Starting phenix.real_space_refine on Sat Aug 23 03:50:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fiy_31606/08_2025/7fiy_31606_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fiy_31606/08_2025/7fiy_31606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fiy_31606/08_2025/7fiy_31606_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fiy_31606/08_2025/7fiy_31606_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fiy_31606/08_2025/7fiy_31606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fiy_31606/08_2025/7fiy_31606.map" } resolution = 3.4 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= 0.083 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 54 5.16 5 C 5983 2.51 5 N 1638 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9367 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2974 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 12, 'TRANS': 346} Chain breaks: 4 Chain: "P" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1948 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'CLR': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 1.83, per 1000 atoms: 0.20 Number of scatterers: 9367 At special positions: 0 Unit cell: (79.254, 102.816, 171.36, 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 54 16.00 O 1692 8.00 N 1638 7.00 C 5983 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 70 " distance=2.03 Simple disulfide: pdb=" SG CYS R 61 " - pdb=" SG CYS R 103 " distance=2.03 Simple disulfide: pdb=" SG CYS R 84 " - pdb=" SG CYS R 118 " distance=2.03 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=2.03 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: 0.78 Conformation dependent library (CDL) restraints added in 298.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 43.8% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'R' and resid 31 through 49 Processing helix chain 'R' and resid 115 through 119 Processing helix chain 'R' and resid 124 through 162 removed outlier: 3.872A pdb=" N LEU R 128 " --> pdb=" O ASN R 124 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP R 129 " --> pdb=" O GLU R 125 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR R 142 " --> pdb=" O GLN R 138 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU R 159 " --> pdb=" O ALA R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 166 Processing helix chain 'R' and resid 167 through 194 removed outlier: 3.826A pdb=" N ILE R 172 " --> pdb=" O THR R 168 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS R 173 " --> pdb=" O ARG R 169 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG R 192 " --> pdb=" O LEU R 188 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 246 removed outlier: 3.554A pdb=" N LEU R 245 " --> pdb=" O LEU R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 281 Proline residue: R 267 - end of helix removed outlier: 3.556A pdb=" N ILE R 272 " --> pdb=" O ALA R 268 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 292 through 328 removed outlier: 3.585A pdb=" N TRP R 296 " --> pdb=" O VAL R 292 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE R 298 " --> pdb=" O ALA R 294 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE R 299 " --> pdb=" O ILE R 295 " (cutoff:3.500A) Proline residue: R 302 - end of helix removed outlier: 3.578A pdb=" N SER R 323 " --> pdb=" O GLY R 319 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG R 328 " --> pdb=" O LYS R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 351 Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 352 through 364 removed outlier: 3.908A pdb=" N VAL R 356 " --> pdb=" O VAL R 352 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE R 357 " --> pdb=" O HIS R 353 " (cutoff:3.500A) Proline residue: R 359 - end of helix Processing helix chain 'R' and resid 366 through 394 removed outlier: 3.832A pdb=" N ARG R 370 " --> pdb=" O ARG R 366 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE R 371 " --> pdb=" O GLY R 367 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE R 378 " --> pdb=" O LEU R 374 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE R 383 " --> pdb=" O PHE R 379 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY R 385 " --> pdb=" O SER R 381 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE R 386 " --> pdb=" O SER R 382 " (cutoff:3.500A) Processing helix chain 'R' and resid 396 through 414 Processing helix chain 'P' and resid 2 through 29 Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.921A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.585A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.643A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.650A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.480A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.696A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.522A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.670A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.504A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.910A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 78 through 83 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 213 removed outlier: 4.169A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.495A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.826A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.794A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.875A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.791A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.781A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.546A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 7.109A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1332 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: 1.24 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3005 1.34 - 1.46: 1886 1.46 - 1.58: 4617 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 9580 Sorted by residual: bond pdb=" C GLY A 52 " pdb=" O GLY A 52 " ideal model delta sigma weight residual 1.235 1.270 -0.035 1.35e-02 5.49e+03 6.84e+00 bond pdb=" C SER A 51 " pdb=" N GLY A 52 " ideal model delta sigma weight residual 1.331 1.357 -0.027 1.46e-02 4.69e+03 3.37e+00 bond pdb=" C5 CLR R 602 " pdb=" C6 CLR R 602 " ideal model delta sigma weight residual 1.332 1.300 0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" C5 CLR R 606 " pdb=" C6 CLR R 606 " ideal model delta sigma weight residual 1.332 1.300 0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" C ALA R 358 " pdb=" N PRO R 359 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.45e+00 ... (remaining 9575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 12597 2.05 - 4.11: 352 4.11 - 6.16: 43 6.16 - 8.22: 11 8.22 - 10.27: 4 Bond angle restraints: 13007 Sorted by residual: angle pdb=" N GLY R 198 " pdb=" CA GLY R 198 " pdb=" C GLY R 198 " ideal model delta sigma weight residual 112.34 121.31 -8.97 2.04e+00 2.40e-01 1.93e+01 angle pdb=" C CYS R 216 " pdb=" N ARG R 217 " pdb=" CA ARG R 217 " ideal model delta sigma weight residual 120.38 126.29 -5.91 1.37e+00 5.33e-01 1.86e+01 angle pdb=" N VAL R 248 " pdb=" CA VAL R 248 " pdb=" C VAL R 248 " ideal model delta sigma weight residual 106.21 110.24 -4.03 1.07e+00 8.73e-01 1.42e+01 angle pdb=" N AIB P 2 " pdb=" CA AIB P 2 " pdb=" C AIB P 2 " ideal model delta sigma weight residual 111.00 121.27 -10.27 2.80e+00 1.28e-01 1.35e+01 angle pdb=" CA GLN R 364 " pdb=" CB GLN R 364 " pdb=" CG GLN R 364 " ideal model delta sigma weight residual 114.10 121.38 -7.28 2.00e+00 2.50e-01 1.33e+01 ... (remaining 13002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.81: 5698 14.81 - 29.62: 212 29.62 - 44.43: 58 44.43 - 59.24: 1 59.24 - 74.04: 1 Dihedral angle restraints: 5970 sinusoidal: 2630 harmonic: 3340 Sorted by residual: dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 159.68 20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA TYR N 60 " pdb=" C TYR N 60 " pdb=" N THR N 61 " pdb=" CA THR N 61 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ASP B 291 " pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 5967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1278 0.082 - 0.163: 134 0.163 - 0.245: 21 0.245 - 0.326: 6 0.326 - 0.408: 7 Chirality restraints: 1446 Sorted by residual: chirality pdb=" C14 CLR R 605 " pdb=" C13 CLR R 605 " pdb=" C15 CLR R 605 " pdb=" C8 CLR R 605 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" C14 CLR R 604 " pdb=" C13 CLR R 604 " pdb=" C15 CLR R 604 " pdb=" C8 CLR R 604 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" C14 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C15 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.71 0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 1443 not shown) Planarity restraints: 1628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 198 " -0.049 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO R 199 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO R 199 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 199 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 360 " -0.042 5.00e-02 4.00e+02 6.36e-02 6.46e+00 pdb=" N PRO A 361 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO A 332 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.035 5.00e-02 4.00e+02 ... (remaining 1625 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2184 2.80 - 3.33: 8203 3.33 - 3.85: 14573 3.85 - 4.38: 16660 4.38 - 4.90: 29943 Nonbonded interactions: 71563 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.275 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.306 3.040 nonbonded pdb=" OG SER R 342 " pdb=" O LEU A 393 " model vdw 2.314 3.040 nonbonded pdb=" OD1 ASN A 292 " pdb=" OG1 THR A 364 " model vdw 2.334 3.040 nonbonded pdb=" OE2 GLU R 282 " pdb=" OG1 THR R 284 " model vdw 2.334 3.040 ... (remaining 71558 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.490 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 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 : 0.004 0.050 9585 Z= 0.204 Angle : 0.822 10.274 13017 Z= 0.449 Chirality : 0.062 0.408 1446 Planarity : 0.006 0.073 1628 Dihedral : 8.340 74.045 3799 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.22), residues: 1123 helix: -0.08 (0.20), residues: 434 sheet: -0.95 (0.33), residues: 226 loop : -1.09 (0.25), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 278 TYR 0.026 0.002 TYR P 1 PHE 0.024 0.002 PHE R 177 TRP 0.036 0.002 TRP A 281 HIS 0.014 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9580) covalent geometry : angle 0.82031 (13007) SS BOND : bond 0.00184 ( 5) SS BOND : angle 2.16046 ( 10) hydrogen bonds : bond 0.26274 ( 460) hydrogen bonds : angle 7.51969 ( 1332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 67 MET cc_start: 0.6978 (mtt) cc_final: 0.6194 (mtp) REVERT: R 252 GLU cc_start: 0.5603 (pt0) cc_final: 0.5106 (tp30) REVERT: R 376 PHE cc_start: 0.7091 (t80) cc_final: 0.6600 (t80) REVERT: P 19 GLN cc_start: 0.8365 (mt0) cc_final: 0.8164 (mt0) REVERT: P 22 PHE cc_start: 0.8598 (t80) cc_final: 0.8351 (t80) REVERT: A 343 ASP cc_start: 0.7501 (t70) cc_final: 0.7246 (t70) REVERT: G 52 THR cc_start: 0.8571 (m) cc_final: 0.8223 (p) REVERT: N 67 ARG cc_start: 0.6618 (mtp180) cc_final: 0.6199 (mtp180) REVERT: N 83 MET cc_start: 0.7568 (mtp) cc_final: 0.7287 (mtp) REVERT: N 109 ASP cc_start: 0.6532 (p0) cc_final: 0.6308 (p0) REVERT: N 125 THR cc_start: 0.8495 (m) cc_final: 0.8291 (t) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1024 time to fit residues: 36.0068 Evaluate side-chains 160 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.0770 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 173 HIS R 230 ASN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 156 GLN B 239 ASN B 266 HIS B 268 ASN N 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.196502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.154565 restraints weight = 10901.270| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 3.11 r_work: 0.3283 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 9585 Z= 0.274 Angle : 0.689 7.804 13017 Z= 0.364 Chirality : 0.045 0.147 1446 Planarity : 0.005 0.058 1628 Dihedral : 5.397 34.305 1664 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.05 % Allowed : 10.29 % Favored : 86.66 % 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 aren not related in a simple way. whole: 0.50 (0.24), residues: 1123 helix: 1.97 (0.23), residues: 450 sheet: -0.76 (0.33), residues: 238 loop : -0.71 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 370 TYR 0.050 0.003 TYR R 36 PHE 0.020 0.002 PHE R 379 TRP 0.023 0.002 TRP A 281 HIS 0.011 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00647 ( 9580) covalent geometry : angle 0.68798 (13007) SS BOND : bond 0.00272 ( 5) SS BOND : angle 1.31411 ( 10) hydrogen bonds : bond 0.05672 ( 460) hydrogen bonds : angle 4.72988 ( 1332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: R 39 TRP cc_start: 0.8753 (t60) cc_final: 0.8276 (t60) REVERT: R 67 MET cc_start: 0.7197 (mtt) cc_final: 0.6330 (mtp) REVERT: R 87 TYR cc_start: 0.7826 (p90) cc_final: 0.7618 (p90) REVERT: R 376 PHE cc_start: 0.7916 (t80) cc_final: 0.7039 (t80) REVERT: R 389 SER cc_start: 0.8631 (t) cc_final: 0.8385 (p) REVERT: P 9 ASP cc_start: 0.8512 (t0) cc_final: 0.8199 (t0) REVERT: P 24 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8406 (mm-40) REVERT: A 339 TYR cc_start: 0.8662 (m-80) cc_final: 0.8379 (m-80) REVERT: N 83 MET cc_start: 0.8131 (mtp) cc_final: 0.7925 (mtp) REVERT: N 109 ASP cc_start: 0.7156 (p0) cc_final: 0.6815 (p0) REVERT: N 117 TYR cc_start: 0.8542 (m-80) cc_final: 0.8317 (m-80) REVERT: N 125 THR cc_start: 0.8563 (m) cc_final: 0.8337 (t) outliers start: 30 outliers final: 17 residues processed: 201 average time/residue: 0.0891 time to fit residues: 23.8889 Evaluate side-chains 165 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 308 LEU Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 84 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN B 44 GLN B 75 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN N 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.198218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.156966 restraints weight = 10822.116| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.92 r_work: 0.3315 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9585 Z= 0.150 Angle : 0.571 8.068 13017 Z= 0.295 Chirality : 0.041 0.163 1446 Planarity : 0.004 0.054 1628 Dihedral : 5.086 32.275 1664 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.85 % Allowed : 11.71 % Favored : 85.44 % 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 aren not related in a simple way. whole: 0.83 (0.25), residues: 1123 helix: 2.42 (0.23), residues: 455 sheet: -0.76 (0.34), residues: 221 loop : -0.69 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 46 TYR 0.039 0.002 TYR R 36 PHE 0.014 0.002 PHE R 379 TRP 0.017 0.001 TRP N 47 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9580) covalent geometry : angle 0.56944 (13007) SS BOND : bond 0.00438 ( 5) SS BOND : angle 1.77950 ( 10) hydrogen bonds : bond 0.04601 ( 460) hydrogen bonds : angle 4.30286 ( 1332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: R 39 TRP cc_start: 0.8947 (t60) cc_final: 0.8439 (t60) REVERT: R 67 MET cc_start: 0.7174 (mtt) cc_final: 0.6501 (mtp) REVERT: R 87 TYR cc_start: 0.8314 (p90) cc_final: 0.7847 (p90) REVERT: R 181 MET cc_start: 0.8401 (tpp) cc_final: 0.8041 (tpp) REVERT: R 376 PHE cc_start: 0.7993 (t80) cc_final: 0.7043 (t80) REVERT: P 9 ASP cc_start: 0.8487 (t0) cc_final: 0.8106 (t0) REVERT: P 24 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8473 (mm-40) REVERT: A 339 TYR cc_start: 0.8569 (m-80) cc_final: 0.8327 (m-80) REVERT: G 52 THR cc_start: 0.8851 (m) cc_final: 0.8407 (p) REVERT: N 67 ARG cc_start: 0.7639 (mtp180) cc_final: 0.7412 (mtp180) REVERT: N 69 THR cc_start: 0.8235 (m) cc_final: 0.7789 (p) REVERT: N 109 ASP cc_start: 0.7178 (p0) cc_final: 0.6852 (p0) REVERT: N 117 TYR cc_start: 0.8423 (m-80) cc_final: 0.8171 (m-80) REVERT: N 125 THR cc_start: 0.8684 (m) cc_final: 0.8457 (t) outliers start: 28 outliers final: 18 residues processed: 178 average time/residue: 0.0824 time to fit residues: 19.8310 Evaluate side-chains 159 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 0.0470 chunk 90 optimal weight: 0.0010 chunk 38 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 overall best weight: 0.9686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.208758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.169889 restraints weight = 11669.111| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 3.26 r_work: 0.3601 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9585 Z= 0.156 Angle : 0.566 9.238 13017 Z= 0.293 Chirality : 0.041 0.201 1446 Planarity : 0.004 0.054 1628 Dihedral : 4.983 38.532 1664 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.75 % Allowed : 13.24 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.25), residues: 1123 helix: 2.76 (0.23), residues: 448 sheet: -0.82 (0.34), residues: 218 loop : -0.64 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 46 TYR 0.033 0.002 TYR R 36 PHE 0.013 0.001 PHE B 199 TRP 0.016 0.001 TRP N 47 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9580) covalent geometry : angle 0.55985 (13007) SS BOND : bond 0.00154 ( 5) SS BOND : angle 3.04263 ( 10) hydrogen bonds : bond 0.04158 ( 460) hydrogen bonds : angle 4.11200 ( 1332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.317 Fit side-chains REVERT: R 39 TRP cc_start: 0.8991 (t60) cc_final: 0.8459 (t60) REVERT: R 67 MET cc_start: 0.7230 (mtt) cc_final: 0.6649 (mtp) REVERT: R 87 TYR cc_start: 0.8455 (p90) cc_final: 0.8034 (p90) REVERT: P 16 LYS cc_start: 0.9297 (mmtm) cc_final: 0.9089 (mmmm) REVERT: P 24 GLN cc_start: 0.8929 (mm-40) cc_final: 0.8628 (mm-40) REVERT: A 339 TYR cc_start: 0.8588 (m-80) cc_final: 0.8313 (m-80) REVERT: B 234 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8245 (t80) REVERT: G 52 THR cc_start: 0.8892 (m) cc_final: 0.8399 (p) REVERT: G 62 ARG cc_start: 0.8563 (pmt-80) cc_final: 0.8331 (pmt-80) REVERT: G 63 GLU cc_start: 0.6748 (mt-10) cc_final: 0.5581 (pt0) REVERT: N 109 ASP cc_start: 0.7048 (p0) cc_final: 0.6699 (p0) REVERT: N 117 TYR cc_start: 0.8414 (m-80) cc_final: 0.8100 (m-80) outliers start: 27 outliers final: 19 residues processed: 161 average time/residue: 0.0902 time to fit residues: 19.5473 Evaluate side-chains 154 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.207282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.167019 restraints weight = 11562.396| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 3.31 r_work: 0.3586 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9585 Z= 0.171 Angle : 0.571 8.379 13017 Z= 0.294 Chirality : 0.041 0.182 1446 Planarity : 0.004 0.052 1628 Dihedral : 4.927 38.239 1664 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.46 % Allowed : 12.53 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.25), residues: 1123 helix: 2.80 (0.23), residues: 444 sheet: -0.96 (0.34), residues: 226 loop : -0.60 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 46 TYR 0.028 0.002 TYR R 36 PHE 0.015 0.001 PHE P 22 TRP 0.014 0.001 TRP R 233 HIS 0.010 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9580) covalent geometry : angle 0.56588 (13007) SS BOND : bond 0.00169 ( 5) SS BOND : angle 2.67778 ( 10) hydrogen bonds : bond 0.04012 ( 460) hydrogen bonds : angle 4.11856 ( 1332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.226 Fit side-chains REVERT: R 39 TRP cc_start: 0.8961 (t60) cc_final: 0.8676 (t60) REVERT: R 67 MET cc_start: 0.7274 (mtt) cc_final: 0.6735 (mtp) REVERT: R 87 TYR cc_start: 0.8453 (p90) cc_final: 0.7959 (p90) REVERT: R 181 MET cc_start: 0.8394 (tpp) cc_final: 0.8141 (tpp) REVERT: R 324 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7972 (mmtt) REVERT: R 376 PHE cc_start: 0.7925 (t80) cc_final: 0.7683 (t80) REVERT: P 16 LYS cc_start: 0.9307 (mmtm) cc_final: 0.9106 (mmmm) REVERT: A 339 TYR cc_start: 0.8666 (m-80) cc_final: 0.8318 (m-80) REVERT: B 234 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8104 (t80) REVERT: G 62 ARG cc_start: 0.8625 (pmt-80) cc_final: 0.8406 (pmt-80) REVERT: G 63 GLU cc_start: 0.6746 (mt-10) cc_final: 0.5634 (pt0) REVERT: N 91 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8542 (t) REVERT: N 109 ASP cc_start: 0.7096 (p0) cc_final: 0.6736 (p0) REVERT: N 117 TYR cc_start: 0.8454 (m-80) cc_final: 0.8075 (m-80) outliers start: 34 outliers final: 21 residues processed: 162 average time/residue: 0.0896 time to fit residues: 19.5779 Evaluate side-chains 156 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 324 LYS Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 0.0030 chunk 89 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 73 optimal weight: 0.0050 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 2 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 24 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.209753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.166719 restraints weight = 11562.323| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 3.60 r_work: 0.3561 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9585 Z= 0.116 Angle : 0.532 7.581 13017 Z= 0.275 Chirality : 0.039 0.179 1446 Planarity : 0.003 0.051 1628 Dihedral : 4.720 42.193 1664 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.95 % Allowed : 13.34 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.25), residues: 1123 helix: 2.89 (0.23), residues: 445 sheet: -0.72 (0.34), residues: 222 loop : -0.61 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 52 TYR 0.026 0.001 TYR R 36 PHE 0.020 0.001 PHE P 22 TRP 0.013 0.001 TRP R 233 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9580) covalent geometry : angle 0.52876 (13007) SS BOND : bond 0.00164 ( 5) SS BOND : angle 2.29055 ( 10) hydrogen bonds : bond 0.03655 ( 460) hydrogen bonds : angle 3.95079 ( 1332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: R 39 TRP cc_start: 0.9021 (t60) cc_final: 0.8726 (t60) REVERT: R 67 MET cc_start: 0.7221 (mtt) cc_final: 0.6729 (mtp) REVERT: R 269 LEU cc_start: 0.8061 (tt) cc_final: 0.7817 (tp) REVERT: R 318 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8542 (mm) REVERT: R 376 PHE cc_start: 0.7884 (t80) cc_final: 0.7678 (t80) REVERT: R 387 LEU cc_start: 0.8360 (mt) cc_final: 0.8043 (mt) REVERT: P 16 LYS cc_start: 0.9268 (mmtm) cc_final: 0.9063 (mmmm) REVERT: A 339 TYR cc_start: 0.8673 (m-80) cc_final: 0.8342 (m-80) REVERT: B 189 SER cc_start: 0.8836 (p) cc_final: 0.8507 (m) REVERT: B 234 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8141 (t80) REVERT: G 62 ARG cc_start: 0.8621 (pmt-80) cc_final: 0.8393 (pmt-80) REVERT: G 63 GLU cc_start: 0.7119 (mt-10) cc_final: 0.5881 (pt0) REVERT: N 109 ASP cc_start: 0.7189 (p0) cc_final: 0.6805 (p0) REVERT: N 117 TYR cc_start: 0.8288 (m-80) cc_final: 0.7990 (m-80) outliers start: 29 outliers final: 19 residues processed: 162 average time/residue: 0.0830 time to fit residues: 18.4067 Evaluate side-chains 151 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 0.0980 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.214450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.167564 restraints weight = 11982.240| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 4.14 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9585 Z= 0.190 Angle : 0.584 9.847 13017 Z= 0.301 Chirality : 0.041 0.197 1446 Planarity : 0.004 0.051 1628 Dihedral : 4.934 55.797 1664 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.05 % Allowed : 13.85 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.25), residues: 1123 helix: 2.75 (0.23), residues: 448 sheet: -0.86 (0.34), residues: 227 loop : -0.61 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 52 TYR 0.025 0.002 TYR N 94 PHE 0.016 0.001 PHE B 199 TRP 0.016 0.001 TRP N 47 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 9580) covalent geometry : angle 0.58020 (13007) SS BOND : bond 0.00159 ( 5) SS BOND : angle 2.56389 ( 10) hydrogen bonds : bond 0.03927 ( 460) hydrogen bonds : angle 4.08623 ( 1332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: R 67 MET cc_start: 0.7236 (mtt) cc_final: 0.6537 (mtp) REVERT: R 269 LEU cc_start: 0.7764 (tt) cc_final: 0.7493 (tp) REVERT: R 318 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8498 (mm) REVERT: P 26 LEU cc_start: 0.8315 (mt) cc_final: 0.7989 (tt) REVERT: A 339 TYR cc_start: 0.8398 (m-80) cc_final: 0.8064 (m-80) REVERT: B 234 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.7995 (t80) REVERT: G 62 ARG cc_start: 0.8378 (pmt-80) cc_final: 0.8100 (pmt-80) REVERT: G 63 GLU cc_start: 0.7024 (mt-10) cc_final: 0.5912 (pt0) REVERT: N 109 ASP cc_start: 0.6473 (p0) cc_final: 0.6145 (p0) REVERT: N 117 TYR cc_start: 0.8365 (m-80) cc_final: 0.8038 (m-80) outliers start: 30 outliers final: 23 residues processed: 155 average time/residue: 0.0902 time to fit residues: 18.8515 Evaluate side-chains 152 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 281 TYR Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.216718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.168705 restraints weight = 11871.923| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 3.97 r_work: 0.3431 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9585 Z= 0.134 Angle : 0.562 11.634 13017 Z= 0.286 Chirality : 0.040 0.184 1446 Planarity : 0.003 0.051 1628 Dihedral : 4.758 56.903 1664 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.85 % Allowed : 14.15 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.25), residues: 1123 helix: 2.67 (0.24), residues: 452 sheet: -0.69 (0.35), residues: 217 loop : -0.63 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 52 TYR 0.020 0.001 TYR R 141 PHE 0.012 0.001 PHE B 199 TRP 0.041 0.001 TRP R 39 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9580) covalent geometry : angle 0.55949 (13007) SS BOND : bond 0.00107 ( 5) SS BOND : angle 2.03821 ( 10) hydrogen bonds : bond 0.03624 ( 460) hydrogen bonds : angle 4.05080 ( 1332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: R 35 LEU cc_start: 0.9111 (mt) cc_final: 0.8854 (mt) REVERT: R 67 MET cc_start: 0.7262 (mtt) cc_final: 0.6854 (mtp) REVERT: R 269 LEU cc_start: 0.8086 (tt) cc_final: 0.7847 (tp) REVERT: R 318 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8519 (mm) REVERT: P 9 ASP cc_start: 0.8514 (t0) cc_final: 0.8078 (t0) REVERT: A 339 TYR cc_start: 0.8684 (m-80) cc_final: 0.8374 (m-80) REVERT: B 234 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8143 (t80) REVERT: G 62 ARG cc_start: 0.8692 (pmt-80) cc_final: 0.8429 (pmt-80) REVERT: G 63 GLU cc_start: 0.7104 (mt-10) cc_final: 0.5954 (pt0) REVERT: N 109 ASP cc_start: 0.7086 (p0) cc_final: 0.6729 (p0) REVERT: N 117 TYR cc_start: 0.8359 (m-80) cc_final: 0.8019 (m-80) outliers start: 28 outliers final: 24 residues processed: 154 average time/residue: 0.0751 time to fit residues: 16.0987 Evaluate side-chains 156 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 281 TYR Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 100 optimal weight: 0.0010 chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.208540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.167527 restraints weight = 11445.925| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.65 r_work: 0.3425 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9585 Z= 0.168 Angle : 0.581 9.929 13017 Z= 0.297 Chirality : 0.040 0.196 1446 Planarity : 0.004 0.050 1628 Dihedral : 4.756 44.343 1664 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.36 % Allowed : 13.65 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.26), residues: 1123 helix: 2.69 (0.24), residues: 448 sheet: -0.69 (0.35), residues: 217 loop : -0.63 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 52 TYR 0.019 0.002 TYR N 94 PHE 0.014 0.001 PHE B 199 TRP 0.031 0.001 TRP R 39 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 9580) covalent geometry : angle 0.57802 (13007) SS BOND : bond 0.00116 ( 5) SS BOND : angle 2.30355 ( 10) hydrogen bonds : bond 0.03722 ( 460) hydrogen bonds : angle 4.08868 ( 1332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: R 67 MET cc_start: 0.7250 (mtt) cc_final: 0.6840 (mtp) REVERT: R 318 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8466 (mm) REVERT: P 9 ASP cc_start: 0.8533 (t0) cc_final: 0.8093 (t0) REVERT: A 339 TYR cc_start: 0.8715 (m-80) cc_final: 0.8401 (m-80) REVERT: B 234 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.8074 (t80) REVERT: G 62 ARG cc_start: 0.8676 (pmt-80) cc_final: 0.8424 (pmt-80) REVERT: G 63 GLU cc_start: 0.7123 (mt-10) cc_final: 0.5962 (pt0) REVERT: N 105 ARG cc_start: 0.7866 (mtm-85) cc_final: 0.6809 (tpm170) REVERT: N 109 ASP cc_start: 0.7124 (p0) cc_final: 0.6773 (p0) REVERT: N 117 TYR cc_start: 0.8441 (m-80) cc_final: 0.8057 (m-80) outliers start: 33 outliers final: 28 residues processed: 154 average time/residue: 0.0805 time to fit residues: 17.1143 Evaluate side-chains 158 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 281 TYR Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 89 optimal weight: 0.0670 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.209237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.166024 restraints weight = 11572.252| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.61 r_work: 0.3504 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9585 Z= 0.115 Angle : 0.545 9.801 13017 Z= 0.277 Chirality : 0.039 0.183 1446 Planarity : 0.003 0.051 1628 Dihedral : 4.515 44.382 1664 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.85 % Allowed : 14.36 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.26), residues: 1123 helix: 2.73 (0.24), residues: 449 sheet: -0.56 (0.35), residues: 215 loop : -0.60 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.018 0.001 TYR R 141 PHE 0.020 0.001 PHE P 22 TRP 0.029 0.001 TRP R 39 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9580) covalent geometry : angle 0.54219 (13007) SS BOND : bond 0.00146 ( 5) SS BOND : angle 1.94314 ( 10) hydrogen bonds : bond 0.03423 ( 460) hydrogen bonds : angle 3.97495 ( 1332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: R 67 MET cc_start: 0.7272 (mtt) cc_final: 0.6905 (mtp) REVERT: R 318 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8523 (mm) REVERT: R 387 LEU cc_start: 0.8336 (mt) cc_final: 0.8031 (mt) REVERT: A 339 TYR cc_start: 0.8671 (m-80) cc_final: 0.8361 (m-80) REVERT: B 234 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8043 (t80) REVERT: G 62 ARG cc_start: 0.8512 (pmt-80) cc_final: 0.8201 (pmt-80) REVERT: N 105 ARG cc_start: 0.7820 (mtm-85) cc_final: 0.6853 (tpm170) REVERT: N 109 ASP cc_start: 0.7061 (p0) cc_final: 0.6750 (p0) REVERT: N 117 TYR cc_start: 0.8247 (m-80) cc_final: 0.7948 (m-80) outliers start: 28 outliers final: 23 residues processed: 149 average time/residue: 0.0844 time to fit residues: 17.2351 Evaluate side-chains 153 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 91 optimal weight: 0.1980 chunk 64 optimal weight: 0.0050 chunk 31 optimal weight: 0.0270 chunk 98 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.207866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.169537 restraints weight = 11469.184| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 3.06 r_work: 0.3497 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9585 Z= 0.142 Angle : 0.562 9.925 13017 Z= 0.288 Chirality : 0.040 0.188 1446 Planarity : 0.004 0.050 1628 Dihedral : 4.519 50.114 1664 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.65 % Allowed : 14.77 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.26), residues: 1123 helix: 2.64 (0.24), residues: 452 sheet: -0.66 (0.34), residues: 222 loop : -0.51 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.018 0.001 TYR R 36 PHE 0.024 0.001 PHE R 345 TRP 0.027 0.001 TRP R 39 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9580) covalent geometry : angle 0.55985 (13007) SS BOND : bond 0.00149 ( 5) SS BOND : angle 2.02140 ( 10) hydrogen bonds : bond 0.03555 ( 460) hydrogen bonds : angle 3.98612 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1768.94 seconds wall clock time: 30 minutes 58.68 seconds (1858.68 seconds total)