Starting phenix.real_space_refine on Fri Mar 14 03:29:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fiy_31606/03_2025/7fiy_31606_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fiy_31606/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7fiy_31606/03_2025/7fiy_31606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fiy_31606/03_2025/7fiy_31606.map" model { file = "/net/cci-nas-00/data/ceres_data/7fiy_31606/03_2025/7fiy_31606_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fiy_31606/03_2025/7fiy_31606_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.20, per 1000 atoms: 0.66 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: 1.90 Conformation dependent library (CDL) restraints added in 893.9 milliseconds 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: 0.98 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: 2.84 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 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: 1.070 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.390 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:4.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.680 ------------------------------------------------------------------------------- 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 9580 Z= 0.268 Angle : 0.820 10.274 13007 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.036 0.002 TRP A 281 HIS 0.014 0.002 HIS A 220 PHE 0.024 0.002 PHE R 177 TYR 0.026 0.002 TYR P 1 ARG 0.005 0.000 ARG R 278 *********************** 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 : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 67 MET cc_start: 0.6978 (mtt) cc_final: 0.6195 (mtp) REVERT: R 252 GLU cc_start: 0.5603 (pt0) cc_final: 0.5102 (tp30) REVERT: R 376 PHE cc_start: 0.7091 (t80) cc_final: 0.6592 (t80) REVERT: P 19 GLN cc_start: 0.8365 (mt0) cc_final: 0.8163 (mt0) REVERT: P 22 PHE cc_start: 0.8598 (t80) cc_final: 0.8382 (t80) REVERT: A 343 ASP cc_start: 0.7501 (t70) cc_final: 0.7249 (t70) REVERT: G 52 THR cc_start: 0.8571 (m) cc_final: 0.8224 (p) REVERT: N 67 ARG cc_start: 0.6618 (mtp180) cc_final: 0.6196 (mtp180) REVERT: N 83 MET cc_start: 0.7568 (mtp) cc_final: 0.7289 (mtp) REVERT: N 109 ASP cc_start: 0.6532 (p0) cc_final: 0.6307 (p0) REVERT: N 125 THR cc_start: 0.8495 (m) cc_final: 0.8293 (t) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.3008 time to fit residues: 105.0254 Evaluate side-chains 159 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 10.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 156 GLN 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 = 0.4287 r_free = 0.4287 target = 0.198929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.163648 restraints weight = 10617.711| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.61 r_work: 0.3393 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9580 Z= 0.268 Angle : 0.605 6.773 13007 Z= 0.321 Chirality : 0.043 0.139 1446 Planarity : 0.005 0.056 1628 Dihedral : 5.197 34.023 1664 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.55 % Allowed : 10.49 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.24), residues: 1123 helix: 1.96 (0.22), residues: 452 sheet: -0.56 (0.34), residues: 229 loop : -0.72 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 281 HIS 0.009 0.001 HIS A 220 PHE 0.020 0.002 PHE R 379 TYR 0.029 0.002 TYR R 141 ARG 0.008 0.001 ARG R 370 *********************** 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 209 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: R 39 TRP cc_start: 0.8692 (t60) cc_final: 0.8187 (t60) REVERT: R 67 MET cc_start: 0.7224 (mtt) cc_final: 0.6343 (mtp) REVERT: R 87 TYR cc_start: 0.7836 (p90) cc_final: 0.7588 (p90) REVERT: R 252 GLU cc_start: 0.6292 (pt0) cc_final: 0.5479 (tp30) REVERT: R 376 PHE cc_start: 0.7790 (t80) cc_final: 0.7000 (t80) REVERT: P 9 ASP cc_start: 0.8379 (t0) cc_final: 0.8053 (t0) REVERT: P 24 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8350 (mm-40) REVERT: B 189 SER cc_start: 0.8494 (p) cc_final: 0.8267 (m) REVERT: G 52 THR cc_start: 0.8718 (m) cc_final: 0.8389 (p) REVERT: N 109 ASP cc_start: 0.6936 (p0) cc_final: 0.6632 (p0) outliers start: 25 outliers final: 14 residues processed: 196 average time/residue: 0.2524 time to fit residues: 66.2951 Evaluate side-chains 169 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 301 THR 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 55 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 275 SER 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 42 optimal weight: 0.2980 chunk 86 optimal weight: 0.7980 chunk 2 optimal weight: 30.0000 chunk 83 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN 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 = 0.4476 r_free = 0.4476 target = 0.213932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.163182 restraints weight = 11954.189| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 4.67 r_work: 0.3398 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 9580 Z= 0.419 Angle : 0.670 9.279 13007 Z= 0.348 Chirality : 0.045 0.183 1446 Planarity : 0.004 0.054 1628 Dihedral : 5.317 31.038 1664 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.46 % Allowed : 12.12 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1123 helix: 2.45 (0.23), residues: 447 sheet: -0.89 (0.32), residues: 239 loop : -0.53 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 47 HIS 0.012 0.002 HIS A 220 PHE 0.019 0.002 PHE B 199 TYR 0.031 0.003 TYR B 289 ARG 0.004 0.001 ARG B 52 *********************** 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 191 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: R 39 TRP cc_start: 0.9014 (t60) cc_final: 0.8510 (t60) REVERT: R 67 MET cc_start: 0.7054 (mtt) cc_final: 0.6508 (mtp) REVERT: R 87 TYR cc_start: 0.8530 (p90) cc_final: 0.7922 (p90) REVERT: P 9 ASP cc_start: 0.8633 (t0) cc_final: 0.8250 (t0) REVERT: P 24 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8562 (mm-40) REVERT: A 27 GLU cc_start: 0.8514 (tp30) cc_final: 0.8208 (tm-30) REVERT: B 234 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8186 (t80) REVERT: N 105 ARG cc_start: 0.8072 (mpp80) cc_final: 0.7832 (mtm-85) REVERT: N 109 ASP cc_start: 0.7311 (p0) cc_final: 0.6994 (p0) REVERT: N 117 TYR cc_start: 0.8616 (m-80) cc_final: 0.8324 (m-80) outliers start: 34 outliers final: 19 residues processed: 179 average time/residue: 0.2377 time to fit residues: 57.5286 Evaluate side-chains 157 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 301 THR 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 44 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 30 VAL 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 89 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4511 r_free = 0.4511 target = 0.217489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.167380 restraints weight = 11826.621| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 4.04 r_work: 0.3451 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9580 Z= 0.212 Angle : 0.557 10.407 13007 Z= 0.289 Chirality : 0.041 0.201 1446 Planarity : 0.004 0.053 1628 Dihedral : 4.939 38.986 1664 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.85 % Allowed : 13.75 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1123 helix: 2.75 (0.23), residues: 448 sheet: -1.02 (0.34), residues: 217 loop : -0.64 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 233 HIS 0.009 0.001 HIS A 220 PHE 0.013 0.001 PHE B 292 TYR 0.056 0.002 TYR R 36 ARG 0.004 0.000 ARG A 20 *********************** 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 179 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 1.667 Fit side-chains revert: symmetry clash REVERT: R 39 TRP cc_start: 0.9042 (t60) cc_final: 0.8489 (t60) REVERT: R 67 MET cc_start: 0.7168 (mtt) cc_final: 0.6618 (mtp) REVERT: R 87 TYR cc_start: 0.8595 (p90) cc_final: 0.8004 (p90) REVERT: P 16 LYS cc_start: 0.9256 (mmtm) cc_final: 0.9049 (mmmm) REVERT: P 24 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8693 (mm-40) REVERT: A 27 GLU cc_start: 0.8347 (tp30) cc_final: 0.8056 (tm-30) REVERT: B 44 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6707 (tt0) REVERT: B 234 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.7962 (t80) REVERT: G 52 THR cc_start: 0.8870 (m) cc_final: 0.8369 (p) REVERT: G 62 ARG cc_start: 0.8607 (pmt-80) cc_final: 0.8344 (pmt-80) REVERT: G 63 GLU cc_start: 0.6794 (mt-10) cc_final: 0.5609 (pt0) REVERT: N 87 LYS cc_start: 0.8290 (mtmt) cc_final: 0.8053 (mmmt) REVERT: N 109 ASP cc_start: 0.7058 (p0) cc_final: 0.6678 (p0) REVERT: N 117 TYR cc_start: 0.8446 (m-80) cc_final: 0.8110 (m-80) outliers start: 28 outliers final: 17 residues processed: 166 average time/residue: 0.2831 time to fit residues: 64.6084 Evaluate side-chains 156 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 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 A residue 372 ILE Chi-restraints excluded: chain B residue 44 GLN 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 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 35 ASN Chi-restraints excluded: chain N residue 61 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 0.0670 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.217705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.168113 restraints weight = 11788.271| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 4.42 r_work: 0.3440 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9580 Z= 0.193 Angle : 0.531 7.852 13007 Z= 0.276 Chirality : 0.039 0.176 1446 Planarity : 0.003 0.052 1628 Dihedral : 4.777 37.455 1664 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.95 % Allowed : 13.24 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1123 helix: 2.85 (0.23), residues: 447 sheet: -0.91 (0.33), residues: 225 loop : -0.56 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 233 HIS 0.009 0.001 HIS A 220 PHE 0.014 0.001 PHE P 22 TYR 0.046 0.002 TYR R 36 ARG 0.003 0.000 ARG B 22 *********************** 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 177 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: R 39 TRP cc_start: 0.9035 (t60) cc_final: 0.8496 (t60) REVERT: R 67 MET cc_start: 0.7210 (mtt) cc_final: 0.6636 (mtp) REVERT: R 87 TYR cc_start: 0.8615 (p90) cc_final: 0.8034 (p90) REVERT: R 269 LEU cc_start: 0.8103 (tt) cc_final: 0.7851 (tp) REVERT: R 376 PHE cc_start: 0.7936 (t80) cc_final: 0.7681 (t80) REVERT: A 27 GLU cc_start: 0.8380 (tp30) cc_final: 0.8087 (tm-30) REVERT: B 234 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8016 (t80) REVERT: G 62 ARG cc_start: 0.8606 (pmt-80) cc_final: 0.8349 (pmt-80) REVERT: G 63 GLU cc_start: 0.6929 (mt-10) cc_final: 0.5647 (pt0) REVERT: N 91 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8594 (t) REVERT: N 109 ASP cc_start: 0.7228 (p0) cc_final: 0.6846 (p0) REVERT: N 117 TYR cc_start: 0.8464 (m-80) cc_final: 0.8061 (m-80) outliers start: 29 outliers final: 20 residues processed: 167 average time/residue: 0.2647 time to fit residues: 60.8868 Evaluate side-chains 155 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 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 223 THR 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 61 THR Chi-restraints excluded: chain N residue 83 MET 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 75 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 84 optimal weight: 0.3980 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.217928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.167474 restraints weight = 11852.666| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 4.52 r_work: 0.3469 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9580 Z= 0.198 Angle : 0.536 7.378 13007 Z= 0.278 Chirality : 0.039 0.177 1446 Planarity : 0.003 0.051 1628 Dihedral : 4.720 44.592 1664 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.75 % Allowed : 14.36 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1123 helix: 2.88 (0.23), residues: 447 sheet: -0.75 (0.34), residues: 223 loop : -0.60 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 233 HIS 0.008 0.001 HIS A 220 PHE 0.019 0.001 PHE P 22 TYR 0.043 0.002 TYR R 36 ARG 0.005 0.000 ARG N 105 *********************** 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 166 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: R 39 TRP cc_start: 0.9037 (t60) cc_final: 0.8524 (t60) REVERT: R 67 MET cc_start: 0.7243 (mtt) cc_final: 0.6680 (mtp) REVERT: R 269 LEU cc_start: 0.8071 (tt) cc_final: 0.7841 (tp) REVERT: R 318 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8505 (mm) REVERT: R 376 PHE cc_start: 0.7975 (t80) cc_final: 0.7769 (t80) REVERT: A 27 GLU cc_start: 0.8349 (tp30) cc_final: 0.8072 (tm-30) REVERT: A 50 GLU cc_start: 0.6586 (tp30) cc_final: 0.6342 (tp30) REVERT: G 62 ARG cc_start: 0.8631 (pmt-80) cc_final: 0.8356 (pmt-80) REVERT: G 63 GLU cc_start: 0.7096 (mt-10) cc_final: 0.5811 (pt0) REVERT: N 91 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8570 (t) REVERT: N 109 ASP cc_start: 0.7189 (p0) cc_final: 0.6834 (p0) REVERT: N 117 TYR cc_start: 0.8404 (m-80) cc_final: 0.8041 (m-80) outliers start: 27 outliers final: 22 residues processed: 158 average time/residue: 0.2481 time to fit residues: 52.7636 Evaluate side-chains 151 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 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 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 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 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 Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 290 ASN P 19 GLN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** B 88 ASN ** 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 = 0.4476 r_free = 0.4476 target = 0.214169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.166494 restraints weight = 11866.200| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 4.18 r_work: 0.3334 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9580 Z= 0.319 Angle : 0.591 7.663 13007 Z= 0.308 Chirality : 0.041 0.198 1446 Planarity : 0.004 0.050 1628 Dihedral : 5.010 59.748 1664 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.56 % Allowed : 14.15 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1123 helix: 2.83 (0.23), residues: 450 sheet: -0.87 (0.34), residues: 220 loop : -0.70 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 47 HIS 0.010 0.001 HIS A 220 PHE 0.016 0.002 PHE B 199 TYR 0.039 0.002 TYR R 36 ARG 0.003 0.000 ARG G 27 *********************** 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 171 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 1.115 Fit side-chains REVERT: R 39 TRP cc_start: 0.9037 (t60) cc_final: 0.8581 (t60) REVERT: R 67 MET cc_start: 0.7322 (mtt) cc_final: 0.6606 (mtp) REVERT: R 188 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7952 (mm) REVERT: R 269 LEU cc_start: 0.8143 (tt) cc_final: 0.7923 (tp) REVERT: R 318 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8450 (mm) REVERT: P 9 ASP cc_start: 0.8565 (t0) cc_final: 0.8122 (t0) REVERT: P 24 GLN cc_start: 0.9091 (mt0) cc_final: 0.8767 (mm-40) REVERT: P 26 LEU cc_start: 0.8847 (mt) cc_final: 0.8525 (tt) REVERT: A 27 GLU cc_start: 0.8457 (tp30) cc_final: 0.8154 (tm-30) REVERT: B 234 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8045 (t80) REVERT: G 62 ARG cc_start: 0.8649 (pmt-80) cc_final: 0.8368 (pmt-80) REVERT: G 63 GLU cc_start: 0.7076 (mt-10) cc_final: 0.5797 (pt0) REVERT: N 91 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8602 (t) REVERT: N 109 ASP cc_start: 0.7117 (p0) cc_final: 0.6741 (p0) REVERT: N 117 TYR cc_start: 0.8611 (m-80) cc_final: 0.8274 (m-80) outliers start: 35 outliers final: 25 residues processed: 162 average time/residue: 0.3238 time to fit residues: 72.2285 Evaluate side-chains 158 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 188 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 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 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 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 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 17 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4501 r_free = 0.4501 target = 0.216681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.169467 restraints weight = 11959.771| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 3.79 r_work: 0.3511 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9580 Z= 0.216 Angle : 0.547 7.345 13007 Z= 0.284 Chirality : 0.040 0.189 1446 Planarity : 0.003 0.050 1628 Dihedral : 4.739 51.630 1664 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.46 % Allowed : 14.36 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1123 helix: 2.77 (0.23), residues: 454 sheet: -0.75 (0.35), residues: 216 loop : -0.70 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 47 HIS 0.008 0.001 HIS A 220 PHE 0.012 0.001 PHE B 199 TYR 0.038 0.002 TYR R 36 ARG 0.003 0.000 ARG G 27 *********************** 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 170 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: R 39 TRP cc_start: 0.9057 (t60) cc_final: 0.8593 (t60) REVERT: R 67 MET cc_start: 0.7285 (mtt) cc_final: 0.6598 (mtp) REVERT: R 188 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7775 (mm) REVERT: R 269 LEU cc_start: 0.8089 (tt) cc_final: 0.7863 (tp) REVERT: R 318 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8464 (mm) REVERT: P 9 ASP cc_start: 0.8541 (t0) cc_final: 0.8090 (t0) REVERT: P 26 LEU cc_start: 0.8855 (mt) cc_final: 0.8513 (tt) REVERT: A 27 GLU cc_start: 0.8424 (tp30) cc_final: 0.8110 (tm-30) REVERT: B 17 GLN cc_start: 0.8969 (pp30) cc_final: 0.8760 (pp30) REVERT: G 62 ARG cc_start: 0.8605 (pmt-80) cc_final: 0.8315 (pmt-80) REVERT: G 63 GLU cc_start: 0.7044 (mt-10) cc_final: 0.5884 (pt0) REVERT: N 91 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8566 (t) REVERT: N 109 ASP cc_start: 0.7077 (p0) cc_final: 0.6729 (p0) REVERT: N 117 TYR cc_start: 0.8405 (m-80) cc_final: 0.8059 (m-80) outliers start: 34 outliers final: 30 residues processed: 160 average time/residue: 0.2423 time to fit residues: 52.6757 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 : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 188 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 281 TYR Chi-restraints excluded: chain R residue 306 THR 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 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 146 LEU 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 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 Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 40.0000 chunk 25 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 57 optimal weight: 0.0070 chunk 58 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- 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 = 0.4449 r_free = 0.4449 target = 0.208235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.165217 restraints weight = 11506.035| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 3.44 r_work: 0.3547 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9580 Z= 0.187 Angle : 0.541 8.048 13007 Z= 0.280 Chirality : 0.039 0.180 1446 Planarity : 0.003 0.050 1628 Dihedral : 4.537 42.008 1664 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.46 % Allowed : 14.36 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1123 helix: 2.80 (0.23), residues: 454 sheet: -0.62 (0.35), residues: 214 loop : -0.73 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.007 0.001 HIS A 220 PHE 0.011 0.001 PHE R 379 TYR 0.037 0.001 TYR R 36 ARG 0.002 0.000 ARG G 27 *********************** 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 166 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: R 39 TRP cc_start: 0.9052 (t60) cc_final: 0.8651 (t60) REVERT: R 67 MET cc_start: 0.7311 (mtt) cc_final: 0.6627 (mtp) REVERT: R 188 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7746 (mm) REVERT: R 318 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8505 (mm) REVERT: R 373 LYS cc_start: 0.7949 (ttpt) cc_final: 0.7613 (tttt) REVERT: P 26 LEU cc_start: 0.8756 (mt) cc_final: 0.8447 (tt) REVERT: A 27 GLU cc_start: 0.8403 (tp30) cc_final: 0.8098 (tm-30) REVERT: G 62 ARG cc_start: 0.8527 (pmt-80) cc_final: 0.8253 (pmt-80) REVERT: G 63 GLU cc_start: 0.7090 (mt-10) cc_final: 0.5957 (pt0) REVERT: N 91 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8571 (t) REVERT: N 109 ASP cc_start: 0.7041 (p0) cc_final: 0.6704 (p0) REVERT: N 117 TYR cc_start: 0.8302 (m-80) cc_final: 0.7952 (m-80) outliers start: 34 outliers final: 30 residues processed: 156 average time/residue: 0.2388 time to fit residues: 50.8261 Evaluate side-chains 161 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 188 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 299 ILE Chi-restraints excluded: chain R residue 306 THR 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 320 THR 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 146 LEU 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 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 Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 42 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 110 optimal weight: 0.0030 chunk 96 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 = 0.4485 r_free = 0.4485 target = 0.210329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.171363 restraints weight = 11544.516| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 3.19 r_work: 0.3633 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 0.047 9580 Z= 0.199 Angle : 0.545 8.131 13007 Z= 0.283 Chirality : 0.039 0.183 1446 Planarity : 0.004 0.050 1628 Dihedral : 4.502 46.200 1664 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.26 % Allowed : 14.66 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1123 helix: 2.72 (0.23), residues: 457 sheet: -0.65 (0.35), residues: 216 loop : -0.78 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.008 0.001 HIS A 220 PHE 0.024 0.001 PHE R 345 TYR 0.030 0.001 TYR R 36 ARG 0.006 0.000 ARG A 20 ********************** 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 163 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.952 Fit side-chains REVERT: R 39 TRP cc_start: 0.9072 (t60) cc_final: 0.8651 (t60) REVERT: R 67 MET cc_start: 0.7294 (mtt) cc_final: 0.6581 (mtp) REVERT: R 188 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7625 (mm) REVERT: R 318 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8509 (mm) REVERT: R 373 LYS cc_start: 0.8015 (ttpt) cc_final: 0.7766 (tttt) REVERT: P 26 LEU cc_start: 0.8749 (mt) cc_final: 0.8462 (tt) REVERT: A 27 GLU cc_start: 0.8312 (tp30) cc_final: 0.8034 (tm-30) REVERT: A 339 TYR cc_start: 0.8623 (m-80) cc_final: 0.8332 (m-80) REVERT: G 62 ARG cc_start: 0.8413 (pmt-80) cc_final: 0.8098 (pmt-80) REVERT: N 91 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8571 (t) REVERT: N 105 ARG cc_start: 0.7603 (mtm-85) cc_final: 0.6825 (tpm170) REVERT: N 109 ASP cc_start: 0.6923 (p0) cc_final: 0.6590 (p0) REVERT: N 117 TYR cc_start: 0.8286 (m-80) cc_final: 0.7944 (m-80) outliers start: 32 outliers final: 28 residues processed: 153 average time/residue: 0.2480 time to fit residues: 50.9405 Evaluate side-chains 157 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 188 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 306 THR 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 320 THR 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 146 LEU 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 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 Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 110 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 87 optimal weight: 0.8980 chunk 47 optimal weight: 0.0370 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 = 0.4499 r_free = 0.4499 target = 0.211839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.169217 restraints weight = 11522.750| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 3.42 r_work: 0.3536 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9580 Z= 0.161 Angle : 0.530 8.209 13007 Z= 0.274 Chirality : 0.039 0.178 1446 Planarity : 0.003 0.050 1628 Dihedral : 4.356 50.755 1664 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.05 % Allowed : 14.97 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1123 helix: 2.79 (0.23), residues: 457 sheet: -0.59 (0.35), residues: 216 loop : -0.76 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 233 HIS 0.007 0.001 HIS A 220 PHE 0.022 0.001 PHE R 345 TYR 0.030 0.001 TYR R 36 ARG 0.005 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5176.47 seconds wall clock time: 92 minutes 38.88 seconds (5558.88 seconds total)