Starting phenix.real_space_refine on Sat Aug 23 01:09:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yn5_39415/08_2025/8yn5_39415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yn5_39415/08_2025/8yn5_39415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yn5_39415/08_2025/8yn5_39415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yn5_39415/08_2025/8yn5_39415.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yn5_39415/08_2025/8yn5_39415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yn5_39415/08_2025/8yn5_39415.map" } resolution = 2.7 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= 0.014 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 59 5.16 5 C 5814 2.51 5 N 1519 2.21 5 O 1655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 9047 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1769 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" 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: "E" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2301 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 148 Unusual residues: {'CLR': 5, 'HSM': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 1.73, per 1000 atoms: 0.19 Number of scatterers: 9047 At special positions: 0 Unit cell: (105.93, 104.86, 116.63, 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 59 16.00 O 1655 8.00 N 1519 7.00 C 5814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 188 " distance=2.03 Simple disulfide: pdb=" SG CYS R 384 " - pdb=" SG CYS R 388 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 353.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 40.1% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.524A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.125A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.387A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.018A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.716A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.511A pdb=" N THR E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 62 removed outlier: 4.048A pdb=" N VAL R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET R 56 " --> pdb=" O ASN R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 86 Processing helix chain 'R' and resid 86 through 97 Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 103 through 137 removed outlier: 3.744A pdb=" N LEU R 109 " --> pdb=" O GLY R 105 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL R 136 " --> pdb=" O ARG R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 146 Processing helix chain 'R' and resid 148 through 179 removed outlier: 3.942A pdb=" N TYR R 167 " --> pdb=" O ALA R 163 " (cutoff:3.500A) Proline residue: R 169 - end of helix removed outlier: 4.753A pdb=" N GLU R 175 " --> pdb=" O ILE R 171 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYR R 176 " --> pdb=" O LEU R 172 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY R 179 " --> pdb=" O GLU R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 207 removed outlier: 3.698A pdb=" N ILE R 200 " --> pdb=" O TRP R 196 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU R 205 " --> pdb=" O THR R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 236 removed outlier: 3.779A pdb=" N TYR R 222 " --> pdb=" O ASN R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 385 Proline residue: R 373 - end of helix removed outlier: 3.515A pdb=" N ALA R 383 " --> pdb=" O ILE R 379 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS R 384 " --> pdb=" O ILE R 380 " (cutoff:3.500A) Processing helix chain 'R' and resid 390 through 416 removed outlier: 3.583A pdb=" N TYR R 394 " --> pdb=" O PRO R 390 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU R 395 " --> pdb=" O ASP R 391 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU R 400 " --> pdb=" O THR R 396 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU R 401 " --> pdb=" O SER R 397 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TRP R 402 " --> pdb=" O PHE R 398 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA R 406 " --> pdb=" O TRP R 402 " (cutoff:3.500A) Proline residue: R 409 - end of helix Proline residue: R 413 - end of helix Processing helix chain 'R' and resid 416 through 427 removed outlier: 3.633A pdb=" N ARG R 421 " --> pdb=" O HIS R 417 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU R 426 " --> pdb=" O ALA R 422 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.161A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.652A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.799A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.860A 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: 5.963A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.076A 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: 6.287A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.661A 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: 4.379A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.291A 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: 6.573A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.693A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 11 removed outlier: 5.997A pdb=" N ARG E 37 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N TRP E 46 " --> pdb=" O ARG E 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 11 removed outlier: 4.328A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.105A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1335 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: 1.52 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2870 1.34 - 1.46: 2222 1.46 - 1.58: 4081 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 9257 Sorted by residual: bond pdb=" CG HSM R 701 " pdb=" ND1 HSM R 701 " ideal model delta sigma weight residual 1.383 1.339 0.044 2.00e-02 2.50e+03 4.79e+00 bond pdb=" C5 CLR R 703 " pdb=" C6 CLR R 703 " ideal model delta sigma weight residual 1.332 1.297 0.035 2.00e-02 2.50e+03 3.11e+00 bond pdb=" C5 CLR R 704 " pdb=" C6 CLR R 704 " ideal model delta sigma weight residual 1.332 1.299 0.033 2.00e-02 2.50e+03 2.74e+00 bond pdb=" C5 CLR R 706 " pdb=" C6 CLR R 706 " ideal model delta sigma weight residual 1.332 1.300 0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" C5 CLR R 705 " pdb=" C6 CLR R 705 " ideal model delta sigma weight residual 1.332 1.300 0.032 2.00e-02 2.50e+03 2.56e+00 ... (remaining 9252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 12360 1.63 - 3.26: 154 3.26 - 4.90: 44 4.90 - 6.53: 17 6.53 - 8.16: 4 Bond angle restraints: 12579 Sorted by residual: angle pdb=" C13 CLR R 702 " pdb=" C17 CLR R 702 " pdb=" C20 CLR R 702 " ideal model delta sigma weight residual 119.60 111.44 8.16 3.00e+00 1.11e-01 7.40e+00 angle pdb=" C13 CLR R 706 " pdb=" C17 CLR R 706 " pdb=" C20 CLR R 706 " ideal model delta sigma weight residual 119.60 112.32 7.28 3.00e+00 1.11e-01 5.89e+00 angle pdb=" C13 CLR R 703 " pdb=" C17 CLR R 703 " pdb=" C20 CLR R 703 " ideal model delta sigma weight residual 119.60 112.45 7.15 3.00e+00 1.11e-01 5.69e+00 angle pdb=" C13 CLR R 705 " pdb=" C17 CLR R 705 " pdb=" C20 CLR R 705 " ideal model delta sigma weight residual 119.60 112.45 7.15 3.00e+00 1.11e-01 5.68e+00 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 126.08 -4.54 1.91e+00 2.74e-01 5.65e+00 ... (remaining 12574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.60: 5389 15.60 - 31.21: 234 31.21 - 46.81: 51 46.81 - 62.41: 12 62.41 - 78.02: 2 Dihedral angle restraints: 5688 sinusoidal: 2377 harmonic: 3311 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TRP B 339 " pdb=" C TRP B 339 " pdb=" N ASN B 340 " pdb=" CA ASN B 340 " ideal model delta harmonic sigma weight residual 180.00 161.59 18.41 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1351 0.097 - 0.194: 69 0.194 - 0.290: 5 0.290 - 0.387: 5 0.387 - 0.484: 5 Chirality restraints: 1435 Sorted by residual: chirality pdb=" C14 CLR R 702 " pdb=" C13 CLR R 702 " pdb=" C15 CLR R 702 " pdb=" C8 CLR R 702 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" C14 CLR R 706 " pdb=" C13 CLR R 706 " pdb=" C15 CLR R 706 " pdb=" C8 CLR R 706 " both_signs ideal model delta sigma weight residual False -2.32 -2.79 0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" C14 CLR R 705 " pdb=" C13 CLR R 705 " pdb=" C15 CLR R 705 " pdb=" C8 CLR R 705 " both_signs ideal model delta sigma weight residual False -2.32 -2.78 0.46 2.00e-01 2.50e+01 5.26e+00 ... (remaining 1432 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 408 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO R 409 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO R 409 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 409 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO B 236 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 209 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.74e+00 pdb=" N PRO R 210 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO R 210 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 210 " 0.019 5.00e-02 4.00e+02 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 868 2.75 - 3.29: 8730 3.29 - 3.82: 15344 3.82 - 4.36: 19145 4.36 - 4.90: 32635 Nonbonded interactions: 76722 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.209 3.040 nonbonded pdb=" O SER E 29 " pdb=" OG SER E 52 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.263 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.304 3.040 nonbonded pdb=" NZ LYS A 209 " pdb=" OD2 ASP B 228 " model vdw 2.305 3.120 ... (remaining 76717 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.800 Find NCS groups from input model: 0.060 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:7.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 : 0.002 0.044 9261 Z= 0.113 Angle : 0.529 8.161 12587 Z= 0.236 Chirality : 0.056 0.484 1435 Planarity : 0.003 0.052 1557 Dihedral : 9.599 78.016 3542 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.42 % Allowed : 2.72 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.24), residues: 1125 helix: 1.56 (0.25), residues: 408 sheet: 0.96 (0.29), residues: 292 loop : 0.19 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 37 TYR 0.010 0.001 TYR E 190 PHE 0.009 0.001 PHE B 199 TRP 0.009 0.001 TRP B 82 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9257) covalent geometry : angle 0.52905 (12579) SS BOND : bond 0.00148 ( 4) SS BOND : angle 0.45045 ( 8) hydrogen bonds : bond 0.23203 ( 471) hydrogen bonds : angle 6.75741 ( 1335) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 189 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6689 (tp30) REVERT: A 240 MET cc_start: 0.7255 (tpp) cc_final: 0.7035 (tpp) REVERT: A 255 ASN cc_start: 0.8996 (m-40) cc_final: 0.8773 (m-40) REVERT: A 275 GLU cc_start: 0.8204 (tt0) cc_final: 0.7617 (tm-30) REVERT: A 318 GLU cc_start: 0.8627 (tt0) cc_final: 0.8360 (tt0) REVERT: B 46 ARG cc_start: 0.7835 (mtp-110) cc_final: 0.7615 (mtp180) REVERT: R 151 ARG cc_start: 0.7985 (mtt-85) cc_final: 0.7645 (ttm110) REVERT: R 417 HIS cc_start: 0.8191 (t70) cc_final: 0.7963 (t70) outliers start: 4 outliers final: 3 residues processed: 193 average time/residue: 0.7211 time to fit residues: 146.8236 Evaluate side-chains 143 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 195 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 91 HIS B 175 GLN B 176 GLN B 259 GLN C 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.151746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.104032 restraints weight = 10504.041| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.78 r_work: 0.2988 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9261 Z= 0.157 Angle : 0.555 6.755 12587 Z= 0.294 Chirality : 0.042 0.153 1435 Planarity : 0.004 0.049 1557 Dihedral : 5.627 45.618 1572 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.78 % Allowed : 10.15 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.25), residues: 1125 helix: 2.35 (0.25), residues: 412 sheet: 0.88 (0.29), residues: 291 loop : 0.08 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 150 TYR 0.016 0.001 TYR R 392 PHE 0.019 0.001 PHE R 344 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9257) covalent geometry : angle 0.55480 (12579) SS BOND : bond 0.00410 ( 4) SS BOND : angle 0.94858 ( 8) hydrogen bonds : bond 0.05484 ( 471) hydrogen bonds : angle 4.83486 ( 1335) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.401 Fit side-chains REVERT: A 255 ASN cc_start: 0.8920 (m-40) cc_final: 0.8675 (m-40) REVERT: B 19 ARG cc_start: 0.8284 (ttp80) cc_final: 0.7831 (ttp-110) REVERT: B 215 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: B 217 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.7762 (pmt) REVERT: B 260 GLU cc_start: 0.9006 (tt0) cc_final: 0.8782 (tt0) REVERT: R 141 SER cc_start: 0.9128 (t) cc_final: 0.8819 (p) REVERT: R 176 TYR cc_start: 0.8053 (m-10) cc_final: 0.7838 (m-10) REVERT: R 417 HIS cc_start: 0.8374 (t70) cc_final: 0.8159 (t70) outliers start: 17 outliers final: 11 residues processed: 156 average time/residue: 0.6895 time to fit residues: 113.9574 Evaluate side-chains 142 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 212 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 35 ASN B 175 GLN B 220 GLN C 59 ASN E 183 GLN E 194 ASN R 145 GLN R 226 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.154289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112755 restraints weight = 10447.282| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.69 r_work: 0.3017 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9261 Z= 0.115 Angle : 0.501 6.751 12587 Z= 0.263 Chirality : 0.041 0.149 1435 Planarity : 0.004 0.051 1557 Dihedral : 5.006 48.340 1568 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.20 % Allowed : 11.30 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.25), residues: 1125 helix: 2.67 (0.25), residues: 410 sheet: 0.90 (0.30), residues: 275 loop : -0.02 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.012 0.001 TYR E 190 PHE 0.010 0.001 PHE B 199 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9257) covalent geometry : angle 0.50052 (12579) SS BOND : bond 0.00291 ( 4) SS BOND : angle 0.67946 ( 8) hydrogen bonds : bond 0.04240 ( 471) hydrogen bonds : angle 4.43408 ( 1335) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 255 ASN cc_start: 0.8774 (m-40) cc_final: 0.8493 (m-40) REVERT: B 19 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7721 (ttp-110) REVERT: B 170 ASP cc_start: 0.8878 (t70) cc_final: 0.8550 (t70) REVERT: B 260 GLU cc_start: 0.8944 (tt0) cc_final: 0.8740 (tt0) REVERT: R 41 MET cc_start: 0.7885 (mtp) cc_final: 0.7641 (mtm) REVERT: R 141 SER cc_start: 0.9074 (t) cc_final: 0.8694 (p) REVERT: R 176 TYR cc_start: 0.8041 (m-10) cc_final: 0.7780 (m-10) REVERT: R 417 HIS cc_start: 0.8332 (t70) cc_final: 0.8115 (t70) outliers start: 21 outliers final: 12 residues processed: 156 average time/residue: 0.6569 time to fit residues: 108.8487 Evaluate side-chains 139 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 212 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 71 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 16 ASN B 35 ASN B 175 GLN C 59 ASN R 145 GLN R 226 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.153978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110664 restraints weight = 10698.507| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.77 r_work: 0.3015 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9261 Z= 0.119 Angle : 0.506 9.817 12587 Z= 0.262 Chirality : 0.041 0.148 1435 Planarity : 0.004 0.051 1557 Dihedral : 4.924 46.142 1568 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.09 % Allowed : 12.66 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.25), residues: 1125 helix: 2.77 (0.25), residues: 411 sheet: 0.77 (0.30), residues: 276 loop : -0.03 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.016 0.001 TYR R 392 PHE 0.021 0.001 PHE R 344 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9257) covalent geometry : angle 0.50586 (12579) SS BOND : bond 0.00326 ( 4) SS BOND : angle 0.65153 ( 8) hydrogen bonds : bond 0.04004 ( 471) hydrogen bonds : angle 4.30790 ( 1335) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 255 ASN cc_start: 0.8714 (m-40) cc_final: 0.8460 (m-40) REVERT: B 19 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7787 (ttp-110) REVERT: B 170 ASP cc_start: 0.8901 (t70) cc_final: 0.8545 (t70) REVERT: R 141 SER cc_start: 0.9048 (t) cc_final: 0.8687 (p) REVERT: R 176 TYR cc_start: 0.8126 (m-10) cc_final: 0.7801 (m-10) REVERT: R 344 PHE cc_start: 0.6915 (t80) cc_final: 0.6183 (t80) outliers start: 20 outliers final: 13 residues processed: 146 average time/residue: 0.6680 time to fit residues: 103.4659 Evaluate side-chains 144 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 64 SER Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 212 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 0.0370 chunk 63 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 18 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 35 ASN B 175 GLN R 145 GLN R 226 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.102867 restraints weight = 10621.694| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.85 r_work: 0.2936 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9261 Z= 0.101 Angle : 0.483 8.063 12587 Z= 0.250 Chirality : 0.040 0.144 1435 Planarity : 0.004 0.050 1557 Dihedral : 4.789 47.021 1568 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.51 % Allowed : 12.55 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.25), residues: 1125 helix: 2.92 (0.25), residues: 411 sheet: 0.68 (0.30), residues: 276 loop : -0.01 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.013 0.001 TYR E 190 PHE 0.015 0.001 PHE R 344 TRP 0.015 0.001 TRP B 82 HIS 0.007 0.001 HIS R 417 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 9257) covalent geometry : angle 0.48270 (12579) SS BOND : bond 0.00306 ( 4) SS BOND : angle 0.55723 ( 8) hydrogen bonds : bond 0.03653 ( 471) hydrogen bonds : angle 4.16664 ( 1335) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 255 ASN cc_start: 0.8655 (m-40) cc_final: 0.8386 (m-40) REVERT: A 276 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7905 (mm-30) REVERT: B 19 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7725 (ttm-80) REVERT: B 46 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8130 (mtp180) REVERT: B 170 ASP cc_start: 0.8872 (t70) cc_final: 0.8499 (t70) REVERT: E 160 ARG cc_start: 0.7623 (ttp-110) cc_final: 0.6950 (ttm110) REVERT: E 180 ARG cc_start: 0.8815 (mtt90) cc_final: 0.8594 (mtt90) REVERT: R 141 SER cc_start: 0.8831 (t) cc_final: 0.8606 (p) REVERT: R 176 TYR cc_start: 0.8143 (m-10) cc_final: 0.7871 (m-10) REVERT: R 344 PHE cc_start: 0.7015 (t80) cc_final: 0.6455 (t80) outliers start: 24 outliers final: 15 residues processed: 161 average time/residue: 0.5261 time to fit residues: 89.8743 Evaluate side-chains 155 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 417 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 83 optimal weight: 0.0040 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 16 ASN B 35 ASN B 175 GLN B 220 GLN R 145 GLN R 226 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.150737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.102178 restraints weight = 10588.197| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.84 r_work: 0.2917 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9261 Z= 0.109 Angle : 0.490 11.377 12587 Z= 0.253 Chirality : 0.040 0.142 1435 Planarity : 0.004 0.050 1557 Dihedral : 4.759 45.714 1568 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.41 % Allowed : 13.81 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.25), residues: 1125 helix: 2.94 (0.25), residues: 412 sheet: 0.60 (0.30), residues: 278 loop : 0.05 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.016 0.001 TYR R 392 PHE 0.014 0.001 PHE R 193 TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 417 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9257) covalent geometry : angle 0.48991 (12579) SS BOND : bond 0.00272 ( 4) SS BOND : angle 0.56580 ( 8) hydrogen bonds : bond 0.03700 ( 471) hydrogen bonds : angle 4.15101 ( 1335) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 240 MET cc_start: 0.7101 (tpt) cc_final: 0.6853 (tpp) REVERT: A 248 LYS cc_start: 0.8861 (mttt) cc_final: 0.8530 (mtpp) REVERT: A 255 ASN cc_start: 0.8665 (m-40) cc_final: 0.8413 (m-40) REVERT: A 276 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7874 (mm-30) REVERT: B 19 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7746 (ttm-80) REVERT: B 46 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8192 (mtp180) REVERT: B 170 ASP cc_start: 0.8873 (t70) cc_final: 0.8486 (t70) REVERT: E 160 ARG cc_start: 0.7601 (ttp-110) cc_final: 0.6926 (ttm110) REVERT: E 180 ARG cc_start: 0.8798 (mtt90) cc_final: 0.8589 (mtt90) REVERT: R 141 SER cc_start: 0.8811 (t) cc_final: 0.8593 (p) REVERT: R 176 TYR cc_start: 0.8129 (m-10) cc_final: 0.7793 (m-10) REVERT: R 344 PHE cc_start: 0.7091 (t80) cc_final: 0.6418 (t80) outliers start: 23 outliers final: 19 residues processed: 156 average time/residue: 0.5264 time to fit residues: 87.1026 Evaluate side-chains 161 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 417 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 0.0670 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 35 ASN B 175 GLN E 186 GLN R 145 GLN R 226 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.149028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.103460 restraints weight = 10699.438| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.83 r_work: 0.2898 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9261 Z= 0.134 Angle : 0.509 10.202 12587 Z= 0.263 Chirality : 0.041 0.141 1435 Planarity : 0.004 0.051 1557 Dihedral : 4.854 45.090 1568 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.72 % Allowed : 13.91 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.25), residues: 1125 helix: 2.93 (0.25), residues: 411 sheet: 0.64 (0.30), residues: 277 loop : 0.03 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.012 0.001 TYR E 102 PHE 0.010 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS R 417 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9257) covalent geometry : angle 0.50858 (12579) SS BOND : bond 0.00309 ( 4) SS BOND : angle 0.68839 ( 8) hydrogen bonds : bond 0.03941 ( 471) hydrogen bonds : angle 4.22652 ( 1335) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 248 LYS cc_start: 0.8816 (mttt) cc_final: 0.8461 (mtpp) REVERT: A 255 ASN cc_start: 0.8687 (m-40) cc_final: 0.8406 (m-40) REVERT: B 19 ARG cc_start: 0.8172 (ttp80) cc_final: 0.7671 (ttm-80) REVERT: B 46 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8184 (mtp180) REVERT: B 170 ASP cc_start: 0.8854 (t70) cc_final: 0.8438 (t70) REVERT: E 160 ARG cc_start: 0.7468 (ttp-110) cc_final: 0.6877 (ttm110) REVERT: E 218 ARG cc_start: 0.7917 (mpp-170) cc_final: 0.7701 (mpp80) REVERT: R 141 SER cc_start: 0.8800 (t) cc_final: 0.8583 (p) REVERT: R 176 TYR cc_start: 0.8126 (m-10) cc_final: 0.7806 (m-10) REVERT: R 344 PHE cc_start: 0.7104 (t80) cc_final: 0.6530 (t80) outliers start: 26 outliers final: 15 residues processed: 154 average time/residue: 0.7221 time to fit residues: 117.7189 Evaluate side-chains 153 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 417 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 104 optimal weight: 20.0000 chunk 41 optimal weight: 0.0970 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 16 ASN B 35 ASN B 175 GLN E 183 GLN E 186 GLN R 145 GLN R 226 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.101011 restraints weight = 10609.516| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.82 r_work: 0.2898 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9261 Z= 0.121 Angle : 0.502 9.656 12587 Z= 0.259 Chirality : 0.040 0.136 1435 Planarity : 0.004 0.051 1557 Dihedral : 4.800 45.720 1568 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.72 % Allowed : 14.02 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.25), residues: 1125 helix: 2.91 (0.25), residues: 412 sheet: 0.53 (0.29), residues: 286 loop : 0.11 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.016 0.001 TYR R 392 PHE 0.014 0.001 PHE R 193 TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 417 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9257) covalent geometry : angle 0.50150 (12579) SS BOND : bond 0.00302 ( 4) SS BOND : angle 0.59838 ( 8) hydrogen bonds : bond 0.03775 ( 471) hydrogen bonds : angle 4.18442 ( 1335) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.414 Fit side-chains REVERT: A 248 LYS cc_start: 0.8803 (mttt) cc_final: 0.8475 (mtpp) REVERT: A 255 ASN cc_start: 0.8719 (m-40) cc_final: 0.8461 (m-40) REVERT: B 19 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7689 (ttm-80) REVERT: B 46 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8134 (mtp180) REVERT: B 170 ASP cc_start: 0.8868 (t70) cc_final: 0.8432 (t70) REVERT: E 18 LYS cc_start: 0.8581 (ttmt) cc_final: 0.8333 (tptt) REVERT: E 160 ARG cc_start: 0.7500 (ttp-110) cc_final: 0.6894 (ttm110) REVERT: E 218 ARG cc_start: 0.7956 (mpp-170) cc_final: 0.7742 (mpp80) REVERT: R 141 SER cc_start: 0.8816 (t) cc_final: 0.8597 (p) REVERT: R 176 TYR cc_start: 0.8151 (m-10) cc_final: 0.7838 (m-10) REVERT: R 344 PHE cc_start: 0.7166 (t80) cc_final: 0.6631 (t80) outliers start: 26 outliers final: 20 residues processed: 154 average time/residue: 0.7014 time to fit residues: 114.3940 Evaluate side-chains 155 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 155 LYS Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 417 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 16 ASN B 35 ASN B 175 GLN E 183 GLN E 186 GLN R 145 GLN R 226 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.146599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.100604 restraints weight = 10601.839| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.84 r_work: 0.2850 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9261 Z= 0.217 Angle : 0.572 9.164 12587 Z= 0.298 Chirality : 0.043 0.154 1435 Planarity : 0.004 0.052 1557 Dihedral : 5.112 43.805 1568 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.51 % Allowed : 14.33 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.25), residues: 1125 helix: 2.93 (0.24), residues: 404 sheet: 0.67 (0.29), residues: 282 loop : 0.07 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.016 0.002 TYR E 102 PHE 0.014 0.002 PHE B 151 TRP 0.013 0.002 TRP B 63 HIS 0.007 0.001 HIS R 417 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 9257) covalent geometry : angle 0.57157 (12579) SS BOND : bond 0.00438 ( 4) SS BOND : angle 0.90968 ( 8) hydrogen bonds : bond 0.04556 ( 471) hydrogen bonds : angle 4.43543 ( 1335) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.374 Fit side-chains REVERT: A 248 LYS cc_start: 0.8798 (mttt) cc_final: 0.8448 (mtpp) REVERT: A 255 ASN cc_start: 0.8814 (m-40) cc_final: 0.8564 (m-40) REVERT: B 19 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7674 (ttm-80) REVERT: B 46 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8068 (mtp180) REVERT: B 170 ASP cc_start: 0.8788 (t70) cc_final: 0.8320 (t70) REVERT: E 18 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8036 (ttpt) REVERT: E 160 ARG cc_start: 0.7486 (ttp-110) cc_final: 0.6877 (ttm110) REVERT: E 183 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8467 (pt0) REVERT: R 141 SER cc_start: 0.9054 (t) cc_final: 0.8689 (p) REVERT: R 176 TYR cc_start: 0.8138 (m-10) cc_final: 0.7810 (m-10) REVERT: R 344 PHE cc_start: 0.7158 (t80) cc_final: 0.6646 (t80) outliers start: 24 outliers final: 17 residues processed: 149 average time/residue: 0.7502 time to fit residues: 118.1957 Evaluate side-chains 150 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 417 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 35 ASN B 175 GLN E 183 GLN E 186 GLN R 145 GLN R 226 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.148691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.099443 restraints weight = 10526.358| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.84 r_work: 0.2874 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9261 Z= 0.136 Angle : 0.523 9.158 12587 Z= 0.272 Chirality : 0.041 0.134 1435 Planarity : 0.004 0.051 1557 Dihedral : 4.947 47.240 1568 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.30 % Allowed : 14.44 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.25), residues: 1125 helix: 2.95 (0.24), residues: 405 sheet: 0.63 (0.30), residues: 281 loop : 0.07 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.017 0.001 TYR R 392 PHE 0.021 0.001 PHE R 193 TRP 0.015 0.001 TRP B 82 HIS 0.007 0.001 HIS R 417 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9257) covalent geometry : angle 0.52276 (12579) SS BOND : bond 0.00290 ( 4) SS BOND : angle 0.58716 ( 8) hydrogen bonds : bond 0.03993 ( 471) hydrogen bonds : angle 4.30842 ( 1335) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.372 Fit side-chains REVERT: A 248 LYS cc_start: 0.8866 (mttt) cc_final: 0.8504 (mtpp) REVERT: A 255 ASN cc_start: 0.8797 (m-40) cc_final: 0.8559 (m-40) REVERT: B 19 ARG cc_start: 0.8225 (ttp80) cc_final: 0.7727 (ttm-80) REVERT: B 46 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8101 (mtp180) REVERT: B 170 ASP cc_start: 0.8905 (t70) cc_final: 0.8463 (t70) REVERT: E 18 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8058 (ttpt) REVERT: E 160 ARG cc_start: 0.7532 (ttp-110) cc_final: 0.6919 (ttm110) REVERT: E 183 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8460 (pt0) REVERT: E 218 ARG cc_start: 0.8019 (mpp-170) cc_final: 0.7758 (mpp80) REVERT: R 141 SER cc_start: 0.9062 (t) cc_final: 0.8696 (p) REVERT: R 176 TYR cc_start: 0.8148 (m-10) cc_final: 0.7811 (m-10) outliers start: 22 outliers final: 18 residues processed: 150 average time/residue: 0.7161 time to fit residues: 113.4304 Evaluate side-chains 152 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 417 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 48 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 105 optimal weight: 0.7980 chunk 60 optimal weight: 0.0570 chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 35 ASN B 175 GLN E 186 GLN R 145 GLN R 226 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.150077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.101951 restraints weight = 10488.628| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.80 r_work: 0.2917 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9261 Z= 0.104 Angle : 0.506 10.198 12587 Z= 0.262 Chirality : 0.040 0.132 1435 Planarity : 0.004 0.050 1557 Dihedral : 4.768 47.493 1568 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.99 % Allowed : 15.17 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.25), residues: 1125 helix: 2.91 (0.25), residues: 412 sheet: 0.52 (0.30), residues: 280 loop : 0.03 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 219 TYR 0.017 0.001 TYR E 190 PHE 0.010 0.001 PHE B 199 TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS R 417 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 9257) covalent geometry : angle 0.50636 (12579) SS BOND : bond 0.00223 ( 4) SS BOND : angle 0.47674 ( 8) hydrogen bonds : bond 0.03627 ( 471) hydrogen bonds : angle 4.19003 ( 1335) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4192.34 seconds wall clock time: 72 minutes 14.93 seconds (4334.93 seconds total)