0.044 0.142 1916 Planarity : 0.003 0.030 2510 Dihedral : 4.140 25.537 1790 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.70 % Allowed : 13.55 % Favored : 83.75 % 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 aren not related in a simple way. whole: -0.09 (0.20), residues: 1650 helix: 1.54 (0.24), residues: 490 sheet: 0.13 (0.28), residues: 348 loop : -1.18 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 126 TYR 0.029 0.002 TYR B 208 PHE 0.018 0.002 PHE B 52 TRP 0.015 0.001 TRP E 126 HIS 0.019 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00372 (13794) covalent geometry : angle 0.55913 (18630) SS BOND : bond 0.00221 ( 4) SS BOND : angle 1.65702 ( 8) hydrogen bonds : bond 0.03833 ( 605) hydrogen bonds : angle 4.38363 ( 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 302 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 263 time to evaluate : 0.373 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: 0.8616 (mptt) cc_final: 0.7558 (tptt) REVERT: A 192 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8631 (mmt-90) REVERT: A 226 ASP cc_start: 0.8501 (t70) cc_final: 0.7592 (t0) REVERT: A 297 GLN cc_start: 0.8692 (mt0) cc_final: 0.8439 (mt0) REVERT: B 289 TYR cc_start: 0.9023 (m-80) cc_final: 0.8766 (m-10) REVERT: B 355 ILE cc_start: 0.7799 (tt) cc_final: 0.7565 (tt) REVERT: C 70 GLN cc_start: 0.9109 (pp30) cc_final: 0.8400 (pp30) REVERT: C 75 HIS cc_start: 0.8949 (OUTLIER) cc_final: 0.8555 (t-90) REVERT: C 132 ASN cc_start: 0.9073 (t0) cc_final: 0.8639 (t0) REVERT: D 89 ASP cc_start: 0.8238 (p0) cc_final: 0.8001 (p0) REVERT: D 129 ASP cc_start: 0.7062 (t0) cc_final: 0.6545 (t0) REVERT: E 48 TYR cc_start: 0.8671 (p90) cc_final: 0.8394 (p90) REVERT: E 79 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8632 (pt0) REVERT: E 118 ILE cc_start: 0.8440 (mm) cc_final: 0.8040 (mm) REVERT: E 137 VAL cc_start: 0.8103 (t) cc_final: 0.7778 (p) REVERT: F 215 MET cc_start: 0.8656 (mtp) cc_final: 0.8341 (mtm) REVERT: G 48 ASP cc_start: 0.8662 (t0) cc_final: 0.8223 (m-30) REVERT: G 49 GLN cc_start: 0.9003 (pp30) cc_final: 0.8786 (pp30) REVERT: G 52 ILE cc_start: 0.9327 (tp) cc_final: 0.8913 (tt) REVERT: G 73 GLN cc_start: 0.8270 (pp30) cc_final: 0.8035 (pp30) REVERT: G 135 TYR cc_start: 0.7643 (m-80) cc_final: 0.7363 (m-80) REVERT: G 140 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7188 (tt0) REVERT: H 75 HIS cc_start: 0.9111 (m-70) cc_final: 0.8403 (m-70) REVERT: H 117 LEU cc_start: 0.8198 (tp) cc_final: 0.7952 (tp) REVERT: H 126 ARG cc_start: 0.8571 (ttp-110) cc_final: 0.8175 (ptp-110) REVERT: H 132 ASN cc_start: 0.7500 (t0) cc_final: 0.7121 (t0) outliers start: 39 outliers final: 20 residues processed: 287 average time/residue: 0.1058 time to fit residues: 43.1828 Evaluate side-chains 251 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 79 GLN 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: 3.9990 chunk 45 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 164 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 191 GLN C 49 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.156772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.094729 restraints weight = 19959.180| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.08 r_work: 0.2937 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13798 Z= 0.223 Angle : 0.597 9.242 18638 Z= 0.315 Chirality : 0.047 0.204 1916 Planarity : 0.004 0.036 2510 Dihedral : 4.354 22.747 1788 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.39 % Allowed : 14.45 % Favored : 82.16 % 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 aren not related in a simple way. whole: -0.30 (0.20), residues: 1650 helix: 1.44 (0.24), residues: 492 sheet: -0.34 (0.28), residues: 366 loop : -1.18 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 126 TYR 0.025 0.002 TYR B 208 PHE 0.025 0.002 PHE H 77 TRP 0.018 0.002 TRP E 126 HIS 0.016 0.001 HIS G 80 Details of bonding type rmsd covalent geometry : bond 0.00522 (13794) covalent geometry : angle 0.59641 (18630) SS BOND : bond 0.00253 ( 4) SS BOND : angle 1.82441 ( 8) hydrogen bonds : bond 0.03970 ( 605) hydrogen bonds : angle 4.42917 ( 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: 49 poor density : 240 time to evaluate : 0.522 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: 0.8725 (mptt) cc_final: 0.7556 (tptt) REVERT: A 297 GLN cc_start: 0.8865 (mt0) cc_final: 0.8599 (mt0) REVERT: A 350 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7494 (mtm-85) REVERT: B 289 TYR cc_start: 0.9130 (m-80) cc_final: 0.8895 (m-10) REVERT: B 355 ILE cc_start: 0.7660 (tt) cc_final: 0.7435 (tt) REVERT: C 57 GLU cc_start: 0.9272 (pt0) cc_final: 0.9010 (pt0) REVERT: C 71 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8738 (mp0) REVERT: C 75 HIS cc_start: 0.8888 (OUTLIER) cc_final: 0.8684 (t-90) REVERT: C 132 ASN cc_start: 0.9133 (t0) cc_final: 0.8676 (t0) REVERT: D 71 GLU cc_start: 0.9421 (mt-10) cc_final: 0.9203 (mp0) REVERT: D 129 ASP cc_start: 0.7237 (t0) cc_final: 0.6493 (t0) REVERT: D 131 ASN cc_start: 0.8192 (p0) cc_final: 0.7946 (p0) REVERT: E 118 ILE cc_start: 0.8523 (mm) cc_final: 0.8236 (mm) REVERT: E 207 TYR cc_start: 0.8144 (t80) cc_final: 0.7815 (t80) REVERT: G 48 ASP cc_start: 0.8735 (t0) cc_final: 0.8251 (m-30) REVERT: G 49 GLN cc_start: 0.9041 (pp30) cc_final: 0.8697 (pp30) REVERT: G 71 GLU cc_start: 0.9127 (tt0) cc_final: 0.8496 (tm-30) REVERT: G 73 GLN cc_start: 0.8468 (pp30) cc_final: 0.8246 (pp30) REVERT: G 140 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7158 (tt0) REVERT: H 75 HIS cc_start: 0.9153 (m-70) cc_final: 0.8463 (m-70) REVERT: H 86 ASN cc_start: 0.8836 (t0) cc_final: 0.7923 (t0) REVERT: H 112 MET cc_start: 0.8646 (tpp) cc_final: 0.8272 (tpp) REVERT: H 116 GLU cc_start: 0.8739 (mp0) cc_final: 0.8474 (mp0) REVERT: H 132 ASN cc_start: 0.7867 (t0) cc_final: 0.7200 (t0) outliers start: 49 outliers final: 32 residues processed: 271 average time/residue: 0.1105 time to fit residues: 43.4892 Evaluate side-chains 257 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 A residue 311 HIS 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 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 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 79 GLN 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 G residue 89 ASP 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: 0.9980 chunk 68 optimal weight: 7.9990 chunk 162 optimal weight: 0.0980 chunk 69 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.0670 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS B 162 ASN B 191 GLN C 49 GLN C 86 ASN ** 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 80 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 = 0.4036 r_free = 0.4036 target = 0.159329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098203 restraints weight = 19713.304| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.83 r_work: 0.3018 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 13798 Z= 0.111 Angle : 0.544 9.478 18638 Z= 0.287 Chirality : 0.044 0.160 1916 Planarity : 0.004 0.075 2510 Dihedral : 4.176 21.894 1788 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.07 % Allowed : 16.53 % Favored : 81.40 % 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 aren not related in a simple way. whole: -0.21 (0.20), residues: 1650 helix: 1.36 (0.24), residues: 492 sheet: 0.22 (0.30), residues: 308 loop : -1.21 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 350 TYR 0.023 0.001 TYR B 208 PHE 0.030 0.001 PHE A 296 TRP 0.012 0.001 TRP F 126 HIS 0.012 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00243 (13794) covalent geometry : angle 0.54296 (18630) SS BOND : bond 0.00324 ( 4) SS BOND : angle 1.59893 ( 8) hydrogen bonds : bond 0.03459 ( 605) hydrogen bonds : angle 4.19095 ( 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 276 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 0.407 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: A 159 LYS cc_start: 0.8635 (mptt) cc_final: 0.7517 (tptt) REVERT: A 226 ASP cc_start: 0.8512 (t70) cc_final: 0.7546 (t0) REVERT: B 295 HIS cc_start: 0.8847 (m90) cc_final: 0.8641 (m90) REVERT: C 57 GLU cc_start: 0.9218 (pt0) cc_final: 0.8892 (pt0) REVERT: C 62 LYS cc_start: 0.8811 (tptt) cc_final: 0.8572 (tptt) REVERT: C 71 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8886 (mp0) REVERT: C 132 ASN cc_start: 0.9122 (t0) cc_final: 0.8705 (t0) REVERT: D 53 MET cc_start: 0.9464 (mmp) cc_final: 0.9112 (mmm) REVERT: D 68 SER cc_start: 0.9564 (t) cc_final: 0.9300 (t) REVERT: D 89 ASP cc_start: 0.8175 (p0) cc_final: 0.7950 (p0) REVERT: D 112 MET cc_start: 0.8750 (tmm) cc_final: 0.8510 (tmm) REVERT: D 129 ASP cc_start: 0.7295 (t0) cc_final: 0.6765 (t0) REVERT: E 118 ILE cc_start: 0.8443 (mm) cc_final: 0.8204 (mm) REVERT: G 47 HIS cc_start: 0.9144 (m-70) cc_final: 0.8806 (m-70) REVERT: G 53 MET cc_start: 0.9018 (mmt) cc_final: 0.8729 (mmm) REVERT: G 71 GLU cc_start: 0.9118 (tt0) cc_final: 0.8533 (tm-30) REVERT: G 73 GLN cc_start: 0.8509 (pp30) cc_final: 0.8294 (pp30) REVERT: G 140 GLU cc_start: 0.7736 (mt-10) cc_final: 0.6868 (mt-10) REVERT: H 75 HIS cc_start: 0.9112 (m-70) cc_final: 0.8409 (m-70) REVERT: H 86 ASN cc_start: 0.8971 (t0) cc_final: 0.8185 (t0) REVERT: H 132 ASN cc_start: 0.7824 (t0) cc_final: 0.7348 (t0) outliers start: 30 outliers final: 23 residues processed: 262 average time/residue: 0.1061 time to fit residues: 40.1960 Evaluate side-chains 248 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 311 HIS 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 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 178 HIS 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 F residue 297 GLN Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 86 ASN 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: 10.0000 chunk 9 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 165 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN B 191 GLN ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 HIS F 79 GLN F 191 GLN G 70 GLN G 86 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 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 = 0.4002 r_free = 0.4002 target = 0.156497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.097719 restraints weight = 19777.473| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.18 r_work: 0.2928 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13798 Z= 0.215 Angle : 0.592 9.029 18638 Z= 0.313 Chirality : 0.047 0.239 1916 Planarity : 0.004 0.066 2510 Dihedral : 4.324 23.272 1788 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.53 % Allowed : 16.87 % Favored : 79.60 % 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 aren not related in a simple way. whole: -0.26 (0.20), residues: 1650 helix: 1.32 (0.23), residues: 492 sheet: 0.04 (0.29), residues: 336 loop : -1.21 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 126 TYR 0.027 0.002 TYR G 138 PHE 0.024 0.002 PHE H 77 TRP 0.015 0.002 TRP E 126 HIS 0.017 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00508 (13794) covalent geometry : angle 0.59125 (18630) SS BOND : bond 0.00182 ( 4) SS BOND : angle 1.66407 ( 8) hydrogen bonds : bond 0.03809 ( 605) hydrogen bonds : angle 4.40299 ( 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 277 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 226 time to evaluate : 0.348 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: 0.8694 (mptt) cc_final: 0.7572 (tptt) REVERT: A 350 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7505 (mtm-85) REVERT: B 207 TYR cc_start: 0.9429 (t80) cc_final: 0.8930 (t80) REVERT: B 295 HIS cc_start: 0.8996 (m90) cc_final: 0.8755 (m90) REVERT: C 62 LYS cc_start: 0.8977 (tptt) cc_final: 0.8768 (tptt) REVERT: C 71 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8990 (mp0) REVERT: C 75 HIS cc_start: 0.8786 (OUTLIER) cc_final: 0.8495 (t-90) REVERT: C 132 ASN cc_start: 0.9154 (t0) cc_final: 0.8704 (t0) REVERT: D 53 MET cc_start: 0.9562 (mmp) cc_final: 0.9145 (mmm) REVERT: D 89 ASP cc_start: 0.8227 (p0) cc_final: 0.7985 (p0) REVERT: D 112 MET cc_start: 0.8713 (tmm) cc_final: 0.8382 (tmm) REVERT: D 127 ASP cc_start: 0.8834 (m-30) cc_final: 0.8530 (m-30) REVERT: D 129 ASP cc_start: 0.7542 (t0) cc_final: 0.6950 (t70) REVERT: D 131 ASN cc_start: 0.8397 (p0) cc_final: 0.8194 (p0) REVERT: E 330 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8186 (mt-10) REVERT: G 47 HIS cc_start: 0.9204 (m-70) cc_final: 0.8881 (m-70) REVERT: G 71 GLU cc_start: 0.9161 (tt0) cc_final: 0.8581 (tm-30) REVERT: G 73 GLN cc_start: 0.8521 (pp30) cc_final: 0.8266 (pp30) REVERT: G 75 HIS cc_start: 0.8398 (OUTLIER) cc_final: 0.7936 (m-70) REVERT: G 140 GLU cc_start: 0.7925 (mt-10) cc_final: 0.6675 (mt-10) REVERT: H 75 HIS cc_start: 0.9136 (m-70) cc_final: 0.8434 (m-70) REVERT: H 86 ASN cc_start: 0.9085 (t0) cc_final: 0.8879 (t0) REVERT: H 126 ARG cc_start: 0.8821 (ttp-110) cc_final: 0.8477 (ptp-110) REVERT: H 132 ASN cc_start: 0.8090 (t0) cc_final: 0.7435 (t0) outliers start: 51 outliers final: 38 residues processed: 255 average time/residue: 0.1058 time to fit residues: 39.2023 Evaluate side-chains 251 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 311 HIS 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 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 95 THR 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 236 MET 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 74 LEU Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 101 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 139 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 162 optimal weight: 50.0000 chunk 10 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN B 191 GLN ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.156934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.095431 restraints weight = 19876.901| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.16 r_work: 0.2936 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3420 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 : 0.580 9.557 18638 Z= 0.307 Chirality : 0.045 0.162 1916 Planarity : 0.004 0.056 2510 Dihedral : 4.294 23.398 1788 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.46 % Allowed : 17.50 % Favored : 79.05 % 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 aren not related in a simple way. whole: -0.27 (0.20), residues: 1650 helix: 1.28 (0.23), residues: 492 sheet: -0.09 (0.29), residues: 348 loop : -1.14 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 350 TYR 0.033 0.002 TYR C 138 PHE 0.025 0.002 PHE A 296 TRP 0.014 0.001 TRP E 126 HIS 0.016 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00396 (13794) covalent geometry : angle 0.57895 (18630) SS BOND : bond 0.00627 ( 4) SS BOND : angle 1.99442 ( 8) hydrogen bonds : bond 0.03683 ( 605) hydrogen bonds : angle 4.35570 ( 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 277 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 0.363 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: A 159 LYS cc_start: 0.8689 (mptt) cc_final: 0.7572 (tptt) REVERT: B 207 TYR cc_start: 0.9404 (t80) cc_final: 0.8978 (t80) REVERT: B 295 HIS cc_start: 0.9002 (m90) cc_final: 0.8765 (m-70) REVERT: B 306 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8257 (pm20) REVERT: B 354 MET cc_start: 0.8747 (tmm) cc_final: 0.8187 (tmm) REVERT: C 62 LYS cc_start: 0.9062 (tptt) cc_final: 0.8856 (tptt) REVERT: C 75 HIS cc_start: 0.8819 (OUTLIER) cc_final: 0.8450 (t70) REVERT: C 126 ARG cc_start: 0.8821 (ttp80) cc_final: 0.8585 (ttp80) REVERT: C 132 ASN cc_start: 0.9166 (t0) cc_final: 0.8784 (t0) REVERT: D 53 MET cc_start: 0.9593 (mmp) cc_final: 0.9217 (mmp) REVERT: D 67 MET cc_start: 0.8361 (tpp) cc_final: 0.8090 (tpp) REVERT: D 89 ASP cc_start: 0.8210 (p0) cc_final: 0.7979 (p0) REVERT: D 112 MET cc_start: 0.8688 (tmm) cc_final: 0.8305 (tmm) REVERT: D 127 ASP cc_start: 0.8843 (m-30) cc_final: 0.8537 (m-30) REVERT: D 129 ASP cc_start: 0.7680 (t0) cc_final: 0.7211 (t70) REVERT: E 330 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8173 (mt-10) REVERT: F 191 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8688 (tp40) REVERT: G 47 HIS cc_start: 0.9229 (m-70) cc_final: 0.8881 (m-70) REVERT: G 71 GLU cc_start: 0.9141 (tt0) cc_final: 0.8584 (tm-30) REVERT: G 73 GLN cc_start: 0.8517 (pp30) cc_final: 0.8300 (pp30) REVERT: G 75 HIS cc_start: 0.8481 (OUTLIER) cc_final: 0.8017 (m-70) REVERT: G 112 MET cc_start: 0.8495 (tmm) cc_final: 0.8178 (tmm) REVERT: G 140 GLU cc_start: 0.7697 (mt-10) cc_final: 0.6510 (mt-10) REVERT: H 75 HIS cc_start: 0.9118 (m-70) cc_final: 0.8405 (m-70) REVERT: H 126 ARG cc_start: 0.8888 (ttp-110) cc_final: 0.8548 (ptp-110) REVERT: H 132 ASN cc_start: 0.8110 (t0) cc_final: 0.7460 (t0) outliers start: 50 outliers final: 37 residues processed: 258 average time/residue: 0.0979 time to fit residues: 36.7060 Evaluate side-chains 255 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 A residue 311 HIS 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 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 236 MET Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain E residue 291 GLU 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 G residue 70 GLN Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 59 VAL 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: 7.9990 chunk 100 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 139 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 152 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 4 optimal weight: 0.0670 chunk 144 optimal weight: 3.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN B 191 GLN ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.158716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096872 restraints weight = 19495.934| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.16 r_work: 0.2942 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3531 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= 0.176 Angle : 0.596 10.497 18638 Z= 0.313 Chirality : 0.046 0.187 1916 Planarity : 0.004 0.055 2510 Dihedral : 4.306 23.653 1788 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.46 % Allowed : 18.33 % Favored : 78.22 % 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 aren not related in a simple way. whole: -0.26 (0.20), residues: 1650 helix: 1.19 (0.23), residues: 504 sheet: 0.05 (0.29), residues: 336 loop : -1.14 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 126 TYR 0.036 0.002 TYR C 138 PHE 0.031 0.002 PHE A 296 TRP 0.014 0.001 TRP E 126 HIS 0.013 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00410 (13794) covalent geometry : angle 0.59472 (18630) SS BOND : bond 0.00238 ( 4) SS BOND : angle 1.76689 ( 8) hydrogen bonds : bond 0.03704 ( 605) hydrogen bonds : angle 4.35030 ( 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 273 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 0.474 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: 0.8627 (mptt) cc_final: 0.7538 (tptt) REVERT: B 207 TYR cc_start: 0.9347 (t80) cc_final: 0.8843 (t80) REVERT: B 289 TYR cc_start: 0.8977 (m-10) cc_final: 0.8760 (m-10) REVERT: B 295 HIS cc_start: 0.9000 (m90) cc_final: 0.8727 (m90) REVERT: B 306 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8220 (pm20) REVERT: B 354 MET cc_start: 0.8688 (tmm) cc_final: 0.8125 (tmm) REVERT: C 62 LYS cc_start: 0.9114 (tptt) cc_final: 0.8899 (tptt) REVERT: C 75 HIS cc_start: 0.8826 (OUTLIER) cc_final: 0.8444 (t70) REVERT: C 132 ASN cc_start: 0.9179 (t0) cc_final: 0.8786 (t0) REVERT: D 53 MET cc_start: 0.9607 (mmp) cc_final: 0.9235 (mmp) REVERT: D 67 MET cc_start: 0.8607 (tpp) cc_final: 0.8341 (tpp) REVERT: D 89 ASP cc_start: 0.8265 (p0) cc_final: 0.8032 (p0) REVERT: D 112 MET cc_start: 0.8622 (tmm) cc_final: 0.8247 (tmm) REVERT: D 127 ASP cc_start: 0.8874 (m-30) cc_final: 0.8600 (m-30) REVERT: E 192 ARG cc_start: 0.8311 (ttm110) cc_final: 0.7944 (mmt180) REVERT: E 232 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8348 (ttpt) REVERT: E 352 LEU cc_start: 0.8031 (tp) cc_final: 0.7641 (tt) REVERT: G 47 HIS cc_start: 0.9179 (m-70) cc_final: 0.8822 (m-70) REVERT: G 71 GLU cc_start: 0.9114 (tt0) cc_final: 0.8863 (pt0) REVERT: G 73 GLN cc_start: 0.8560 (pp30) cc_final: 0.8298 (pp30) REVERT: G 75 HIS cc_start: 0.8288 (OUTLIER) cc_final: 0.8018 (m-70) REVERT: G 112 MET cc_start: 0.8507 (tmm) cc_final: 0.8153 (tmm) REVERT: G 132 ASN cc_start: 0.8805 (t0) cc_final: 0.7860 (t0) REVERT: G 140 GLU cc_start: 0.7661 (mt-10) cc_final: 0.6177 (mt-10) REVERT: H 75 HIS cc_start: 0.9092 (m-70) cc_final: 0.8364 (m-70) REVERT: H 86 ASN cc_start: 0.8861 (t0) cc_final: 0.8085 (t0) REVERT: H 126 ARG cc_start: 0.8938 (ttp-110) cc_final: 0.8613 (ptp-110) REVERT: H 132 ASN cc_start: 0.8113 (t0) cc_final: 0.7391 (t0) outliers start: 50 outliers final: 37 residues processed: 254 average time/residue: 0.1276 time to fit residues: 46.6072 Evaluate side-chains 250 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 209 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 A residue 311 HIS 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 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 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 178 HIS Chi-restraints excluded: chain E residue 190 CYS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 236 MET 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 G residue 137 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 0.0030 chunk 15 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN B 191 GLN ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN G 73 GLN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.158921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.097350 restraints weight = 19436.699| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.30 r_work: 0.2927 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3647 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= 0.174 Angle : 0.601 12.212 18638 Z= 0.318 Chirality : 0.046 0.199 1916 Planarity : 0.004 0.054 2510 Dihedral : 4.295 23.808 1788 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.25 % Allowed : 18.88 % Favored : 77.87 % 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 aren not related in a simple way. whole: -0.26 (0.20), residues: 1650 helix: 1.10 (0.23), residues: 504 sheet: 0.09 (0.29), residues: 336 loop : -1.10 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 117 TYR 0.030 0.002 TYR C 138 PHE 0.036 0.002 PHE A 296 TRP 0.013 0.001 TRP E 126 HIS 0.010 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00407 (13794) covalent geometry : angle 0.59837 (18630) SS BOND : bond 0.00749 ( 4) SS BOND : angle 2.53088 ( 8) hydrogen bonds : bond 0.03703 ( 605) hydrogen bonds : angle 4.39835 ( 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: 47 poor density : 218 time to evaluate : 0.602 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: A 159 LYS cc_start: 0.8649 (mptt) cc_final: 0.7556 (tptt) REVERT: B 207 TYR cc_start: 0.9375 (t80) cc_final: 0.8921 (t80) REVERT: B 295 HIS cc_start: 0.9018 (m90) cc_final: 0.8733 (m90) REVERT: B 306 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8257 (pm20) REVERT: B 354 MET cc_start: 0.8702 (tmm) cc_final: 0.8134 (tmm) REVERT: C 62 LYS cc_start: 0.9118 (tptt) cc_final: 0.8888 (tptt) REVERT: C 75 HIS cc_start: 0.8747 (OUTLIER) cc_final: 0.8310 (t70) REVERT: C 132 ASN cc_start: 0.9188 (t0) cc_final: 0.8802 (t0) REVERT: D 53 MET cc_start: 0.9598 (mmp) cc_final: 0.9225 (mmp) REVERT: D 67 MET cc_start: 0.8715 (tpp) cc_final: 0.8450 (tpp) REVERT: D 89 ASP cc_start: 0.8260 (p0) cc_final: 0.8030 (p0) REVERT: D 112 MET cc_start: 0.8606 (tmm) cc_final: 0.8156 (tmm) REVERT: D 127 ASP cc_start: 0.8873 (m-30) cc_final: 0.8592 (m-30) REVERT: E 137 VAL cc_start: 0.8095 (t) cc_final: 0.7861 (p) REVERT: E 207 TYR cc_start: 0.8079 (t80) cc_final: 0.7812 (t80) REVERT: E 232 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8230 (ttpt) REVERT: E 352 LEU cc_start: 0.8073 (tp) cc_final: 0.7606 (tt) REVERT: G 47 HIS cc_start: 0.9200 (m-70) cc_final: 0.8818 (m-70) REVERT: G 70 GLN cc_start: 0.8300 (pm20) cc_final: 0.7987 (pm20) REVERT: G 71 GLU cc_start: 0.9106 (tt0) cc_final: 0.8547 (tm-30) REVERT: G 73 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8322 (pp30) REVERT: G 75 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7706 (m-70) REVERT: G 112 MET cc_start: 0.8533 (tmm) cc_final: 0.8184 (tmm) REVERT: G 132 ASN cc_start: 0.8829 (t0) cc_final: 0.7900 (t0) REVERT: G 140 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6047 (mt-10) REVERT: H 86 ASN cc_start: 0.8897 (t0) cc_final: 0.8035 (t0) REVERT: H 126 ARG cc_start: 0.8943 (ttp-110) cc_final: 0.8427 (ptp-110) REVERT: H 132 ASN cc_start: 0.8110 (t0) cc_final: 0.7482 (t0) outliers start: 47 outliers final: 38 residues processed: 248 average time/residue: 0.1269 time to fit residues: 45.3371 Evaluate side-chains 253 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 A residue 311 HIS 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 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 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 178 HIS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 236 MET 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 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 G residue 73 GLN Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 MET 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: 0.9980 chunk 129 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN ** H 55 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 = 0.4031 r_free = 0.4031 target = 0.159815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.096979 restraints weight = 19651.071| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.37 r_work: 0.2934 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13798 Z= 0.137 Angle : 0.621 19.302 18638 Z= 0.323 Chirality : 0.046 0.211 1916 Planarity : 0.004 0.065 2510 Dihedral : 4.227 23.501 1788 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.70 % Allowed : 19.64 % Favored : 77.66 % 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 aren not related in a simple way. whole: -0.15 (0.20), residues: 1650 helix: 1.14 (0.24), residues: 504 sheet: 0.11 (0.29), residues: 344 loop : -0.98 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 117 TYR 0.028 0.002 TYR C 138 PHE 0.047 0.002 PHE A 296 TRP 0.013 0.001 TRP F 126 HIS 0.009 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00315 (13794) covalent geometry : angle 0.61968 (18630) SS BOND : bond 0.00202 ( 4) SS BOND : angle 2.07062 ( 8) hydrogen bonds : bond 0.03580 ( 605) hydrogen bonds : angle 4.36192 ( 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 265 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 226 time to evaluate : 0.628 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: A 159 LYS cc_start: 0.8591 (mptt) cc_final: 0.7490 (tptt) REVERT: B 207 TYR cc_start: 0.9350 (t80) cc_final: 0.8817 (t80) REVERT: B 295 HIS cc_start: 0.9029 (m90) cc_final: 0.8739 (m90) REVERT: B 354 MET cc_start: 0.8721 (tmm) cc_final: 0.8163 (tmm) REVERT: C 75 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.8259 (t70) REVERT: C 126 ARG cc_start: 0.8812 (ttp80) cc_final: 0.8495 (ttp80) REVERT: C 132 ASN cc_start: 0.9187 (t0) cc_final: 0.8782 (t0) REVERT: D 53 MET cc_start: 0.9608 (mmp) cc_final: 0.9260 (mmp) REVERT: D 67 MET cc_start: 0.8736 (tpp) cc_final: 0.8343 (tpp) REVERT: D 89 ASP cc_start: 0.8247 (p0) cc_final: 0.8042 (p0) REVERT: D 112 MET cc_start: 0.8605 (tmm) cc_final: 0.8158 (tmm) REVERT: D 127 ASP cc_start: 0.8868 (m-30) cc_final: 0.8579 (m-30) REVERT: E 137 VAL cc_start: 0.8078 (t) cc_final: 0.7852 (p) REVERT: E 207 TYR cc_start: 0.8067 (t80) cc_final: 0.7789 (t80) REVERT: E 291 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8854 (pm20) REVERT: E 330 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8100 (mt-10) REVERT: E 352 LEU cc_start: 0.8002 (tp) cc_final: 0.7532 (tt) REVERT: G 47 HIS cc_start: 0.9207 (m-70) cc_final: 0.8831 (m-70) REVERT: G 70 GLN cc_start: 0.8382 (pm20) cc_final: 0.8034 (pm20) REVERT: G 71 GLU cc_start: 0.9104 (tt0) cc_final: 0.8606 (pt0) REVERT: G 73 GLN cc_start: 0.8608 (pp30) cc_final: 0.8351 (pp30) REVERT: G 75 HIS cc_start: 0.8172 (OUTLIER) cc_final: 0.7839 (m-70) REVERT: G 112 MET cc_start: 0.8526 (tmm) cc_final: 0.8149 (tmm) REVERT: G 140 GLU cc_start: 0.7648 (mt-10) cc_final: 0.6273 (mt-10) REVERT: H 86 ASN cc_start: 0.8842 (t0) cc_final: 0.8017 (t0) REVERT: H 126 ARG cc_start: 0.8959 (ttp-110) cc_final: 0.8411 (ptp-110) REVERT: H 132 ASN cc_start: 0.8161 (t0) cc_final: 0.7548 (t0) outliers start: 39 outliers final: 32 residues processed: 252 average time/residue: 0.1243 time to fit residues: 45.4560 Evaluate side-chains 257 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 222 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 A residue 311 HIS 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 94 SER 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 178 HIS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 236 MET 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 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 G residue 137 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 59 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 138 optimal weight: 0.0270 overall best weight: 0.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN ** H 55 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 = 0.4035 r_free = 0.4035 target = 0.158915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.098612 restraints weight = 20045.769| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.11 r_work: 0.2974 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13798 Z= 0.133 Angle : 0.637 17.085 18638 Z= 0.336 Chirality : 0.046 0.211 1916 Planarity : 0.004 0.055 2510 Dihedral : 4.200 23.162 1788 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.42 % Allowed : 20.40 % Favored : 77.18 % 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 aren not related in a simple way. whole: -0.12 (0.20), residues: 1650 helix: 1.19 (0.24), residues: 486 sheet: 0.16 (0.29), residues: 344 loop : -0.96 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 350 TYR 0.029 0.002 TYR C 138 PHE 0.034 0.001 PHE A 296 TRP 0.013 0.001 TRP F 126 HIS 0.014 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00304 (13794) covalent geometry : angle 0.63573 (18630) SS BOND : bond 0.00144 ( 4) SS BOND : angle 1.85403 ( 8) hydrogen bonds : bond 0.03643 ( 605) hydrogen bonds : angle 4.39178 ( 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 263 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 0.567 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: A 159 LYS cc_start: 0.8623 (mptt) cc_final: 0.7557 (tptt) REVERT: B 117 ARG cc_start: 0.7327 (mmm160) cc_final: 0.6975 (mmm160) REVERT: B 207 TYR cc_start: 0.9390 (t80) cc_final: 0.8909 (t80) REVERT: B 295 HIS cc_start: 0.9026 (m90) cc_final: 0.8733 (m90) REVERT: B 354 MET cc_start: 0.8798 (tmm) cc_final: 0.8219 (tmm) REVERT: C 126 ARG cc_start: 0.8766 (ttp80) cc_final: 0.8465 (ttp80) REVERT: C 132 ASN cc_start: 0.9180 (t0) cc_final: 0.8796 (t0) REVERT: D 53 MET cc_start: 0.9608 (mmp) cc_final: 0.9277 (mmp) REVERT: D 67 MET cc_start: 0.8678 (tpp) cc_final: 0.8255 (tpp) REVERT: D 112 MET cc_start: 0.8607 (tmm) cc_final: 0.8155 (tmm) REVERT: D 127 ASP cc_start: 0.8770 (m-30) cc_final: 0.8480 (m-30) REVERT: E 207 TYR cc_start: 0.8115 (t80) cc_final: 0.7872 (t80) REVERT: E 291 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8848 (pm20) REVERT: E 330 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8080 (mt-10) REVERT: E 352 LEU cc_start: 0.8125 (tp) cc_final: 0.7647 (tt) REVERT: G 47 HIS cc_start: 0.9178 (m-70) cc_final: 0.8820 (m-70) REVERT: G 70 GLN cc_start: 0.8440 (pm20) cc_final: 0.8068 (pm20) REVERT: G 71 GLU cc_start: 0.9053 (tt0) cc_final: 0.8581 (pt0) REVERT: G 75 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7947 (m-70) REVERT: G 112 MET cc_start: 0.8499 (tmm) cc_final: 0.8131 (tmm) REVERT: G 140 GLU cc_start: 0.7585 (mt-10) cc_final: 0.6244 (mt-10) REVERT: H 86 ASN cc_start: 0.8877 (t0) cc_final: 0.8062 (t0) REVERT: H 126 ARG cc_start: 0.8900 (ttp-110) cc_final: 0.8529 (ptp-110) REVERT: H 132 ASN cc_start: 0.8157 (t0) cc_final: 0.7545 (t0) outliers start: 35 outliers final: 29 residues processed: 250 average time/residue: 0.1230 time to fit residues: 44.5937 Evaluate side-chains 248 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 311 HIS 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 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 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 221 THR Chi-restraints excluded: chain E residue 236 MET 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 20 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 67 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN ** H 55 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 = 0.4044 r_free = 0.4044 target = 0.159590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.099877 restraints weight = 20044.608| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.05 r_work: 0.2999 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13798 Z= 0.127 Angle : 0.643 16.873 18638 Z= 0.337 Chirality : 0.045 0.190 1916 Planarity : 0.004 0.048 2510 Dihedral : 4.129 22.734 1788 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.14 % Allowed : 21.02 % 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 aren not related in a simple way. whole: 0.00 (0.20), residues: 1650 helix: 1.25 (0.24), residues: 478 sheet: 0.33 (0.30), residues: 334 loop : -0.86 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 126 TYR 0.029 0.002 TYR B 289 PHE 0.051 0.001 PHE A 296 TRP 0.013 0.001 TRP F 126 HIS 0.013 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00290 (13794) covalent geometry : angle 0.64216 (18630) SS BOND : bond 0.00134 ( 4) SS BOND : angle 1.76643 ( 8) hydrogen bonds : bond 0.03600 ( 605) hydrogen bonds : angle 4.32123 ( 1836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3279.08 seconds wall clock time: 56 minutes 47.51 seconds (3407.51 seconds total)