Starting phenix.real_space_refine on Fri Sep 11 06:57:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cfn_30345/09_2026/7cfn_30345.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cfn_30345/09_2026/7cfn_30345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cfn_30345/09_2026/7cfn_30345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cfn_30345/09_2026/7cfn_30345.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7cfn_30345/09_2026/7cfn_30345.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cfn_30345/09_2026/7cfn_30345.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cfn_30345/09_2026/7cfn_30345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cfn_30345/09_2026/7cfn_30345.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 5158 2.51 5 N 1416 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8112 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1930 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1914 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 232, 1914 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1932 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2587 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2076 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 274, 2070 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 252} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 274, 2070 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 252} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2121 Chain: "R" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 111 Unusual residues: {'CLR': 1, 'FX0': 2, 'PLM': 1} Classifications: {'undetermined': 4, 'water': 1} Link IDs: {None: 4} Time building chain proxies: 2.63, per 1000 atoms: 0.32 Number of scatterers: 8112 At special positions: 0 Unit cell: (79.092, 115.596, 119.652, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1492 8.00 N 1416 7.00 C 5158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 155 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 462.1 milliseconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 10 sheets defined 42.9% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.571A pdb=" N ARG A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.553A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.569A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.501A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.276A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.753A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.704A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.621A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 6 through 23 removed outlier: 4.037A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.754A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.748A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 42 removed outlier: 3.987A pdb=" N ALA R 31 " --> pdb=" O LEU R 27 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP R 42 " --> pdb=" O GLY R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 47 removed outlier: 3.900A pdb=" N ARG R 46 " --> pdb=" O ASP R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 67 removed outlier: 3.581A pdb=" N CYS R 52 " --> pdb=" O PRO R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 75 removed outlier: 3.903A pdb=" N TRP R 75 " --> pdb=" O PRO R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 116 removed outlier: 4.151A pdb=" N LEU R 87 " --> pdb=" O TRP R 83 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL R 88 " --> pdb=" O SER R 84 " (cutoff:3.500A) Proline residue: R 92 - end of helix Processing helix chain 'R' and resid 123 through 140 removed outlier: 3.558A pdb=" N ALA R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) Proline residue: R 135 - end of helix Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 156 through 161 Processing helix chain 'R' and resid 162 through 173 Processing helix chain 'R' and resid 175 through 207 removed outlier: 4.365A pdb=" N ALA R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 236 removed outlier: 3.797A pdb=" N ALA R 217 " --> pdb=" O ALA R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 252 removed outlier: 3.785A pdb=" N TYR R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL R 241 " --> pdb=" O TRP R 237 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU R 252 " --> pdb=" O VAL R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 275 removed outlier: 4.498A pdb=" N THR R 261 " --> pdb=" O LEU R 257 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU R 262 " --> pdb=" O GLY R 258 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER R 264 " --> pdb=" O GLY R 260 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER R 272 " --> pdb=" O LEU R 268 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA R 273 " --> pdb=" O GLY R 269 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA R 274 " --> pdb=" O SER R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 282 Processing helix chain 'R' and resid 284 through 289 removed outlier: 3.842A pdb=" N THR R 288 " --> pdb=" O ASP R 284 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.864A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.649A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.895A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.665A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.773A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.661A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.711A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.611A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.062A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.733A pdb=" N LEU N 81 " --> pdb=" O LEU N 20 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.757A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1111 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1954 1.33 - 1.45: 1779 1.45 - 1.58: 4492 1.58 - 1.70: 1 1.70 - 1.82: 63 Bond restraints: 8289 Sorted by residual: bond pdb=" C27 FX0 R 401 " pdb=" O04 FX0 R 401 " ideal model delta sigma weight residual 1.251 1.359 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C27 FX0 R 403 " pdb=" O04 FX0 R 403 " ideal model delta sigma weight residual 1.251 1.358 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C ALA R 289 " pdb=" N PRO R 290 " ideal model delta sigma weight residual 1.334 1.429 -0.095 2.34e-02 1.83e+03 1.65e+01 bond pdb=" C HIS A 387 " pdb=" O HIS A 387 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.94e+00 bond pdb=" C LEU A 388 " pdb=" O LEU A 388 " ideal model delta sigma weight residual 1.237 1.208 0.029 1.17e-02 7.31e+03 6.09e+00 ... (remaining 8284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 10627 1.95 - 3.91: 525 3.91 - 5.86: 81 5.86 - 7.82: 30 7.82 - 9.77: 10 Bond angle restraints: 11273 Sorted by residual: angle pdb=" N VAL R 170 " pdb=" CA VAL R 170 " pdb=" C VAL R 170 " ideal model delta sigma weight residual 110.72 115.97 -5.25 1.01e+00 9.80e-01 2.71e+01 angle pdb=" N LEU R 90 " pdb=" CA LEU R 90 " pdb=" C LEU R 90 " ideal model delta sigma weight residual 111.69 117.96 -6.27 1.23e+00 6.61e-01 2.60e+01 angle pdb=" N GLU A 392 " pdb=" CA GLU A 392 " pdb=" C GLU A 392 " ideal model delta sigma weight residual 110.80 118.87 -8.07 2.13e+00 2.20e-01 1.43e+01 angle pdb=" C ASP B 66 " pdb=" N SER B 67 " pdb=" CA SER B 67 " ideal model delta sigma weight residual 123.47 129.26 -5.79 1.53e+00 4.27e-01 1.43e+01 angle pdb=" CA ALA R 91 " pdb=" C ALA R 91 " pdb=" N PRO R 92 " ideal model delta sigma weight residual 120.93 117.35 3.58 1.06e+00 8.90e-01 1.14e+01 ... (remaining 11268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.71: 4607 14.71 - 29.42: 222 29.42 - 44.13: 70 44.13 - 58.83: 9 58.83 - 73.54: 9 Dihedral angle restraints: 4917 sinusoidal: 1928 harmonic: 2989 Sorted by residual: dihedral pdb=" CA ASP A 331 " pdb=" C ASP A 331 " pdb=" N PRO A 332 " pdb=" CA PRO A 332 " ideal model delta harmonic sigma weight residual -180.00 -153.57 -26.43 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ASP B 195 " pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta harmonic sigma weight residual -180.00 -156.36 -23.64 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 4914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1031 0.077 - 0.154: 215 0.154 - 0.231: 28 0.231 - 0.308: 6 0.308 - 0.385: 2 Chirality restraints: 1282 Sorted by residual: chirality pdb=" CA GLU A 392 " pdb=" N GLU A 392 " pdb=" C GLU A 392 " pdb=" CB GLU A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA LEU R 90 " pdb=" N LEU R 90 " pdb=" C LEU R 90 " pdb=" CB LEU R 90 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB VAL A 241 " pdb=" CA VAL A 241 " pdb=" CG1 VAL A 241 " pdb=" CG2 VAL A 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 1279 not shown) Planarity restraints: 1433 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.81e+00 pdb=" N PRO N 88 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 289 " -0.042 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO R 290 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO R 290 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 290 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " -0.024 2.00e-02 2.50e+03 1.60e-02 6.36e+00 pdb=" CG TRP A 281 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " -0.011 2.00e-02 2.50e+03 ... (remaining 1430 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 48 2.56 - 3.15: 6006 3.15 - 3.73: 12132 3.73 - 4.32: 16769 4.32 - 4.90: 28921 Nonbonded interactions: 63876 Sorted by model distance: nonbonded pdb=" CD2 LEU A 394 " pdb=" OXT LEU A 394 " model vdw 1.979 3.460 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.296 3.040 nonbonded pdb=" O ARG B 22 " pdb=" NE2 GLN B 259 " model vdw 2.337 3.120 ... (remaining 63871 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.070 Find NCS groups from input model: 0.040 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.008 0.108 8292 Z= 0.332 Angle : 1.039 9.772 11279 Z= 0.543 Chirality : 0.064 0.385 1282 Planarity : 0.007 0.074 1433 Dihedral : 10.518 73.543 2982 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.12 % Allowed : 3.31 % Favored : 96.57 % 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: -2.77 (0.22), residues: 1020 helix: -1.41 (0.21), residues: 398 sheet: -1.88 (0.31), residues: 236 loop : -2.04 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 342 TYR 0.021 0.003 TYR A 339 PHE 0.026 0.003 PHE B 151 TRP 0.040 0.004 TRP A 281 HIS 0.013 0.003 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.33 ( 8289) covalent geometry : angle 1.03880 / 0.54 (11273) SS BOND : bond 0.00535 / 0.26 ( 3) SS BOND : angle 0.89410 / 0.45 ( 6) hydrogen bonds : bond 0.19234 / 11.88 ( 386) hydrogen bonds : angle 6.97273 / 4.90 ( 1111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.7813 (m-30) cc_final: 0.7568 (m-30) REVERT: A 35 GLN cc_start: 0.7176 (mt0) cc_final: 0.6666 (mp10) REVERT: A 40 THR cc_start: 0.8881 (t) cc_final: 0.8556 (m) REVERT: A 60 MET cc_start: 0.4235 (ptt) cc_final: 0.3658 (pmt) REVERT: A 284 ASP cc_start: 0.8170 (m-30) cc_final: 0.7847 (m-30) REVERT: B 155 ASN cc_start: 0.7960 (t0) cc_final: 0.7641 (t0) REVERT: B 186 ASP cc_start: 0.7886 (p0) cc_final: 0.7593 (p0) REVERT: B 323 ASP cc_start: 0.7911 (m-30) cc_final: 0.7587 (m-30) REVERT: G 21 MET cc_start: 0.7013 (ttt) cc_final: 0.6603 (ttm) REVERT: R 116 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7848 (mtt-85) REVERT: R 204 ARG cc_start: 0.6992 (ttt90) cc_final: 0.6508 (ttm110) REVERT: R 254 ARG cc_start: 0.7701 (ptm-80) cc_final: 0.6946 (ptt180) REVERT: R 268 LEU cc_start: 0.8111 (tt) cc_final: 0.7754 (tp) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.5972 time to fit residues: 109.3953 Evaluate side-chains 111 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 213 GLN A 371 ASN B 44 GLN B 237 ASN B 295 ASN B 340 ASN R 93 ASN ** R 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.156819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119810 restraints weight = 24074.437| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 5.31 r_work: 0.3022 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8292 Z= 0.122 Angle : 0.641 11.954 11279 Z= 0.307 Chirality : 0.043 0.280 1282 Planarity : 0.004 0.049 1433 Dihedral : 5.438 40.395 1160 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.84 % Allowed : 12.31 % Favored : 84.85 % 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: -0.75 (0.25), residues: 1020 helix: 0.96 (0.25), residues: 388 sheet: -1.27 (0.33), residues: 227 loop : -1.40 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 38 TYR 0.020 0.001 TYR R 251 PHE 0.012 0.001 PHE A 212 TRP 0.020 0.002 TRP R 149 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 8289) covalent geometry : angle 0.64048 / 0.31 (11273) SS BOND : bond 0.00204 / 0.09 ( 3) SS BOND : angle 0.85418 / 0.37 ( 6) hydrogen bonds : bond 0.04609 / 3.03 ( 386) hydrogen bonds : angle 4.71977 / 3.25 ( 1111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7456 (mm) cc_final: 0.7221 (mt) REVERT: A 35 GLN cc_start: 0.7047 (mt0) cc_final: 0.6510 (mp10) REVERT: A 40 THR cc_start: 0.8653 (t) cc_final: 0.8310 (m) REVERT: A 220 HIS cc_start: 0.8919 (m-70) cc_final: 0.8542 (m-70) REVERT: A 284 ASP cc_start: 0.8672 (m-30) cc_final: 0.8054 (m-30) REVERT: A 356 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.6846 (ttt180) REVERT: A 392 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7982 (mt-10) REVERT: B 49 ARG cc_start: 0.8457 (mpt180) cc_final: 0.8255 (mmt-90) REVERT: B 155 ASN cc_start: 0.7834 (t0) cc_final: 0.7510 (t0) REVERT: B 254 ASP cc_start: 0.8662 (t0) cc_final: 0.8260 (t0) REVERT: B 268 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7814 (m110) REVERT: B 323 ASP cc_start: 0.7764 (m-30) cc_final: 0.7355 (m-30) REVERT: G 21 MET cc_start: 0.7180 (ttt) cc_final: 0.6970 (ttm) REVERT: N 50 ASP cc_start: 0.8475 (p0) cc_final: 0.8200 (p0) REVERT: R 116 ARG cc_start: 0.8321 (mtt-85) cc_final: 0.8085 (mtt-85) REVERT: R 251 TYR cc_start: 0.8428 (t80) cc_final: 0.8148 (t80) REVERT: R 254 ARG cc_start: 0.7585 (ptm-80) cc_final: 0.6816 (ptt180) REVERT: R 268 LEU cc_start: 0.8028 (tt) cc_final: 0.7677 (tp) outliers start: 24 outliers final: 6 residues processed: 154 average time/residue: 0.5254 time to fit residues: 86.3151 Evaluate side-chains 128 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain R residue 123 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 0.0010 chunk 49 optimal weight: 0.0000 chunk 43 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 44 optimal weight: 0.0010 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN B 237 ASN R 93 ASN ** R 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.157446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.120191 restraints weight = 20400.171| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 4.67 r_work: 0.3043 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8292 Z= 0.110 Angle : 0.597 9.754 11279 Z= 0.284 Chirality : 0.042 0.279 1282 Planarity : 0.004 0.043 1433 Dihedral : 4.926 37.458 1160 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.49 % Allowed : 14.91 % Favored : 82.60 % 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 (0.26), residues: 1020 helix: 1.56 (0.26), residues: 399 sheet: -1.02 (0.33), residues: 231 loop : -1.16 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 317 TYR 0.017 0.001 TYR R 251 PHE 0.012 0.001 PHE A 212 TRP 0.027 0.002 TRP R 149 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 8289) covalent geometry : angle 0.59695 / 0.28 (11273) SS BOND : bond 0.00507 / 0.26 ( 3) SS BOND : angle 0.73016 / 0.31 ( 6) hydrogen bonds : bond 0.03854 / 2.57 ( 386) hydrogen bonds : angle 4.29031 / 2.95 ( 1111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7629 (mm) cc_final: 0.7394 (mt) REVERT: A 35 GLN cc_start: 0.7158 (mt0) cc_final: 0.6622 (mp10) REVERT: A 209 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: A 220 HIS cc_start: 0.8885 (m-70) cc_final: 0.8267 (m-70) REVERT: A 309 GLU cc_start: 0.7599 (mp0) cc_final: 0.7363 (mp0) REVERT: A 392 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: B 155 ASN cc_start: 0.7904 (t0) cc_final: 0.7593 (t0) REVERT: B 254 ASP cc_start: 0.8636 (t0) cc_final: 0.8244 (t0) REVERT: B 323 ASP cc_start: 0.7716 (m-30) cc_final: 0.7355 (m-30) REVERT: B 331 SER cc_start: 0.9178 (t) cc_final: 0.8912 (p) REVERT: N 7 SER cc_start: 0.7868 (p) cc_final: 0.7567 (m) REVERT: R 116 ARG cc_start: 0.8176 (mtt-85) cc_final: 0.7932 (mtt-85) REVERT: R 254 ARG cc_start: 0.7402 (ptm-80) cc_final: 0.6784 (ptt180) REVERT: R 268 LEU cc_start: 0.8066 (tt) cc_final: 0.7763 (tp) outliers start: 21 outliers final: 9 residues processed: 140 average time/residue: 0.5298 time to fit residues: 79.0150 Evaluate side-chains 128 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 160 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 0.0270 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 81 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 ASN ** R 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.157234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.121615 restraints weight = 26926.588| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 5.97 r_work: 0.2995 rms_B_bonded: 5.21 restraints_weight: 2.0000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8292 Z= 0.109 Angle : 0.586 9.299 11279 Z= 0.276 Chirality : 0.041 0.291 1282 Planarity : 0.004 0.043 1433 Dihedral : 4.731 36.878 1160 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.96 % Allowed : 14.79 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.27), residues: 1020 helix: 1.95 (0.27), residues: 399 sheet: -0.72 (0.34), residues: 229 loop : -1.02 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 317 TYR 0.018 0.001 TYR R 251 PHE 0.014 0.001 PHE A 212 TRP 0.033 0.001 TRP R 149 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 8289) covalent geometry : angle 0.58552 / 0.28 (11273) SS BOND : bond 0.00173 / 0.07 ( 3) SS BOND : angle 0.86127 / 0.45 ( 6) hydrogen bonds : bond 0.03598 / 2.41 ( 386) hydrogen bonds : angle 4.11129 / 2.81 ( 1111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7604 (mm) cc_final: 0.7378 (mt) REVERT: A 35 GLN cc_start: 0.7173 (mt0) cc_final: 0.6616 (mp10) REVERT: A 392 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8017 (mt-10) REVERT: B 19 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6820 (ttp-170) REVERT: B 155 ASN cc_start: 0.7871 (t0) cc_final: 0.7390 (t0) REVERT: B 254 ASP cc_start: 0.8632 (t0) cc_final: 0.8245 (t0) REVERT: B 323 ASP cc_start: 0.7591 (m-30) cc_final: 0.7264 (m-30) REVERT: N 7 SER cc_start: 0.7850 (p) cc_final: 0.7584 (m) REVERT: R 116 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7820 (mtt-85) REVERT: R 158 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8455 (mp10) REVERT: R 254 ARG cc_start: 0.7358 (ptm-80) cc_final: 0.6699 (ptt180) REVERT: R 268 LEU cc_start: 0.8001 (tt) cc_final: 0.7723 (tp) outliers start: 25 outliers final: 5 residues processed: 140 average time/residue: 0.4604 time to fit residues: 69.2768 Evaluate side-chains 123 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 157 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112655 restraints weight = 20579.818| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 4.64 r_work: 0.2955 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8292 Z= 0.205 Angle : 0.669 9.415 11279 Z= 0.323 Chirality : 0.046 0.290 1282 Planarity : 0.004 0.037 1433 Dihedral : 4.987 40.457 1160 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.49 % Allowed : 17.16 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.26), residues: 1020 helix: 1.76 (0.26), residues: 406 sheet: -0.76 (0.33), residues: 231 loop : -1.00 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 96 TYR 0.017 0.002 TYR R 251 PHE 0.021 0.002 PHE N 108 TRP 0.040 0.002 TRP R 149 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 ( 8289) covalent geometry : angle 0.66915 / 0.32 (11273) SS BOND : bond 0.00299 / 0.15 ( 3) SS BOND : angle 1.10465 / 0.65 ( 6) hydrogen bonds : bond 0.04609 / 3.08 ( 386) hydrogen bonds : angle 4.28368 / 2.94 ( 1111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7574 (mm) cc_final: 0.7310 (mt) REVERT: A 35 GLN cc_start: 0.7501 (mt0) cc_final: 0.6833 (mp10) REVERT: A 209 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: A 220 HIS cc_start: 0.8842 (m-70) cc_final: 0.8395 (m-70) REVERT: B 18 ILE cc_start: 0.8096 (mt) cc_final: 0.7860 (mp) REVERT: B 19 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6782 (tpp80) REVERT: B 67 SER cc_start: 0.8571 (t) cc_final: 0.8335 (t) REVERT: B 155 ASN cc_start: 0.7986 (t0) cc_final: 0.7669 (t0) REVERT: B 254 ASP cc_start: 0.8612 (t0) cc_final: 0.8200 (t0) REVERT: B 323 ASP cc_start: 0.7631 (m-30) cc_final: 0.7196 (m-30) REVERT: G 21 MET cc_start: 0.7716 (tmt) cc_final: 0.7400 (tmm) REVERT: N 7 SER cc_start: 0.7928 (p) cc_final: 0.7619 (m) REVERT: N 69 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8338 (m) REVERT: N 110 VAL cc_start: 0.9115 (t) cc_final: 0.8538 (m) REVERT: R 33 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6859 (mp) REVERT: R 158 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8510 (mp10) REVERT: R 254 ARG cc_start: 0.7372 (ptm-80) cc_final: 0.6805 (ptt180) REVERT: R 268 LEU cc_start: 0.8082 (tt) cc_final: 0.7720 (tp) outliers start: 21 outliers final: 6 residues processed: 124 average time/residue: 0.4528 time to fit residues: 60.0676 Evaluate side-chains 124 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 157 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 chunk 16 optimal weight: 30.0000 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.151461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114401 restraints weight = 25511.050| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 5.55 r_work: 0.2926 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8292 Z= 0.170 Angle : 0.635 10.057 11279 Z= 0.305 Chirality : 0.044 0.305 1282 Planarity : 0.004 0.057 1433 Dihedral : 4.938 43.160 1160 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.84 % Allowed : 17.51 % Favored : 79.64 % 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: 0.35 (0.26), residues: 1020 helix: 1.87 (0.26), residues: 411 sheet: -0.69 (0.33), residues: 229 loop : -0.96 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 317 TYR 0.017 0.001 TYR R 251 PHE 0.017 0.002 PHE N 108 TRP 0.048 0.002 TRP R 149 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 8289) covalent geometry : angle 0.63473 / 0.30 (11273) SS BOND : bond 0.00246 / 0.12 ( 3) SS BOND : angle 0.88321 / 0.47 ( 6) hydrogen bonds : bond 0.04235 / 2.83 ( 386) hydrogen bonds : angle 4.19023 / 2.87 ( 1111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7460 (mm) cc_final: 0.7209 (mt) REVERT: A 35 GLN cc_start: 0.7360 (mt0) cc_final: 0.6728 (mp10) REVERT: A 209 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: A 220 HIS cc_start: 0.8842 (m-70) cc_final: 0.8414 (m-70) REVERT: A 392 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7993 (mt-10) REVERT: B 18 ILE cc_start: 0.7992 (mt) cc_final: 0.7757 (mp) REVERT: B 19 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6740 (tpp80) REVERT: B 67 SER cc_start: 0.8463 (t) cc_final: 0.8208 (t) REVERT: B 150 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.6762 (mmt90) REVERT: B 155 ASN cc_start: 0.7965 (t0) cc_final: 0.7627 (t0) REVERT: B 186 ASP cc_start: 0.8340 (p0) cc_final: 0.7748 (p0) REVERT: B 234 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8714 (m-80) REVERT: B 246 ASP cc_start: 0.8106 (m-30) cc_final: 0.7704 (m-30) REVERT: B 254 ASP cc_start: 0.8586 (t0) cc_final: 0.8138 (t0) REVERT: B 323 ASP cc_start: 0.7538 (m-30) cc_final: 0.7097 (m-30) REVERT: N 7 SER cc_start: 0.7826 (p) cc_final: 0.7490 (m) REVERT: R 158 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8461 (mp10) REVERT: R 254 ARG cc_start: 0.7350 (ptm-80) cc_final: 0.6748 (ptt180) REVERT: R 268 LEU cc_start: 0.8017 (tt) cc_final: 0.7639 (tp) outliers start: 24 outliers final: 7 residues processed: 124 average time/residue: 0.4977 time to fit residues: 65.9610 Evaluate side-chains 121 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 157 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 62 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 0.0070 chunk 74 optimal weight: 0.9980 overall best weight: 0.8800 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.153938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106800 restraints weight = 30003.165| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 4.41 r_work: 0.2974 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8292 Z= 0.121 Angle : 0.588 10.000 11279 Z= 0.282 Chirality : 0.042 0.313 1282 Planarity : 0.004 0.037 1433 Dihedral : 4.782 44.775 1160 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.13 % Allowed : 18.22 % Favored : 79.64 % 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: 0.56 (0.27), residues: 1020 helix: 2.08 (0.26), residues: 411 sheet: -0.60 (0.33), residues: 229 loop : -0.87 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 317 TYR 0.015 0.001 TYR R 251 PHE 0.014 0.001 PHE N 108 TRP 0.048 0.002 TRP R 149 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 8289) covalent geometry : angle 0.58793 / 0.28 (11273) SS BOND : bond 0.00210 / 0.10 ( 3) SS BOND : angle 0.76644 / 0.38 ( 6) hydrogen bonds : bond 0.03743 / 2.51 ( 386) hydrogen bonds : angle 4.04845 / 2.78 ( 1111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7434 (mm) cc_final: 0.7199 (mt) REVERT: A 35 GLN cc_start: 0.7259 (mt0) cc_final: 0.6648 (mp10) REVERT: A 46 LEU cc_start: 0.8229 (tt) cc_final: 0.7983 (tp) REVERT: A 209 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: A 220 HIS cc_start: 0.8843 (m-70) cc_final: 0.8507 (m-70) REVERT: A 392 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7924 (mt-10) REVERT: B 67 SER cc_start: 0.8432 (t) cc_final: 0.8123 (t) REVERT: B 155 ASN cc_start: 0.7970 (t0) cc_final: 0.7603 (t0) REVERT: B 186 ASP cc_start: 0.8333 (p0) cc_final: 0.7773 (p0) REVERT: B 246 ASP cc_start: 0.8078 (m-30) cc_final: 0.7690 (m-30) REVERT: B 254 ASP cc_start: 0.8533 (t0) cc_final: 0.8115 (t0) REVERT: B 323 ASP cc_start: 0.7526 (m-30) cc_final: 0.7113 (m-30) REVERT: G 21 MET cc_start: 0.7704 (tmt) cc_final: 0.7303 (tmm) REVERT: N 7 SER cc_start: 0.7831 (p) cc_final: 0.7519 (m) REVERT: R 254 ARG cc_start: 0.7338 (ptm-80) cc_final: 0.6739 (ptt180) REVERT: R 268 LEU cc_start: 0.8018 (tt) cc_final: 0.7656 (tp) outliers start: 18 outliers final: 7 residues processed: 132 average time/residue: 0.4701 time to fit residues: 66.5952 Evaluate side-chains 123 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 157 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 75 optimal weight: 0.0270 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.149404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.111245 restraints weight = 18508.678| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 4.03 r_work: 0.2960 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8292 Z= 0.216 Angle : 0.672 10.398 11279 Z= 0.327 Chirality : 0.046 0.309 1282 Planarity : 0.004 0.035 1433 Dihedral : 4.987 48.084 1160 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.60 % Allowed : 17.87 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.38 (0.26), residues: 1020 helix: 1.87 (0.26), residues: 411 sheet: -0.70 (0.33), residues: 231 loop : -0.88 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 317 TYR 0.019 0.001 TYR A 339 PHE 0.019 0.002 PHE N 108 TRP 0.049 0.002 TRP R 149 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.22 ( 8289) covalent geometry : angle 0.67182 / 0.33 (11273) SS BOND : bond 0.00359 / 0.18 ( 3) SS BOND : angle 0.86938 / 0.45 ( 6) hydrogen bonds : bond 0.04531 / 3.03 ( 386) hydrogen bonds : angle 4.22969 / 2.91 ( 1111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7534 (mm) cc_final: 0.7257 (mt) REVERT: A 35 GLN cc_start: 0.7384 (mt0) cc_final: 0.6699 (mp10) REVERT: A 209 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: A 220 HIS cc_start: 0.8802 (m-70) cc_final: 0.8373 (m-70) REVERT: A 392 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: B 67 SER cc_start: 0.8620 (t) cc_final: 0.8253 (t) REVERT: B 150 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.6731 (mmt90) REVERT: B 155 ASN cc_start: 0.8036 (t0) cc_final: 0.7682 (t0) REVERT: B 197 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6594 (mmm160) REVERT: B 246 ASP cc_start: 0.8082 (m-30) cc_final: 0.7701 (m-30) REVERT: B 254 ASP cc_start: 0.8557 (t0) cc_final: 0.8156 (t0) REVERT: B 323 ASP cc_start: 0.7593 (m-30) cc_final: 0.7173 (m-30) REVERT: G 21 MET cc_start: 0.7737 (tmt) cc_final: 0.7363 (tmm) REVERT: N 7 SER cc_start: 0.7849 (p) cc_final: 0.7542 (m) REVERT: R 33 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6814 (mp) REVERT: R 254 ARG cc_start: 0.7401 (ptm-80) cc_final: 0.6809 (ptt180) REVERT: R 268 LEU cc_start: 0.8071 (tt) cc_final: 0.7687 (tp) outliers start: 22 outliers final: 8 residues processed: 125 average time/residue: 0.5183 time to fit residues: 69.0956 Evaluate side-chains 123 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 157 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 51 optimal weight: 0.2980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 292 ASN ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.151581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.104087 restraints weight = 30062.393| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 4.09 r_work: 0.2959 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8292 Z= 0.151 Angle : 0.635 10.113 11279 Z= 0.306 Chirality : 0.044 0.316 1282 Planarity : 0.004 0.036 1433 Dihedral : 4.892 50.218 1160 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.66 % Allowed : 19.41 % Favored : 78.93 % 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: 0.48 (0.27), residues: 1020 helix: 2.00 (0.26), residues: 411 sheet: -0.70 (0.33), residues: 231 loop : -0.85 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 317 TYR 0.015 0.001 TYR R 251 PHE 0.014 0.001 PHE N 108 TRP 0.049 0.002 TRP R 149 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 8289) covalent geometry : angle 0.63460 / 0.31 (11273) SS BOND : bond 0.00264 / 0.13 ( 3) SS BOND : angle 0.76476 / 0.39 ( 6) hydrogen bonds : bond 0.04050 / 2.71 ( 386) hydrogen bonds : angle 4.14204 / 2.88 ( 1111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7410 (mm) cc_final: 0.7162 (mt) REVERT: A 35 GLN cc_start: 0.7304 (mt0) cc_final: 0.6657 (mp10) REVERT: A 209 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: A 220 HIS cc_start: 0.8817 (m-70) cc_final: 0.8489 (m-70) REVERT: A 392 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: B 13 GLN cc_start: 0.8076 (tp40) cc_final: 0.7658 (tp40) REVERT: B 67 SER cc_start: 0.8560 (t) cc_final: 0.8211 (t) REVERT: B 150 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.6727 (mmt90) REVERT: B 155 ASN cc_start: 0.7978 (t0) cc_final: 0.7615 (t0) REVERT: B 246 ASP cc_start: 0.8072 (m-30) cc_final: 0.7640 (m-30) REVERT: B 254 ASP cc_start: 0.8495 (t0) cc_final: 0.8093 (t0) REVERT: B 258 ASP cc_start: 0.6720 (t70) cc_final: 0.6470 (t0) REVERT: B 323 ASP cc_start: 0.7528 (m-30) cc_final: 0.7071 (m-30) REVERT: G 21 MET cc_start: 0.7717 (tmt) cc_final: 0.7400 (tmm) REVERT: N 7 SER cc_start: 0.7834 (p) cc_final: 0.7534 (m) REVERT: R 254 ARG cc_start: 0.7349 (ptm-80) cc_final: 0.6776 (ptt180) REVERT: R 268 LEU cc_start: 0.8045 (tt) cc_final: 0.7674 (tp) outliers start: 14 outliers final: 9 residues processed: 123 average time/residue: 0.5128 time to fit residues: 67.4350 Evaluate side-chains 123 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 157 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.108610 restraints weight = 12903.169| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.76 r_work: 0.3067 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8292 Z= 0.139 Angle : 0.626 10.039 11279 Z= 0.303 Chirality : 0.043 0.320 1282 Planarity : 0.004 0.036 1433 Dihedral : 4.854 51.198 1160 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.78 % Allowed : 19.41 % Favored : 78.82 % 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: 0.61 (0.27), residues: 1020 helix: 2.21 (0.26), residues: 404 sheet: -0.71 (0.33), residues: 231 loop : -0.80 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 317 TYR 0.014 0.001 TYR R 251 PHE 0.014 0.001 PHE N 108 TRP 0.046 0.002 TRP R 149 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 8289) covalent geometry : angle 0.62581 / 0.30 (11273) SS BOND : bond 0.00246 / 0.12 ( 3) SS BOND : angle 0.73056 / 0.37 ( 6) hydrogen bonds : bond 0.03885 / 2.60 ( 386) hydrogen bonds : angle 4.11080 / 2.86 ( 1111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7485 (mm) cc_final: 0.7245 (mt) REVERT: A 35 GLN cc_start: 0.7387 (mt0) cc_final: 0.6738 (mp10) REVERT: A 46 LEU cc_start: 0.8286 (tt) cc_final: 0.8013 (tp) REVERT: A 209 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7326 (tm-30) REVERT: A 220 HIS cc_start: 0.8700 (m-70) cc_final: 0.8298 (m-70) REVERT: A 392 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: B 13 GLN cc_start: 0.8174 (tp40) cc_final: 0.7708 (tp40) REVERT: B 67 SER cc_start: 0.8537 (t) cc_final: 0.8180 (t) REVERT: B 150 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.6714 (mmt90) REVERT: B 155 ASN cc_start: 0.8035 (t0) cc_final: 0.7673 (t0) REVERT: B 246 ASP cc_start: 0.7905 (m-30) cc_final: 0.7519 (m-30) REVERT: B 254 ASP cc_start: 0.8403 (t0) cc_final: 0.8032 (t0) REVERT: B 323 ASP cc_start: 0.7547 (m-30) cc_final: 0.7151 (m-30) REVERT: N 7 SER cc_start: 0.7854 (p) cc_final: 0.7563 (m) REVERT: N 120 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7819 (mp10) REVERT: R 254 ARG cc_start: 0.7397 (ptm-80) cc_final: 0.6886 (ptt180) REVERT: R 268 LEU cc_start: 0.8102 (tt) cc_final: 0.7730 (tp) outliers start: 15 outliers final: 9 residues processed: 120 average time/residue: 0.5059 time to fit residues: 64.7497 Evaluate side-chains 125 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 157 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 50 optimal weight: 0.1980 chunk 97 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 93 optimal weight: 0.3980 chunk 71 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.155097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117637 restraints weight = 18480.663| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 4.10 r_work: 0.3041 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8292 Z= 0.113 Angle : 0.605 9.727 11279 Z= 0.291 Chirality : 0.042 0.323 1282 Planarity : 0.004 0.037 1433 Dihedral : 4.768 52.252 1160 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.54 % Allowed : 19.53 % Favored : 78.93 % 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: 0.73 (0.27), residues: 1020 helix: 2.34 (0.26), residues: 404 sheet: -0.61 (0.34), residues: 224 loop : -0.80 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 317 TYR 0.014 0.001 TYR R 251 PHE 0.014 0.001 PHE A 212 TRP 0.043 0.002 TRP R 149 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 8289) covalent geometry : angle 0.60458 / 0.29 (11273) SS BOND : bond 0.00221 / 0.10 ( 3) SS BOND : angle 0.66987 / 0.31 ( 6) hydrogen bonds : bond 0.03433 / 2.31 ( 386) hydrogen bonds : angle 4.00586 / 2.80 ( 1111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2866.94 seconds wall clock time: 49 minutes 37.56 seconds (2977.56 seconds total)