Starting phenix.real_space_refine on Wed Aug 5 23:05:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10fa_75124/08_2026/10fa_75124.cif Found real_map, /net/cci-nas-00/data/ceres_data/10fa_75124/08_2026/10fa_75124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10fa_75124/08_2026/10fa_75124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10fa_75124/08_2026/10fa_75124.map" model { file = "/net/cci-nas-00/data/ceres_data/10fa_75124/08_2026/10fa_75124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10fa_75124/08_2026/10fa_75124.cif" } resolution = 3.52 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= 0.001 sd= 0.041 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 84 5.16 5 C 7536 2.51 5 N 2116 2.21 5 O 2184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11924 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2980 Classifications: {'peptide': 373} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 352} Chain breaks: 1 Chain: "B" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2980 Classifications: {'peptide': 373} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 352} Chain breaks: 1 Chain: "C" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2980 Classifications: {'peptide': 373} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 352} Chain breaks: 1 Chain: "D" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2980 Classifications: {'peptide': 373} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 352} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2392 SG CYS A 302 103.992 67.626 55.108 1.00 54.18 S ATOM 2406 SG CYS A 304 101.278 67.645 52.357 1.00 46.20 S ATOM 2431 SG CYS A 307 100.208 67.580 56.101 1.00 45.04 S ATOM 5372 SG CYS B 302 91.881 71.316 24.850 1.00 39.29 S ATOM 5386 SG CYS B 304 93.461 69.661 27.958 1.00 36.30 S ATOM 5411 SG CYS B 307 93.788 67.971 24.561 1.00 36.75 S ATOM 8352 SG CYS C 302 40.405 33.079 55.112 1.00 55.08 S ATOM 8366 SG CYS C 304 43.120 33.059 52.358 1.00 47.07 S ATOM 8391 SG CYS C 307 44.191 33.127 56.098 1.00 45.90 S ATOM 11332 SG CYS D 302 52.521 29.389 24.843 1.00 38.80 S ATOM 11346 SG CYS D 304 50.941 31.039 27.951 1.00 35.88 S ATOM 11371 SG CYS D 307 50.612 32.733 24.557 1.00 36.54 S Time building chain proxies: 2.47, per 1000 atoms: 0.21 Number of scatterers: 11924 At special positions: 0 Unit cell: (145.35, 101.65, 80.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 84 16.00 O 2184 8.00 N 2116 7.00 C 7536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 457.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" ND1 HIS A 333 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 302 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 304 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 307 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" ND1 HIS B 333 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 304 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 307 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 302 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" ND1 HIS C 333 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 304 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 302 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 307 " pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" ND1 HIS D 333 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 307 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 304 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 302 " Number of angles added : 12 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 20 sheets defined 48.9% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 66 through 73 removed outlier: 3.745A pdb=" N LEU A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 151 through 177 Processing helix chain 'A' and resid 191 through 206 Processing helix chain 'A' and resid 220 through 232 Processing helix chain 'A' and resid 248 through 258 removed outlier: 3.575A pdb=" N ARG A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 273 Processing helix chain 'A' and resid 288 through 292 Processing helix chain 'A' and resid 304 through 310 removed outlier: 3.518A pdb=" N ASN A 309 " --> pdb=" O TYR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.551A pdb=" N LEU A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 351 removed outlier: 3.593A pdb=" N ALA A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 365 removed outlier: 3.579A pdb=" N GLN A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 59 through 64 Processing helix chain 'B' and resid 66 through 73 removed outlier: 3.650A pdb=" N LEU B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 123 through 134 removed outlier: 3.581A pdb=" N GLN B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR B 132 " --> pdb=" O MET B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 176 removed outlier: 3.513A pdb=" N LYS B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 206 Processing helix chain 'B' and resid 220 through 232 removed outlier: 3.572A pdb=" N GLU B 229 " --> pdb=" O HIS B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 removed outlier: 3.550A pdb=" N VAL B 253 " --> pdb=" O PRO B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 273 Processing helix chain 'B' and resid 288 through 292 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 311 through 321 Processing helix chain 'B' and resid 324 through 327 Processing helix chain 'B' and resid 328 through 352 removed outlier: 3.832A pdb=" N HIS B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 365 removed outlier: 3.636A pdb=" N GLN B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 66 through 73 removed outlier: 3.739A pdb=" N LEU C 72 " --> pdb=" O GLU C 68 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 151 through 177 Processing helix chain 'C' and resid 191 through 206 Processing helix chain 'C' and resid 220 through 232 Processing helix chain 'C' and resid 248 through 258 Processing helix chain 'C' and resid 266 through 273 Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 304 through 310 removed outlier: 3.518A pdb=" N ASN C 309 " --> pdb=" O TYR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 322 removed outlier: 3.545A pdb=" N LEU C 315 " --> pdb=" O SER C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 351 removed outlier: 3.643A pdb=" N ALA C 327 " --> pdb=" O GLU C 323 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN C 330 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 365 removed outlier: 3.579A pdb=" N GLN C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 66 through 73 removed outlier: 3.594A pdb=" N LEU D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 91 through 96 Processing helix chain 'D' and resid 123 through 134 Processing helix chain 'D' and resid 151 through 176 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 220 through 232 removed outlier: 3.512A pdb=" N ARG D 226 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU D 229 " --> pdb=" O HIS D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 257 removed outlier: 3.555A pdb=" N VAL D 253 " --> pdb=" O PRO D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 273 Processing helix chain 'D' and resid 288 through 292 Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 311 through 321 Processing helix chain 'D' and resid 328 through 352 removed outlier: 3.842A pdb=" N HIS D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 365 removed outlier: 3.636A pdb=" N GLN D 365 " --> pdb=" O PHE D 361 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 9 removed outlier: 7.055A pdb=" N ARG A 14 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N THR A 8 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA A 12 " --> pdb=" O THR A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.450A pdb=" N CYS A 28 " --> pdb=" O PHE A 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 33 removed outlier: 4.098A pdb=" N ASN A 57 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 54 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ASP A 89 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLY A 56 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET A 140 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 139 " --> pdb=" O PHE A 183 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE A 185 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 279 removed outlier: 3.521A pdb=" N LEU A 277 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 9 removed outlier: 6.063A pdb=" N PHE B 3 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B 18 " --> pdb=" O PHE B 3 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU B 5 " --> pdb=" O ARG B 16 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG B 16 " --> pdb=" O LEU B 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AA8, first strand: chain 'B' and resid 32 through 33 removed outlier: 4.005A pdb=" N ASN B 57 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 54 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASP B 89 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLY B 56 " --> pdb=" O ASP B 89 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE B 86 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N MET B 140 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR B 88 " --> pdb=" O MET B 140 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 139 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ILE B 185 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 102 through 104 Processing sheet with id=AB1, first strand: chain 'B' and resid 278 through 279 removed outlier: 3.536A pdb=" N GLY B 282 " --> pdb=" O VAL B 279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 9 removed outlier: 7.097A pdb=" N ARG C 14 " --> pdb=" O ASP C 6 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N THR C 8 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA C 12 " --> pdb=" O THR C 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.766A pdb=" N CYS C 28 " --> pdb=" O PHE C 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 32 through 33 removed outlier: 4.008A pdb=" N ASN C 57 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE C 54 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASP C 89 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY C 56 " --> pdb=" O ASP C 89 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET C 140 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 103 through 104 removed outlier: 3.566A pdb=" N HIS C 110 " --> pdb=" O LYS C 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 276 through 279 removed outlier: 3.513A pdb=" N LEU C 277 " --> pdb=" O VAL C 284 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 2 through 9 removed outlier: 6.094A pdb=" N PHE D 3 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL D 18 " --> pdb=" O PHE D 3 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU D 5 " --> pdb=" O ARG D 16 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG D 16 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 28 through 30 removed outlier: 6.592A pdb=" N CYS D 28 " --> pdb=" O PHE D 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 32 through 33 removed outlier: 3.978A pdb=" N ASN D 57 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE D 54 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASP D 89 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLY D 56 " --> pdb=" O ASP D 89 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE D 86 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N MET D 140 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR D 88 " --> pdb=" O MET D 140 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL D 139 " --> pdb=" O PHE D 183 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ILE D 185 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY D 209 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 102 through 104 Processing sheet with id=AC2, first strand: chain 'D' and resid 278 through 279 removed outlier: 3.563A pdb=" N GLY D 282 " --> pdb=" O VAL D 279 " (cutoff:3.500A) 542 hydrogen bonds defined for protein. 1542 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: 1.48 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4018 1.34 - 1.46: 2664 1.46 - 1.58: 5374 1.58 - 1.70: 0 1.70 - 1.81: 136 Bond restraints: 12192 Sorted by residual: bond pdb=" C MET A 267 " pdb=" N PRO A 268 " ideal model delta sigma weight residual 1.335 1.359 -0.023 1.30e-02 5.92e+03 3.22e+00 bond pdb=" C MET C 267 " pdb=" N PRO C 268 " ideal model delta sigma weight residual 1.334 1.360 -0.026 1.51e-02 4.39e+03 2.94e+00 bond pdb=" CB GLU C 355 " pdb=" CG GLU C 355 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" CB GLU A 355 " pdb=" CG GLU A 355 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.37e+00 bond pdb=" CB GLU B 350 " pdb=" CG GLU B 350 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 ... (remaining 12187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 15871 1.24 - 2.49: 450 2.49 - 3.73: 100 3.73 - 4.97: 15 4.97 - 6.21: 8 Bond angle restraints: 16444 Sorted by residual: angle pdb=" CB GLU A 355 " pdb=" CG GLU A 355 " pdb=" CD GLU A 355 " ideal model delta sigma weight residual 112.60 117.54 -4.94 1.70e+00 3.46e-01 8.43e+00 angle pdb=" CA GLU C 355 " pdb=" CB GLU C 355 " pdb=" CG GLU C 355 " ideal model delta sigma weight residual 114.10 119.85 -5.75 2.00e+00 2.50e-01 8.25e+00 angle pdb=" CB GLU D 350 " pdb=" CG GLU D 350 " pdb=" CD GLU D 350 " ideal model delta sigma weight residual 112.60 117.40 -4.80 1.70e+00 3.46e-01 7.96e+00 angle pdb=" CB GLU C 355 " pdb=" CG GLU C 355 " pdb=" CD GLU C 355 " ideal model delta sigma weight residual 112.60 117.33 -4.73 1.70e+00 3.46e-01 7.73e+00 angle pdb=" CA GLU A 355 " pdb=" CB GLU A 355 " pdb=" CG GLU A 355 " ideal model delta sigma weight residual 114.10 119.62 -5.52 2.00e+00 2.50e-01 7.61e+00 ... (remaining 16439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 6378 17.80 - 35.59: 699 35.59 - 53.39: 194 53.39 - 71.18: 32 71.18 - 88.98: 13 Dihedral angle restraints: 7316 sinusoidal: 3088 harmonic: 4228 Sorted by residual: dihedral pdb=" CA ASP A 360 " pdb=" CB ASP A 360 " pdb=" CG ASP A 360 " pdb=" OD1 ASP A 360 " ideal model delta sinusoidal sigma weight residual -30.00 -88.59 58.59 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP C 360 " pdb=" CB ASP C 360 " pdb=" CG ASP C 360 " pdb=" OD1 ASP C 360 " ideal model delta sinusoidal sigma weight residual -30.00 -88.57 58.57 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASN A 288 " pdb=" CB ASN A 288 " pdb=" CG ASN A 288 " pdb=" OD1 ASN A 288 " ideal model delta sinusoidal sigma weight residual -90.00 -164.57 74.57 2 2.00e+01 2.50e-03 1.12e+01 ... (remaining 7313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1119 0.031 - 0.063: 411 0.063 - 0.094: 108 0.094 - 0.126: 76 0.126 - 0.157: 6 Chirality restraints: 1720 Sorted by residual: chirality pdb=" CG LEU C 354 " pdb=" CB LEU C 354 " pdb=" CD1 LEU C 354 " pdb=" CD2 LEU C 354 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CG LEU A 354 " pdb=" CB LEU A 354 " pdb=" CD1 LEU A 354 " pdb=" CD2 LEU A 354 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ILE B 235 " pdb=" N ILE B 235 " pdb=" C ILE B 235 " pdb=" CB ILE B 235 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 1717 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 42 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO D 43 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 43 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 43 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 42 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO B 43 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 43 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 43 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 369 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO D 370 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 370 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 370 " 0.023 5.00e-02 4.00e+02 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 6066 3.01 - 3.48: 11839 3.48 - 3.96: 18824 3.96 - 4.43: 22137 4.43 - 4.90: 36588 Nonbonded interactions: 95454 Sorted by model distance: nonbonded pdb=" N ASP B 151 " pdb=" OD1 ASP B 151 " model vdw 2.538 3.120 nonbonded pdb=" N GLU A 355 " pdb=" OE1 GLU A 355 " model vdw 2.539 3.120 nonbonded pdb=" N ASP D 151 " pdb=" OD1 ASP D 151 " model vdw 2.539 3.120 nonbonded pdb=" N GLU C 355 " pdb=" OE1 GLU C 355 " model vdw 2.542 3.120 nonbonded pdb=" N ASP A 75 " pdb=" OD1 ASP A 75 " model vdw 2.552 3.120 ... (remaining 95449 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.490 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 0.046 12208 Z= 0.113 Angle : 0.534 6.213 16456 Z= 0.295 Chirality : 0.040 0.157 1720 Planarity : 0.004 0.042 2172 Dihedral : 15.966 88.980 4628 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.18 % Allowed : 18.34 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.20), residues: 1476 helix: -0.81 (0.18), residues: 700 sheet: -0.20 (0.43), residues: 136 loop : -0.26 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 328 TYR 0.008 0.001 TYR B 210 PHE 0.009 0.001 PHE C 121 TRP 0.004 0.001 TRP B 62 HIS 0.004 0.000 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (12192) covalent geometry : angle 0.53142 / 0.30 (16444) hydrogen bonds : bond 0.26378 / 17.69 ( 542) hydrogen bonds : angle 7.96693 / 5.46 ( 1542) metal coordination : bond 0.01959 / 1.00 ( 16) metal coordination : angle 1.93623 / 1.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.8206 (mtp) cc_final: 0.7940 (mtm) REVERT: A 267 MET cc_start: 0.6945 (ptm) cc_final: 0.6590 (ttp) REVERT: A 288 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7695 (t0) REVERT: A 342 MET cc_start: 0.6697 (mmm) cc_final: 0.6383 (mtp) REVERT: C 41 MET cc_start: 0.8628 (mtp) cc_final: 0.8239 (mtp) REVERT: C 223 ASP cc_start: 0.8056 (m-30) cc_final: 0.7819 (m-30) REVERT: C 342 MET cc_start: 0.7398 (mmm) cc_final: 0.6915 (mmm) outliers start: 15 outliers final: 9 residues processed: 161 average time/residue: 0.0925 time to fit residues: 22.1263 Evaluate side-chains 151 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 57 ASN Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 217 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.172007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135870 restraints weight = 14366.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.139700 restraints weight = 9346.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.142305 restraints weight = 6993.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.144044 restraints weight = 5744.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.145107 restraints weight = 5025.924| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12208 Z= 0.145 Angle : 0.521 5.991 16456 Z= 0.278 Chirality : 0.043 0.143 1720 Planarity : 0.005 0.039 2172 Dihedral : 5.194 66.153 1679 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.76 % Allowed : 14.89 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.21), residues: 1476 helix: 0.23 (0.18), residues: 760 sheet: 0.70 (0.48), residues: 128 loop : -0.29 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 328 TYR 0.010 0.001 TYR A 191 PHE 0.009 0.001 PHE A 111 TRP 0.004 0.001 TRP A 152 HIS 0.005 0.001 HIS D 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (12192) covalent geometry : angle 0.51971 / 0.28 (16444) hydrogen bonds : bond 0.04989 / 3.40 ( 542) hydrogen bonds : angle 4.84952 / 3.35 ( 1542) metal coordination : bond 0.02006 / 1.11 ( 16) metal coordination : angle 1.31169 / 0.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 0.298 Fit side-chains REVERT: A 41 MET cc_start: 0.8862 (mmm) cc_final: 0.8416 (mtm) REVERT: A 244 MET cc_start: 0.8218 (mtp) cc_final: 0.7972 (mtm) REVERT: A 338 TYR cc_start: 0.8563 (m-80) cc_final: 0.8074 (m-80) REVERT: A 342 MET cc_start: 0.7157 (mmm) cc_final: 0.6898 (mmm) REVERT: B 234 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7186 (mt0) REVERT: C 41 MET cc_start: 0.8620 (mtp) cc_final: 0.8189 (mtp) REVERT: C 320 ARG cc_start: 0.7552 (ttm170) cc_final: 0.6963 (ttp-170) REVERT: C 338 TYR cc_start: 0.8514 (m-80) cc_final: 0.8090 (m-80) outliers start: 48 outliers final: 32 residues processed: 188 average time/residue: 0.0863 time to fit residues: 24.4202 Evaluate side-chains 175 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 57 ASN Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 281 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 14 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 94 GLN ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.169189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133419 restraints weight = 14563.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137162 restraints weight = 9472.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.139695 restraints weight = 7125.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.141313 restraints weight = 5860.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142524 restraints weight = 5149.136| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12208 Z= 0.205 Angle : 0.548 6.526 16456 Z= 0.288 Chirality : 0.045 0.153 1720 Planarity : 0.005 0.045 2172 Dihedral : 5.081 50.662 1676 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.15 % Allowed : 15.60 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.21), residues: 1476 helix: 0.54 (0.19), residues: 760 sheet: 0.76 (0.44), residues: 156 loop : -0.50 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 328 TYR 0.010 0.001 TYR D 191 PHE 0.011 0.002 PHE A 19 TRP 0.005 0.001 TRP A 152 HIS 0.010 0.002 HIS B 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.20 (12192) covalent geometry : angle 0.54668 / 0.29 (16444) hydrogen bonds : bond 0.04662 / 3.17 ( 542) hydrogen bonds : angle 4.61832 / 3.19 ( 1542) metal coordination : bond 0.02854 / 1.56 ( 16) metal coordination : angle 1.40211 / 0.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 145 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.8892 (mmm) cc_final: 0.8482 (mtm) REVERT: A 244 MET cc_start: 0.8224 (mtp) cc_final: 0.7974 (mtm) REVERT: A 338 TYR cc_start: 0.8680 (m-80) cc_final: 0.8162 (m-80) REVERT: B 234 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7250 (mt0) REVERT: C 320 ARG cc_start: 0.7659 (ttm170) cc_final: 0.7152 (ttp-170) REVERT: C 338 TYR cc_start: 0.8658 (m-80) cc_final: 0.8211 (m-80) outliers start: 53 outliers final: 35 residues processed: 192 average time/residue: 0.0867 time to fit residues: 25.0781 Evaluate side-chains 174 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 57 ASN Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 317 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 114 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN C 180 ASN C 317 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.170997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135198 restraints weight = 14468.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.139033 restraints weight = 9368.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141611 restraints weight = 7009.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.143269 restraints weight = 5752.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.144360 restraints weight = 5042.524| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12208 Z= 0.154 Angle : 0.513 6.195 16456 Z= 0.267 Chirality : 0.044 0.195 1720 Planarity : 0.004 0.044 2172 Dihedral : 4.768 48.709 1674 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.61 % Allowed : 15.67 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1476 helix: 0.74 (0.19), residues: 760 sheet: 0.72 (0.41), residues: 176 loop : -0.50 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 328 TYR 0.008 0.001 TYR D 191 PHE 0.010 0.001 PHE B 173 TRP 0.005 0.001 TRP A 152 HIS 0.007 0.001 HIS D 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (12192) covalent geometry : angle 0.51210 / 0.27 (16444) hydrogen bonds : bond 0.04002 / 2.73 ( 542) hydrogen bonds : angle 4.38341 / 3.02 ( 1542) metal coordination : bond 0.02328 / 1.28 ( 16) metal coordination : angle 1.30265 / 0.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 149 time to evaluate : 0.423 Fit side-chains REVERT: A 244 MET cc_start: 0.8211 (mtp) cc_final: 0.7972 (mtm) REVERT: A 338 TYR cc_start: 0.8654 (m-80) cc_final: 0.8164 (m-80) REVERT: B 234 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7163 (mt0) REVERT: C 320 ARG cc_start: 0.7656 (ttm170) cc_final: 0.7136 (ttp-170) REVERT: C 338 TYR cc_start: 0.8606 (m-80) cc_final: 0.8179 (m-10) REVERT: D 229 GLU cc_start: 0.8128 (tp30) cc_final: 0.7355 (mm-30) REVERT: D 353 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7703 (mttm) outliers start: 46 outliers final: 31 residues processed: 188 average time/residue: 0.0869 time to fit residues: 24.4111 Evaluate side-chains 174 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 57 ASN Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 99 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.171286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135606 restraints weight = 14451.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.139452 restraints weight = 9365.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141915 restraints weight = 6999.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.143783 restraints weight = 5755.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144946 restraints weight = 5016.109| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12208 Z= 0.152 Angle : 0.509 6.153 16456 Z= 0.264 Chirality : 0.044 0.212 1720 Planarity : 0.004 0.040 2172 Dihedral : 4.732 48.604 1674 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.84 % Allowed : 16.38 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.22), residues: 1476 helix: 0.83 (0.19), residues: 760 sheet: 0.83 (0.44), residues: 156 loop : -0.46 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 328 TYR 0.015 0.001 TYR B 310 PHE 0.010 0.001 PHE B 173 TRP 0.004 0.001 TRP B 62 HIS 0.007 0.001 HIS D 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (12192) covalent geometry : angle 0.50837 / 0.26 (16444) hydrogen bonds : bond 0.03849 / 2.62 ( 542) hydrogen bonds : angle 4.26988 / 2.95 ( 1542) metal coordination : bond 0.02198 / 1.21 ( 16) metal coordination : angle 1.20130 / 0.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 0.411 Fit side-chains REVERT: A 244 MET cc_start: 0.8205 (mtp) cc_final: 0.7981 (mtm) REVERT: A 338 TYR cc_start: 0.8642 (m-80) cc_final: 0.8144 (m-80) REVERT: B 234 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7156 (mt0) REVERT: C 320 ARG cc_start: 0.7653 (ttm170) cc_final: 0.6998 (ttp-170) REVERT: C 338 TYR cc_start: 0.8600 (m-80) cc_final: 0.8172 (m-80) REVERT: D 125 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.5913 (mp0) REVERT: D 229 GLU cc_start: 0.8100 (tp30) cc_final: 0.7321 (mm-30) REVERT: D 353 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7702 (mttm) outliers start: 49 outliers final: 36 residues processed: 188 average time/residue: 0.0876 time to fit residues: 24.6324 Evaluate side-chains 181 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 57 ASN Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 52 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 146 optimal weight: 0.0670 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 87 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.172648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.136923 restraints weight = 14414.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.140841 restraints weight = 9311.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.143481 restraints weight = 6929.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.145249 restraints weight = 5666.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146461 restraints weight = 4932.040| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12208 Z= 0.131 Angle : 0.495 6.340 16456 Z= 0.255 Chirality : 0.043 0.149 1720 Planarity : 0.004 0.039 2172 Dihedral : 4.663 48.263 1674 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.00 % Allowed : 16.22 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.22), residues: 1476 helix: 0.90 (0.19), residues: 760 sheet: 0.85 (0.45), residues: 156 loop : -0.39 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 328 TYR 0.014 0.001 TYR D 310 PHE 0.009 0.001 PHE B 173 TRP 0.005 0.001 TRP B 62 HIS 0.006 0.001 HIS D 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (12192) covalent geometry : angle 0.49391 / 0.26 (16444) hydrogen bonds : bond 0.03658 / 2.49 ( 542) hydrogen bonds : angle 4.17546 / 2.88 ( 1542) metal coordination : bond 0.01860 / 1.03 ( 16) metal coordination : angle 1.07743 / 0.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 0.258 Fit side-chains REVERT: A 244 MET cc_start: 0.8179 (mtp) cc_final: 0.7956 (mtm) REVERT: A 338 TYR cc_start: 0.8608 (m-80) cc_final: 0.8082 (m-80) REVERT: B 190 VAL cc_start: 0.9148 (OUTLIER) cc_final: 0.8937 (t) REVERT: B 234 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7138 (mt0) REVERT: C 94 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.6824 (mp10) REVERT: C 320 ARG cc_start: 0.7627 (ttm170) cc_final: 0.6976 (ttp-170) REVERT: C 338 TYR cc_start: 0.8594 (m-80) cc_final: 0.8154 (m-80) REVERT: D 125 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.5914 (mp0) REVERT: D 229 GLU cc_start: 0.8089 (tp30) cc_final: 0.7315 (mm-30) REVERT: D 353 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7674 (mttm) outliers start: 51 outliers final: 36 residues processed: 188 average time/residue: 0.0814 time to fit residues: 23.1098 Evaluate side-chains 176 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 57 ASN Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 117 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 115 optimal weight: 0.0970 chunk 89 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.171938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136625 restraints weight = 14342.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140473 restraints weight = 9277.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.142906 restraints weight = 6937.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.144766 restraints weight = 5710.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145912 restraints weight = 4981.512| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12208 Z= 0.140 Angle : 0.506 6.780 16456 Z= 0.260 Chirality : 0.043 0.149 1720 Planarity : 0.004 0.038 2172 Dihedral : 4.675 48.703 1674 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.00 % Allowed : 16.30 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.22), residues: 1476 helix: 0.92 (0.19), residues: 760 sheet: 0.82 (0.44), residues: 156 loop : -0.40 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 328 TYR 0.013 0.001 TYR D 310 PHE 0.009 0.001 PHE B 173 TRP 0.005 0.001 TRP B 62 HIS 0.006 0.001 HIS D 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (12192) covalent geometry : angle 0.50575 / 0.26 (16444) hydrogen bonds : bond 0.03631 / 2.47 ( 542) hydrogen bonds : angle 4.15314 / 2.87 ( 1542) metal coordination : bond 0.01881 / 1.04 ( 16) metal coordination : angle 1.01977 / 0.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 139 time to evaluate : 0.273 Fit side-chains REVERT: A 244 MET cc_start: 0.8173 (mtp) cc_final: 0.7955 (mtm) REVERT: A 338 TYR cc_start: 0.8630 (m-80) cc_final: 0.8094 (m-80) REVERT: B 190 VAL cc_start: 0.9150 (OUTLIER) cc_final: 0.8930 (t) REVERT: B 234 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7125 (mt0) REVERT: C 94 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.6841 (mp10) REVERT: C 320 ARG cc_start: 0.7666 (ttm170) cc_final: 0.6998 (ttp-170) REVERT: C 338 TYR cc_start: 0.8613 (m-80) cc_final: 0.8115 (m-80) REVERT: D 125 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.5843 (mp0) REVERT: D 190 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8927 (t) REVERT: D 229 GLU cc_start: 0.8073 (tp30) cc_final: 0.7312 (mm-30) REVERT: D 353 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7681 (mttm) outliers start: 51 outliers final: 38 residues processed: 184 average time/residue: 0.0804 time to fit residues: 22.1718 Evaluate side-chains 179 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 57 ASN Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 70 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 chunk 125 optimal weight: 0.0670 chunk 62 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN A 276 HIS A 288 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 HIS ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.174948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139817 restraints weight = 14258.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143780 restraints weight = 9171.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.146421 restraints weight = 6826.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.148222 restraints weight = 5582.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.149288 restraints weight = 4860.233| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12208 Z= 0.104 Angle : 0.489 7.245 16456 Z= 0.250 Chirality : 0.042 0.146 1720 Planarity : 0.004 0.037 2172 Dihedral : 4.563 47.553 1674 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.45 % Allowed : 16.69 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.22), residues: 1476 helix: 1.04 (0.19), residues: 760 sheet: 0.91 (0.45), residues: 156 loop : -0.29 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 287 TYR 0.011 0.001 TYR D 310 PHE 0.008 0.001 PHE B 121 TRP 0.004 0.000 TRP B 62 HIS 0.004 0.001 HIS D 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (12192) covalent geometry : angle 0.48899 / 0.25 (16444) hydrogen bonds : bond 0.03352 / 2.30 ( 542) hydrogen bonds : angle 4.02357 / 2.79 ( 1542) metal coordination : bond 0.01207 / 0.68 ( 16) metal coordination : angle 0.79770 / 0.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 0.445 Fit side-chains REVERT: A 244 MET cc_start: 0.8139 (mtp) cc_final: 0.7783 (mtm) REVERT: A 267 MET cc_start: 0.6596 (ptm) cc_final: 0.6323 (ttp) REVERT: A 338 TYR cc_start: 0.8535 (m-80) cc_final: 0.8038 (m-80) REVERT: B 125 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6031 (mp0) REVERT: B 190 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8906 (t) REVERT: B 234 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7135 (mt0) REVERT: C 94 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.6860 (mp10) REVERT: C 320 ARG cc_start: 0.7577 (ttm170) cc_final: 0.6947 (ttp-170) REVERT: C 338 TYR cc_start: 0.8512 (m-80) cc_final: 0.8029 (m-80) REVERT: D 125 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.5828 (mp0) REVERT: D 190 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8922 (t) REVERT: D 229 GLU cc_start: 0.8089 (tp30) cc_final: 0.7328 (mm-30) REVERT: D 353 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7604 (mttm) outliers start: 44 outliers final: 29 residues processed: 180 average time/residue: 0.0808 time to fit residues: 22.2220 Evaluate side-chains 174 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 57 ASN Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 134 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN C 317 HIS ** D 94 GLN ** 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 = 0.4038 r_free = 0.4038 target = 0.175425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.140073 restraints weight = 14362.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.144046 restraints weight = 9266.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.146725 restraints weight = 6878.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148525 restraints weight = 5615.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.149693 restraints weight = 4888.442| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12208 Z= 0.113 Angle : 0.501 7.793 16456 Z= 0.255 Chirality : 0.042 0.151 1720 Planarity : 0.004 0.041 2172 Dihedral : 4.532 46.971 1674 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.98 % Allowed : 17.63 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.22), residues: 1476 helix: 1.05 (0.19), residues: 760 sheet: 1.04 (0.42), residues: 176 loop : -0.28 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 328 TYR 0.011 0.001 TYR D 310 PHE 0.021 0.001 PHE A 93 TRP 0.005 0.001 TRP B 62 HIS 0.006 0.001 HIS C 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (12192) covalent geometry : angle 0.50109 / 0.26 (16444) hydrogen bonds : bond 0.03310 / 2.26 ( 542) hydrogen bonds : angle 4.01496 / 2.78 ( 1542) metal coordination : bond 0.01281 / 0.72 ( 16) metal coordination : angle 0.74663 / 0.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.337 Fit side-chains REVERT: A 244 MET cc_start: 0.8127 (mtp) cc_final: 0.7754 (mtm) REVERT: A 338 TYR cc_start: 0.8554 (m-80) cc_final: 0.8075 (m-80) REVERT: B 125 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6026 (mp0) REVERT: B 190 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8915 (t) REVERT: B 234 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7131 (mt0) REVERT: C 94 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.6837 (mp10) REVERT: C 320 ARG cc_start: 0.7593 (ttm170) cc_final: 0.6982 (ttp-170) REVERT: C 338 TYR cc_start: 0.8498 (m-80) cc_final: 0.8142 (m-80) REVERT: D 125 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5855 (mp0) REVERT: D 190 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8920 (t) REVERT: D 229 GLU cc_start: 0.8088 (tp30) cc_final: 0.7326 (mm-30) REVERT: D 353 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7603 (mttm) outliers start: 38 outliers final: 26 residues processed: 174 average time/residue: 0.0846 time to fit residues: 22.2325 Evaluate side-chains 169 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 10 optimal weight: 0.0980 chunk 44 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.169672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134347 restraints weight = 14564.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138081 restraints weight = 9472.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140594 restraints weight = 7127.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.142155 restraints weight = 5878.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143423 restraints weight = 5166.852| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12208 Z= 0.213 Angle : 0.591 8.431 16456 Z= 0.302 Chirality : 0.046 0.185 1720 Planarity : 0.004 0.040 2172 Dihedral : 4.692 49.119 1672 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.13 % Allowed : 17.55 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.22), residues: 1476 helix: 0.84 (0.19), residues: 760 sheet: 0.81 (0.41), residues: 176 loop : -0.48 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 172 TYR 0.014 0.001 TYR B 310 PHE 0.011 0.002 PHE B 173 TRP 0.007 0.001 TRP B 62 HIS 0.011 0.002 HIS D 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.21 (12192) covalent geometry : angle 0.58989 / 0.30 (16444) hydrogen bonds : bond 0.03995 / 2.72 ( 542) hydrogen bonds : angle 4.24506 / 2.95 ( 1542) metal coordination : bond 0.02653 / 1.47 ( 16) metal coordination : angle 1.19494 / 0.71 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.417 Fit side-chains REVERT: A 41 MET cc_start: 0.8865 (mmm) cc_final: 0.8508 (mtm) REVERT: A 338 TYR cc_start: 0.8741 (m-80) cc_final: 0.8172 (m-80) REVERT: A 342 MET cc_start: 0.7369 (mmm) cc_final: 0.6855 (mmm) REVERT: B 234 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7177 (mt0) REVERT: C 94 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.7065 (mp10) REVERT: C 338 TYR cc_start: 0.8705 (m-80) cc_final: 0.8211 (m-80) REVERT: D 125 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.5888 (mp0) REVERT: D 353 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7760 (mttm) outliers start: 40 outliers final: 31 residues processed: 179 average time/residue: 0.0786 time to fit residues: 21.5420 Evaluate side-chains 177 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 30 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 8 optimal weight: 0.0070 chunk 107 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN A 317 HIS ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 HIS ** D 94 GLN ** 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 = 0.4014 r_free = 0.4014 target = 0.172933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137524 restraints weight = 14398.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141338 restraints weight = 9376.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143998 restraints weight = 7007.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145673 restraints weight = 5742.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146918 restraints weight = 5024.034| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12208 Z= 0.137 Angle : 0.538 8.180 16456 Z= 0.274 Chirality : 0.043 0.155 1720 Planarity : 0.004 0.038 2172 Dihedral : 4.584 47.822 1672 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.06 % Allowed : 17.71 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.22), residues: 1476 helix: 0.90 (0.19), residues: 760 sheet: 0.81 (0.42), residues: 176 loop : -0.38 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 328 TYR 0.011 0.001 TYR B 310 PHE 0.012 0.001 PHE B 111 TRP 0.005 0.001 TRP B 62 HIS 0.006 0.001 HIS D 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (12192) covalent geometry : angle 0.53713 / 0.27 (16444) hydrogen bonds : bond 0.03601 / 2.47 ( 542) hydrogen bonds : angle 4.12466 / 2.87 ( 1542) metal coordination : bond 0.01778 / 1.00 ( 16) metal coordination : angle 1.06152 / 0.62 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1634.01 seconds wall clock time: 28 minutes 51.87 seconds (1731.87 seconds total)