Starting phenix.real_space_refine on Tue Apr 29 20:02:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yn5_39415/04_2025/8yn5_39415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yn5_39415/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8yn5_39415/04_2025/8yn5_39415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yn5_39415/04_2025/8yn5_39415.map" model { file = "/net/cci-nas-00/data/ceres_data/8yn5_39415/04_2025/8yn5_39415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yn5_39415/04_2025/8yn5_39415.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, '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: 5.93, per 1000 atoms: 0.66 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: 2.48 Conformation dependent library (CDL) restraints added in 983.8 milliseconds 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: 1.09 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: 2.54 Time building geometry restraints manager: 2.88 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.740 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:17.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.960 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (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 TRP 0.009 0.001 TRP B 82 HIS 0.002 0.001 HIS B 183 PHE 0.009 0.001 PHE B 199 TYR 0.010 0.001 TYR E 190 ARG 0.002 0.000 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.23203 ( 471) hydrogen bonds : angle 6.75741 ( 1335) SS BOND : bond 0.00148 ( 4) SS BOND : angle 0.45045 ( 8) covalent geometry : bond 0.00238 ( 9257) covalent geometry : angle 0.52905 (12579) *********************** 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 : 0.979 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: 1.5832 time to fit residues: 323.6847 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 : 0.991 ------------------------------------------------------------------------------- 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 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.154088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112142 restraints weight = 10344.726| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.66 r_work: 0.3035 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9261 Z= 0.128 Angle : 0.535 7.075 12587 Z= 0.281 Chirality : 0.041 0.144 1435 Planarity : 0.004 0.047 1557 Dihedral : 5.536 45.122 1572 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.78 % Allowed : 9.83 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.25), residues: 1125 helix: 2.39 (0.25), residues: 412 sheet: 0.87 (0.30), residues: 280 loop : 0.11 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.020 0.001 PHE R 344 TYR 0.018 0.001 TYR R 392 ARG 0.003 0.000 ARG R 381 Details of bonding type rmsd hydrogen bonds : bond 0.05142 ( 471) hydrogen bonds : angle 4.76173 ( 1335) SS BOND : bond 0.00342 ( 4) SS BOND : angle 0.86674 ( 8) covalent geometry : bond 0.00265 ( 9257) covalent geometry : angle 0.53451 (12579) *********************** 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 165 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.946 Fit side-chains REVERT: A 255 ASN cc_start: 0.8835 (m-40) cc_final: 0.8540 (m-40) REVERT: B 19 ARG cc_start: 0.8211 (ttp80) cc_final: 0.7743 (ttp-110) REVERT: B 258 ASP cc_start: 0.8587 (t70) cc_final: 0.8353 (t70) REVERT: B 260 GLU cc_start: 0.8988 (tt0) cc_final: 0.8758 (tt0) REVERT: R 141 SER cc_start: 0.9032 (t) cc_final: 0.8711 (p) REVERT: R 176 TYR cc_start: 0.7981 (m-10) cc_final: 0.7740 (m-10) REVERT: R 417 HIS cc_start: 0.8257 (t70) cc_final: 0.7986 (OUTLIER) outliers start: 17 outliers final: 13 residues processed: 157 average time/residue: 1.3858 time to fit residues: 231.6306 Evaluate side-chains 141 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 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 E residue 186 GLN Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 E 183 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 = 0.3757 r_free = 0.3757 target = 0.152133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.108353 restraints weight = 10541.856| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.78 r_work: 0.2955 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9261 Z= 0.163 Angle : 0.539 6.863 12587 Z= 0.283 Chirality : 0.042 0.153 1435 Planarity : 0.004 0.052 1557 Dihedral : 5.324 46.647 1570 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.30 % Allowed : 10.88 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.25), residues: 1125 helix: 2.61 (0.25), residues: 409 sheet: 0.86 (0.29), residues: 286 loop : -0.03 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS E 34 PHE 0.012 0.001 PHE B 151 TYR 0.013 0.001 TYR E 102 ARG 0.005 0.000 ARG R 151 Details of bonding type rmsd hydrogen bonds : bond 0.04753 ( 471) hydrogen bonds : angle 4.58237 ( 1335) SS BOND : bond 0.00405 ( 4) SS BOND : angle 0.90024 ( 8) covalent geometry : bond 0.00371 ( 9257) covalent geometry : angle 0.53870 (12579) *********************** 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 158 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 255 ASN cc_start: 0.8854 (m-40) cc_final: 0.8600 (m-40) REVERT: B 19 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7717 (ttp-110) REVERT: B 46 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8067 (mtp180) REVERT: R 41 MET cc_start: 0.7906 (mtp) cc_final: 0.7661 (mtm) REVERT: R 86 PHE cc_start: 0.8529 (t80) cc_final: 0.8324 (t80) REVERT: R 141 SER cc_start: 0.9122 (t) cc_final: 0.8756 (p) REVERT: R 176 TYR cc_start: 0.8055 (m-10) cc_final: 0.7767 (m-10) outliers start: 22 outliers final: 11 residues processed: 146 average time/residue: 1.3708 time to fit residues: 212.3054 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 : 0.942 ------------------------------------------------------------------------------- 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 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 192 MET Chi-restraints excluded: chain R residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 54 optimal weight: 0.0770 chunk 16 optimal weight: 10.0000 chunk 94 optimal weight: 0.3980 chunk 111 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 194 ASN 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 = 0.3784 r_free = 0.3784 target = 0.154492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111543 restraints weight = 10449.741| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.71 r_work: 0.3007 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9261 Z= 0.108 Angle : 0.500 9.974 12587 Z= 0.260 Chirality : 0.040 0.146 1435 Planarity : 0.004 0.050 1557 Dihedral : 4.938 47.325 1568 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.20 % Allowed : 12.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.25), residues: 1125 helix: 2.70 (0.25), residues: 412 sheet: 0.77 (0.30), residues: 276 loop : 0.00 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.008 0.001 HIS R 417 PHE 0.009 0.001 PHE B 199 TYR 0.016 0.001 TYR E 190 ARG 0.007 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 471) hydrogen bonds : angle 4.34334 ( 1335) SS BOND : bond 0.00317 ( 4) SS BOND : angle 0.63244 ( 8) covalent geometry : bond 0.00230 ( 9257) covalent geometry : angle 0.50028 (12579) *********************** 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 157 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 255 ASN cc_start: 0.8769 (m-40) cc_final: 0.8507 (m-40) REVERT: B 19 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7781 (ttp-110) REVERT: C 20 LYS cc_start: 0.8539 (mttm) cc_final: 0.8310 (mtpt) REVERT: R 141 SER cc_start: 0.9045 (t) cc_final: 0.8683 (p) REVERT: R 176 TYR cc_start: 0.8090 (m-10) cc_final: 0.7763 (m-10) outliers start: 21 outliers final: 10 residues processed: 146 average time/residue: 1.3579 time to fit residues: 210.6837 Evaluate side-chains 141 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 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 R residue 95 VAL Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 417 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.0030 chunk 83 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 79 optimal weight: 0.0060 chunk 106 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 66 optimal weight: 0.0010 chunk 51 optimal weight: 3.9990 overall best weight: 0.5214 ------------------------------------------------------------------------------- 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 R 417 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113048 restraints weight = 10478.677| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.73 r_work: 0.3070 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9261 Z= 0.099 Angle : 0.483 7.925 12587 Z= 0.250 Chirality : 0.040 0.144 1435 Planarity : 0.004 0.049 1557 Dihedral : 4.795 47.249 1568 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.20 % Allowed : 13.28 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.25), residues: 1125 helix: 2.88 (0.25), residues: 412 sheet: 0.66 (0.30), residues: 277 loop : 0.01 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.007 0.001 HIS R 417 PHE 0.022 0.001 PHE R 344 TYR 0.012 0.001 TYR E 190 ARG 0.006 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 471) hydrogen bonds : angle 4.18573 ( 1335) SS BOND : bond 0.00274 ( 4) SS BOND : angle 0.52034 ( 8) covalent geometry : bond 0.00210 ( 9257) covalent geometry : angle 0.48277 (12579) *********************** 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 168 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 255 ASN cc_start: 0.8699 (m-40) cc_final: 0.8452 (m-40) REVERT: B 19 ARG cc_start: 0.8292 (ttp80) cc_final: 0.7819 (ttp-110) REVERT: B 170 ASP cc_start: 0.8899 (t70) cc_final: 0.8664 (t70) REVERT: E 160 ARG cc_start: 0.7676 (ttp-110) cc_final: 0.7029 (ttm110) REVERT: E 180 ARG cc_start: 0.8832 (mtt90) cc_final: 0.8599 (mtt90) REVERT: R 141 SER cc_start: 0.8854 (t) cc_final: 0.8634 (p) REVERT: R 176 TYR cc_start: 0.8137 (m-10) cc_final: 0.7872 (m-10) outliers start: 21 outliers final: 13 residues processed: 161 average time/residue: 1.3705 time to fit residues: 233.9098 Evaluate side-chains 157 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain B residue 327 VAL 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 E residue 195 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 212 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3728 r_free = 0.3728 target = 0.150783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.102269 restraints weight = 10529.298| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.83 r_work: 0.2915 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9261 Z= 0.109 Angle : 0.496 11.390 12587 Z= 0.255 Chirality : 0.040 0.142 1435 Planarity : 0.004 0.049 1557 Dihedral : 4.831 46.245 1568 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.51 % Allowed : 14.02 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.25), residues: 1125 helix: 2.91 (0.25), residues: 412 sheet: 0.63 (0.30), residues: 277 loop : 0.01 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 417 PHE 0.016 0.001 PHE R 193 TYR 0.015 0.001 TYR R 392 ARG 0.004 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 471) hydrogen bonds : angle 4.15251 ( 1335) SS BOND : bond 0.00275 ( 4) SS BOND : angle 0.56348 ( 8) covalent geometry : bond 0.00241 ( 9257) covalent geometry : angle 0.49596 (12579) *********************** 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 177 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6721 (tp30) REVERT: A 243 MET cc_start: 0.8717 (tpt) cc_final: 0.8240 (tpt) REVERT: A 248 LYS cc_start: 0.8780 (mttt) cc_final: 0.8447 (mtpp) REVERT: A 255 ASN cc_start: 0.8681 (m-40) cc_final: 0.8407 (m-40) REVERT: A 318 GLU cc_start: 0.8677 (tt0) cc_final: 0.8444 (tt0) REVERT: B 19 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7734 (ttm-80) REVERT: B 170 ASP cc_start: 0.8884 (t70) cc_final: 0.8626 (t70) REVERT: B 215 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8041 (mm-30) REVERT: B 258 ASP cc_start: 0.8676 (t70) cc_final: 0.8371 (t70) REVERT: E 160 ARG cc_start: 0.7579 (ttp-110) cc_final: 0.6925 (ttm110) REVERT: R 104 ARG cc_start: 0.6796 (tpt-90) cc_final: 0.6408 (tpt-90) REVERT: R 141 SER cc_start: 0.8817 (t) cc_final: 0.8598 (p) REVERT: R 176 TYR cc_start: 0.8135 (m-10) cc_final: 0.7854 (m-10) REVERT: R 193 PHE cc_start: 0.8917 (t80) cc_final: 0.8616 (t80) outliers start: 24 outliers final: 18 residues processed: 165 average time/residue: 1.4683 time to fit residues: 256.2202 Evaluate side-chains 161 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE 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 84 SER 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 95 VAL Chi-restraints excluded: chain R residue 212 LEU 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 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 0.0270 chunk 108 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.9442 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.149626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.100864 restraints weight = 10663.711| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.84 r_work: 0.2900 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9261 Z= 0.118 Angle : 0.498 10.491 12587 Z= 0.257 Chirality : 0.040 0.142 1435 Planarity : 0.004 0.049 1557 Dihedral : 4.815 45.737 1568 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.72 % Allowed : 14.23 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.25), residues: 1125 helix: 2.93 (0.25), residues: 413 sheet: 0.62 (0.30), residues: 277 loop : 0.03 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 417 PHE 0.013 0.001 PHE R 193 TYR 0.011 0.001 TYR E 102 ARG 0.005 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 471) hydrogen bonds : angle 4.17659 ( 1335) SS BOND : bond 0.00292 ( 4) SS BOND : angle 0.62454 ( 8) covalent geometry : bond 0.00263 ( 9257) covalent geometry : angle 0.49825 (12579) *********************** 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 170 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 248 LYS cc_start: 0.8799 (mttt) cc_final: 0.8454 (mtpp) REVERT: A 255 ASN cc_start: 0.8682 (m-40) cc_final: 0.8397 (m-40) REVERT: B 19 ARG cc_start: 0.8188 (ttp80) cc_final: 0.7711 (ttm-80) REVERT: B 46 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8180 (mtp180) REVERT: B 170 ASP cc_start: 0.8905 (t70) cc_final: 0.8657 (t70) REVERT: B 258 ASP cc_start: 0.8703 (t70) cc_final: 0.8381 (t70) REVERT: E 160 ARG cc_start: 0.7592 (ttp-110) cc_final: 0.6938 (ttm110) REVERT: E 186 GLN cc_start: 0.8761 (pt0) cc_final: 0.8534 (pt0) REVERT: E 218 ARG cc_start: 0.7951 (mpp-170) cc_final: 0.7700 (mpp80) REVERT: R 104 ARG cc_start: 0.6804 (tpt-90) cc_final: 0.6402 (tpt-90) REVERT: R 141 SER cc_start: 0.8822 (t) cc_final: 0.8604 (p) REVERT: R 176 TYR cc_start: 0.8151 (m-10) cc_final: 0.7811 (m-10) REVERT: R 193 PHE cc_start: 0.8724 (t80) cc_final: 0.8518 (t80) outliers start: 26 outliers final: 19 residues processed: 158 average time/residue: 1.3742 time to fit residues: 230.0097 Evaluate side-chains 159 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 327 VAL Chi-restraints excluded: chain E residue 18 LYS 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 195 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 212 LEU 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 99 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 98 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 108 optimal weight: 0.0670 chunk 22 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 269 ASN A 322 HIS A 331 ASN A 333 GLN B 16 ASN B 35 ASN B 175 GLN R 145 GLN R 226 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.150557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.102070 restraints weight = 10709.170| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.84 r_work: 0.2920 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9261 Z= 0.104 Angle : 0.488 9.707 12587 Z= 0.252 Chirality : 0.040 0.135 1435 Planarity : 0.004 0.049 1557 Dihedral : 4.753 45.894 1568 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.30 % Allowed : 14.75 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.25), residues: 1125 helix: 2.93 (0.25), residues: 413 sheet: 0.61 (0.30), residues: 277 loop : 0.05 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 417 PHE 0.011 0.001 PHE R 193 TYR 0.016 0.001 TYR R 392 ARG 0.005 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 471) hydrogen bonds : angle 4.09157 ( 1335) SS BOND : bond 0.00268 ( 4) SS BOND : angle 0.55928 ( 8) covalent geometry : bond 0.00227 ( 9257) covalent geometry : angle 0.48756 (12579) *********************** 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 168 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 248 LYS cc_start: 0.8757 (mttt) cc_final: 0.8437 (mtpp) REVERT: A 255 ASN cc_start: 0.8657 (m-40) cc_final: 0.8404 (m-40) REVERT: B 19 ARG cc_start: 0.8192 (ttp80) cc_final: 0.7715 (ttm-80) REVERT: B 46 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8160 (mtp180) REVERT: B 170 ASP cc_start: 0.8843 (t70) cc_final: 0.8566 (t70) REVERT: B 258 ASP cc_start: 0.8692 (t70) cc_final: 0.8351 (t70) REVERT: E 160 ARG cc_start: 0.7517 (ttp-110) cc_final: 0.6929 (ttm110) REVERT: E 183 GLN cc_start: 0.8457 (mt0) cc_final: 0.8136 (pt0) REVERT: E 186 GLN cc_start: 0.8744 (pt0) cc_final: 0.8538 (pt0) REVERT: R 141 SER cc_start: 0.8779 (t) cc_final: 0.8557 (p) REVERT: R 176 TYR cc_start: 0.8129 (m-10) cc_final: 0.7786 (m-10) outliers start: 22 outliers final: 17 residues processed: 160 average time/residue: 1.2872 time to fit residues: 218.8188 Evaluate side-chains 160 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 327 VAL Chi-restraints excluded: chain E residue 18 LYS 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 195 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 92 VAL 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 14 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 41 optimal weight: 0.0770 chunk 90 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 43 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 16 ASN B 35 ASN B 175 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 = 0.3733 r_free = 0.3733 target = 0.151307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.103154 restraints weight = 10566.033| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.82 r_work: 0.2941 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9261 Z= 0.096 Angle : 0.481 9.264 12587 Z= 0.249 Chirality : 0.040 0.133 1435 Planarity : 0.004 0.048 1557 Dihedral : 4.649 44.879 1568 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.78 % Allowed : 15.27 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.25), residues: 1125 helix: 2.98 (0.25), residues: 413 sheet: 0.64 (0.30), residues: 275 loop : 0.03 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS R 417 PHE 0.010 0.001 PHE A 189 TYR 0.011 0.001 TYR E 190 ARG 0.005 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 471) hydrogen bonds : angle 4.04177 ( 1335) SS BOND : bond 0.00256 ( 4) SS BOND : angle 0.49616 ( 8) covalent geometry : bond 0.00204 ( 9257) covalent geometry : angle 0.48138 (12579) *********************** 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 161 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 248 LYS cc_start: 0.8794 (mttt) cc_final: 0.8485 (mtpm) REVERT: A 255 ASN cc_start: 0.8604 (m-40) cc_final: 0.8340 (m-40) REVERT: B 19 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7660 (ttm-80) REVERT: B 46 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8125 (mtp180) REVERT: B 170 ASP cc_start: 0.8807 (t70) cc_final: 0.8521 (t70) REVERT: B 258 ASP cc_start: 0.8673 (t70) cc_final: 0.8300 (t70) REVERT: E 86 ARG cc_start: 0.7231 (mtt180) cc_final: 0.6932 (mtp180) REVERT: E 140 MET cc_start: 0.9018 (mmm) cc_final: 0.8609 (mmm) REVERT: E 160 ARG cc_start: 0.7498 (ttp-110) cc_final: 0.6837 (ttm110) REVERT: E 183 GLN cc_start: 0.8424 (mt0) cc_final: 0.8129 (pt0) REVERT: E 186 GLN cc_start: 0.8790 (pt0) cc_final: 0.8571 (pt0) REVERT: R 141 SER cc_start: 0.8718 (t) cc_final: 0.8470 (p) REVERT: R 176 TYR cc_start: 0.8108 (m-10) cc_final: 0.7746 (m-10) outliers start: 17 outliers final: 14 residues processed: 154 average time/residue: 1.3974 time to fit residues: 228.5680 Evaluate side-chains 153 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 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 327 VAL Chi-restraints excluded: chain C residue 58 GLU 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 192 MET Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 206 SER 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 36 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 188 HIS A 269 ASN A 331 ASN B 16 ASN B 35 ASN B 175 GLN 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 = 0.3703 r_free = 0.3703 target = 0.148622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.103665 restraints weight = 10651.177| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.81 r_work: 0.2896 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9261 Z= 0.151 Angle : 0.535 8.955 12587 Z= 0.279 Chirality : 0.042 0.140 1435 Planarity : 0.004 0.050 1557 Dihedral : 4.841 42.940 1568 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.67 % Allowed : 16.00 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1125 helix: 3.05 (0.25), residues: 407 sheet: 0.56 (0.30), residues: 283 loop : 0.13 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS R 417 PHE 0.021 0.001 PHE R 193 TYR 0.016 0.001 TYR R 392 ARG 0.010 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 471) hydrogen bonds : angle 4.23531 ( 1335) SS BOND : bond 0.00318 ( 4) SS BOND : angle 0.78556 ( 8) covalent geometry : bond 0.00344 ( 9257) covalent geometry : angle 0.53511 (12579) ********************** 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 157 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.942 Fit side-chains REVERT: A 33 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7881 (mt-10) REVERT: A 248 LYS cc_start: 0.8793 (mttt) cc_final: 0.8487 (mtpm) REVERT: A 255 ASN cc_start: 0.8710 (m-40) cc_final: 0.8386 (m-40) REVERT: B 19 ARG cc_start: 0.8172 (ttp80) cc_final: 0.7676 (ttm-80) REVERT: B 46 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8081 (mtp180) REVERT: B 170 ASP cc_start: 0.8888 (t70) cc_final: 0.8611 (t70) REVERT: E 86 ARG cc_start: 0.7356 (mtt180) cc_final: 0.7081 (mtt90) REVERT: E 160 ARG cc_start: 0.7481 (ttp-110) cc_final: 0.6869 (ttm110) REVERT: E 186 GLN cc_start: 0.8753 (pt0) cc_final: 0.8550 (pt0) REVERT: R 141 SER cc_start: 0.8777 (t) cc_final: 0.8539 (p) REVERT: R 176 TYR cc_start: 0.8097 (m-10) cc_final: 0.7794 (m-10) outliers start: 16 outliers final: 16 residues processed: 152 average time/residue: 1.3971 time to fit residues: 225.1129 Evaluate side-chains 153 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 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 192 MET Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 212 LEU 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 12 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 188 HIS A 331 ASN B 16 ASN B 35 ASN B 175 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 = 0.3721 r_free = 0.3721 target = 0.150351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.101564 restraints weight = 10573.908| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.84 r_work: 0.2910 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2586 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= 0.111 Angle : 0.506 8.860 12587 Z= 0.263 Chirality : 0.040 0.132 1435 Planarity : 0.004 0.049 1557 Dihedral : 4.763 44.538 1568 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.46 % Allowed : 16.11 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.25), residues: 1125 helix: 2.96 (0.25), residues: 413 sheet: 0.55 (0.30), residues: 278 loop : 0.05 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 417 PHE 0.011 0.001 PHE A 189 TYR 0.015 0.001 TYR E 190 ARG 0.006 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 471) hydrogen bonds : angle 4.16229 ( 1335) SS BOND : bond 0.00258 ( 4) SS BOND : angle 0.61749 ( 8) covalent geometry : bond 0.00244 ( 9257) covalent geometry : angle 0.50608 (12579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8710.20 seconds wall clock time: 150 minutes 56.97 seconds (9056.97 seconds total)