Starting phenix.real_space_refine on Sun May 25 13:07:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jmh_36421/05_2025/8jmh_36421_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jmh_36421/05_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_36421/05_2025/8jmh_36421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jmh_36421/05_2025/8jmh_36421.map" model { file = "/net/cci-nas-00/data/ceres_data/8jmh_36421/05_2025/8jmh_36421_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jmh_36421/05_2025/8jmh_36421_neut_trim.cif" } resolution = 2.5 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= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.83, per 1000 atoms: 0.47 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: 7.31 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.10 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: 9.57 Time building geometry restraints manager: 8.56 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: 0.11 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.450 Extract box with map and model: 1.040 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 55.120 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.090 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:10.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.040 ------------------------------------------------------------------------------- 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 (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: 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 TRP 0.010 0.001 TRP D 355 HIS 0.001 0.000 HIS D 197 PHE 0.012 0.001 PHE C 64 TYR 0.011 0.001 TYR D 241 ARG 0.009 0.000 ARG D 211 Details of bonding type rmsd link_ALPHA1-2 : bond 0.06394 ( 4) link_ALPHA1-2 : angle 2.42325 ( 12) hydrogen bonds : bond 0.16203 ( 984) hydrogen bonds : angle 5.39975 ( 2916) covalent geometry : bond 0.00681 (13780) covalent geometry : angle 0.56975 (18704) *********************** 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 : 2.333 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 2.7144 time to fit residues: 525.6263 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 : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.110978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.081486 restraints weight = 46674.815| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.88 r_work: 0.2790 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.0674 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= 0.148 Angle : 0.536 11.302 18716 Z= 0.287 Chirality : 0.047 1.412 2176 Planarity : 0.004 0.041 2276 Dihedral : 5.431 29.211 1996 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.34 % Allowed : 11.21 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.64 (0.20), residues: 1620 helix: 2.48 (0.14), residues: 1228 sheet: None (None), residues: 0 loop : -0.69 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 355 HIS 0.002 0.001 HIS D 60 PHE 0.013 0.001 PHE B 64 TYR 0.012 0.001 TYR D 241 ARG 0.005 0.000 ARG D 211 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00109 ( 4) link_ALPHA1-2 : angle 1.62758 ( 12) hydrogen bonds : bond 0.05565 ( 984) hydrogen bonds : angle 4.29516 ( 2916) covalent geometry : bond 0.00298 (13780) covalent geometry : angle 0.53477 (18704) *********************** 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 189 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 184 time to evaluate : 2.286 Fit side-chains REVERT: A 94 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7175 (tptp) REVERT: B 94 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7179 (tptp) REVERT: C 94 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7182 (tptp) REVERT: D 180 ARG cc_start: 0.8078 (tpp-160) cc_final: 0.7820 (tpp-160) outliers start: 5 outliers final: 0 residues processed: 185 average time/residue: 3.0019 time to fit residues: 604.3800 Evaluate side-chains 179 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 176 time to evaluate : 2.083 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 123 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.110792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.081206 restraints weight = 47029.427| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.89 r_work: 0.2780 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.0895 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= 0.162 Angle : 0.506 11.274 18716 Z= 0.271 Chirality : 0.047 1.403 2176 Planarity : 0.003 0.047 2276 Dihedral : 4.182 17.806 1996 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.48 % Allowed : 11.62 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.81 (0.20), residues: 1620 helix: 2.66 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : -0.58 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 355 HIS 0.002 0.001 HIS A 60 PHE 0.013 0.001 PHE A 64 TYR 0.011 0.001 TYR B 241 ARG 0.005 0.000 ARG D 211 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00038 ( 4) link_ALPHA1-2 : angle 1.25696 ( 12) hydrogen bonds : bond 0.05092 ( 984) hydrogen bonds : angle 4.07949 ( 2916) covalent geometry : bond 0.00351 (13780) covalent geometry : angle 0.50507 (18704) *********************** 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 186 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 179 time to evaluate : 2.129 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7122 (tptt) REVERT: B 94 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7130 (tptt) REVERT: C 94 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7128 (tptt) REVERT: D 180 ARG cc_start: 0.7972 (tpp-160) cc_final: 0.7709 (tpp-160) outliers start: 7 outliers final: 0 residues processed: 183 average time/residue: 2.9224 time to fit residues: 582.7588 Evaluate side-chains 179 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 176 time to evaluate : 2.038 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 153 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 37 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 = 0.3360 r_free = 0.3360 target = 0.110204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.080492 restraints weight = 47315.966| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.89 r_work: 0.2767 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13784 Z= 0.189 Angle : 0.517 11.296 18716 Z= 0.277 Chirality : 0.047 1.406 2176 Planarity : 0.003 0.049 2276 Dihedral : 3.961 14.463 1996 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.27 % Allowed : 12.70 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.75 (0.20), residues: 1620 helix: 2.63 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : -0.65 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 355 HIS 0.002 0.001 HIS D 197 PHE 0.014 0.001 PHE D 66 TYR 0.012 0.002 TYR B 241 ARG 0.005 0.000 ARG D 211 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00047 ( 4) link_ALPHA1-2 : angle 1.17843 ( 12) hydrogen bonds : bond 0.04969 ( 984) hydrogen bonds : angle 4.01516 ( 2916) covalent geometry : bond 0.00415 (13780) covalent geometry : angle 0.51671 (18704) *********************** 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 186 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 182 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 180 ARG cc_start: 0.8000 (tpp-160) cc_final: 0.7703 (tpp80) outliers start: 4 outliers final: 0 residues processed: 186 average time/residue: 2.9873 time to fit residues: 604.6041 Evaluate side-chains 179 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 129 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.109630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.079914 restraints weight = 47154.997| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.89 r_work: 0.2758 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13784 Z= 0.219 Angle : 0.523 11.300 18716 Z= 0.283 Chirality : 0.048 1.405 2176 Planarity : 0.004 0.054 2276 Dihedral : 3.945 14.053 1996 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.61 % Allowed : 12.70 % 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 (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: 2.69 (0.20), residues: 1620 helix: 2.59 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : -0.71 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 355 HIS 0.003 0.001 HIS D 197 PHE 0.015 0.001 PHE D 66 TYR 0.012 0.002 TYR B 241 ARG 0.007 0.000 ARG B 211 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00024 ( 4) link_ALPHA1-2 : angle 1.16864 ( 12) hydrogen bonds : bond 0.05040 ( 984) hydrogen bonds : angle 4.00123 ( 2916) covalent geometry : bond 0.00491 (13780) covalent geometry : angle 0.52272 (18704) *********************** 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 186 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 177 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.8048 (tpp80) cc_final: 0.7730 (tpp80) REVERT: B 94 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7125 (tptt) REVERT: B 180 ARG cc_start: 0.8049 (tpp80) cc_final: 0.7730 (tpp80) REVERT: C 94 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.7113 (tptt) REVERT: D 180 ARG cc_start: 0.8030 (tpp-160) cc_final: 0.7738 (tpp80) outliers start: 9 outliers final: 3 residues processed: 184 average time/residue: 3.0118 time to fit residues: 605.7070 Evaluate side-chains 181 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain C residue 94 LYS 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 6 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3353 r_free = 0.3353 target = 0.109842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.079921 restraints weight = 47331.232| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.90 r_work: 0.2757 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13784 Z= 0.206 Angle : 0.524 11.295 18716 Z= 0.281 Chirality : 0.048 1.404 2176 Planarity : 0.004 0.057 2276 Dihedral : 3.912 14.152 1996 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.82 % Allowed : 12.57 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.67 (0.20), residues: 1620 helix: 2.57 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.74 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 355 HIS 0.002 0.001 HIS D 197 PHE 0.014 0.001 PHE D 66 TYR 0.012 0.002 TYR B 241 ARG 0.007 0.000 ARG D 211 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00030 ( 4) link_ALPHA1-2 : angle 1.15106 ( 12) hydrogen bonds : bond 0.04960 ( 984) hydrogen bonds : angle 3.98115 ( 2916) covalent geometry : bond 0.00459 (13780) covalent geometry : angle 0.52328 (18704) *********************** 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 187 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7104 (tptt) REVERT: D 180 ARG cc_start: 0.8016 (tpp-160) cc_final: 0.7724 (tpp80) outliers start: 12 outliers final: 3 residues processed: 182 average time/residue: 3.0452 time to fit residues: 603.1889 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 : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LYS 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 42 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3358 r_free = 0.3358 target = 0.110207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.080452 restraints weight = 47177.096| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.89 r_work: 0.2767 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13784 Z= 0.176 Angle : 0.507 11.265 18716 Z= 0.273 Chirality : 0.047 1.399 2176 Planarity : 0.004 0.061 2276 Dihedral : 3.794 14.186 1996 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.54 % Allowed : 12.70 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.76 (0.20), residues: 1620 helix: 2.64 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.69 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 355 HIS 0.002 0.001 HIS D 197 PHE 0.013 0.001 PHE D 66 TYR 0.012 0.001 TYR B 241 ARG 0.009 0.000 ARG B 211 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00059 ( 4) link_ALPHA1-2 : angle 1.07572 ( 12) hydrogen bonds : bond 0.04813 ( 984) hydrogen bonds : angle 3.94850 ( 2916) covalent geometry : bond 0.00387 (13780) covalent geometry : angle 0.50635 (18704) *********************** 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 180 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 180 ARG cc_start: 0.8044 (tpp-160) cc_final: 0.7758 (tpp80) outliers start: 8 outliers final: 4 residues processed: 180 average time/residue: 3.1171 time to fit residues: 608.1281 Evaluate side-chains 177 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 173 time to evaluate : 2.235 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.0770 chunk 96 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.1344 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.110916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.081208 restraints weight = 47103.249| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.89 r_work: 0.2779 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1279 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= 0.142 Angle : 0.491 11.256 18716 Z= 0.264 Chirality : 0.046 1.395 2176 Planarity : 0.004 0.063 2276 Dihedral : 3.703 14.231 1996 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.41 % Allowed : 12.91 % 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 (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: 2.88 (0.20), residues: 1620 helix: 2.72 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.63 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 355 HIS 0.005 0.001 HIS D 290 PHE 0.012 0.001 PHE D 64 TYR 0.013 0.001 TYR B 241 ARG 0.009 0.000 ARG C 211 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00135 ( 4) link_ALPHA1-2 : angle 0.99273 ( 12) hydrogen bonds : bond 0.04635 ( 984) hydrogen bonds : angle 3.91031 ( 2916) covalent geometry : bond 0.00302 (13780) covalent geometry : angle 0.49027 (18704) *********************** 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 180 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 174 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 180 ARG cc_start: 0.8023 (tpp-160) cc_final: 0.7738 (tpp80) outliers start: 6 outliers final: 5 residues processed: 180 average time/residue: 3.1754 time to fit residues: 624.1690 Evaluate side-chains 178 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 173 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 215 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 21 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 123 optimal weight: 0.0000 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.111263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.081489 restraints weight = 47373.956| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.90 r_work: 0.2789 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1355 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 : 0.502 11.238 18716 Z= 0.265 Chirality : 0.046 1.393 2176 Planarity : 0.004 0.067 2276 Dihedral : 3.648 14.246 1996 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.68 % Allowed : 12.98 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 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 TRP 0.011 0.001 TRP D 355 HIS 0.003 0.001 HIS D 290 PHE 0.012 0.001 PHE D 64 TYR 0.012 0.001 TYR D 241 ARG 0.009 0.000 ARG A 211 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00142 ( 4) link_ALPHA1-2 : angle 0.95640 ( 12) hydrogen bonds : bond 0.04577 ( 984) hydrogen bonds : angle 3.88122 ( 2916) covalent geometry : bond 0.00293 (13780) covalent geometry : angle 0.50183 (18704) *********************** 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 190 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7407 (mm-30) REVERT: D 180 ARG cc_start: 0.7995 (tpp-160) cc_final: 0.7714 (tpp80) outliers start: 10 outliers final: 6 residues processed: 187 average time/residue: 3.1395 time to fit residues: 637.4229 Evaluate side-chains 181 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 329 ASN 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 150 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.110767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.081048 restraints weight = 47395.759| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.89 r_work: 0.2778 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1357 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= 0.165 Angle : 0.499 11.254 18716 Z= 0.268 Chirality : 0.047 1.397 2176 Planarity : 0.004 0.068 2276 Dihedral : 3.681 14.206 1996 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.41 % Allowed : 13.25 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.91 (0.20), residues: 1620 helix: 2.74 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.62 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 355 HIS 0.002 0.001 HIS D 197 PHE 0.013 0.001 PHE D 66 TYR 0.012 0.001 TYR B 241 ARG 0.008 0.000 ARG D 211 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00123 ( 4) link_ALPHA1-2 : angle 1.00361 ( 12) hydrogen bonds : bond 0.04666 ( 984) hydrogen bonds : angle 3.88621 ( 2916) covalent geometry : bond 0.00358 (13780) covalent geometry : angle 0.49894 (18704) ********************** 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 180 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 174 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 94 LYS cc_start: 0.7647 (tptp) cc_final: 0.7394 (tptt) REVERT: D 180 ARG cc_start: 0.8006 (tpp-160) cc_final: 0.7714 (tpp80) outliers start: 6 outliers final: 4 residues processed: 180 average time/residue: 3.0773 time to fit residues: 601.1015 Evaluate side-chains 175 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 171 time to evaluate : 1.991 ------------------------------------------------------------------------------- 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 157 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 154 optimal weight: 0.0050 chunk 21 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 74 optimal weight: 0.1980 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.112292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.082673 restraints weight = 47337.854| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.89 r_work: 0.2802 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13784 Z= 0.111 Angle : 0.497 11.212 18716 Z= 0.260 Chirality : 0.046 1.389 2176 Planarity : 0.004 0.069 2276 Dihedral : 3.585 14.234 1996 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.27 % Allowed : 13.65 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 3.06 (0.21), residues: 1620 helix: 2.85 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.57 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 355 HIS 0.001 0.000 HIS D 60 PHE 0.011 0.001 PHE A 64 TYR 0.012 0.001 TYR B 241 ARG 0.009 0.000 ARG A 211 Details of bonding type rmsd link_ALPHA1-2 : bond 0.00178 ( 4) link_ALPHA1-2 : angle 0.88928 ( 12) hydrogen bonds : bond 0.04386 ( 984) hydrogen bonds : angle 3.83921 ( 2916) covalent geometry : bond 0.00223 (13780) covalent geometry : angle 0.49618 (18704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17769.45 seconds wall clock time: 304 minutes 44.92 seconds (18284.92 seconds total)