Starting phenix.real_space_refine on Mon Aug 25 09:22:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jmh_36421/08_2025/8jmh_36421_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jmh_36421/08_2025/8jmh_36421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jmh_36421/08_2025/8jmh_36421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jmh_36421/08_2025/8jmh_36421.map" model { file = "/net/cci-nas-00/data/ceres_data/8jmh_36421/08_2025/8jmh_36421_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jmh_36421/08_2025/8jmh_36421_neut_trim.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 96 5.16 5 C 8872 2.51 5 N 2212 2.21 5 O 2264 1.98 5 H 13812 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27256 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "B" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "C" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "D" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'FRU': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'FRU': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'FRU': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'FRU': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.16, per 1000 atoms: 0.15 Number of scatterers: 27256 At special positions: 0 Unit cell: (116.25, 116.25, 101.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 O 2264 8.00 N 2212 7.00 C 8872 6.00 H 13812 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Links applied ALPHA1-2 " GLC E 1 " - " FRU E 2 " ~> Even though FRU is a beta isomer, an alpha linkage is required... " GLC F 1 " - " FRU F 2 " " GLC G 1 " - " FRU G 2 " " GLC H 1 " - " FRU H 2 " Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 606.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3136 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 58 through 73 Proline residue: A 65 - end of helix removed outlier: 3.858A pdb=" N VAL A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 95 through 123 Processing helix chain 'A' and resid 128 through 164 removed outlier: 3.927A pdb=" N LEU A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 177 through 214 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 242 through 287 removed outlier: 4.551A pdb=" N ASP A 264 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 319 removed outlier: 3.592A pdb=" N PHE A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 339 Processing helix chain 'A' and resid 347 through 382 removed outlier: 4.137A pdb=" N ILE A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'A' and resid 421 through 443 removed outlier: 4.085A pdb=" N GLN A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE A 442 " --> pdb=" O VAL A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 removed outlier: 3.843A pdb=" N GLY A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 73 Proline residue: B 65 - end of helix removed outlier: 3.856A pdb=" N VAL B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'B' and resid 95 through 123 Processing helix chain 'B' and resid 128 through 164 removed outlier: 3.927A pdb=" N LEU B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 177 through 214 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 242 through 287 removed outlier: 4.557A pdb=" N ASP B 264 " --> pdb=" O TRP B 260 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 319 removed outlier: 3.591A pdb=" N PHE B 298 " --> pdb=" O CYS B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 339 Processing helix chain 'B' and resid 347 through 382 removed outlier: 4.135A pdb=" N ILE B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 387 Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'B' and resid 421 through 443 removed outlier: 4.081A pdb=" N GLN B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 450 removed outlier: 3.842A pdb=" N GLY B 450 " --> pdb=" O ASN B 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 73 Proline residue: C 65 - end of helix removed outlier: 3.852A pdb=" N VAL C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 95 through 123 Processing helix chain 'C' and resid 128 through 164 removed outlier: 4.022A pdb=" N LEU C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Proline residue: C 153 - end of helix Processing helix chain 'C' and resid 165 through 168 Processing helix chain 'C' and resid 177 through 214 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 242 through 287 removed outlier: 4.554A pdb=" N ASP C 264 " --> pdb=" O TRP C 260 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 319 removed outlier: 3.590A pdb=" N PHE C 298 " --> pdb=" O CYS C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 339 Processing helix chain 'C' and resid 347 through 382 removed outlier: 4.132A pdb=" N ILE C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 387 Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'C' and resid 421 through 443 removed outlier: 4.064A pdb=" N GLN C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE C 442 " --> pdb=" O VAL C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 450 removed outlier: 3.843A pdb=" N GLY C 450 " --> pdb=" O ASN C 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 73 Proline residue: D 65 - end of helix removed outlier: 3.729A pdb=" N VAL D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'D' and resid 95 through 123 Processing helix chain 'D' and resid 128 through 164 removed outlier: 4.137A pdb=" N LEU D 132 " --> pdb=" O ASN D 128 " (cutoff:3.500A) Proline residue: D 153 - end of helix Processing helix chain 'D' and resid 165 through 168 Processing helix chain 'D' and resid 177 through 214 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 242 through 287 removed outlier: 4.342A pdb=" N ASP D 264 " --> pdb=" O TRP D 260 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 339 removed outlier: 3.536A pdb=" N PHE D 298 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N SER D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 387 removed outlier: 4.015A pdb=" N ILE D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL D 385 " --> pdb=" O ARG D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'D' and resid 421 through 440 Processing helix chain 'D' and resid 443 through 450 removed outlier: 3.734A pdb=" N GLY D 450 " --> pdb=" O ASN D 446 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2916 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: 5.45 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13772 1.03 - 1.23: 40 1.23 - 1.42: 5796 1.42 - 1.61: 7828 1.61 - 1.81: 156 Bond restraints: 27592 Sorted by residual: bond pdb=" C4 FRU G 2 " pdb=" C5 FRU G 2 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C4 FRU E 2 " pdb=" C5 FRU E 2 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C4 FRU F 2 " pdb=" C5 FRU F 2 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C4 FRU H 2 " pdb=" C5 FRU H 2 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C5 FRU F 2 " pdb=" O5 FRU F 2 " ideal model delta sigma weight residual 1.420 1.619 -0.199 2.00e-02 2.50e+03 9.94e+01 ... (remaining 27587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.41: 49804 5.41 - 10.81: 20 10.81 - 16.22: 1 16.22 - 21.62: 0 21.62 - 27.03: 3 Bond angle restraints: 49828 Sorted by residual: angle pdb=" CG2 THR A 54 " pdb=" CB THR A 54 " pdb=" HB THR A 54 " ideal model delta sigma weight residual 108.00 80.97 27.03 3.00e+00 1.11e-01 8.12e+01 angle pdb=" OG1 THR A 54 " pdb=" CB THR A 54 " pdb=" HB THR A 54 " ideal model delta sigma weight residual 109.00 82.70 26.30 3.00e+00 1.11e-01 7.69e+01 angle pdb=" CA THR A 54 " pdb=" CB THR A 54 " pdb=" HB THR A 54 " ideal model delta sigma weight residual 109.00 83.66 25.34 3.00e+00 1.11e-01 7.13e+01 angle pdb=" OG1 THR A 54 " pdb=" CB THR A 54 " pdb=" CG2 THR A 54 " ideal model delta sigma weight residual 109.30 120.58 -11.28 2.00e+00 2.50e-01 3.18e+01 angle pdb=" CA THR A 54 " pdb=" CB THR A 54 " pdb=" CG2 THR A 54 " ideal model delta sigma weight residual 110.50 118.56 -8.06 1.70e+00 3.46e-01 2.25e+01 ... (remaining 49823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.72: 11348 14.72 - 29.44: 1208 29.44 - 44.16: 354 44.16 - 58.89: 153 58.89 - 73.61: 25 Dihedral angle restraints: 13088 sinusoidal: 7084 harmonic: 6004 Sorted by residual: dihedral pdb=" CG LYS D 449 " pdb=" CD LYS D 449 " pdb=" CE LYS D 449 " pdb=" NZ LYS D 449 " ideal model delta sinusoidal sigma weight residual -180.00 -122.72 -57.28 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CG LYS B 449 " pdb=" CD LYS B 449 " pdb=" CE LYS B 449 " pdb=" NZ LYS B 449 " ideal model delta sinusoidal sigma weight residual -180.00 -123.57 -56.43 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CG LYS A 449 " pdb=" CD LYS A 449 " pdb=" CE LYS A 449 " pdb=" NZ LYS A 449 " ideal model delta sinusoidal sigma weight residual -180.00 -123.57 -56.43 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 13085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.280: 2175 0.280 - 0.559: 0 0.559 - 0.839: 0 0.839 - 1.118: 0 1.118 - 1.398: 1 Chirality restraints: 2176 Sorted by residual: chirality pdb=" CB THR A 54 " pdb=" CA THR A 54 " pdb=" OG1 THR A 54 " pdb=" CG2 THR A 54 " both_signs ideal model delta sigma weight residual False 2.55 1.15 1.40 2.00e-01 2.50e+01 4.89e+01 chirality pdb=" C1 GLC E 1 " pdb=" C2 GLC E 1 " pdb=" O5 GLC E 1 " pdb=" O2 FRU E 2 " both_signs ideal model delta sigma weight residual False 2.40 2.34 0.06 2.00e-02 2.50e+03 9.66e+00 chirality pdb=" C1 GLC F 1 " pdb=" C2 GLC F 1 " pdb=" O5 GLC F 1 " pdb=" O2 FRU F 2 " both_signs ideal model delta sigma weight residual False 2.40 2.34 0.06 2.00e-02 2.50e+03 8.51e+00 ... (remaining 2173 not shown) Planarity restraints: 3836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 211 " -0.181 9.50e-02 1.11e+02 6.05e-02 4.26e+00 pdb=" NE ARG D 211 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG D 211 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 211 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D 211 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG D 211 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG D 211 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 211 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG D 211 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 164 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO D 165 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 165 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 165 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 164 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO B 165 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 165 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 165 " 0.016 5.00e-02 4.00e+02 ... (remaining 3833 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1846 2.21 - 2.81: 58108 2.81 - 3.41: 79260 3.41 - 4.00: 102843 4.00 - 4.60: 159628 Nonbonded interactions: 401685 Sorted by model distance: nonbonded pdb=" O ILE D 249 " pdb="HD22 ASN D 253 " model vdw 1.615 2.450 nonbonded pdb=" OD2 ASP A 264 " pdb="HD21 ASN A 330 " model vdw 1.648 2.450 nonbonded pdb=" O PHE B 367 " pdb=" HG1 THR B 371 " model vdw 1.654 2.450 nonbonded pdb=" O PHE C 367 " pdb=" HG1 THR C 371 " model vdw 1.655 2.450 nonbonded pdb=" OD2 ASP C 264 " pdb="HD21 ASN C 330 " model vdw 1.656 2.450 ... (remaining 401680 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.090 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.200 Find NCS groups from input model: 0.360 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 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 : 0.007 0.227 13784 Z= 0.342 Angle : 0.573 11.277 18716 Z= 0.288 Chirality : 0.047 1.398 2176 Planarity : 0.003 0.080 2276 Dihedral : 15.006 73.607 5168 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.07 % Allowed : 11.41 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.05 (0.21), residues: 1620 helix: 2.80 (0.15), residues: 1172 sheet: None (None), residues: 0 loop : -0.13 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 211 TYR 0.011 0.001 TYR D 241 PHE 0.012 0.001 PHE C 64 TRP 0.010 0.001 TRP D 355 HIS 0.001 0.000 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00681 (13780) covalent geometry : angle 0.56975 (18704) hydrogen bonds : bond 0.16203 ( 984) hydrogen bonds : angle 5.39975 ( 2916) link_ALPHA1-2 : bond 0.06394 ( 4) link_ALPHA1-2 : angle 2.42325 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.804 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 1.2121 time to fit residues: 233.6766 Evaluate side-chains 175 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.080991 restraints weight = 46973.049| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.88 r_work: 0.2761 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13784 Z= 0.167 Angle : 0.547 11.308 18716 Z= 0.292 Chirality : 0.048 1.408 2176 Planarity : 0.004 0.041 2276 Dihedral : 5.436 28.547 1996 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.54 % Allowed : 11.21 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.74 (0.20), residues: 1620 helix: 2.58 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.54 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 211 TYR 0.012 0.001 TYR D 241 PHE 0.014 0.001 PHE C 64 TRP 0.009 0.001 TRP D 355 HIS 0.002 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00349 (13780) covalent geometry : angle 0.54541 (18704) hydrogen bonds : bond 0.05528 ( 984) hydrogen bonds : angle 4.28432 ( 2916) link_ALPHA1-2 : bond 0.00357 ( 4) link_ALPHA1-2 : angle 1.67325 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 0.758 Fit side-chains REVERT: A 94 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7101 (tptp) REVERT: B 94 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7102 (tptp) REVERT: C 94 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7122 (tptp) REVERT: D 180 ARG cc_start: 0.7994 (tpp-160) cc_final: 0.7727 (tpp-160) outliers start: 8 outliers final: 1 residues processed: 184 average time/residue: 1.5266 time to fit residues: 304.3964 Evaluate side-chains 182 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 178 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain D residue 329 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 130 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 0.0970 chunk 96 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.082515 restraints weight = 47037.774| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.89 r_work: 0.2802 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13784 Z= 0.126 Angle : 0.488 11.233 18716 Z= 0.262 Chirality : 0.046 1.399 2176 Planarity : 0.003 0.051 2276 Dihedral : 3.913 15.338 1996 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.41 % Allowed : 11.89 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.84 (0.20), residues: 1620 helix: 2.67 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.58 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 211 TYR 0.012 0.001 TYR D 241 PHE 0.012 0.001 PHE D 64 TRP 0.009 0.001 TRP A 355 HIS 0.002 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00255 (13780) covalent geometry : angle 0.48740 (18704) hydrogen bonds : bond 0.04859 ( 984) hydrogen bonds : angle 4.03215 ( 2916) link_ALPHA1-2 : bond 0.00043 ( 4) link_ALPHA1-2 : angle 1.18618 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: D 180 ARG cc_start: 0.7955 (tpp-160) cc_final: 0.7710 (tpp-160) outliers start: 6 outliers final: 3 residues processed: 195 average time/residue: 1.4383 time to fit residues: 304.8482 Evaluate side-chains 183 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 180 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain D residue 329 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 108 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 144 optimal weight: 0.1980 chunk 147 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.081322 restraints weight = 46996.703| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.88 r_work: 0.2786 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13784 Z= 0.171 Angle : 0.507 11.259 18716 Z= 0.271 Chirality : 0.047 1.400 2176 Planarity : 0.003 0.028 2276 Dihedral : 3.773 14.003 1996 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.20 % Allowed : 13.11 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.20), residues: 1620 helix: 2.72 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : -0.58 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 211 TYR 0.012 0.001 TYR B 241 PHE 0.013 0.001 PHE D 64 TRP 0.011 0.001 TRP A 355 HIS 0.002 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00370 (13780) covalent geometry : angle 0.50649 (18704) hydrogen bonds : bond 0.04831 ( 984) hydrogen bonds : angle 3.96421 ( 2916) link_ALPHA1-2 : bond 0.00044 ( 4) link_ALPHA1-2 : angle 1.11718 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 184 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 180 ARG cc_start: 0.7977 (tpp-160) cc_final: 0.7679 (tpp80) outliers start: 3 outliers final: 1 residues processed: 187 average time/residue: 1.5363 time to fit residues: 311.0618 Evaluate side-chains 180 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 215 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.081442 restraints weight = 47033.573| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.88 r_work: 0.2784 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13784 Z= 0.161 Angle : 0.494 11.273 18716 Z= 0.266 Chirality : 0.047 1.401 2176 Planarity : 0.004 0.051 2276 Dihedral : 3.707 14.172 1996 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.48 % Allowed : 12.84 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.20), residues: 1620 helix: 2.71 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.63 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 211 TYR 0.012 0.001 TYR B 241 PHE 0.013 0.001 PHE D 64 TRP 0.011 0.001 TRP A 355 HIS 0.002 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00348 (13780) covalent geometry : angle 0.49357 (18704) hydrogen bonds : bond 0.04759 ( 984) hydrogen bonds : angle 3.93001 ( 2916) link_ALPHA1-2 : bond 0.00073 ( 4) link_ALPHA1-2 : angle 1.04525 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 177 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.7990 (tpp80) cc_final: 0.7646 (tpp80) REVERT: D 94 LYS cc_start: 0.7631 (tptp) cc_final: 0.7287 (tptt) REVERT: D 180 ARG cc_start: 0.7982 (tpp-160) cc_final: 0.7687 (tpp80) outliers start: 7 outliers final: 3 residues processed: 184 average time/residue: 1.4457 time to fit residues: 288.5135 Evaluate side-chains 182 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 179 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain D residue 215 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 132 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.081145 restraints weight = 47016.490| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.89 r_work: 0.2782 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13784 Z= 0.169 Angle : 0.505 11.269 18716 Z= 0.269 Chirality : 0.047 1.401 2176 Planarity : 0.004 0.056 2276 Dihedral : 3.709 14.221 1996 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.34 % Allowed : 13.18 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.86 (0.20), residues: 1620 helix: 2.71 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.65 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 211 TYR 0.012 0.001 TYR B 241 PHE 0.013 0.001 PHE D 64 TRP 0.011 0.001 TRP A 355 HIS 0.002 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00369 (13780) covalent geometry : angle 0.50428 (18704) hydrogen bonds : bond 0.04752 ( 984) hydrogen bonds : angle 3.91673 ( 2916) link_ALPHA1-2 : bond 0.00043 ( 4) link_ALPHA1-2 : angle 1.03148 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 180 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.8035 (tpp80) cc_final: 0.7700 (tpp80) REVERT: D 94 LYS cc_start: 0.7668 (tptp) cc_final: 0.7411 (tptt) REVERT: D 180 ARG cc_start: 0.8003 (tpp-160) cc_final: 0.7709 (tpp80) outliers start: 5 outliers final: 4 residues processed: 185 average time/residue: 1.7112 time to fit residues: 342.0406 Evaluate side-chains 185 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 181 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 215 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.080553 restraints weight = 47133.782| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.89 r_work: 0.2772 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13784 Z= 0.192 Angle : 0.510 11.377 18716 Z= 0.276 Chirality : 0.048 1.447 2176 Planarity : 0.004 0.062 2276 Dihedral : 3.759 14.183 1996 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.34 % Allowed : 13.18 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.84 (0.20), residues: 1620 helix: 2.70 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.67 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 211 TYR 0.012 0.002 TYR B 241 PHE 0.014 0.001 PHE D 66 TRP 0.011 0.001 TRP B 355 HIS 0.002 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00425 (13780) covalent geometry : angle 0.50989 (18704) hydrogen bonds : bond 0.04842 ( 984) hydrogen bonds : angle 3.92160 ( 2916) link_ALPHA1-2 : bond 0.00063 ( 4) link_ALPHA1-2 : angle 1.07475 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 178 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 94 LYS cc_start: 0.7697 (tptp) cc_final: 0.7434 (tptt) REVERT: D 180 ARG cc_start: 0.8057 (tpp-160) cc_final: 0.7770 (tpp80) outliers start: 5 outliers final: 4 residues processed: 183 average time/residue: 1.6907 time to fit residues: 334.6265 Evaluate side-chains 182 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 178 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 215 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 159 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.081609 restraints weight = 47024.381| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.89 r_work: 0.2791 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13784 Z= 0.139 Angle : 0.502 11.263 18716 Z= 0.266 Chirality : 0.046 1.395 2176 Planarity : 0.004 0.064 2276 Dihedral : 3.667 14.204 1996 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.54 % Allowed : 13.18 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.94 (0.20), residues: 1620 helix: 2.77 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.64 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 211 TYR 0.012 0.001 TYR B 241 PHE 0.012 0.001 PHE B 64 TRP 0.011 0.001 TRP A 355 HIS 0.002 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00296 (13780) covalent geometry : angle 0.50129 (18704) hydrogen bonds : bond 0.04610 ( 984) hydrogen bonds : angle 3.88699 ( 2916) link_ALPHA1-2 : bond 0.00128 ( 4) link_ALPHA1-2 : angle 0.98418 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 184 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 94 LYS cc_start: 0.7669 (tptp) cc_final: 0.7405 (tptt) REVERT: D 180 ARG cc_start: 0.7980 (tpp-160) cc_final: 0.7695 (tpp80) REVERT: D 289 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7402 (mm-30) outliers start: 8 outliers final: 3 residues processed: 189 average time/residue: 1.6926 time to fit residues: 345.7932 Evaluate side-chains 183 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 180 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain C residue 215 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 15 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.081104 restraints weight = 47466.635| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.89 r_work: 0.2782 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13784 Z= 0.167 Angle : 0.500 11.263 18716 Z= 0.269 Chirality : 0.047 1.400 2176 Planarity : 0.004 0.072 2276 Dihedral : 3.678 14.172 1996 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.34 % Allowed : 13.18 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.92 (0.20), residues: 1620 helix: 2.76 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.66 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 211 TYR 0.012 0.001 TYR B 241 PHE 0.013 0.001 PHE D 64 TRP 0.011 0.001 TRP D 355 HIS 0.002 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00366 (13780) covalent geometry : angle 0.49924 (18704) hydrogen bonds : bond 0.04689 ( 984) hydrogen bonds : angle 3.88716 ( 2916) link_ALPHA1-2 : bond 0.00082 ( 4) link_ALPHA1-2 : angle 1.00528 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 175 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 94 LYS cc_start: 0.7677 (tptp) cc_final: 0.7405 (tptt) REVERT: D 180 ARG cc_start: 0.8007 (tpp-160) cc_final: 0.7718 (tpp80) outliers start: 5 outliers final: 4 residues processed: 180 average time/residue: 1.3825 time to fit residues: 270.1794 Evaluate side-chains 180 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 176 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 215 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.081150 restraints weight = 47295.759| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.89 r_work: 0.2783 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13784 Z= 0.164 Angle : 0.509 11.239 18716 Z= 0.270 Chirality : 0.047 1.392 2176 Planarity : 0.004 0.068 2276 Dihedral : 3.685 14.133 1996 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.27 % Allowed : 13.59 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.92 (0.20), residues: 1620 helix: 2.75 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.63 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 211 TYR 0.012 0.001 TYR B 241 PHE 0.012 0.001 PHE D 64 TRP 0.011 0.001 TRP D 355 HIS 0.002 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00357 (13780) covalent geometry : angle 0.50870 (18704) hydrogen bonds : bond 0.04677 ( 984) hydrogen bonds : angle 3.87974 ( 2916) link_ALPHA1-2 : bond 0.00103 ( 4) link_ALPHA1-2 : angle 1.00855 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 178 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 94 LYS cc_start: 0.7642 (tptp) cc_final: 0.7390 (tptt) REVERT: D 180 ARG cc_start: 0.8009 (tpp-160) cc_final: 0.7712 (tpp80) outliers start: 4 outliers final: 4 residues processed: 182 average time/residue: 1.4638 time to fit residues: 288.6376 Evaluate side-chains 180 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 176 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 215 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 154 optimal weight: 0.0870 chunk 150 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.111488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.081816 restraints weight = 47220.136| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.89 r_work: 0.2787 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13784 Z= 0.138 Angle : 0.489 11.209 18716 Z= 0.262 Chirality : 0.046 1.388 2176 Planarity : 0.004 0.068 2276 Dihedral : 3.619 14.106 1996 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.20 % Allowed : 13.52 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.99 (0.20), residues: 1620 helix: 2.80 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.61 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 211 TYR 0.012 0.001 TYR B 241 PHE 0.012 0.001 PHE D 64 TRP 0.011 0.001 TRP D 355 HIS 0.002 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00291 (13780) covalent geometry : angle 0.48835 (18704) hydrogen bonds : bond 0.04539 ( 984) hydrogen bonds : angle 3.85469 ( 2916) link_ALPHA1-2 : bond 0.00156 ( 4) link_ALPHA1-2 : angle 0.97134 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8646.95 seconds wall clock time: 147 minutes 16.56 seconds (8836.56 seconds total)