Starting phenix.real_space_refine on Thu Jul 2 11:33:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cz5_30505/07_2026/7cz5_30505.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cz5_30505/07_2026/7cz5_30505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cz5_30505/07_2026/7cz5_30505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cz5_30505/07_2026/7cz5_30505.map" model { file = "/net/cci-nas-00/data/ceres_data/7cz5_30505/07_2026/7cz5_30505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cz5_30505/07_2026/7cz5_30505.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7cz5_30505/07_2026/7cz5_30505.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cz5_30505/07_2026/7cz5_30505.cif" } resolution = 2.6 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 5304 2.51 5 N 1444 2.21 5 O 1542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8336 Number of models: 1 Model: "" Number of chains: 11 Chain: "R" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2155 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1893 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 3 Chain: "P" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 224 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "R" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'CLR': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.52, per 1000 atoms: 0.18 Number of scatterers: 8336 At special positions: 0 Unit cell: (97.344, 97.344, 135.876, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1542 8.00 N 1444 7.00 C 5304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 202 " - pdb=" SG CYS R 272 " distance=2.02 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: 0.52 Conformation dependent library (CDL) restraints added in 349.3 milliseconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 41.4% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'R' and resid 119 through 154 Processing helix chain 'R' and resid 155 through 158 removed outlier: 3.758A pdb=" N HIS R 158 " --> pdb=" O ARG R 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 155 through 158' Processing helix chain 'R' and resid 159 through 187 removed outlier: 3.501A pdb=" N TYR R 163 " --> pdb=" O CYS R 159 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL R 164 " --> pdb=" O PRO R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 233 Processing helix chain 'R' and resid 239 through 268 removed outlier: 3.620A pdb=" N TRP R 243 " --> pdb=" O ARG R 239 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP R 250 " --> pdb=" O VAL R 246 " (cutoff:3.500A) Proline residue: R 253 - end of helix removed outlier: 3.509A pdb=" N PHE R 267 " --> pdb=" O CYS R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 274 removed outlier: 3.672A pdb=" N ASP R 274 " --> pdb=" O ALA R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 309 Proline residue: R 288 - end of helix removed outlier: 3.515A pdb=" N GLY R 298 " --> pdb=" O GLY R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 324 through 339 Proline residue: R 336 - end of helix Processing helix chain 'R' and resid 340 through 343 Processing helix chain 'R' and resid 353 through 363 removed outlier: 3.698A pdb=" N LEU R 358 " --> pdb=" O LEU R 354 " (cutoff:3.500A) Proline residue: R 359 - end of helix Processing helix chain 'R' and resid 364 through 366 No H-bonds generated for 'chain 'R' and resid 364 through 366' Processing helix chain 'R' and resid 367 through 377 Processing helix chain 'R' and resid 380 through 393 removed outlier: 3.737A pdb=" N ARG R 384 " --> pdb=" O ASN R 380 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU R 386 " --> pdb=" O GLU R 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.693A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.707A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.742A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.597A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'P' and resid 2 through 28 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.503A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 22 removed outlier: 4.274A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.691A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.555A 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: 3.759A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.376A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.558A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.681A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.662A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.682A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.615A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.528A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.675A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.561A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1173 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: 1.36 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2565 1.34 - 1.46: 2200 1.46 - 1.59: 3680 1.59 - 1.72: 0 1.72 - 1.84: 62 Bond restraints: 8507 Sorted by residual: bond pdb=" C1 PLM A 401 " pdb=" O1 PLM A 401 " ideal model delta sigma weight residual 1.249 1.342 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C1 PLM R 601 " pdb=" O1 PLM R 601 " ideal model delta sigma weight residual 1.249 1.342 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C1 PLM R 601 " pdb=" O2 PLM R 601 " ideal model delta sigma weight residual 1.249 1.208 0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C1 PLM A 401 " pdb=" O2 PLM A 401 " ideal model delta sigma weight residual 1.249 1.209 0.040 2.00e-02 2.50e+03 4.05e+00 bond pdb=" C1 PLM A 401 " pdb=" C2 PLM A 401 " ideal model delta sigma weight residual 1.542 1.505 0.037 2.00e-02 2.50e+03 3.38e+00 ... (remaining 8502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 11111 1.54 - 3.07: 311 3.07 - 4.61: 63 4.61 - 6.14: 24 6.14 - 7.68: 7 Bond angle restraints: 11516 Sorted by residual: angle pdb=" CA TYR R 133 " pdb=" CB TYR R 133 " pdb=" CG TYR R 133 " ideal model delta sigma weight residual 113.90 119.99 -6.09 1.80e+00 3.09e-01 1.14e+01 angle pdb=" C ILE R 132 " pdb=" N TYR R 133 " pdb=" CA TYR R 133 " ideal model delta sigma weight residual 121.14 115.26 5.88 1.75e+00 3.27e-01 1.13e+01 angle pdb=" N TYR R 226 " pdb=" CA TYR R 226 " pdb=" C TYR R 226 " ideal model delta sigma weight residual 111.28 114.82 -3.54 1.09e+00 8.42e-01 1.06e+01 angle pdb=" CA TRP B 99 " pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 113.60 107.64 5.96 1.90e+00 2.77e-01 9.84e+00 angle pdb=" CA TRP R 219 " pdb=" CB TRP R 219 " pdb=" CG TRP R 219 " ideal model delta sigma weight residual 113.60 108.30 5.30 1.90e+00 2.77e-01 7.78e+00 ... (remaining 11511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4602 17.38 - 34.76: 363 34.76 - 52.14: 49 52.14 - 69.52: 16 69.52 - 86.90: 6 Dihedral angle restraints: 5036 sinusoidal: 2003 harmonic: 3033 Sorted by residual: dihedral pdb=" CB CYS R 202 " pdb=" SG CYS R 202 " pdb=" SG CYS R 272 " pdb=" CB CYS R 272 " ideal model delta sinusoidal sigma weight residual 93.00 51.17 41.83 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CA ILE R 270 " pdb=" C ILE R 270 " pdb=" N ALA R 271 " pdb=" CA ALA R 271 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1222 0.095 - 0.190: 66 0.190 - 0.285: 1 0.285 - 0.380: 1 0.380 - 0.475: 1 Chirality restraints: 1291 Sorted by residual: chirality pdb=" C14 CLR R 602 " pdb=" C13 CLR R 602 " pdb=" C15 CLR R 602 " pdb=" C8 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.79 0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" C10 CLR R 602 " pdb=" C1 CLR R 602 " pdb=" C5 CLR R 602 " pdb=" C9 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.85 -2.52 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C17 CLR R 602 " pdb=" C13 CLR R 602 " pdb=" C16 CLR R 602 " pdb=" C20 CLR R 602 " both_signs ideal model delta sigma weight residual False 2.55 2.81 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1288 not shown) Planarity restraints: 1459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 99 " -0.021 2.00e-02 2.50e+03 1.14e-02 3.27e+00 pdb=" CG TRP B 99 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP B 99 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP B 99 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 99 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 99 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 99 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 99 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 99 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 99 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO G 49 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 1 " 0.012 2.00e-02 2.50e+03 1.16e-02 2.69e+00 pdb=" CG TYR P 1 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR P 1 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR P 1 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR P 1 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR P 1 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR P 1 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR P 1 " -0.001 2.00e-02 2.50e+03 ... (remaining 1456 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 510 2.73 - 3.27: 8139 3.27 - 3.81: 13353 3.81 - 4.36: 17137 4.36 - 4.90: 29252 Nonbonded interactions: 68391 Sorted by model distance: nonbonded pdb=" O GLY N 8 " pdb=" OG1 THR N 122 " model vdw 2.186 3.040 nonbonded pdb=" OD1 ASN R 380 " pdb=" O HOH R 701 " model vdw 2.258 3.040 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.261 3.120 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.296 3.120 nonbonded pdb=" ND2 ASN R 380 " pdb=" OE2 GLU R 382 " model vdw 2.304 3.120 ... (remaining 68386 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: 0.860 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.230 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 0.093 8508 Z= 0.199 Angle : 0.687 7.677 11518 Z= 0.369 Chirality : 0.049 0.475 1291 Planarity : 0.004 0.042 1459 Dihedral : 13.252 86.899 3069 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.24), residues: 1026 helix: -0.70 (0.24), residues: 413 sheet: -0.89 (0.32), residues: 218 loop : -2.23 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 13 TYR 0.027 0.002 TYR P 1 PHE 0.019 0.002 PHE B 151 TRP 0.029 0.002 TRP B 99 HIS 0.014 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 ( 8507) covalent geometry : angle 0.68572 / 0.37 (11516) SS BOND : bond 0.00642 / 0.34 ( 1) SS BOND : angle 2.98886 / 1.62 ( 2) hydrogen bonds : bond 0.15962 / 10.98 ( 409) hydrogen bonds : angle 6.31620 / 4.70 ( 1173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7050 (mmpt) cc_final: 0.6848 (mttp) REVERT: A 230 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7686 (mt-10) REVERT: A 378 ASP cc_start: 0.7294 (m-30) cc_final: 0.7038 (m-30) REVERT: P 27 MET cc_start: 0.2554 (mmm) cc_final: 0.1770 (tmt) REVERT: B 197 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7744 (mtt-85) REVERT: B 337 LYS cc_start: 0.8763 (mttt) cc_final: 0.8466 (mttt) REVERT: G 21 MET cc_start: 0.6371 (tpp) cc_final: 0.5388 (mpt) REVERT: G 29 LYS cc_start: 0.8418 (mmtm) cc_final: 0.8094 (mptm) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.5847 time to fit residues: 84.1564 Evaluate side-chains 104 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 210 HIS R 323 GLN A 14 ASN A 267 GLN A 292 ASN P 8 ASN B 35 ASN B 91 HIS G 18 GLN G 24 ASN N 3 GLN N 84 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.173210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128313 restraints weight = 9306.093| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.00 r_work: 0.3522 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8508 Z= 0.210 Angle : 0.649 9.366 11518 Z= 0.346 Chirality : 0.047 0.212 1291 Planarity : 0.005 0.045 1459 Dihedral : 7.108 56.899 1172 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.35 % Allowed : 7.96 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.25), residues: 1026 helix: 0.28 (0.26), residues: 405 sheet: -0.27 (0.34), residues: 205 loop : -1.87 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 283 TYR 0.037 0.002 TYR R 133 PHE 0.018 0.002 PHE B 151 TRP 0.024 0.002 TRP R 219 HIS 0.015 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 ( 8507) covalent geometry : angle 0.64632 / 0.34 (11516) SS BOND : bond 0.00263 / 0.14 ( 1) SS BOND : angle 4.14460 / 2.31 ( 2) hydrogen bonds : bond 0.05689 / 3.66 ( 409) hydrogen bonds : angle 4.95839 / 3.73 ( 1173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.226 Fit side-chains REVERT: R 270 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7485 (mp) REVERT: R 364 LEU cc_start: 0.7801 (tp) cc_final: 0.7524 (tt) REVERT: A 24 LYS cc_start: 0.7512 (mmpt) cc_final: 0.7227 (ttmm) REVERT: A 378 ASP cc_start: 0.8032 (m-30) cc_final: 0.7731 (m-30) REVERT: P 27 MET cc_start: 0.2678 (mmm) cc_final: 0.1822 (tmt) REVERT: B 44 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8526 (mt0) REVERT: B 59 TYR cc_start: 0.9206 (OUTLIER) cc_final: 0.8379 (t80) REVERT: G 21 MET cc_start: 0.6706 (tpp) cc_final: 0.5374 (mpt) REVERT: G 62 ARG cc_start: 0.6340 (OUTLIER) cc_final: 0.5980 (tpp-160) outliers start: 21 outliers final: 8 residues processed: 119 average time/residue: 0.6302 time to fit residues: 79.2707 Evaluate side-chains 113 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 202 CYS Chi-restraints excluded: chain R residue 270 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain G residue 62 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 60 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 ASN P 8 ASN B 75 GLN B 266 HIS B 268 ASN B 340 ASN N 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.177086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.133081 restraints weight = 9235.311| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.99 r_work: 0.3576 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8508 Z= 0.124 Angle : 0.542 8.831 11518 Z= 0.290 Chirality : 0.043 0.163 1291 Planarity : 0.004 0.044 1459 Dihedral : 6.700 59.975 1172 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.23 % Allowed : 11.10 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.26), residues: 1026 helix: 0.95 (0.27), residues: 405 sheet: -0.23 (0.33), residues: 205 loop : -1.60 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 265 TYR 0.029 0.001 TYR R 133 PHE 0.013 0.001 PHE A 212 TRP 0.020 0.001 TRP R 219 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 8507) covalent geometry : angle 0.54003 / 0.29 (11516) SS BOND : bond 0.00573 / 0.30 ( 1) SS BOND : angle 3.79741 / 2.10 ( 2) hydrogen bonds : bond 0.04497 / 2.89 ( 409) hydrogen bonds : angle 4.44446 / 3.33 ( 1173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: R 364 LEU cc_start: 0.7813 (tp) cc_final: 0.7574 (tt) REVERT: A 24 LYS cc_start: 0.7353 (mmpt) cc_final: 0.7084 (ttmm) REVERT: A 378 ASP cc_start: 0.7967 (m-30) cc_final: 0.7651 (m-30) REVERT: P 27 MET cc_start: 0.2637 (mmm) cc_final: 0.1898 (tmt) REVERT: B 45 MET cc_start: 0.9400 (mtt) cc_final: 0.8776 (mtt) REVERT: B 59 TYR cc_start: 0.9172 (OUTLIER) cc_final: 0.8328 (t80) REVERT: B 172 GLU cc_start: 0.8067 (pp20) cc_final: 0.7827 (pp20) REVERT: G 42 GLU cc_start: 0.7726 (mp0) cc_final: 0.7356 (mp0) REVERT: G 62 ARG cc_start: 0.6300 (OUTLIER) cc_final: 0.5938 (tpp-160) outliers start: 11 outliers final: 3 residues processed: 113 average time/residue: 0.5547 time to fit residues: 66.4189 Evaluate side-chains 99 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 194 HIS Chi-restraints excluded: chain R residue 202 CYS Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 62 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 292 ASN P 8 ASN B 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.174449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.130017 restraints weight = 9375.370| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.00 r_work: 0.3527 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8508 Z= 0.188 Angle : 0.593 8.542 11518 Z= 0.317 Chirality : 0.045 0.173 1291 Planarity : 0.005 0.050 1459 Dihedral : 6.779 56.357 1172 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.58 % Allowed : 12.22 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.26), residues: 1026 helix: 1.11 (0.27), residues: 399 sheet: 0.00 (0.33), residues: 205 loop : -1.56 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 317 TYR 0.029 0.002 TYR R 133 PHE 0.018 0.002 PHE B 199 TRP 0.022 0.002 TRP R 219 HIS 0.011 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 8507) covalent geometry : angle 0.59072 / 0.32 (11516) SS BOND : bond 0.00594 / 0.31 ( 1) SS BOND : angle 3.55946 / 1.96 ( 2) hydrogen bonds : bond 0.05071 / 3.26 ( 409) hydrogen bonds : angle 4.52779 / 3.41 ( 1173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: R 364 LEU cc_start: 0.7813 (tp) cc_final: 0.7560 (tt) REVERT: A 24 LYS cc_start: 0.7580 (mmpt) cc_final: 0.7168 (ttmm) REVERT: A 292 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8739 (m-40) REVERT: A 378 ASP cc_start: 0.8019 (m-30) cc_final: 0.7718 (m-30) REVERT: P 27 MET cc_start: 0.2681 (mmm) cc_final: 0.1778 (tmt) REVERT: B 44 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8509 (mt0) REVERT: B 59 TYR cc_start: 0.9201 (OUTLIER) cc_final: 0.8327 (t80) REVERT: B 175 GLN cc_start: 0.8269 (mm-40) cc_final: 0.8054 (mm110) REVERT: G 62 ARG cc_start: 0.6331 (OUTLIER) cc_final: 0.5961 (tpp-160) outliers start: 23 outliers final: 10 residues processed: 110 average time/residue: 0.6301 time to fit residues: 73.1634 Evaluate side-chains 106 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 TYR Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 194 HIS Chi-restraints excluded: chain R residue 202 CYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 0.0980 chunk 66 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.0470 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 165 HIS A 292 ASN P 8 ASN B 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.177216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.133111 restraints weight = 9323.854| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.00 r_work: 0.3582 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8508 Z= 0.119 Angle : 0.522 8.042 11518 Z= 0.280 Chirality : 0.042 0.166 1291 Planarity : 0.004 0.046 1459 Dihedral : 6.473 58.106 1172 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.24 % Allowed : 13.45 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.26), residues: 1026 helix: 1.33 (0.27), residues: 408 sheet: 0.08 (0.33), residues: 205 loop : -1.47 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 317 TYR 0.027 0.001 TYR R 133 PHE 0.014 0.001 PHE A 212 TRP 0.019 0.001 TRP R 219 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 8507) covalent geometry : angle 0.51954 / 0.28 (11516) SS BOND : bond 0.00491 / 0.26 ( 1) SS BOND : angle 3.57865 / 1.96 ( 2) hydrogen bonds : bond 0.04292 / 2.76 ( 409) hydrogen bonds : angle 4.26008 / 3.20 ( 1173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.305 Fit side-chains REVERT: R 364 LEU cc_start: 0.7813 (tp) cc_final: 0.7576 (tt) REVERT: A 24 LYS cc_start: 0.7432 (mmpt) cc_final: 0.7062 (ttmm) REVERT: A 292 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8539 (m-40) REVERT: A 343 ASP cc_start: 0.8191 (m-30) cc_final: 0.7831 (m-30) REVERT: A 356 ARG cc_start: 0.7260 (ptt180) cc_final: 0.6904 (pmt170) REVERT: A 378 ASP cc_start: 0.7896 (m-30) cc_final: 0.7553 (m-30) REVERT: P 27 MET cc_start: 0.2556 (mmm) cc_final: 0.1793 (tmt) REVERT: B 45 MET cc_start: 0.9417 (mtt) cc_final: 0.8759 (mtt) REVERT: B 59 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.8243 (t80) REVERT: G 21 MET cc_start: 0.6510 (tpp) cc_final: 0.5135 (mpt) REVERT: G 62 ARG cc_start: 0.6373 (OUTLIER) cc_final: 0.6008 (tpp-160) outliers start: 20 outliers final: 9 residues processed: 111 average time/residue: 0.6490 time to fit residues: 76.2556 Evaluate side-chains 104 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 TYR Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 194 HIS Chi-restraints excluded: chain R residue 202 CYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 62 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 94 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.0570 chunk 14 optimal weight: 2.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.178098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.134286 restraints weight = 9232.459| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.99 r_work: 0.3598 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8508 Z= 0.110 Angle : 0.509 7.763 11518 Z= 0.272 Chirality : 0.042 0.164 1291 Planarity : 0.004 0.046 1459 Dihedral : 6.294 59.561 1172 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.24 % Allowed : 14.35 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.26), residues: 1026 helix: 1.52 (0.27), residues: 408 sheet: 0.02 (0.33), residues: 215 loop : -1.31 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 317 TYR 0.026 0.001 TYR R 133 PHE 0.013 0.001 PHE A 212 TRP 0.018 0.001 TRP R 219 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 8507) covalent geometry : angle 0.50709 / 0.27 (11516) SS BOND : bond 0.00459 / 0.24 ( 1) SS BOND : angle 3.47867 / 1.91 ( 2) hydrogen bonds : bond 0.04027 / 2.59 ( 409) hydrogen bonds : angle 4.11095 / 3.09 ( 1173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.293 Fit side-chains REVERT: R 364 LEU cc_start: 0.7824 (tp) cc_final: 0.7590 (tt) REVERT: A 24 LYS cc_start: 0.7370 (mmpt) cc_final: 0.7017 (ttmm) REVERT: A 292 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8569 (m-40) REVERT: A 343 ASP cc_start: 0.8176 (m-30) cc_final: 0.7854 (m-30) REVERT: A 356 ARG cc_start: 0.7243 (ptt180) cc_final: 0.6536 (ptt180) REVERT: A 378 ASP cc_start: 0.7877 (m-30) cc_final: 0.7528 (m-30) REVERT: P 27 MET cc_start: 0.2701 (mmm) cc_final: 0.1923 (tmt) REVERT: B 45 MET cc_start: 0.9414 (mtt) cc_final: 0.8778 (mtt) REVERT: B 59 TYR cc_start: 0.9158 (OUTLIER) cc_final: 0.8277 (t80) REVERT: B 314 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7680 (ttt180) REVERT: G 21 MET cc_start: 0.6444 (tpp) cc_final: 0.5020 (mpt) REVERT: G 46 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8078 (tppp) REVERT: G 62 ARG cc_start: 0.6310 (OUTLIER) cc_final: 0.5956 (tpp-160) outliers start: 20 outliers final: 7 residues processed: 107 average time/residue: 0.6575 time to fit residues: 74.3950 Evaluate side-chains 101 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 TYR Chi-restraints excluded: chain R residue 194 HIS Chi-restraints excluded: chain R residue 202 CYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 59 optimal weight: 0.0870 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.174542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.129960 restraints weight = 9388.156| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.00 r_work: 0.3530 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8508 Z= 0.188 Angle : 0.585 10.090 11518 Z= 0.312 Chirality : 0.045 0.171 1291 Planarity : 0.004 0.046 1459 Dihedral : 6.569 58.272 1172 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.02 % Allowed : 14.46 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.26), residues: 1026 helix: 1.32 (0.26), residues: 409 sheet: 0.19 (0.34), residues: 210 loop : -1.27 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 317 TYR 0.028 0.002 TYR R 133 PHE 0.019 0.002 PHE B 199 TRP 0.021 0.002 TRP R 219 HIS 0.010 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 ( 8507) covalent geometry : angle 0.58341 / 0.31 (11516) SS BOND : bond 0.00542 / 0.29 ( 1) SS BOND : angle 3.44837 / 1.90 ( 2) hydrogen bonds : bond 0.04890 / 3.14 ( 409) hydrogen bonds : angle 4.36436 / 3.29 ( 1173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7577 (mmpt) cc_final: 0.7130 (ttmm) REVERT: A 292 ASN cc_start: 0.8912 (t0) cc_final: 0.8687 (m-40) REVERT: A 356 ARG cc_start: 0.7396 (ptt180) cc_final: 0.7134 (pmm-80) REVERT: A 378 ASP cc_start: 0.8010 (m-30) cc_final: 0.7697 (m-30) REVERT: P 27 MET cc_start: 0.2544 (mmm) cc_final: 0.1755 (tmt) REVERT: B 17 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: B 44 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8563 (mt0) REVERT: B 59 TYR cc_start: 0.9171 (OUTLIER) cc_final: 0.8314 (t80) REVERT: B 314 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7858 (ttt180) outliers start: 18 outliers final: 11 residues processed: 110 average time/residue: 0.6654 time to fit residues: 77.0739 Evaluate side-chains 106 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 TYR Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 194 HIS Chi-restraints excluded: chain R residue 202 CYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 87 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 0.0270 chunk 64 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.179071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.134988 restraints weight = 9282.336| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.02 r_work: 0.3612 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8508 Z= 0.102 Angle : 0.506 8.613 11518 Z= 0.268 Chirality : 0.041 0.160 1291 Planarity : 0.004 0.046 1459 Dihedral : 6.199 59.953 1172 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.46 % Allowed : 15.36 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.26), residues: 1026 helix: 1.65 (0.27), residues: 408 sheet: 0.11 (0.33), residues: 215 loop : -1.16 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 317 TYR 0.025 0.001 TYR R 133 PHE 0.013 0.001 PHE A 212 TRP 0.018 0.001 TRP R 219 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 8507) covalent geometry : angle 0.50412 / 0.27 (11516) SS BOND : bond 0.00380 / 0.20 ( 1) SS BOND : angle 3.52257 / 1.93 ( 2) hydrogen bonds : bond 0.03874 / 2.48 ( 409) hydrogen bonds : angle 4.04746 / 3.04 ( 1173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.320 Fit side-chains REVERT: A 24 LYS cc_start: 0.7378 (mmpt) cc_final: 0.7008 (ttmm) REVERT: A 292 ASN cc_start: 0.8751 (t0) cc_final: 0.8472 (m-40) REVERT: A 343 ASP cc_start: 0.8211 (m-30) cc_final: 0.7825 (m-30) REVERT: A 356 ARG cc_start: 0.7076 (ptt180) cc_final: 0.6230 (ptt180) REVERT: P 27 MET cc_start: 0.2496 (mmm) cc_final: 0.1718 (tmt) REVERT: B 45 MET cc_start: 0.9400 (mtt) cc_final: 0.8778 (mtt) REVERT: B 59 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.8240 (t80) REVERT: B 314 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7596 (ttt180) REVERT: G 21 MET cc_start: 0.6510 (tpp) cc_final: 0.5112 (mpt) REVERT: G 46 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8061 (tppp) outliers start: 13 outliers final: 7 residues processed: 110 average time/residue: 0.6094 time to fit residues: 70.8962 Evaluate side-chains 104 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 TYR Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 194 HIS Chi-restraints excluded: chain R residue 202 CYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 46 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 75 optimal weight: 0.0570 chunk 55 optimal weight: 0.4980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.178723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.134771 restraints weight = 9253.479| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.00 r_work: 0.3554 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8508 Z= 0.107 Angle : 0.510 8.815 11518 Z= 0.270 Chirality : 0.042 0.160 1291 Planarity : 0.004 0.046 1459 Dihedral : 6.009 56.626 1172 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.68 % Allowed : 15.25 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.26), residues: 1026 helix: 1.77 (0.27), residues: 408 sheet: 0.20 (0.33), residues: 215 loop : -1.04 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 317 TYR 0.025 0.001 TYR R 133 PHE 0.013 0.001 PHE B 199 TRP 0.018 0.001 TRP R 219 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 8507) covalent geometry : angle 0.50769 / 0.27 (11516) SS BOND : bond 0.00403 / 0.21 ( 1) SS BOND : angle 3.32439 / 1.82 ( 2) hydrogen bonds : bond 0.03847 / 2.47 ( 409) hydrogen bonds : angle 3.99539 / 3.00 ( 1173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.227 Fit side-chains REVERT: A 24 LYS cc_start: 0.7354 (mmpt) cc_final: 0.6975 (ttmm) REVERT: A 292 ASN cc_start: 0.8731 (t0) cc_final: 0.8516 (m-40) REVERT: A 343 ASP cc_start: 0.8198 (m-30) cc_final: 0.7825 (m-30) REVERT: A 356 ARG cc_start: 0.7057 (ptt180) cc_final: 0.6304 (ptt180) REVERT: P 27 MET cc_start: 0.2497 (mmm) cc_final: 0.1829 (tmt) REVERT: B 59 TYR cc_start: 0.9145 (OUTLIER) cc_final: 0.8251 (t80) REVERT: B 314 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7623 (ttt180) REVERT: G 21 MET cc_start: 0.6443 (tpp) cc_final: 0.5047 (mpt) REVERT: G 46 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8084 (tppp) outliers start: 15 outliers final: 7 residues processed: 108 average time/residue: 0.5970 time to fit residues: 68.2749 Evaluate side-chains 101 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 TYR Chi-restraints excluded: chain R residue 194 HIS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 GLN B 75 GLN N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.176802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.132638 restraints weight = 9305.454| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.00 r_work: 0.3568 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8508 Z= 0.138 Angle : 0.543 9.009 11518 Z= 0.288 Chirality : 0.043 0.171 1291 Planarity : 0.004 0.045 1459 Dihedral : 6.146 57.277 1172 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.46 % Allowed : 15.92 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.26), residues: 1026 helix: 1.68 (0.26), residues: 408 sheet: 0.18 (0.33), residues: 215 loop : -1.04 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 317 TYR 0.026 0.001 TYR R 133 PHE 0.015 0.001 PHE B 199 TRP 0.019 0.001 TRP R 219 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 8507) covalent geometry : angle 0.54000 / 0.29 (11516) SS BOND : bond 0.00390 / 0.21 ( 1) SS BOND : angle 4.57811 / 2.49 ( 2) hydrogen bonds : bond 0.04261 / 2.73 ( 409) hydrogen bonds : angle 4.14168 / 3.12 ( 1173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.241 Fit side-chains REVERT: A 24 LYS cc_start: 0.7449 (mmpt) cc_final: 0.7030 (ttmm) REVERT: A 343 ASP cc_start: 0.8261 (m-30) cc_final: 0.7908 (m-30) REVERT: A 356 ARG cc_start: 0.7112 (ptt180) cc_final: 0.6395 (ptt180) REVERT: P 27 MET cc_start: 0.2428 (mmm) cc_final: 0.1755 (tmt) REVERT: B 45 MET cc_start: 0.9341 (mtt) cc_final: 0.8957 (mtt) REVERT: B 59 TYR cc_start: 0.9176 (OUTLIER) cc_final: 0.8297 (t80) REVERT: B 314 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7747 (ttt180) REVERT: G 21 MET cc_start: 0.6467 (tpp) cc_final: 0.5051 (mpt) REVERT: G 46 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8077 (tppp) outliers start: 13 outliers final: 8 residues processed: 103 average time/residue: 0.5896 time to fit residues: 64.2692 Evaluate side-chains 102 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 TYR Chi-restraints excluded: chain R residue 194 HIS Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 GLN B 75 GLN N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.174676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.129991 restraints weight = 9301.925| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.01 r_work: 0.3534 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8508 Z= 0.172 Angle : 0.581 9.268 11518 Z= 0.307 Chirality : 0.044 0.176 1291 Planarity : 0.004 0.045 1459 Dihedral : 6.366 59.829 1172 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.23 % Allowed : 16.59 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.26), residues: 1026 helix: 1.59 (0.26), residues: 408 sheet: 0.28 (0.34), residues: 211 loop : -1.08 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 317 TYR 0.028 0.002 TYR R 133 PHE 0.018 0.002 PHE A 212 TRP 0.020 0.002 TRP R 219 HIS 0.010 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 8507) covalent geometry : angle 0.57741 / 0.31 (11516) SS BOND : bond 0.00623 / 0.33 ( 1) SS BOND : angle 4.62216 / 2.52 ( 2) hydrogen bonds : bond 0.04710 / 3.03 ( 409) hydrogen bonds : angle 4.29559 / 3.23 ( 1173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3435.80 seconds wall clock time: 59 minutes 6.59 seconds (3546.59 seconds total)