Starting phenix.real_space_refine on Fri Aug 7 02:12:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9of2_70418/08_2026/9of2_70418.cif Found real_map, /net/cci-nas-00/data/ceres_data/9of2_70418/08_2026/9of2_70418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9of2_70418/08_2026/9of2_70418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9of2_70418/08_2026/9of2_70418.map" model { file = "/net/cci-nas-00/data/ceres_data/9of2_70418/08_2026/9of2_70418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9of2_70418/08_2026/9of2_70418.cif" } resolution = 3.7 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= 0.002 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 54 5.49 5 S 81 5.16 5 C 6237 2.51 5 N 1781 2.21 5 O 1996 1.98 5 H 8765 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 18914 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 545 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "B" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 562 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "C" Number of atoms: 4874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 4874 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 4 Chain: "D" Number of atoms: 4092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 4092 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 6 Chain: "E" Number of atoms: 4771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 4771 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain breaks: 3 Chain: "F" Number of atoms: 4070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 4070 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 9, 'TRANS': 242} Chain breaks: 6 Time building chain proxies: 3.12, per 1000 atoms: 0.16 Number of scatterers: 18914 At special positions: 0 Unit cell: (96.216, 112.252, 123.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 81 16.00 P 54 15.00 O 1996 8.00 N 1781 7.00 C 6237 6.00 H 8765 1.00 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: 1.60 Conformation dependent library (CDL) restraints added in 558.8 milliseconds 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 10 sheets defined 42.4% alpha, 23.9% beta 20 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'C' and resid 15 through 38 removed outlier: 3.561A pdb=" N ASP C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 41 No H-bonds generated for 'chain 'C' and resid 39 through 41' Processing helix chain 'C' and resid 44 through 51 removed outlier: 3.966A pdb=" N HIS C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 73 Processing helix chain 'C' and resid 89 through 95 removed outlier: 4.184A pdb=" N LYS C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 120 removed outlier: 4.281A pdb=" N PHE C 118 " --> pdb=" O ASN C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.975A pdb=" N THR C 135 " --> pdb=" O PHE C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.525A pdb=" N MET C 235 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 265 removed outlier: 4.444A pdb=" N GLU C 263 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 280 Processing helix chain 'C' and resid 282 through 284 No H-bonds generated for 'chain 'C' and resid 282 through 284' Processing helix chain 'C' and resid 285 through 300 Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'D' and resid 94 through 116 Processing helix chain 'D' and resid 128 through 142 removed outlier: 3.803A pdb=" N SER D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 173 removed outlier: 3.879A pdb=" N LYS D 165 " --> pdb=" O ASP D 161 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N HIS D 166 " --> pdb=" O GLN D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 198 removed outlier: 3.579A pdb=" N VAL D 196 " --> pdb=" O SER D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 205 removed outlier: 3.627A pdb=" N TRP D 204 " --> pdb=" O PRO D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 213 removed outlier: 3.652A pdb=" N VAL D 213 " --> pdb=" O TYR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 226 removed outlier: 3.596A pdb=" N LEU D 221 " --> pdb=" O ASP D 217 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU D 223 " --> pdb=" O ASP D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 384 Processing helix chain 'D' and resid 387 through 392 removed outlier: 3.846A pdb=" N LEU D 391 " --> pdb=" O GLN D 387 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 387 through 392' Processing helix chain 'D' and resid 404 through 416 removed outlier: 3.800A pdb=" N LEU D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 416 " --> pdb=" O PHE D 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 36 removed outlier: 3.637A pdb=" N ARG E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 54 through 74 removed outlier: 3.713A pdb=" N SER E 62 " --> pdb=" O ARG E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 90 through 95 Processing helix chain 'E' and resid 114 through 119 removed outlier: 4.129A pdb=" N PHE E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 removed outlier: 4.198A pdb=" N THR E 127 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 134 Processing helix chain 'E' and resid 136 through 138 No H-bonds generated for 'chain 'E' and resid 136 through 138' Processing helix chain 'E' and resid 139 through 148 removed outlier: 3.542A pdb=" N ILE E 143 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER E 148 " --> pdb=" O ARG E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 188 Processing helix chain 'E' and resid 231 through 235 removed outlier: 3.759A pdb=" N MET E 235 " --> pdb=" O PRO E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 265 removed outlier: 3.517A pdb=" N LEU E 264 " --> pdb=" O ARG E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 272 removed outlier: 3.572A pdb=" N LEU E 272 " --> pdb=" O PRO E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 280 Processing helix chain 'E' and resid 282 through 284 No H-bonds generated for 'chain 'E' and resid 282 through 284' Processing helix chain 'E' and resid 285 through 299 Processing helix chain 'F' and resid 95 through 116 Processing helix chain 'F' and resid 129 through 142 removed outlier: 3.535A pdb=" N ARG F 133 " --> pdb=" O LEU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 172 removed outlier: 3.643A pdb=" N GLU F 170 " --> pdb=" O HIS F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 194 removed outlier: 3.511A pdb=" N THR F 194 " --> pdb=" O ASP F 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 191 through 194' Processing helix chain 'F' and resid 208 through 213 removed outlier: 3.998A pdb=" N VAL F 213 " --> pdb=" O TYR F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 217 through 226 Processing helix chain 'F' and resid 379 through 384 Processing helix chain 'F' and resid 395 through 400 removed outlier: 3.920A pdb=" N PHE F 399 " --> pdb=" O ASN F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 403 No H-bonds generated for 'chain 'F' and resid 401 through 403' Processing helix chain 'F' and resid 404 through 416 removed outlier: 4.144A pdb=" N VAL F 416 " --> pdb=" O PHE F 412 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 108 through 111 removed outlier: 3.906A pdb=" N PHE C 110 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 223 " --> pdb=" O GLN C 198 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR C 196 " --> pdb=" O MET C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 254 through 257 removed outlier: 6.667A pdb=" N ARG C 247 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N CYS C 257 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU C 245 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N CYS C 336 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 340 " --> pdb=" O GLN C 322 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN C 322 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 302 " --> pdb=" O GLY C 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 307 through 310 Processing sheet with id=AA4, first strand: chain 'D' and resid 186 through 189 removed outlier: 6.709A pdb=" N VAL D 186 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER D 180 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR D 188 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 177 " --> pdb=" O ALA D 339 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D 304 " --> pdb=" O MET D 267 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS D 265 " --> pdb=" O VAL D 306 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 364 through 367 removed outlier: 4.248A pdb=" N TYR D 456 " --> pdb=" O PHE D 446 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 364 through 367 removed outlier: 4.248A pdb=" N TYR D 456 " --> pdb=" O PHE D 446 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET D 439 " --> pdb=" O PHE D 427 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE D 427 " --> pdb=" O MET D 439 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 425 " --> pdb=" O THR D 441 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL D 422 " --> pdb=" O SER F 424 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N MET F 426 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N SER D 424 " --> pdb=" O MET F 426 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE F 427 " --> pdb=" O MET F 439 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER F 442 " --> pdb=" O THR F 460 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR F 460 " --> pdb=" O SER F 442 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR F 456 " --> pdb=" O PHE F 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 110 through 111 removed outlier: 4.334A pdb=" N PHE E 110 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE E 223 " --> pdb=" O GLN E 198 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN E 198 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR E 196 " --> pdb=" O MET E 225 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 254 through 257 removed outlier: 6.981A pdb=" N ILE E 326 " --> pdb=" O GLN E 335 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE E 337 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR E 324 " --> pdb=" O ILE E 337 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N CYS E 339 " --> pdb=" O GLN E 322 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLN E 322 " --> pdb=" O CYS E 339 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN E 341 " --> pdb=" O GLU E 320 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU E 320 " --> pdb=" O ASN E 341 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL E 343 " --> pdb=" O TRP E 318 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N TRP E 318 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL E 302 " --> pdb=" O GLY E 323 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 254 through 257 removed outlier: 6.981A pdb=" N ILE E 326 " --> pdb=" O GLN E 335 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE E 337 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR E 324 " --> pdb=" O ILE E 337 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N CYS E 339 " --> pdb=" O GLN E 322 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLN E 322 " --> pdb=" O CYS E 339 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN E 341 " --> pdb=" O GLU E 320 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU E 320 " --> pdb=" O ASN E 341 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL E 343 " --> pdb=" O TRP E 318 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N TRP E 318 " --> pdb=" O VAL E 343 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 186 through 189 removed outlier: 6.772A pdb=" N VAL F 186 " --> pdb=" O SER F 180 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER F 180 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR F 188 " --> pdb=" O ILE F 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA F 339 " --> pdb=" O PHE F 177 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR F 309 " --> pdb=" O ILE F 340 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY F 310 " --> pdb=" O ARG F 261 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 4.68 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 8726 1.02 - 1.22: 42 1.22 - 1.42: 4320 1.42 - 1.61: 6010 1.61 - 1.81: 126 Bond restraints: 19224 Sorted by residual: bond pdb=" ND2 ASN F 198 " pdb="HD21 ASN F 198 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN F 198 " pdb="HD22 ASN F 198 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" O3' DG B 10 " pdb=" P DC B 11 " ideal model delta sigma weight residual 1.607 1.644 -0.037 1.20e-02 6.94e+03 9.60e+00 bond pdb=" C3' DC B 26 " pdb=" C2' DC B 26 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.29e+00 bond pdb=" C3' DG B 31 " pdb=" C2' DG B 31 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.23e+00 ... (remaining 19219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 32887 1.18 - 2.37: 1162 2.37 - 3.55: 97 3.55 - 4.74: 23 4.74 - 5.92: 7 Bond angle restraints: 34176 Sorted by residual: angle pdb=" N3 DT A 23 " pdb=" C4 DT A 23 " pdb=" O4 DT A 23 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT A 34 " pdb=" C4 DT A 34 " pdb=" O4 DT A 34 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" O4' DG B 19 " pdb=" C4' DG B 19 " pdb=" C3' DG B 19 " ideal model delta sigma weight residual 106.00 103.49 2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" O4' DG B 17 " pdb=" C4' DG B 17 " pdb=" C3' DG B 17 " ideal model delta sigma weight residual 106.00 103.52 2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT A 32 " pdb=" C4 DT A 32 " pdb=" O4 DT A 32 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.62e+01 ... (remaining 34171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.39: 8143 25.39 - 50.79: 768 50.79 - 76.18: 160 76.18 - 101.57: 13 101.57 - 126.97: 1 Dihedral angle restraints: 9085 sinusoidal: 5176 harmonic: 3909 Sorted by residual: dihedral pdb=" CA HIS D 214 " pdb=" C HIS D 214 " pdb=" N PRO D 215 " pdb=" CA PRO D 215 " ideal model delta harmonic sigma weight residual 180.00 -161.90 -18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA TYR E 35 " pdb=" C TYR E 35 " pdb=" N GLU E 36 " pdb=" CA GLU E 36 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" C4' DA A 40 " pdb=" C3' DA A 40 " pdb=" O3' DA A 40 " pdb=" P DG A 41 " ideal model delta sinusoidal sigma weight residual 220.00 93.03 126.97 1 3.50e+01 8.16e-04 1.25e+01 ... (remaining 9082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1041 0.029 - 0.057: 349 0.057 - 0.086: 102 0.086 - 0.114: 94 0.114 - 0.143: 24 Chirality restraints: 1610 Sorted by residual: chirality pdb=" C3' DT A 34 " pdb=" C4' DT A 34 " pdb=" O3' DT A 34 " pdb=" C2' DT A 34 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" P DC B 11 " pdb=" OP1 DC B 11 " pdb=" OP2 DC B 11 " pdb=" O5' DC B 11 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" C3' DC A 29 " pdb=" C4' DC A 29 " pdb=" O3' DC A 29 " pdb=" C2' DC A 29 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 1607 not shown) Planarity restraints: 2667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 198 " -0.176 2.00e-02 2.50e+03 1.76e-01 4.64e+02 pdb=" CG ASN F 198 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN F 198 " 0.168 2.00e-02 2.50e+03 pdb=" ND2 ASN F 198 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN F 198 " 0.249 2.00e-02 2.50e+03 pdb="HD22 ASN F 198 " -0.253 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN F 198 " 0.019 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" N GLN F 199 " -0.063 2.00e-02 2.50e+03 pdb=" CA GLN F 199 " 0.015 2.00e-02 2.50e+03 pdb=" H GLN F 199 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 311 " -0.013 2.00e-02 2.50e+03 2.39e-02 5.72e+00 pdb=" N LYS C 312 " 0.041 2.00e-02 2.50e+03 pdb=" CA LYS C 312 " -0.010 2.00e-02 2.50e+03 pdb=" H LYS C 312 " -0.018 2.00e-02 2.50e+03 ... (remaining 2664 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 1859 2.24 - 2.83: 38225 2.83 - 3.42: 43949 3.42 - 4.01: 61197 4.01 - 4.60: 93249 Nonbonded interactions: 238479 Sorted by model distance: nonbonded pdb=" OE1 GLU C 17 " pdb=" H GLU C 17 " model vdw 1.649 2.450 nonbonded pdb=" H SER E 249 " pdb=" O LYS E 253 " model vdw 1.652 2.450 nonbonded pdb=" O GLN C 123 " pdb=" HG1 THR C 127 " model vdw 1.676 2.450 nonbonded pdb=" HB2 SER C 304 " pdb="HG21 THR C 321 " model vdw 1.678 2.440 nonbonded pdb=" O GLN E 123 " pdb=" HG1 THR E 127 " model vdw 1.697 2.450 ... (remaining 238474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and ((resid 20 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid \ 21 and (name N or name CA or name C or name O or name CB or name CG or name OD1 \ or name OD2)) or (resid 22 and (name N or name CA or name C or name O or name CB \ )) or resid 23 through 74 or resid 87 through 203 or resid 219 through 359)) selection = (chain 'E' and (resid 20 through 178 or (resid 179 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)) or (resid 180 and (name N or name CA or name C or name O )) or re \ sid 181 through 327 or (resid 328 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name ND2)) or (resid 329 and (name N or name C \ A or name C or name O or name CB or name CG or name CD )) or resid 333 through 3 \ 59)) } ncs_group { reference = (chain 'D' and (resid 94 through 118 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD )) or (resid 127 and (name N or n \ ame CA or name C or name O or name CB or name CG or name OD1 or name OD2)) or re \ sid 128 through 269 or resid 303 through 464)) selection = (chain 'F' and (resid 94 through 142 or resid 156 through 314 or resid 335 throu \ gh 429 or (resid 430 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 431 th \ rough 464)) } 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: 5.810 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: 0.110 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.500 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 0.040 10459 Z= 0.266 Angle : 0.511 5.922 14329 Z= 0.389 Chirality : 0.040 0.143 1610 Planarity : 0.002 0.039 1626 Dihedral : 21.040 126.967 4002 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 25.63 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.29), residues: 1069 helix: 2.24 (0.31), residues: 346 sheet: -1.09 (0.37), residues: 240 loop : 0.21 (0.31), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 26 TYR 0.004 0.001 TYR C 316 PHE 0.004 0.001 PHE C 98 TRP 0.002 0.000 TRP D 438 HIS 0.003 0.000 HIS D 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.27 (10459) covalent geometry : angle 0.51075 / 0.39 (14329) hydrogen bonds : bond 0.22613 / 25.41 ( 412) hydrogen bonds : angle 9.32339 / 11.61 ( 1121) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 MET cc_start: 0.8936 (tpp) cc_final: 0.8683 (mmm) REVERT: D 159 LEU cc_start: 0.8489 (mm) cc_final: 0.8286 (mm) REVERT: D 160 THR cc_start: 0.8872 (p) cc_final: 0.8642 (p) REVERT: E 119 MET cc_start: 0.8921 (mpp) cc_final: 0.8434 (mmt) REVERT: E 252 MET cc_start: 0.8510 (mmp) cc_final: 0.8206 (tpt) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2481 time to fit residues: 75.5073 Evaluate side-chains 116 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.115805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.091946 restraints weight = 53470.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.095865 restraints weight = 25706.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098426 restraints weight = 15978.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.099979 restraints weight = 11637.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.101121 restraints weight = 9491.781| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 10459 Z= 0.227 Angle : 0.575 8.478 14329 Z= 0.326 Chirality : 0.042 0.188 1610 Planarity : 0.004 0.038 1626 Dihedral : 19.121 140.367 1771 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.26 % Allowed : 25.63 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.28), residues: 1069 helix: 1.97 (0.30), residues: 346 sheet: -1.25 (0.32), residues: 279 loop : -0.16 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.007 0.001 TYR E 202 PHE 0.017 0.001 PHE C 134 TRP 0.005 0.001 TRP E 190 HIS 0.005 0.001 HIS E 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.23 (10459) covalent geometry : angle 0.57535 / 0.33 (14329) hydrogen bonds : bond 0.06107 / 6.91 ( 412) hydrogen bonds : angle 6.23128 / 7.93 ( 1121) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 MET cc_start: 0.8901 (tpp) cc_final: 0.8658 (mmm) REVERT: D 214 HIS cc_start: 0.6914 (OUTLIER) cc_final: 0.6084 (p-80) REVERT: E 119 MET cc_start: 0.9129 (mpp) cc_final: 0.8760 (mmt) REVERT: E 252 MET cc_start: 0.9253 (mmp) cc_final: 0.8948 (tpt) REVERT: F 134 MET cc_start: 0.8523 (mtm) cc_final: 0.8314 (mtm) outliers start: 13 outliers final: 6 residues processed: 121 average time/residue: 0.2410 time to fit residues: 40.4385 Evaluate side-chains 109 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 400 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 41 optimal weight: 0.0980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 GLN D 214 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.114834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.090949 restraints weight = 52742.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.094785 restraints weight = 25240.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.097325 restraints weight = 15655.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.098992 restraints weight = 11365.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099962 restraints weight = 9148.635| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10459 Z= 0.143 Angle : 0.497 6.039 14329 Z= 0.283 Chirality : 0.040 0.196 1610 Planarity : 0.003 0.037 1626 Dihedral : 18.833 139.719 1771 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.84 % Allowed : 24.66 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.28), residues: 1069 helix: 1.82 (0.30), residues: 349 sheet: -1.27 (0.32), residues: 272 loop : -0.28 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 440 TYR 0.008 0.001 TYR C 327 PHE 0.017 0.001 PHE E 244 TRP 0.006 0.001 TRP F 438 HIS 0.008 0.001 HIS D 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (10459) covalent geometry : angle 0.49650 / 0.28 (14329) hydrogen bonds : bond 0.04776 / 5.41 ( 412) hydrogen bonds : angle 5.67505 / 7.25 ( 1121) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 289 MET cc_start: 0.9222 (mmm) cc_final: 0.8986 (mmm) REVERT: E 119 MET cc_start: 0.9119 (mpp) cc_final: 0.8734 (mmt) REVERT: E 179 ARG cc_start: 0.8096 (mtm180) cc_final: 0.7821 (mtp180) REVERT: E 252 MET cc_start: 0.9256 (mmp) cc_final: 0.8852 (tpt) outliers start: 19 outliers final: 13 residues processed: 126 average time/residue: 0.2294 time to fit residues: 40.4221 Evaluate side-chains 114 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 CYS Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 400 CYS Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 461 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.119946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.095579 restraints weight = 51901.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.099595 restraints weight = 25147.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.102178 restraints weight = 15840.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.103755 restraints weight = 11642.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.104849 restraints weight = 9544.047| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10459 Z= 0.180 Angle : 0.512 6.639 14329 Z= 0.292 Chirality : 0.040 0.223 1610 Planarity : 0.003 0.038 1626 Dihedral : 18.717 141.346 1771 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.93 % Allowed : 24.76 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.27), residues: 1069 helix: 1.65 (0.30), residues: 357 sheet: -1.33 (0.31), residues: 277 loop : -0.49 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 99 TYR 0.007 0.001 TYR F 188 PHE 0.015 0.001 PHE E 244 TRP 0.006 0.001 TRP F 438 HIS 0.034 0.001 HIS D 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (10459) covalent geometry : angle 0.51247 / 0.29 (14329) hydrogen bonds : bond 0.04288 / 4.87 ( 412) hydrogen bonds : angle 5.31741 / 6.81 ( 1121) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 32 GLU cc_start: 0.7852 (tp30) cc_final: 0.7500 (tp30) REVERT: E 119 MET cc_start: 0.9139 (mpp) cc_final: 0.8730 (mmt) REVERT: E 179 ARG cc_start: 0.8072 (mtm180) cc_final: 0.7841 (mtp180) outliers start: 20 outliers final: 17 residues processed: 120 average time/residue: 0.2178 time to fit residues: 37.2333 Evaluate side-chains 112 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 CYS Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 400 CYS Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 461 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 GLN D 214 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.119257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.094902 restraints weight = 51907.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.098885 restraints weight = 25106.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.101450 restraints weight = 15850.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103067 restraints weight = 11689.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.103954 restraints weight = 9546.862| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10459 Z= 0.161 Angle : 0.488 9.245 14329 Z= 0.277 Chirality : 0.039 0.158 1610 Planarity : 0.003 0.038 1626 Dihedral : 18.622 140.879 1771 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.74 % Allowed : 24.47 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.27), residues: 1069 helix: 1.55 (0.30), residues: 363 sheet: -1.37 (0.31), residues: 277 loop : -0.54 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 100 TYR 0.007 0.001 TYR C 342 PHE 0.014 0.001 PHE E 244 TRP 0.005 0.001 TRP F 438 HIS 0.023 0.001 HIS D 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (10459) covalent geometry : angle 0.48776 / 0.28 (14329) hydrogen bonds : bond 0.04076 / 4.61 ( 412) hydrogen bonds : angle 5.14184 / 6.58 ( 1121) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 119 MET cc_start: 0.9122 (mpp) cc_final: 0.8715 (mmt) REVERT: E 179 ARG cc_start: 0.8105 (mtm180) cc_final: 0.7858 (mtp180) REVERT: E 252 MET cc_start: 0.9050 (mmt) cc_final: 0.8827 (mmm) outliers start: 18 outliers final: 16 residues processed: 107 average time/residue: 0.2224 time to fit residues: 33.5741 Evaluate side-chains 110 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 CYS Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 461 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.118540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.094364 restraints weight = 51196.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.098278 restraints weight = 24826.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.100795 restraints weight = 15712.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.102430 restraints weight = 11624.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103351 restraints weight = 9491.953| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10459 Z= 0.155 Angle : 0.477 7.791 14329 Z= 0.270 Chirality : 0.039 0.156 1610 Planarity : 0.003 0.038 1626 Dihedral : 18.588 142.252 1771 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.03 % Allowed : 23.69 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.27), residues: 1069 helix: 1.64 (0.30), residues: 357 sheet: -1.43 (0.31), residues: 277 loop : -0.47 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 342 TYR 0.007 0.001 TYR C 342 PHE 0.014 0.001 PHE E 244 TRP 0.005 0.001 TRP F 438 HIS 0.003 0.001 HIS E 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (10459) covalent geometry : angle 0.47651 / 0.27 (14329) hydrogen bonds : bond 0.03937 / 4.46 ( 412) hydrogen bonds : angle 5.03207 / 6.43 ( 1121) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 289 MET cc_start: 0.9126 (mmm) cc_final: 0.8861 (mmm) REVERT: E 119 MET cc_start: 0.9099 (mpp) cc_final: 0.8702 (mmt) REVERT: E 179 ARG cc_start: 0.8120 (mtm180) cc_final: 0.7871 (mtp180) REVERT: E 252 MET cc_start: 0.9092 (mmt) cc_final: 0.8881 (mmm) outliers start: 21 outliers final: 17 residues processed: 112 average time/residue: 0.2096 time to fit residues: 33.2501 Evaluate side-chains 110 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 CYS Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 461 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 2 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.114005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.089724 restraints weight = 51291.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.093495 restraints weight = 25177.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.095975 restraints weight = 16043.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.097513 restraints weight = 11903.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.098501 restraints weight = 9812.268| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10459 Z= 0.268 Angle : 0.565 4.868 14329 Z= 0.319 Chirality : 0.041 0.163 1610 Planarity : 0.004 0.045 1626 Dihedral : 18.573 145.600 1771 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.71 % Allowed : 23.40 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.27), residues: 1069 helix: 1.23 (0.29), residues: 355 sheet: -1.69 (0.31), residues: 279 loop : -0.85 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 100 TYR 0.015 0.002 TYR D 450 PHE 0.018 0.002 PHE E 244 TRP 0.008 0.001 TRP F 438 HIS 0.006 0.001 HIS C 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.27 (10459) covalent geometry : angle 0.56525 / 0.32 (14329) hydrogen bonds : bond 0.04813 / 5.45 ( 412) hydrogen bonds : angle 5.16020 / 6.59 ( 1121) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 179 ARG cc_start: 0.8146 (mtm180) cc_final: 0.7896 (mtp180) outliers start: 28 outliers final: 18 residues processed: 115 average time/residue: 0.1860 time to fit residues: 30.5279 Evaluate side-chains 105 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 CYS Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 400 CYS Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 441 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 97 optimal weight: 0.4980 chunk 42 optimal weight: 0.3980 chunk 60 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.116462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.092581 restraints weight = 50610.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.096423 restraints weight = 24027.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.098968 restraints weight = 15194.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.100554 restraints weight = 11158.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.101445 restraints weight = 9106.932| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10459 Z= 0.112 Angle : 0.466 4.594 14329 Z= 0.264 Chirality : 0.039 0.160 1610 Planarity : 0.003 0.038 1626 Dihedral : 18.496 145.151 1771 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.35 % Allowed : 24.37 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.27), residues: 1069 helix: 1.51 (0.30), residues: 354 sheet: -1.55 (0.31), residues: 282 loop : -0.50 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 185 TYR 0.010 0.001 TYR D 450 PHE 0.014 0.001 PHE E 244 TRP 0.007 0.001 TRP F 438 HIS 0.004 0.001 HIS E 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (10459) covalent geometry : angle 0.46552 / 0.26 (14329) hydrogen bonds : bond 0.03807 / 4.29 ( 412) hydrogen bonds : angle 4.86172 / 6.24 ( 1121) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 289 MET cc_start: 0.9163 (mmm) cc_final: 0.8608 (mmm) REVERT: D 343 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8000 (mp) REVERT: E 179 ARG cc_start: 0.8110 (mtm180) cc_final: 0.7874 (mtp180) outliers start: 14 outliers final: 11 residues processed: 103 average time/residue: 0.2290 time to fit residues: 33.0813 Evaluate side-chains 100 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 408 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 76 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.116612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.092404 restraints weight = 51034.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.096389 restraints weight = 24698.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.098941 restraints weight = 15503.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.100563 restraints weight = 11390.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.101454 restraints weight = 9281.379| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10459 Z= 0.135 Angle : 0.464 4.559 14329 Z= 0.262 Chirality : 0.039 0.157 1610 Planarity : 0.003 0.037 1626 Dihedral : 18.469 145.635 1771 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.64 % Allowed : 23.98 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.27), residues: 1069 helix: 1.60 (0.30), residues: 354 sheet: -1.53 (0.31), residues: 279 loop : -0.48 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 185 TYR 0.008 0.001 TYR D 450 PHE 0.013 0.001 PHE F 363 TRP 0.007 0.001 TRP F 438 HIS 0.003 0.001 HIS D 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10459) covalent geometry : angle 0.46355 / 0.26 (14329) hydrogen bonds : bond 0.03729 / 4.25 ( 412) hydrogen bonds : angle 4.76170 / 6.07 ( 1121) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 289 MET cc_start: 0.9173 (mmm) cc_final: 0.8638 (mmm) REVERT: D 343 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8018 (mp) REVERT: E 179 ARG cc_start: 0.8103 (mtm180) cc_final: 0.7875 (mtp180) REVERT: E 235 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7560 (mtt) outliers start: 17 outliers final: 13 residues processed: 101 average time/residue: 0.2248 time to fit residues: 32.0004 Evaluate side-chains 101 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 235 MET Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 433 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 106 optimal weight: 0.0870 chunk 6 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.116684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.092622 restraints weight = 50970.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.096523 restraints weight = 24386.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099043 restraints weight = 15399.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.100642 restraints weight = 11363.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.101541 restraints weight = 9265.300| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 10459 Z= 0.181 Angle : 0.766 59.199 14329 Z= 0.477 Chirality : 0.039 0.225 1610 Planarity : 0.003 0.037 1626 Dihedral : 18.467 145.643 1771 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.45 % Allowed : 24.47 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.27), residues: 1069 helix: 1.60 (0.30), residues: 354 sheet: -1.53 (0.31), residues: 279 loop : -0.48 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 185 TYR 0.012 0.001 TYR F 188 PHE 0.012 0.001 PHE F 363 TRP 0.006 0.001 TRP F 438 HIS 0.003 0.000 HIS D 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 (10459) covalent geometry : angle 0.76606 / 0.48 (14329) hydrogen bonds : bond 0.03701 / 4.22 ( 412) hydrogen bonds : angle 4.75677 / 6.07 ( 1121) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 289 MET cc_start: 0.9176 (mmm) cc_final: 0.8636 (mmm) REVERT: D 343 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8017 (mp) REVERT: E 179 ARG cc_start: 0.8102 (mtm180) cc_final: 0.7872 (mtp180) REVERT: E 235 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7511 (mtt) outliers start: 15 outliers final: 13 residues processed: 96 average time/residue: 0.2168 time to fit residues: 29.5523 Evaluate side-chains 101 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 CYS Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 235 MET Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 433 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.5980 chunk 76 optimal weight: 0.0670 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 93 optimal weight: 2.9990 chunk 6 optimal weight: 0.0470 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 44 optimal weight: 0.0770 overall best weight: 0.1974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.116178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092057 restraints weight = 50769.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096004 restraints weight = 24459.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.098530 restraints weight = 15372.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.100145 restraints weight = 11309.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.101126 restraints weight = 9190.139| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 10459 Z= 0.181 Angle : 0.766 59.199 14329 Z= 0.477 Chirality : 0.039 0.225 1610 Planarity : 0.003 0.037 1626 Dihedral : 18.467 145.643 1771 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.45 % Allowed : 24.56 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.27), residues: 1069 helix: 1.60 (0.30), residues: 354 sheet: -1.53 (0.31), residues: 279 loop : -0.48 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 185 TYR 0.012 0.001 TYR F 188 PHE 0.012 0.001 PHE F 363 TRP 0.006 0.001 TRP F 438 HIS 0.003 0.000 HIS D 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 (10459) covalent geometry : angle 0.76606 / 0.48 (14329) hydrogen bonds : bond 0.03701 / 4.22 ( 412) hydrogen bonds : angle 4.75677 / 6.07 ( 1121) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2880.24 seconds wall clock time: 50 minutes 1.64 seconds (3001.64 seconds total)