Starting phenix.real_space_refine on Sat Sep 12 17:30:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ru0_24692/09_2026/7ru0_24692.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru0_24692/09_2026/7ru0_24692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ru0_24692/09_2026/7ru0_24692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru0_24692/09_2026/7ru0_24692.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ru0_24692/09_2026/7ru0_24692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru0_24692/09_2026/7ru0_24692.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ru0_24692/09_2026/7ru0_24692.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ru0_24692/09_2026/7ru0_24692.cif" } resolution = 4.3 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6008 atoms to isotropic. 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 P 4 5.49 5 S 28 5.16 5 C 8044 2.51 5 N 2040 2.21 5 O 2168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12284 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3049 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 2 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 2.32, per 1000 atoms: 0.19 Number of scatterers: 12284 At special positions: 0 Unit cell: (111.282, 110.191, 113.464, 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 28 16.00 P 4 15.00 O 2168 8.00 N 2040 7.00 C 8044 6.00 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 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 420.4 milliseconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2912 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 59.6% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 11 through 36 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 43 through 56 removed outlier: 3.568A pdb=" N ALA A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 removed outlier: 3.574A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 removed outlier: 4.256A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU A 107 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 122 removed outlier: 4.167A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 158 removed outlier: 3.639A pdb=" N GLY A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 223 removed outlier: 3.551A pdb=" N SER A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 246 removed outlier: 3.502A pdb=" N GLU A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 307 through 314 removed outlier: 3.731A pdb=" N ILE A 314 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.658A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 removed outlier: 4.029A pdb=" N LEU A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 43 through 56 removed outlier: 3.568A pdb=" N ALA B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 removed outlier: 3.574A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 112 removed outlier: 4.256A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU B 107 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 110 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 122 removed outlier: 4.168A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 158 removed outlier: 3.640A pdb=" N GLY B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE B 143 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 223 removed outlier: 3.551A pdb=" N SER B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 246 removed outlier: 3.502A pdb=" N GLU B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 307 through 314 removed outlier: 3.730A pdb=" N ILE B 314 " --> pdb=" O ILE B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.658A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 removed outlier: 4.029A pdb=" N LEU B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 43 through 56 removed outlier: 3.569A pdb=" N ALA C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.574A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 112 removed outlier: 4.256A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU C 107 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 110 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 122 removed outlier: 4.168A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 158 removed outlier: 3.639A pdb=" N GLY C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE C 143 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 223 removed outlier: 3.551A pdb=" N SER C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 246 removed outlier: 3.502A pdb=" N GLU C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 256 through 266 Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 307 through 314 removed outlier: 3.731A pdb=" N ILE C 314 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 402 removed outlier: 3.658A pdb=" N SER C 402 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 417 removed outlier: 4.028A pdb=" N LEU C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 43 through 56 removed outlier: 3.568A pdb=" N ALA D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 89 removed outlier: 3.574A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 removed outlier: 4.256A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU D 107 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 110 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 122 removed outlier: 4.168A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 158 removed outlier: 3.640A pdb=" N GLY D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE D 143 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU D 158 " --> pdb=" O GLY D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 223 removed outlier: 3.550A pdb=" N SER D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 246 removed outlier: 3.502A pdb=" N GLU D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 256 through 266 Processing helix chain 'D' and resid 272 through 277 Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 307 through 314 removed outlier: 3.730A pdb=" N ILE D 314 " --> pdb=" O ILE D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 402 removed outlier: 3.658A pdb=" N SER D 402 " --> pdb=" O ASP D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 417 removed outlier: 4.029A pdb=" N LEU D 414 " --> pdb=" O GLN D 410 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 319 through 322 removed outlier: 8.525A pdb=" N ASP A 388 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN A 342 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 340 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 348 Processing sheet with id=AA3, first strand: chain 'B' and resid 319 through 322 removed outlier: 8.525A pdb=" N ASP B 388 " --> pdb=" O ASN B 342 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN B 342 " --> pdb=" O ASP B 388 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE B 340 " --> pdb=" O TYR B 390 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 346 through 348 Processing sheet with id=AA5, first strand: chain 'C' and resid 319 through 322 removed outlier: 8.524A pdb=" N ASP C 388 " --> pdb=" O ASN C 342 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN C 342 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE C 340 " --> pdb=" O TYR C 390 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 346 through 348 Processing sheet with id=AA7, first strand: chain 'D' and resid 319 through 322 removed outlier: 8.525A pdb=" N ASP D 388 " --> pdb=" O ASN D 342 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN D 342 " --> pdb=" O ASP D 388 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE D 340 " --> pdb=" O TYR D 390 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 346 through 348 632 hydrogen bonds defined for protein. 1788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3718 1.34 - 1.46: 1954 1.46 - 1.57: 6840 1.57 - 1.69: 8 1.69 - 1.81: 48 Bond restraints: 12568 Sorted by residual: bond pdb=" C SER B 157 " pdb=" N LEU B 158 " ideal model delta sigma weight residual 1.332 1.223 0.109 1.31e-02 5.83e+03 6.91e+01 bond pdb=" C SER A 157 " pdb=" N LEU A 158 " ideal model delta sigma weight residual 1.332 1.223 0.109 1.31e-02 5.83e+03 6.86e+01 bond pdb=" C SER D 157 " pdb=" N LEU D 158 " ideal model delta sigma weight residual 1.332 1.223 0.108 1.31e-02 5.83e+03 6.83e+01 bond pdb=" C SER C 157 " pdb=" N LEU C 158 " ideal model delta sigma weight residual 1.332 1.224 0.108 1.31e-02 5.83e+03 6.78e+01 bond pdb=" C LEU C 283 " pdb=" N ARG C 284 " ideal model delta sigma weight residual 1.335 1.243 0.092 1.38e-02 5.25e+03 4.44e+01 ... (remaining 12563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 16093 2.02 - 4.03: 790 4.03 - 6.05: 117 6.05 - 8.07: 88 8.07 - 10.08: 52 Bond angle restraints: 17140 Sorted by residual: angle pdb=" O SER C 157 " pdb=" C SER C 157 " pdb=" N LEU C 158 " ideal model delta sigma weight residual 122.07 115.71 6.36 1.03e+00 9.43e-01 3.82e+01 angle pdb=" O SER B 157 " pdb=" C SER B 157 " pdb=" N LEU B 158 " ideal model delta sigma weight residual 122.07 115.71 6.36 1.03e+00 9.43e-01 3.82e+01 angle pdb=" O SER A 157 " pdb=" C SER A 157 " pdb=" N LEU A 158 " ideal model delta sigma weight residual 122.07 115.71 6.36 1.03e+00 9.43e-01 3.81e+01 angle pdb=" O SER D 157 " pdb=" C SER D 157 " pdb=" N LEU D 158 " ideal model delta sigma weight residual 122.07 115.71 6.36 1.03e+00 9.43e-01 3.81e+01 angle pdb=" N ARG B 284 " pdb=" CA ARG B 284 " pdb=" C ARG B 284 " ideal model delta sigma weight residual 111.82 105.17 6.65 1.16e+00 7.43e-01 3.29e+01 ... (remaining 17135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 7124 24.08 - 48.16: 392 48.16 - 72.24: 20 72.24 - 96.32: 8 96.32 - 120.39: 8 Dihedral angle restraints: 7552 sinusoidal: 3044 harmonic: 4508 Sorted by residual: dihedral pdb=" C5' CMP C 501 " pdb=" O5' CMP C 501 " pdb=" P CMP C 501 " pdb=" O1P CMP C 501 " ideal model delta sinusoidal sigma weight residual 60.00 -179.61 -120.39 1 2.00e+01 2.50e-03 3.61e+01 dihedral pdb=" C5' CMP D 501 " pdb=" O5' CMP D 501 " pdb=" P CMP D 501 " pdb=" O1P CMP D 501 " ideal model delta sinusoidal sigma weight residual 60.00 -179.63 -120.37 1 2.00e+01 2.50e-03 3.61e+01 dihedral pdb=" C5' CMP A 501 " pdb=" O5' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual 60.00 -179.63 -120.37 1 2.00e+01 2.50e-03 3.61e+01 ... (remaining 7549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1492 0.059 - 0.118: 448 0.118 - 0.177: 101 0.177 - 0.236: 3 0.236 - 0.295: 8 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA LYS D 298 " pdb=" N LYS D 298 " pdb=" C LYS D 298 " pdb=" CB LYS D 298 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA LYS B 298 " pdb=" N LYS B 298 " pdb=" C LYS B 298 " pdb=" CB LYS B 298 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA LYS C 298 " pdb=" N LYS C 298 " pdb=" C LYS C 298 " pdb=" CB LYS C 298 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 2049 not shown) Planarity restraints: 2100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 232 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C HIS A 232 " -0.055 2.00e-02 2.50e+03 pdb=" O HIS A 232 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 233 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 232 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C HIS C 232 " 0.055 2.00e-02 2.50e+03 pdb=" O HIS C 232 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG C 233 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 232 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.93e+00 pdb=" C HIS D 232 " 0.055 2.00e-02 2.50e+03 pdb=" O HIS D 232 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG D 233 " -0.018 2.00e-02 2.50e+03 ... (remaining 2097 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 386 2.70 - 3.25: 12358 3.25 - 3.80: 19248 3.80 - 4.35: 23937 4.35 - 4.90: 37952 Nonbonded interactions: 93881 Sorted by model distance: nonbonded pdb=" O LEU B 158 " pdb=" CD1 LEU B 158 " model vdw 2.146 3.460 nonbonded pdb=" O LEU C 158 " pdb=" CD1 LEU C 158 " model vdw 2.147 3.460 nonbonded pdb=" O LEU D 158 " pdb=" CD1 LEU D 158 " model vdw 2.147 3.460 nonbonded pdb=" O LEU A 158 " pdb=" CD1 LEU A 158 " model vdw 2.148 3.460 nonbonded pdb=" O GLY C 293 " pdb=" NZ LYS C 298 " model vdw 2.202 3.120 ... (remaining 93876 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.470 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4843 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 : 0.005 0.109 12568 Z= 0.313 Angle : 1.145 10.082 17140 Z= 0.579 Chirality : 0.059 0.295 2052 Planarity : 0.007 0.049 2100 Dihedral : 14.180 120.394 4640 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -3.06 (0.20), residues: 1512 helix: -1.65 (0.15), residues: 908 sheet: -0.84 (0.58), residues: 88 loop : -2.70 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 391 TYR 0.023 0.002 TYR A 404 PHE 0.016 0.002 PHE C 309 TRP 0.013 0.002 TRP C 264 HIS 0.024 0.003 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.31 (12568) covalent geometry : angle 1.14486 / 0.58 (17140) hydrogen bonds : bond 0.16374 / 10.81 ( 632) hydrogen bonds : angle 6.53623 / 4.66 ( 1788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8709 (mt) cc_final: 0.7996 (mt) REVERT: A 104 LEU cc_start: 0.7719 (pp) cc_final: 0.6954 (mm) REVERT: A 224 LYS cc_start: 0.1293 (tmtt) cc_final: 0.0869 (ttmt) REVERT: A 235 ARG cc_start: 0.6404 (mtp180) cc_final: 0.5637 (mmt180) REVERT: A 261 ASP cc_start: 0.7496 (m-30) cc_final: 0.7021 (m-30) REVERT: A 353 GLU cc_start: 0.8267 (tp30) cc_final: 0.8042 (tm-30) REVERT: A 390 TYR cc_start: 0.6292 (m-80) cc_final: 0.5534 (m-80) REVERT: B 40 PHE cc_start: 0.7031 (t80) cc_final: 0.6792 (t80) REVERT: B 100 LEU cc_start: 0.8651 (mt) cc_final: 0.8304 (mt) REVERT: B 312 ASP cc_start: 0.6036 (m-30) cc_final: 0.5721 (p0) REVERT: B 313 ILE cc_start: 0.6768 (pt) cc_final: 0.6559 (pt) REVERT: B 329 ILE cc_start: 0.5495 (pt) cc_final: 0.5118 (pt) REVERT: B 339 TYR cc_start: 0.4402 (m-10) cc_final: 0.3798 (m-80) REVERT: B 414 LEU cc_start: 0.6641 (tt) cc_final: 0.6232 (mm) REVERT: C 29 ARG cc_start: 0.6152 (tmt170) cc_final: 0.4951 (mpt180) REVERT: C 39 LEU cc_start: 0.7503 (mm) cc_final: 0.7277 (mp) REVERT: C 81 ARG cc_start: 0.0610 (ptt180) cc_final: 0.0184 (ptt180) REVERT: C 261 ASP cc_start: 0.7545 (m-30) cc_final: 0.6868 (m-30) REVERT: C 390 TYR cc_start: 0.5832 (m-80) cc_final: 0.5351 (m-80) REVERT: D 29 ARG cc_start: 0.6304 (tmt170) cc_final: 0.5128 (mpt180) REVERT: D 40 PHE cc_start: 0.7360 (t80) cc_final: 0.7134 (t80) REVERT: D 81 ARG cc_start: 0.0895 (ptt180) cc_final: 0.0589 (ptt180) REVERT: D 100 LEU cc_start: 0.8646 (mt) cc_final: 0.8256 (mt) REVERT: D 104 LEU cc_start: 0.7700 (pp) cc_final: 0.7010 (mm) REVERT: D 235 ARG cc_start: 0.6488 (mtp180) cc_final: 0.5768 (mmt180) REVERT: D 261 ASP cc_start: 0.7688 (m-30) cc_final: 0.7018 (m-30) REVERT: D 390 TYR cc_start: 0.6500 (m-80) cc_final: 0.5929 (m-80) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.1155 time to fit residues: 60.5004 Evaluate side-chains 211 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 HIS A 196 GLN A 217 ASN B 196 GLN B 217 ASN ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN C 196 GLN C 217 ASN C 410 GLN D 196 GLN D 217 ASN D 410 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.251382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.226560 restraints weight = 141810.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.230010 restraints weight = 72377.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.230148 restraints weight = 59266.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.229686 restraints weight = 57104.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.229580 restraints weight = 54824.983| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 12568 Z= 0.219 Angle : 0.945 10.656 17140 Z= 0.448 Chirality : 0.049 0.155 2052 Planarity : 0.007 0.058 2100 Dihedral : 7.813 65.825 1752 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.76 % Allowed : 9.45 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.22 (0.21), residues: 1512 helix: -0.85 (0.17), residues: 896 sheet: -0.50 (0.57), residues: 88 loop : -2.61 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 238 TYR 0.025 0.002 TYR D 357 PHE 0.017 0.002 PHE C 242 TRP 0.023 0.002 TRP B 264 HIS 0.012 0.002 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (12568) covalent geometry : angle 0.94524 / 0.45 (17140) hydrogen bonds : bond 0.04776 / 3.10 ( 632) hydrogen bonds : angle 5.20568 / 3.75 ( 1788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 241 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.7129 (pp) cc_final: 0.5821 (mm) REVERT: A 218 ILE cc_start: 0.3529 (OUTLIER) cc_final: 0.2795 (tp) REVERT: A 261 ASP cc_start: 0.7112 (m-30) cc_final: 0.6835 (m-30) REVERT: A 368 GLU cc_start: 0.5920 (pm20) cc_final: 0.5191 (pm20) REVERT: A 373 LEU cc_start: 0.5373 (OUTLIER) cc_final: 0.5096 (tp) REVERT: B 410 GLN cc_start: 0.7154 (tp40) cc_final: 0.6934 (tp-100) REVERT: C 218 ILE cc_start: 0.3370 (OUTLIER) cc_final: 0.2756 (tp) REVERT: C 232 HIS cc_start: 0.5607 (t-90) cc_final: 0.5126 (t70) REVERT: D 203 ILE cc_start: 0.8262 (tp) cc_final: 0.8041 (tp) REVERT: D 218 ILE cc_start: 0.3387 (OUTLIER) cc_final: 0.2663 (tp) REVERT: D 261 ASP cc_start: 0.6851 (m-30) cc_final: 0.6603 (m-30) REVERT: D 339 TYR cc_start: 0.4549 (m-10) cc_final: 0.4108 (m-80) outliers start: 10 outliers final: 3 residues processed: 248 average time/residue: 0.0932 time to fit residues: 34.0781 Evaluate side-chains 201 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 194 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 55 optimal weight: 0.7980 chunk 129 optimal weight: 0.0870 chunk 35 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 79 optimal weight: 0.0470 chunk 25 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN A 410 GLN B 217 ASN ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN D 217 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.256560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.231858 restraints weight = 141259.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.235973 restraints weight = 75446.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.235374 restraints weight = 61890.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.235361 restraints weight = 60725.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.235452 restraints weight = 56160.557| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5977 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12568 Z= 0.151 Angle : 0.832 8.605 17140 Z= 0.388 Chirality : 0.045 0.165 2052 Planarity : 0.006 0.062 2100 Dihedral : 7.164 65.185 1752 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.65 (0.22), residues: 1512 helix: -0.38 (0.17), residues: 900 sheet: -0.16 (0.56), residues: 88 loop : -2.45 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 403 TYR 0.020 0.002 TYR C 270 PHE 0.022 0.002 PHE B 366 TRP 0.012 0.001 TRP B 264 HIS 0.007 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (12568) covalent geometry : angle 0.83232 / 0.39 (17140) hydrogen bonds : bond 0.04108 / 2.67 ( 632) hydrogen bonds : angle 4.78808 / 3.41 ( 1788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.6727 (pp) cc_final: 0.5718 (mm) REVERT: A 261 ASP cc_start: 0.7162 (m-30) cc_final: 0.6917 (m-30) REVERT: A 368 GLU cc_start: 0.5781 (pm20) cc_final: 0.5374 (pm20) REVERT: A 391 ARG cc_start: 0.7531 (tpt-90) cc_final: 0.7204 (tpp80) REVERT: B 19 ILE cc_start: 0.7383 (pt) cc_final: 0.7158 (pt) REVERT: D 339 TYR cc_start: 0.4661 (m-10) cc_final: 0.4089 (m-80) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.0743 time to fit residues: 26.3200 Evaluate side-chains 182 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 84 optimal weight: 0.0870 chunk 120 optimal weight: 0.3980 chunk 143 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 0.0040 chunk 111 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 141 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.4170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN B 217 ASN B 364 GLN C 196 GLN C 217 ASN D 196 GLN D 217 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.253177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.228426 restraints weight = 143366.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.232617 restraints weight = 77065.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.232104 restraints weight = 64000.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.232424 restraints weight = 59831.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.232172 restraints weight = 58241.223| |-----------------------------------------------------------------------------| r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12568 Z= 0.144 Angle : 0.812 8.614 17140 Z= 0.373 Chirality : 0.044 0.153 2052 Planarity : 0.005 0.064 2100 Dihedral : 6.597 62.637 1752 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.39 (0.22), residues: 1512 helix: -0.06 (0.18), residues: 884 sheet: 0.03 (0.56), residues: 88 loop : -2.52 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 377 TYR 0.028 0.001 TYR B 26 PHE 0.016 0.002 PHE C 366 TRP 0.011 0.001 TRP B 264 HIS 0.010 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (12568) covalent geometry : angle 0.81231 / 0.37 (17140) hydrogen bonds : bond 0.03741 / 2.46 ( 632) hydrogen bonds : angle 4.53055 / 3.21 ( 1788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.7056 (pp) cc_final: 0.5977 (mm) REVERT: A 368 GLU cc_start: 0.5630 (pm20) cc_final: 0.5239 (pm20) REVERT: B 296 ILE cc_start: 0.5891 (mm) cc_final: 0.5578 (mt) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.0726 time to fit residues: 24.1341 Evaluate side-chains 179 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 133 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 15 optimal weight: 0.0170 chunk 140 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 102 optimal weight: 0.0270 chunk 0 optimal weight: 8.9990 chunk 126 optimal weight: 0.1980 chunk 85 optimal weight: 0.0370 chunk 62 optimal weight: 2.9990 overall best weight: 0.2154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN A 410 GLN B 217 ASN C 217 ASN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.253719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.229595 restraints weight = 144952.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.236027 restraints weight = 77914.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.233717 restraints weight = 70784.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.233638 restraints weight = 61721.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.233483 restraints weight = 60193.441| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12568 Z= 0.137 Angle : 0.796 8.317 17140 Z= 0.363 Chirality : 0.044 0.156 2052 Planarity : 0.005 0.066 2100 Dihedral : 6.242 59.356 1752 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.02 (0.22), residues: 1512 helix: 0.31 (0.18), residues: 852 sheet: 0.10 (0.56), residues: 88 loop : -2.34 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 377 TYR 0.017 0.001 TYR A 357 PHE 0.014 0.001 PHE C 366 TRP 0.009 0.001 TRP C 176 HIS 0.009 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (12568) covalent geometry : angle 0.79580 / 0.36 (17140) hydrogen bonds : bond 0.03616 / 2.35 ( 632) hydrogen bonds : angle 4.33772 / 3.08 ( 1788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.6805 (pp) cc_final: 0.5769 (mm) REVERT: B 296 ILE cc_start: 0.6209 (mm) cc_final: 0.5470 (mt) REVERT: C 317 LEU cc_start: 0.6482 (mt) cc_final: 0.6193 (tp) outliers start: 1 outliers final: 1 residues processed: 208 average time/residue: 0.0768 time to fit residues: 25.7554 Evaluate side-chains 176 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 83 optimal weight: 3.9990 chunk 16 optimal weight: 0.0270 chunk 48 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 36 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN A 232 HIS B 217 ASN C 196 GLN C 217 ASN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 217 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.251690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.227540 restraints weight = 142460.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.232092 restraints weight = 74484.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.231218 restraints weight = 61676.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.231214 restraints weight = 60570.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.231017 restraints weight = 55824.717| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12568 Z= 0.140 Angle : 0.798 8.223 17140 Z= 0.366 Chirality : 0.045 0.184 2052 Planarity : 0.006 0.067 2100 Dihedral : 6.000 54.704 1752 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.98 (0.22), residues: 1512 helix: 0.36 (0.18), residues: 864 sheet: 0.16 (0.55), residues: 88 loop : -2.42 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 235 TYR 0.019 0.001 TYR A 270 PHE 0.015 0.001 PHE B 366 TRP 0.007 0.001 TRP B 264 HIS 0.006 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (12568) covalent geometry : angle 0.79803 / 0.37 (17140) hydrogen bonds : bond 0.03622 / 2.37 ( 632) hydrogen bonds : angle 4.28750 / 3.04 ( 1788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.6834 (pp) cc_final: 0.5857 (mm) REVERT: B 339 TYR cc_start: 0.3915 (m-80) cc_final: 0.3481 (m-80) REVERT: C 317 LEU cc_start: 0.6441 (mt) cc_final: 0.6208 (tp) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.0787 time to fit residues: 25.2364 Evaluate side-chains 167 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 81 optimal weight: 0.6980 chunk 130 optimal weight: 0.0470 chunk 125 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 0.0670 chunk 140 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN A 410 GLN B 217 ASN C 217 ASN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN D 410 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.251233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.226957 restraints weight = 141238.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.234735 restraints weight = 77413.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.231952 restraints weight = 67246.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.231960 restraints weight = 61568.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.231525 restraints weight = 57972.002| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5996 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12568 Z= 0.136 Angle : 0.805 9.328 17140 Z= 0.367 Chirality : 0.045 0.157 2052 Planarity : 0.006 0.071 2100 Dihedral : 5.820 52.484 1752 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.94 (0.22), residues: 1512 helix: 0.44 (0.18), residues: 864 sheet: 0.12 (0.55), residues: 88 loop : -2.48 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 235 TYR 0.017 0.001 TYR A 270 PHE 0.015 0.001 PHE B 366 TRP 0.008 0.001 TRP C 176 HIS 0.004 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (12568) covalent geometry : angle 0.80540 / 0.37 (17140) hydrogen bonds : bond 0.03580 / 2.32 ( 632) hydrogen bonds : angle 4.25401 / 3.03 ( 1788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.7212 (pp) cc_final: 0.6133 (mm) REVERT: B 339 TYR cc_start: 0.3752 (m-80) cc_final: 0.3431 (m-80) REVERT: B 391 ARG cc_start: 0.8038 (tpt90) cc_final: 0.7820 (tpp80) REVERT: B 410 GLN cc_start: 0.6325 (tp40) cc_final: 0.6081 (tp-100) REVERT: C 317 LEU cc_start: 0.6441 (mt) cc_final: 0.6229 (tp) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.0821 time to fit residues: 27.3565 Evaluate side-chains 177 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 52 optimal weight: 0.9990 chunk 140 optimal weight: 0.0070 chunk 150 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 81 optimal weight: 0.0470 chunk 147 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 74 optimal weight: 0.0060 overall best weight: 1.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN B 196 GLN B 217 ASN C 196 GLN C 217 ASN D 196 GLN D 217 ASN D 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.244820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.218609 restraints weight = 144485.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.223708 restraints weight = 72008.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.223443 restraints weight = 61692.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.222421 restraints weight = 61965.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.222161 restraints weight = 56345.377| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.6241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12568 Z= 0.193 Angle : 0.898 10.448 17140 Z= 0.419 Chirality : 0.047 0.159 2052 Planarity : 0.006 0.057 2100 Dihedral : 5.968 51.053 1752 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.17 (0.22), residues: 1512 helix: 0.08 (0.17), residues: 892 sheet: 0.29 (0.55), residues: 88 loop : -2.43 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 268 TYR 0.021 0.002 TYR A 270 PHE 0.016 0.002 PHE C 366 TRP 0.019 0.002 TRP B 264 HIS 0.007 0.002 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (12568) covalent geometry : angle 0.89822 / 0.42 (17140) hydrogen bonds : bond 0.04240 / 2.76 ( 632) hydrogen bonds : angle 4.69395 / 3.35 ( 1788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.7435 (pp) cc_final: 0.6342 (mm) REVERT: A 251 GLU cc_start: 0.6452 (tp30) cc_final: 0.5974 (tp30) REVERT: A 261 ASP cc_start: 0.7358 (m-30) cc_final: 0.7068 (m-30) REVERT: B 261 ASP cc_start: 0.7463 (m-30) cc_final: 0.7092 (m-30) REVERT: B 339 TYR cc_start: 0.4433 (m-80) cc_final: 0.3731 (m-80) REVERT: B 389 LEU cc_start: 0.7914 (tp) cc_final: 0.7661 (tp) REVERT: C 389 LEU cc_start: 0.7595 (tp) cc_final: 0.7328 (tp) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.0827 time to fit residues: 27.0896 Evaluate side-chains 166 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 47 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN A 410 GLN B 217 ASN C 217 ASN D 217 ASN D 232 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.247080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.220471 restraints weight = 138786.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.225264 restraints weight = 73895.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.224556 restraints weight = 61185.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.224427 restraints weight = 60556.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.224336 restraints weight = 55429.634| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.6482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12568 Z= 0.159 Angle : 0.850 10.480 17140 Z= 0.392 Chirality : 0.046 0.222 2052 Planarity : 0.006 0.052 2100 Dihedral : 5.811 49.943 1752 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.08 (0.22), residues: 1512 helix: 0.20 (0.17), residues: 888 sheet: 0.31 (0.55), residues: 88 loop : -2.46 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 268 TYR 0.018 0.001 TYR A 270 PHE 0.015 0.001 PHE C 366 TRP 0.011 0.001 TRP D 264 HIS 0.004 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (12568) covalent geometry : angle 0.84998 / 0.39 (17140) hydrogen bonds : bond 0.03820 / 2.51 ( 632) hydrogen bonds : angle 4.53579 / 3.22 ( 1788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.7418 (pp) cc_final: 0.6361 (mm) REVERT: B 38 SER cc_start: 0.9199 (p) cc_final: 0.8711 (t) REVERT: B 261 ASP cc_start: 0.7572 (m-30) cc_final: 0.7234 (m-30) REVERT: B 339 TYR cc_start: 0.4000 (m-80) cc_final: 0.3360 (m-80) REVERT: B 391 ARG cc_start: 0.8116 (tpt90) cc_final: 0.7887 (tpp80) REVERT: D 225 LEU cc_start: 0.2706 (pt) cc_final: 0.1718 (tp) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.0807 time to fit residues: 26.5284 Evaluate side-chains 170 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 138 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 107 optimal weight: 0.0980 chunk 148 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN B 217 ASN B 410 GLN C 196 GLN C 217 ASN C 410 GLN D 196 GLN D 217 ASN D 410 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.246906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.220680 restraints weight = 140411.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.228138 restraints weight = 74760.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.225328 restraints weight = 65562.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.225258 restraints weight = 60520.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.224970 restraints weight = 55672.643| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12568 Z= 0.150 Angle : 0.844 9.787 17140 Z= 0.387 Chirality : 0.046 0.189 2052 Planarity : 0.005 0.050 2100 Dihedral : 5.687 48.447 1752 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.97 (0.22), residues: 1512 helix: 0.29 (0.18), residues: 888 sheet: 0.01 (0.48), residues: 112 loop : -2.45 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 235 TYR 0.015 0.001 TYR A 270 PHE 0.014 0.001 PHE C 366 TRP 0.011 0.001 TRP C 176 HIS 0.004 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (12568) covalent geometry : angle 0.84404 / 0.39 (17140) hydrogen bonds : bond 0.03756 / 2.43 ( 632) hydrogen bonds : angle 4.44119 / 3.17 ( 1788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.7361 (pp) cc_final: 0.6362 (mm) REVERT: A 334 MET cc_start: 0.6154 (mpp) cc_final: 0.4581 (tpt) REVERT: B 38 SER cc_start: 0.9200 (p) cc_final: 0.8748 (t) REVERT: B 261 ASP cc_start: 0.7283 (m-30) cc_final: 0.6950 (m-30) REVERT: B 339 TYR cc_start: 0.4292 (m-80) cc_final: 0.3543 (m-80) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.0834 time to fit residues: 26.5788 Evaluate side-chains 167 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 126 optimal weight: 0.0970 chunk 91 optimal weight: 4.9990 chunk 21 optimal weight: 0.0060 chunk 83 optimal weight: 7.9990 chunk 29 optimal weight: 0.0030 chunk 124 optimal weight: 0.9980 chunk 150 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 0.0170 chunk 4 optimal weight: 4.9990 overall best weight: 0.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN A 410 GLN B 217 ASN C 217 ASN C 410 GLN D 217 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.249982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.223897 restraints weight = 142839.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.231254 restraints weight = 78395.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.229356 restraints weight = 67112.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.229255 restraints weight = 59921.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.229107 restraints weight = 57067.368| |-----------------------------------------------------------------------------| r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.6760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12568 Z= 0.136 Angle : 0.822 9.447 17140 Z= 0.373 Chirality : 0.045 0.151 2052 Planarity : 0.005 0.049 2100 Dihedral : 5.527 46.631 1752 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.86 (0.22), residues: 1512 helix: 0.41 (0.18), residues: 884 sheet: -0.04 (0.48), residues: 112 loop : -2.43 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 391 TYR 0.012 0.001 TYR A 270 PHE 0.020 0.001 PHE B 40 TRP 0.012 0.001 TRP B 176 HIS 0.004 0.000 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (12568) covalent geometry : angle 0.82228 / 0.37 (17140) hydrogen bonds : bond 0.03581 / 2.36 ( 632) hydrogen bonds : angle 4.26482 / 3.04 ( 1788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1627.09 seconds wall clock time: 28 minutes 59.61 seconds (1739.61 seconds total)