Starting phenix.real_space_refine on Fri Aug 22 23:19:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cz5_30505/08_2025/7cz5_30505.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cz5_30505/08_2025/7cz5_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 { model { file = "/net/cci-nas-00/data/ceres_data/7cz5_30505/08_2025/7cz5_30505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cz5_30505/08_2025/7cz5_30505.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cz5_30505/08_2025/7cz5_30505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cz5_30505/08_2025/7cz5_30505.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.51, 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: 0.72 Conformation dependent library (CDL) restraints added in 454.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.18 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: 1.18 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 4651 17.38 - 34.76: 370 34.76 - 52.14: 49 52.14 - 69.52: 16 69.52 - 86.90: 6 Dihedral angle restraints: 5092 sinusoidal: 2059 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 5089 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: 0.690 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.910 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.030 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:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 : 13.226 86.899 3125 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 aren 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 covalent geometry : bond 0.00430 ( 8507) covalent geometry : angle 0.68572 (11516) SS BOND : bond 0.00642 ( 1) SS BOND : angle 2.98886 ( 2) hydrogen bonds : bond 0.15962 ( 409) hydrogen bonds : angle 6.31620 ( 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 : 0.338 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: 0.5675 time to fit residues: 81.5534 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 : 0.254 ------------------------------------------------------------------------------- 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: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 210 HIS R 323 GLN A 14 ASN A 267 GLN A 292 ASN P 8 ASN B 35 ASN B 91 HIS B 340 ASN G 18 GLN G 24 ASN N 3 GLN N 84 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.173275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.128531 restraints weight = 9308.744| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.99 r_work: 0.3522 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8508 Z= 0.211 Angle : 0.649 9.559 11518 Z= 0.346 Chirality : 0.047 0.205 1291 Planarity : 0.005 0.045 1459 Dihedral : 7.148 57.487 1228 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.69 % Allowed : 7.74 % Favored : 89.57 % 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 aren not related in a simple way. whole: -1.04 (0.25), residues: 1026 helix: 0.28 (0.26), residues: 405 sheet: -0.24 (0.34), residues: 205 loop : -1.87 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 covalent geometry : bond 0.00494 ( 8507) covalent geometry : angle 0.64631 (11516) SS BOND : bond 0.00664 ( 1) SS BOND : angle 4.40457 ( 2) hydrogen bonds : bond 0.05657 ( 409) hydrogen bonds : angle 4.95447 ( 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 134 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.219 Fit side-chains REVERT: R 270 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7481 (mp) REVERT: R 364 LEU cc_start: 0.7848 (tp) cc_final: 0.7579 (tt) REVERT: A 24 LYS cc_start: 0.7520 (mmpt) cc_final: 0.7233 (ttmm) REVERT: A 378 ASP cc_start: 0.8072 (m-30) cc_final: 0.7776 (m-30) REVERT: P 27 MET cc_start: 0.2680 (mmm) cc_final: 0.1826 (tmt) REVERT: B 44 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8528 (mt0) REVERT: B 59 TYR cc_start: 0.9211 (OUTLIER) cc_final: 0.8417 (t80) REVERT: G 21 MET cc_start: 0.6714 (tpp) cc_final: 0.5380 (mpt) REVERT: G 42 GLU cc_start: 0.7805 (mp0) cc_final: 0.7480 (mp0) REVERT: G 62 ARG cc_start: 0.6345 (OUTLIER) cc_final: 0.5984 (tpp-160) outliers start: 24 outliers final: 9 residues processed: 120 average time/residue: 0.6262 time to fit residues: 79.3491 Evaluate side-chains 113 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 224 VAL 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: 0.0870 chunk 69 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN P 8 ASN B 75 GLN B 175 GLN B 266 HIS B 268 ASN N 3 GLN N 120 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.178331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.134350 restraints weight = 9246.089| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.00 r_work: 0.3602 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8508 Z= 0.114 Angle : 0.526 8.753 11518 Z= 0.281 Chirality : 0.042 0.176 1291 Planarity : 0.004 0.044 1459 Dihedral : 6.576 59.682 1228 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.23 % Allowed : 10.76 % Favored : 88.00 % 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 aren not related in a simple way. whole: -0.38 (0.26), residues: 1026 helix: 1.02 (0.27), residues: 405 sheet: -0.19 (0.33), residues: 205 loop : -1.55 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 317 TYR 0.029 0.001 TYR R 133 PHE 0.014 0.001 PHE A 212 TRP 0.019 0.001 TRP R 219 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8507) covalent geometry : angle 0.52324 (11516) SS BOND : bond 0.00508 ( 1) SS BOND : angle 3.77126 ( 2) hydrogen bonds : bond 0.04259 ( 409) hydrogen bonds : angle 4.35034 ( 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 120 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: R 364 LEU cc_start: 0.7817 (tp) cc_final: 0.7594 (tt) REVERT: A 24 LYS cc_start: 0.7296 (mmpt) cc_final: 0.7038 (ttmm) REVERT: A 343 ASP cc_start: 0.8209 (m-30) cc_final: 0.7832 (m-30) REVERT: A 378 ASP cc_start: 0.7905 (m-30) cc_final: 0.7574 (m-30) REVERT: P 27 MET cc_start: 0.2591 (mmm) cc_final: 0.1857 (tmt) REVERT: B 45 MET cc_start: 0.9410 (mtt) cc_final: 0.8788 (mtt) REVERT: B 59 TYR cc_start: 0.9166 (OUTLIER) cc_final: 0.8313 (t80) REVERT: B 172 GLU cc_start: 0.8058 (pp20) cc_final: 0.7787 (pp20) REVERT: G 42 GLU cc_start: 0.7746 (mp0) cc_final: 0.7360 (mp0) REVERT: G 62 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.5958 (tpp-160) outliers start: 11 outliers final: 2 residues processed: 115 average time/residue: 0.5576 time to fit residues: 67.8672 Evaluate side-chains 98 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 194 HIS Chi-restraints excluded: chain R residue 202 CYS 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: 7.9990 chunk 2 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4123 r_free = 0.4123 target = 0.174871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.130407 restraints weight = 9394.861| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.01 r_work: 0.3529 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1614 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= 0.184 Angle : 0.581 8.570 11518 Z= 0.311 Chirality : 0.045 0.170 1291 Planarity : 0.005 0.054 1459 Dihedral : 6.734 56.114 1228 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.69 % Allowed : 11.88 % Favored : 85.43 % 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 aren not related in a simple way. whole: -0.21 (0.26), residues: 1026 helix: 1.17 (0.27), residues: 399 sheet: 0.04 (0.33), residues: 205 loop : -1.52 (0.29), 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 0.021 0.002 PHE P 6 TRP 0.021 0.002 TRP R 219 HIS 0.011 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8507) covalent geometry : angle 0.57902 (11516) SS BOND : bond 0.00570 ( 1) SS BOND : angle 3.53922 ( 2) hydrogen bonds : bond 0.04951 ( 409) hydrogen bonds : angle 4.46180 ( 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 124 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: R 364 LEU cc_start: 0.7804 (tp) cc_final: 0.7555 (tt) REVERT: A 24 LYS cc_start: 0.7557 (mmpt) cc_final: 0.7159 (ttmm) REVERT: A 292 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8682 (m-40) REVERT: A 378 ASP cc_start: 0.7997 (m-30) cc_final: 0.7691 (m-30) REVERT: P 27 MET cc_start: 0.2679 (mmm) cc_final: 0.1804 (tmt) REVERT: B 44 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8499 (mt0) REVERT: B 59 TYR cc_start: 0.9174 (OUTLIER) cc_final: 0.8311 (t80) REVERT: G 38 MET cc_start: 0.8398 (ttm) cc_final: 0.8146 (ttp) REVERT: G 42 GLU cc_start: 0.7790 (mp0) cc_final: 0.7387 (mp0) REVERT: G 62 ARG cc_start: 0.6338 (OUTLIER) cc_final: 0.5968 (tpp-160) outliers start: 24 outliers final: 10 residues processed: 111 average time/residue: 0.6037 time to fit residues: 70.8937 Evaluate side-chains 105 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 224 VAL 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 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: 3.9990 chunk 66 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS A 292 ASN P 8 ASN B 75 GLN B 175 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.177362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.133243 restraints weight = 9334.355| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.00 r_work: 0.3574 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1802 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= 0.118 Angle : 0.519 8.039 11518 Z= 0.278 Chirality : 0.042 0.165 1291 Planarity : 0.004 0.046 1459 Dihedral : 6.444 57.361 1228 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.47 % Allowed : 13.12 % Favored : 84.42 % 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 aren not related in a simple way. whole: -0.01 (0.26), residues: 1026 helix: 1.35 (0.27), residues: 408 sheet: 0.11 (0.33), residues: 205 loop : -1.46 (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 0.019 0.001 PHE P 6 TRP 0.020 0.001 TRP R 219 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8507) covalent geometry : angle 0.51717 (11516) SS BOND : bond 0.00476 ( 1) SS BOND : angle 3.53046 ( 2) hydrogen bonds : bond 0.04281 ( 409) hydrogen bonds : angle 4.22884 ( 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 120 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.299 Fit side-chains REVERT: R 364 LEU cc_start: 0.7809 (tp) cc_final: 0.7575 (tt) REVERT: A 24 LYS cc_start: 0.7407 (mmpt) cc_final: 0.7042 (ttmm) REVERT: A 292 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8556 (m-40) REVERT: A 343 ASP cc_start: 0.8174 (m-30) cc_final: 0.7830 (m-30) REVERT: A 378 ASP cc_start: 0.7909 (m-30) cc_final: 0.7563 (m-30) REVERT: P 27 MET cc_start: 0.2538 (mmm) cc_final: 0.1783 (tmt) REVERT: B 45 MET cc_start: 0.9404 (mtt) cc_final: 0.8741 (mtt) REVERT: B 59 TYR cc_start: 0.9158 (OUTLIER) cc_final: 0.8284 (t80) REVERT: G 21 MET cc_start: 0.6467 (tpp) cc_final: 0.5104 (mpt) REVERT: G 42 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: G 46 LYS cc_start: 0.8420 (mmtt) cc_final: 0.8056 (tppp) REVERT: G 62 ARG cc_start: 0.6318 (OUTLIER) cc_final: 0.5947 (tpp-160) outliers start: 22 outliers final: 8 residues processed: 111 average time/residue: 0.5252 time to fit residues: 61.8639 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 : 0.306 ------------------------------------------------------------------------------- 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 42 GLU 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: 4.9990 chunk 27 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 59 optimal weight: 0.4980 chunk 98 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 52 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4168 r_free = 0.4168 target = 0.179159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.135454 restraints weight = 9234.828| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.99 r_work: 0.3614 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2023 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 : 0.496 7.712 11518 Z= 0.265 Chirality : 0.041 0.162 1291 Planarity : 0.004 0.046 1459 Dihedral : 6.212 58.647 1228 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.91 % Allowed : 14.35 % Favored : 83.74 % 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 aren not related in a simple way. whole: 0.23 (0.26), residues: 1026 helix: 1.57 (0.27), residues: 408 sheet: 0.09 (0.33), residues: 215 loop : -1.30 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 317 TYR 0.025 0.001 TYR R 133 PHE 0.016 0.001 PHE P 6 TRP 0.018 0.001 TRP R 219 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 8507) covalent geometry : angle 0.49422 (11516) SS BOND : bond 0.00440 ( 1) SS BOND : angle 3.43469 ( 2) hydrogen bonds : bond 0.03870 ( 409) hydrogen bonds : angle 4.03156 ( 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 119 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.329 Fit side-chains REVERT: R 364 LEU cc_start: 0.7814 (tp) cc_final: 0.7595 (tt) REVERT: A 24 LYS cc_start: 0.7328 (mmpt) cc_final: 0.6996 (ttmm) REVERT: A 292 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8559 (m-40) REVERT: A 343 ASP cc_start: 0.8117 (m-30) cc_final: 0.7758 (m-30) REVERT: P 27 MET cc_start: 0.2704 (mmm) cc_final: 0.1947 (tmt) REVERT: B 59 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.8261 (t80) REVERT: B 314 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7627 (ttt180) REVERT: B 337 LYS cc_start: 0.8832 (mttt) cc_final: 0.8587 (mttt) REVERT: G 21 MET cc_start: 0.6427 (tpp) cc_final: 0.5031 (mpt) REVERT: G 38 MET cc_start: 0.8471 (ttp) cc_final: 0.8250 (ttm) REVERT: G 42 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: G 46 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8092 (tppp) outliers start: 17 outliers final: 7 residues processed: 112 average time/residue: 0.5833 time to fit residues: 69.2830 Evaluate side-chains 103 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 A residue 386 MET 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 42 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 75 optimal weight: 0.0980 chunk 88 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 75 GLN B 340 ASN N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.177070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.132876 restraints weight = 9421.851| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.02 r_work: 0.3573 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8508 Z= 0.133 Angle : 0.525 7.791 11518 Z= 0.281 Chirality : 0.043 0.164 1291 Planarity : 0.004 0.045 1459 Dihedral : 6.286 58.633 1228 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.24 % Allowed : 14.46 % Favored : 83.30 % 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 aren not related in a simple way. whole: 0.27 (0.26), residues: 1026 helix: 1.52 (0.27), residues: 409 sheet: 0.12 (0.33), residues: 215 loop : -1.18 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 317 TYR 0.027 0.001 TYR R 133 PHE 0.015 0.001 PHE B 199 TRP 0.019 0.001 TRP R 219 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8507) covalent geometry : angle 0.52326 (11516) SS BOND : bond 0.00468 ( 1) SS BOND : angle 3.38634 ( 2) hydrogen bonds : bond 0.04238 ( 409) hydrogen bonds : angle 4.12328 ( 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 118 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.367 Fit side-chains REVERT: R 198 SER cc_start: 0.7587 (t) cc_final: 0.7385 (m) REVERT: A 24 LYS cc_start: 0.7417 (mmpt) cc_final: 0.7051 (ttmm) REVERT: A 292 ASN cc_start: 0.8811 (t0) cc_final: 0.8585 (m-40) REVERT: A 343 ASP cc_start: 0.8272 (m-30) cc_final: 0.7919 (m-30) REVERT: P 27 MET cc_start: 0.2753 (mmm) cc_final: 0.1904 (tmt) REVERT: B 59 TYR cc_start: 0.9165 (OUTLIER) cc_final: 0.8303 (t80) REVERT: B 314 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7747 (ttt180) REVERT: G 21 MET cc_start: 0.6410 (tpp) cc_final: 0.5019 (mpt) REVERT: G 42 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: G 46 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8096 (tppp) REVERT: G 62 ARG cc_start: 0.6326 (OUTLIER) cc_final: 0.5956 (tpp-160) outliers start: 20 outliers final: 9 residues processed: 109 average time/residue: 0.6791 time to fit residues: 78.3188 Evaluate side-chains 104 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 386 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 42 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 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 = 0.4155 r_free = 0.4155 target = 0.177829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.133889 restraints weight = 9305.394| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.00 r_work: 0.3591 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2099 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= 0.118 Angle : 0.522 9.952 11518 Z= 0.275 Chirality : 0.042 0.161 1291 Planarity : 0.004 0.046 1459 Dihedral : 6.145 59.019 1228 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.13 % Allowed : 14.80 % 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 aren not related in a simple way. whole: 0.38 (0.26), residues: 1026 helix: 1.61 (0.27), residues: 409 sheet: 0.13 (0.33), residues: 215 loop : -1.09 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 317 TYR 0.026 0.001 TYR R 133 PHE 0.014 0.001 PHE A 212 TRP 0.018 0.001 TRP R 219 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8507) covalent geometry : angle 0.52053 (11516) SS BOND : bond 0.00394 ( 1) SS BOND : angle 3.41880 ( 2) hydrogen bonds : bond 0.04055 ( 409) hydrogen bonds : angle 4.06464 ( 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 123 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.289 Fit side-chains REVERT: A 24 LYS cc_start: 0.7407 (mmpt) cc_final: 0.7029 (ttmm) REVERT: A 292 ASN cc_start: 0.8737 (t0) cc_final: 0.8531 (m-40) REVERT: A 343 ASP cc_start: 0.8221 (m-30) cc_final: 0.7856 (m-30) REVERT: A 356 ARG cc_start: 0.7153 (ptt180) cc_final: 0.6470 (ptt180) REVERT: P 27 MET cc_start: 0.2654 (mmm) cc_final: 0.1830 (tmt) REVERT: B 45 MET cc_start: 0.9324 (mtt) cc_final: 0.8939 (mtt) REVERT: B 59 TYR cc_start: 0.9170 (OUTLIER) cc_final: 0.8273 (t80) REVERT: B 314 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7671 (ttt180) REVERT: G 21 MET cc_start: 0.6401 (tpp) cc_final: 0.5012 (mpt) REVERT: G 38 MET cc_start: 0.8344 (ttm) cc_final: 0.8083 (ttp) REVERT: G 42 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: G 46 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8118 (tppp) outliers start: 19 outliers final: 11 residues processed: 116 average time/residue: 0.6926 time to fit residues: 84.9285 Evaluate side-chains 110 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 R residue 304 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.5594 > 50: distance: 18 - 99: 28.155 distance: 41 - 64: 20.479 distance: 59 - 64: 20.330 distance: 64 - 65: 19.822 distance: 65 - 66: 22.497 distance: 65 - 68: 25.304 distance: 66 - 67: 16.672 distance: 66 - 73: 14.813 distance: 68 - 69: 14.651 distance: 69 - 70: 16.692 distance: 70 - 71: 10.470 distance: 70 - 72: 22.224 distance: 73 - 74: 31.717 distance: 74 - 75: 5.905 distance: 74 - 77: 18.011 distance: 75 - 76: 14.145 distance: 75 - 81: 24.052 distance: 77 - 78: 31.396 distance: 78 - 79: 26.920 distance: 78 - 80: 19.936 distance: 81 - 82: 25.739 distance: 82 - 83: 28.960 distance: 82 - 85: 26.438 distance: 83 - 84: 25.323 distance: 83 - 89: 28.360 distance: 84 - 100: 23.058 distance: 85 - 86: 28.888 distance: 85 - 87: 23.062 distance: 86 - 88: 14.709 distance: 89 - 90: 20.939 distance: 90 - 91: 12.681 distance: 90 - 93: 33.008 distance: 91 - 92: 42.803 distance: 91 - 94: 20.817 distance: 94 - 95: 5.187 distance: 95 - 96: 6.250 distance: 95 - 98: 24.934 distance: 96 - 97: 6.696 distance: 96 - 100: 15.413 distance: 100 - 101: 12.761 distance: 101 - 102: 27.399 distance: 101 - 104: 14.820 distance: 102 - 103: 29.522 distance: 102 - 114: 9.293 distance: 104 - 105: 16.713 distance: 105 - 106: 17.547 distance: 105 - 107: 4.345 distance: 106 - 108: 7.408 distance: 107 - 109: 6.811 distance: 107 - 110: 7.072 distance: 108 - 109: 5.502 distance: 111 - 113: 4.932 distance: 112 - 113: 6.576 distance: 114 - 115: 29.552 distance: 115 - 116: 29.950 distance: 115 - 118: 15.925 distance: 116 - 117: 11.093 distance: 116 - 122: 21.077 distance: 118 - 119: 35.254 distance: 119 - 120: 5.374 distance: 119 - 121: 13.574 distance: 122 - 123: 19.487 distance: 123 - 124: 11.769 distance: 123 - 126: 12.647 distance: 124 - 125: 13.817 distance: 124 - 130: 23.167 distance: 126 - 127: 5.272 distance: 127 - 128: 15.433 distance: 127 - 129: 38.473 distance: 130 - 131: 10.825 distance: 131 - 132: 8.857 distance: 132 - 133: 12.933 distance: 132 - 138: 21.197 distance: 134 - 135: 14.124 distance: 135 - 136: 17.686 distance: 135 - 137: 17.515 distance: 138 - 139: 16.275 distance: 140 - 141: 4.980 distance: 140 - 146: 32.322 distance: 142 - 143: 5.225 distance: 143 - 144: 3.966 distance: 143 - 145: 21.225