Starting phenix.real_space_refine on Thu Jan 16 00:24:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yn5_39415/01_2025/8yn5_39415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yn5_39415/01_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_39415/01_2025/8yn5_39415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yn5_39415/01_2025/8yn5_39415.map" model { file = "/net/cci-nas-00/data/ceres_data/8yn5_39415/01_2025/8yn5_39415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yn5_39415/01_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-5571/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: 5.11, per 1000 atoms: 0.56 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: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.06 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: 2.87 Time building geometry restraints manager: 2.57 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: 0.010 Normalize map: mean=0, sd=1: 0.450 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: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.530 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.010 ------------------------------------------------------------------------------- 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 9257 Z= 0.163 Angle : 0.529 8.161 12579 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 *********************** 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 : 0.951 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: 1.4569 time to fit residues: 297.5336 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 : 1.029 ------------------------------------------------------------------------------- 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 = 0.112143 restraints weight = 10344.727| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.66 r_work: 0.3036 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 9257 Z= 0.172 Angle : 0.535 7.075 12579 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 *********************** 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 : 0.951 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: 0.8588 (t70) cc_final: 0.8354 (t70) REVERT: B 260 GLU cc_start: 0.8987 (tt0) cc_final: 0.8757 (tt0) REVERT: R 141 SER cc_start: 0.9031 (t) cc_final: 0.8711 (p) REVERT: R 176 TYR cc_start: 0.7978 (m-10) cc_final: 0.7737 (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: 1.3587 time to fit residues: 226.9098 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 : 0.958 ------------------------------------------------------------------------------- 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: 0.7980 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 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: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.151921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.108230 restraints weight = 10542.473| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.78 r_work: 0.2952 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9257 Z= 0.261 Angle : 0.547 6.930 12579 Z= 0.288 Chirality : 0.042 0.153 1435 Planarity : 0.004 0.052 1557 Dihedral : 5.370 45.936 1570 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.41 % Allowed : 10.77 % 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: 1.81 (0.25), residues: 1125 helix: 2.71 (0.25), residues: 403 sheet: 0.86 (0.29), residues: 286 loop : 0.04 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS E 34 PHE 0.012 0.001 PHE B 151 TYR 0.013 0.001 TYR E 102 ARG 0.006 0.000 ARG R 151 *********************** 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 161 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: A 255 ASN cc_start: 0.8874 (m-40) cc_final: 0.8621 (m-40) REVERT: A 283 LEU cc_start: 0.9002 (tp) cc_final: 0.8795 (tm) REVERT: B 19 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7721 (ttp-110) REVERT: B 46 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8077 (mtp180) REVERT: B 260 GLU cc_start: 0.8955 (tt0) cc_final: 0.8755 (tt0) REVERT: R 41 MET cc_start: 0.7912 (mtp) cc_final: 0.7677 (mtm) REVERT: R 86 PHE cc_start: 0.8522 (t80) cc_final: 0.8314 (t80) REVERT: R 141 SER cc_start: 0.9129 (t) cc_final: 0.8773 (p) REVERT: R 176 TYR cc_start: 0.8034 (m-10) cc_final: 0.7723 (m-10) REVERT: R 417 HIS cc_start: 0.8264 (t70) cc_final: 0.8063 (t70) outliers start: 23 outliers final: 12 residues processed: 149 average time/residue: 1.4090 time to fit residues: 222.5468 Evaluate side-chains 143 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 84 SER 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: 1.9990 chunk 54 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 R 226 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.152082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.108515 restraints weight = 10379.134| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.73 r_work: 0.2953 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9257 Z= 0.247 Angle : 0.536 6.887 12579 Z= 0.282 Chirality : 0.042 0.151 1435 Planarity : 0.004 0.053 1557 Dihedral : 5.185 46.573 1568 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.82 % Allowed : 11.92 % 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: 1.75 (0.24), residues: 1125 helix: 2.71 (0.24), residues: 403 sheet: 0.68 (0.29), residues: 286 loop : 0.07 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS E 34 PHE 0.018 0.001 PHE R 344 TYR 0.015 0.001 TYR R 392 ARG 0.007 0.000 ARG B 219 *********************** 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 160 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 248 LYS cc_start: 0.8812 (mttt) cc_final: 0.8465 (mtpp) REVERT: A 255 ASN cc_start: 0.8880 (m-40) cc_final: 0.8623 (m-40) REVERT: B 19 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7753 (ttp-110) REVERT: B 46 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8120 (mtp180) REVERT: B 260 GLU cc_start: 0.8955 (tt0) cc_final: 0.8754 (tt0) REVERT: R 141 SER cc_start: 0.9130 (t) cc_final: 0.8765 (p) REVERT: R 176 TYR cc_start: 0.8131 (m-10) cc_final: 0.7841 (m-10) outliers start: 27 outliers final: 15 residues processed: 148 average time/residue: 1.4452 time to fit residues: 226.8515 Evaluate side-chains 144 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 62 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 186 GLN 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 108 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 79 optimal weight: 0.0770 chunk 106 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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 C 59 ASN E 194 ASN R 145 GLN R 417 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.154030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.110892 restraints weight = 10453.741| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.82 r_work: 0.3033 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9257 Z= 0.157 Angle : 0.498 9.929 12579 Z= 0.258 Chirality : 0.040 0.145 1435 Planarity : 0.004 0.051 1557 Dihedral : 4.950 49.097 1568 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.78 % Allowed : 13.49 % Favored : 84.73 % 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: 2.75 (0.25), residues: 411 sheet: 0.69 (0.30), residues: 276 loop : -0.00 (0.29), residues: 438 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 0.010 0.001 PHE B 199 TYR 0.013 0.001 TYR E 190 ARG 0.005 0.000 ARG B 219 *********************** 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 165 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6866 (tp30) REVERT: A 248 LYS cc_start: 0.8777 (mttt) cc_final: 0.8469 (mtpp) REVERT: A 255 ASN cc_start: 0.8771 (m-40) cc_final: 0.8502 (m-40) REVERT: B 19 ARG cc_start: 0.8269 (ttp80) cc_final: 0.7818 (ttm-80) REVERT: E 186 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8592 (pt0) REVERT: R 141 SER cc_start: 0.9078 (t) cc_final: 0.8722 (p) REVERT: R 176 TYR cc_start: 0.8144 (m-10) cc_final: 0.7841 (m-10) REVERT: R 344 PHE cc_start: 0.6975 (t80) cc_final: 0.6415 (t80) outliers start: 17 outliers final: 13 residues processed: 159 average time/residue: 1.4311 time to fit residues: 240.6904 Evaluate side-chains 145 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL 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 95 VAL Chi-restraints excluded: chain R residue 212 LEU 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 8 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 87 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 chunk 104 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 4 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: A 269 ASN B 16 ASN B 35 ASN B 175 GLN R 145 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 = 0.3715 r_free = 0.3715 target = 0.149581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.101060 restraints weight = 10580.515| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.83 r_work: 0.2905 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9257 Z= 0.156 Angle : 0.496 7.879 12579 Z= 0.256 Chirality : 0.040 0.144 1435 Planarity : 0.004 0.051 1557 Dihedral : 4.894 48.109 1568 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.51 % Allowed : 13.70 % 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 (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: 1.80 (0.25), residues: 1125 helix: 2.85 (0.25), residues: 412 sheet: 0.59 (0.30), residues: 278 loop : 0.03 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.007 0.001 HIS R 417 PHE 0.016 0.001 PHE R 193 TYR 0.016 0.001 TYR R 392 ARG 0.005 0.000 ARG B 219 *********************** 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 164 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: A 240 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6816 (tpp) REVERT: A 248 LYS cc_start: 0.8733 (mttt) cc_final: 0.8419 (mtpp) REVERT: A 255 ASN cc_start: 0.8726 (m-40) cc_final: 0.8438 (m-40) REVERT: B 19 ARG cc_start: 0.8193 (ttp80) cc_final: 0.7710 (ttm-80) REVERT: E 160 ARG cc_start: 0.7529 (ttp-110) cc_final: 0.6933 (ttm110) REVERT: E 186 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8612 (pt0) REVERT: R 104 ARG cc_start: 0.6782 (tpt-90) cc_final: 0.6372 (tpt-90) REVERT: R 141 SER cc_start: 0.8997 (t) cc_final: 0.8667 (p) REVERT: R 176 TYR cc_start: 0.8163 (m-10) cc_final: 0.7895 (m-10) REVERT: R 193 PHE cc_start: 0.8914 (t80) cc_final: 0.8568 (t80) outliers start: 24 outliers final: 16 residues processed: 156 average time/residue: 1.4680 time to fit residues: 242.3993 Evaluate side-chains 157 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 328 ASP 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 38 MET 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 186 GLN Chi-restraints excluded: chain E residue 192 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 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 = 0.3690 r_free = 0.3690 target = 0.147433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.098298 restraints weight = 10623.282| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.82 r_work: 0.2837 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9257 Z= 0.263 Angle : 0.551 11.073 12579 Z= 0.285 Chirality : 0.042 0.145 1435 Planarity : 0.004 0.052 1557 Dihedral : 5.079 46.477 1568 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.24 % Allowed : 13.70 % 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: 1.84 (0.25), residues: 1125 helix: 2.90 (0.24), residues: 406 sheet: 0.61 (0.29), residues: 281 loop : 0.06 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS R 417 PHE 0.014 0.001 PHE R 193 TYR 0.014 0.001 TYR E 102 ARG 0.009 0.000 ARG E 191 *********************** 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 172 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6733 (tp30) REVERT: A 240 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6757 (tpp) REVERT: A 248 LYS cc_start: 0.8733 (mttt) cc_final: 0.8408 (mtpp) REVERT: A 255 ASN cc_start: 0.8833 (m-40) cc_final: 0.8569 (m-40) REVERT: B 19 ARG cc_start: 0.8195 (ttp80) cc_final: 0.7700 (ttm-80) REVERT: B 46 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8133 (mtp180) REVERT: E 160 ARG cc_start: 0.7526 (ttp-110) cc_final: 0.6902 (ttm110) REVERT: R 104 ARG cc_start: 0.6823 (tpt-90) cc_final: 0.6412 (tpt-90) REVERT: R 141 SER cc_start: 0.9068 (t) cc_final: 0.8703 (p) REVERT: R 176 TYR cc_start: 0.8157 (m-10) cc_final: 0.7838 (m-10) outliers start: 31 outliers final: 22 residues processed: 157 average time/residue: 1.4906 time to fit residues: 247.3312 Evaluate side-chains 169 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 MET 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 181 THR 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 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 155 VAL Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain R residue 43 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 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: 8.9990 chunk 44 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 56 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.146301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.100023 restraints weight = 10680.945| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.88 r_work: 0.2836 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9257 Z= 0.326 Angle : 0.578 10.176 12579 Z= 0.300 Chirality : 0.043 0.152 1435 Planarity : 0.004 0.052 1557 Dihedral : 5.238 46.921 1568 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.62 % Allowed : 14.12 % 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 (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: 1.76 (0.25), residues: 1125 helix: 2.79 (0.24), residues: 404 sheet: 0.55 (0.29), residues: 286 loop : 0.09 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.007 0.001 HIS R 417 PHE 0.013 0.001 PHE B 151 TYR 0.017 0.002 TYR E 102 ARG 0.005 0.000 ARG B 219 *********************** 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 167 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.968 Fit side-chains REVERT: A 207 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6711 (tp30) REVERT: A 240 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6846 (tpp) REVERT: A 248 LYS cc_start: 0.8753 (mttt) cc_final: 0.8399 (mtpp) REVERT: A 255 ASN cc_start: 0.8845 (m-40) cc_final: 0.8634 (m-40) REVERT: B 19 ARG cc_start: 0.8163 (ttp80) cc_final: 0.7635 (ttp-110) REVERT: B 46 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8079 (mtp180) REVERT: E 160 ARG cc_start: 0.7510 (ttp-110) cc_final: 0.6884 (ttm110) REVERT: E 183 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8471 (pt0) REVERT: E 218 ARG cc_start: 0.7998 (mpp-170) cc_final: 0.7763 (mpp80) REVERT: R 104 ARG cc_start: 0.6830 (tpt-90) cc_final: 0.6417 (tpt-90) REVERT: R 141 SER cc_start: 0.9109 (t) cc_final: 0.8737 (p) REVERT: R 176 TYR cc_start: 0.8140 (m-10) cc_final: 0.7789 (m-10) outliers start: 25 outliers final: 20 residues processed: 156 average time/residue: 1.5199 time to fit residues: 250.3688 Evaluate side-chains 164 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 MET 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 181 THR 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 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 183 GLN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain R residue 43 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 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: 2.9990 chunk 11 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.0060 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 90 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 overall best weight: 0.4554 ------------------------------------------------------------------------------- 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** B 16 ASN B 35 ASN B 175 GLN R 145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.150369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.101683 restraints weight = 10542.687| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.84 r_work: 0.2909 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9257 Z= 0.133 Angle : 0.506 9.970 12579 Z= 0.261 Chirality : 0.040 0.133 1435 Planarity : 0.004 0.050 1557 Dihedral : 4.883 51.032 1568 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.30 % Allowed : 14.33 % 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 (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: 1.75 (0.25), residues: 1125 helix: 2.85 (0.25), residues: 411 sheet: 0.50 (0.30), residues: 278 loop : -0.00 (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 0.021 0.001 PHE R 193 TYR 0.019 0.001 TYR E 190 ARG 0.008 0.000 ARG E 191 *********************** 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 177 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.051 Fit side-chains REVERT: A 207 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6769 (tp30) REVERT: A 240 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6757 (tpp) REVERT: A 248 LYS cc_start: 0.8782 (mttt) cc_final: 0.8453 (mtpp) REVERT: A 255 ASN cc_start: 0.8772 (m-40) cc_final: 0.8505 (m-40) REVERT: B 19 ARG cc_start: 0.8200 (ttp80) cc_final: 0.7702 (ttm-80) REVERT: B 170 ASP cc_start: 0.8899 (t70) cc_final: 0.8636 (t70) REVERT: E 160 ARG cc_start: 0.7536 (ttp-110) cc_final: 0.6900 (ttm110) REVERT: E 218 ARG cc_start: 0.7952 (mpp-170) cc_final: 0.7728 (mpp80) REVERT: R 56 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7235 (mtt) REVERT: R 141 SER cc_start: 0.9038 (t) cc_final: 0.8669 (p) REVERT: R 176 TYR cc_start: 0.8122 (m-10) cc_final: 0.7767 (m-10) outliers start: 22 outliers final: 16 residues processed: 168 average time/residue: 1.4226 time to fit residues: 253.2196 Evaluate side-chains 155 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 278 ILE 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 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 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 R residue 43 LEU Chi-restraints excluded: chain R residue 56 MET 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 36 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 322 HIS A 331 ASN B 16 ASN B 35 ASN B 175 GLN B 220 GLN R 145 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.149589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.100312 restraints weight = 10635.866| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.85 r_work: 0.2892 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9257 Z= 0.171 Angle : 0.510 9.506 12579 Z= 0.265 Chirality : 0.040 0.132 1435 Planarity : 0.004 0.051 1557 Dihedral : 4.880 48.216 1568 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.67 % Allowed : 15.69 % Favored : 82.64 % 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: 2.97 (0.24), residues: 406 sheet: 0.49 (0.30), residues: 280 loop : 0.13 (0.30), residues: 439 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 0.010 0.001 PHE B 199 TYR 0.016 0.001 TYR R 392 ARG 0.007 0.000 ARG B 219 ********************** 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 : 1.014 Fit side-chains REVERT: A 207 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6732 (tp30) REVERT: A 240 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6738 (tpp) REVERT: A 248 LYS cc_start: 0.8769 (mttt) cc_final: 0.8452 (mtpp) REVERT: A 255 ASN cc_start: 0.8733 (m-40) cc_final: 0.8434 (m-40) REVERT: B 19 ARG cc_start: 0.8194 (ttp80) cc_final: 0.7706 (ttm-80) REVERT: B 170 ASP cc_start: 0.8919 (t70) cc_final: 0.8655 (t70) REVERT: E 86 ARG cc_start: 0.7455 (mtt180) cc_final: 0.7238 (mtt90) REVERT: E 160 ARG cc_start: 0.7549 (ttp-110) cc_final: 0.6933 (ttm110) REVERT: E 218 ARG cc_start: 0.7960 (mpp-170) cc_final: 0.7737 (mpp80) REVERT: R 141 SER cc_start: 0.8990 (t) cc_final: 0.8665 (p) REVERT: R 176 TYR cc_start: 0.8079 (m-10) cc_final: 0.7748 (m-10) outliers start: 16 outliers final: 15 residues processed: 151 average time/residue: 1.4217 time to fit residues: 227.9124 Evaluate side-chains 151 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 278 ILE 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 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 18 LYS 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 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 12 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 331 ASN B 16 ASN B 35 ASN B 175 GLN R 145 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.149989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.101394 restraints weight = 10498.735| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.81 r_work: 0.2884 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9257 Z= 0.178 Angle : 0.515 9.277 12579 Z= 0.267 Chirality : 0.041 0.133 1435 Planarity : 0.004 0.051 1557 Dihedral : 4.852 46.933 1568 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.88 % Allowed : 16.00 % Favored : 82.11 % 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: 1.75 (0.25), residues: 1125 helix: 2.83 (0.24), residues: 412 sheet: 0.50 (0.30), residues: 279 loop : 0.01 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.007 0.001 HIS R 417 PHE 0.021 0.001 PHE R 193 TYR 0.011 0.001 TYR E 102 ARG 0.009 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8035.31 seconds wall clock time: 142 minutes 13.79 seconds (8533.79 seconds total)