Starting phenix.real_space_refine on Fri Sep 27 22:18:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru0_24692/09_2024/7ru0_24692.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru0_24692/09_2024/7ru0_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru0_24692/09_2024/7ru0_24692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru0_24692/09_2024/7ru0_24692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru0_24692/09_2024/7ru0_24692.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru0_24692/09_2024/7ru0_24692.cif" } resolution = 4.3 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= 0.004 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'RNA': 1} Modifications used: {'rna3p': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 6.67, per 1000 atoms: 0.54 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: 3.31 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.09 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: 3.30 Time building geometry restraints manager: 3.81 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: 16105 2.02 - 4.03: 782 4.03 - 6.05: 125 6.05 - 8.07: 84 8.07 - 10.08: 44 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 - 28.68: 7308 28.68 - 57.36: 208 57.36 - 86.03: 28 86.03 - 114.71: 0 114.71 - 143.39: 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: 1496 0.059 - 0.118: 448 0.118 - 0.177: 101 0.177 - 0.236: 3 0.236 - 0.295: 4 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: 0.00 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: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 29.250 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4769 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= 0.324 Angle : 1.125 10.082 17140 Z= 0.583 Chirality : 0.057 0.295 2052 Planarity : 0.007 0.049 2100 Dihedral : 14.475 143.388 4640 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.30 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 (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 (0.20), 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 TRP 0.013 0.002 TRP C 264 HIS 0.024 0.003 HIS B 232 PHE 0.016 0.002 PHE C 309 TYR 0.023 0.002 TYR A 404 ARG 0.010 0.001 ARG D 391 *********************** 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 fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 1.362 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: 0.5535 (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: 0.7359 (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: 0.8257 (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: 0.2716 time to fit residues: 139.6730 Evaluate side-chains 211 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 217 ASN ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN C 217 ASN C 410 GLN D 217 ASN D 410 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4980 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12568 Z= 0.273 Angle : 0.856 10.803 17140 Z= 0.418 Chirality : 0.047 0.151 2052 Planarity : 0.006 0.058 2100 Dihedral : 12.300 179.934 1752 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.91 % Allowed : 8.46 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.13 (0.21), residues: 1512 helix: -0.76 (0.17), residues: 896 sheet: -0.54 (0.57), residues: 88 loop : -2.60 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 264 HIS 0.012 0.002 HIS D 232 PHE 0.016 0.002 PHE C 242 TYR 0.025 0.002 TYR D 357 ARG 0.009 0.001 ARG A 238 *********************** 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 255 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 243 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8536 (mt) cc_final: 0.8058 (mt) REVERT: A 104 LEU cc_start: 0.7979 (pp) cc_final: 0.7062 (mm) REVERT: A 140 LEU cc_start: 0.4258 (mm) cc_final: 0.4026 (mm) REVERT: A 218 ILE cc_start: 0.1397 (OUTLIER) cc_final: 0.1118 (tp) REVERT: A 261 ASP cc_start: 0.7570 (m-30) cc_final: 0.7243 (m-30) REVERT: A 337 ASP cc_start: 0.5301 (p0) cc_final: 0.4821 (p0) REVERT: A 353 GLU cc_start: 0.8231 (tp30) cc_final: 0.7925 (tm-30) REVERT: A 368 GLU cc_start: 0.6543 (pm20) cc_final: 0.5947 (pm20) REVERT: A 373 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6440 (tp) REVERT: B 182 THR cc_start: 0.6620 (m) cc_final: 0.5979 (p) REVERT: B 218 ILE cc_start: 0.1063 (OUTLIER) cc_final: 0.0749 (tp) REVERT: B 270 TYR cc_start: 0.4902 (t80) cc_final: 0.4568 (t80) REVERT: B 329 ILE cc_start: 0.5480 (pt) cc_final: 0.5127 (pt) REVERT: B 339 TYR cc_start: 0.4707 (m-10) cc_final: 0.4477 (m-80) REVERT: C 140 LEU cc_start: 0.4481 (mm) cc_final: 0.4257 (mm) REVERT: C 218 ILE cc_start: 0.1242 (OUTLIER) cc_final: 0.0940 (tp) REVERT: C 235 ARG cc_start: 0.5895 (mtp180) cc_final: 0.5442 (mpt180) REVERT: C 261 ASP cc_start: 0.7307 (m-30) cc_final: 0.7103 (m-30) REVERT: C 270 TYR cc_start: 0.4818 (t80) cc_final: 0.4450 (t80) REVERT: C 357 TYR cc_start: 0.5746 (m-80) cc_final: 0.5471 (m-80) REVERT: C 366 PHE cc_start: 0.6877 (p90) cc_final: 0.6577 (p90) REVERT: C 373 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6548 (tt) REVERT: D 218 ILE cc_start: 0.1307 (OUTLIER) cc_final: 0.1005 (tp) REVERT: D 261 ASP cc_start: 0.7411 (m-30) cc_final: 0.7110 (m-30) REVERT: D 339 TYR cc_start: 0.4702 (m-10) cc_final: 0.3967 (m-80) REVERT: D 340 PHE cc_start: 0.7392 (m-10) cc_final: 0.6996 (m-10) REVERT: D 357 TYR cc_start: 0.6388 (m-80) cc_final: 0.5982 (m-80) outliers start: 12 outliers final: 2 residues processed: 251 average time/residue: 0.2210 time to fit residues: 80.9845 Evaluate side-chains 200 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 192 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 0.2980 chunk 137 optimal weight: 0.3980 chunk 47 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 217 ASN B 217 ASN ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN C 232 HIS D 217 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5004 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12568 Z= 0.239 Angle : 0.811 8.498 17140 Z= 0.390 Chirality : 0.045 0.164 2052 Planarity : 0.006 0.061 2100 Dihedral : 11.791 179.459 1752 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.22), residues: 1512 helix: -0.36 (0.17), residues: 900 sheet: -0.18 (0.56), residues: 88 loop : -2.42 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 264 HIS 0.007 0.001 HIS D 232 PHE 0.017 0.002 PHE D 366 TYR 0.017 0.002 TYR D 404 ARG 0.012 0.001 ARG B 403 *********************** 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 213 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8519 (mt) cc_final: 0.8024 (mt) REVERT: A 104 LEU cc_start: 0.7959 (pp) cc_final: 0.7077 (mm) REVERT: A 261 ASP cc_start: 0.7545 (m-30) cc_final: 0.7214 (m-30) REVERT: A 334 MET cc_start: 0.6350 (tpt) cc_final: 0.5761 (mpp) REVERT: A 353 GLU cc_start: 0.8235 (tp30) cc_final: 0.7900 (tm-30) REVERT: A 368 GLU cc_start: 0.6202 (pm20) cc_final: 0.5904 (pm20) REVERT: B 40 PHE cc_start: 0.7253 (t80) cc_final: 0.6979 (t80) REVERT: B 140 LEU cc_start: 0.4988 (mm) cc_final: 0.4783 (mm) REVERT: B 270 TYR cc_start: 0.4632 (t80) cc_final: 0.4225 (t80) REVERT: B 329 ILE cc_start: 0.5482 (pt) cc_final: 0.5210 (pt) REVERT: B 369 MET cc_start: 0.3997 (mtt) cc_final: 0.3778 (mtm) REVERT: C 140 LEU cc_start: 0.4752 (mm) cc_final: 0.4546 (mm) REVERT: C 235 ARG cc_start: 0.5698 (mtp180) cc_final: 0.5344 (mpt180) REVERT: C 261 ASP cc_start: 0.7188 (m-30) cc_final: 0.6967 (m-30) REVERT: C 270 TYR cc_start: 0.4588 (t80) cc_final: 0.4110 (t80) REVERT: C 357 TYR cc_start: 0.5352 (m-80) cc_final: 0.5017 (m-10) REVERT: C 366 PHE cc_start: 0.7166 (p90) cc_final: 0.6782 (p90) REVERT: D 140 LEU cc_start: 0.4773 (mm) cc_final: 0.4545 (mm) REVERT: D 261 ASP cc_start: 0.7308 (m-30) cc_final: 0.6990 (m-30) REVERT: D 340 PHE cc_start: 0.7652 (m-10) cc_final: 0.7273 (m-10) REVERT: D 357 TYR cc_start: 0.6524 (m-80) cc_final: 0.6305 (m-80) REVERT: D 369 MET cc_start: 0.6930 (mmt) cc_final: 0.6702 (mmm) REVERT: D 391 ARG cc_start: 0.6344 (tpt-90) cc_final: 0.5606 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1973 time to fit residues: 64.3540 Evaluate side-chains 185 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 15 optimal weight: 0.0970 chunk 65 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 146 optimal weight: 0.1980 chunk 72 optimal weight: 8.9990 chunk 131 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 217 ASN C 217 ASN D 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4983 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12568 Z= 0.205 Angle : 0.775 8.877 17140 Z= 0.366 Chirality : 0.044 0.154 2052 Planarity : 0.005 0.066 2100 Dihedral : 11.280 176.357 1752 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.22), residues: 1512 helix: -0.07 (0.18), residues: 888 sheet: -0.01 (0.55), residues: 88 loop : -2.53 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 176 HIS 0.008 0.001 HIS C 232 PHE 0.020 0.002 PHE D 366 TYR 0.013 0.001 TYR A 404 ARG 0.006 0.000 ARG A 377 *********************** 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 202 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.387 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8546 (mt) cc_final: 0.8121 (mt) REVERT: A 104 LEU cc_start: 0.7998 (pp) cc_final: 0.7227 (mm) REVERT: A 261 ASP cc_start: 0.7566 (m-30) cc_final: 0.7262 (m-30) REVERT: A 334 MET cc_start: 0.6261 (tpt) cc_final: 0.5701 (mpp) REVERT: A 353 GLU cc_start: 0.8287 (tp30) cc_final: 0.7950 (tm-30) REVERT: A 368 GLU cc_start: 0.6428 (pm20) cc_final: 0.5948 (pm20) REVERT: B 40 PHE cc_start: 0.7316 (t80) cc_final: 0.7015 (t80) REVERT: B 270 TYR cc_start: 0.4488 (t80) cc_final: 0.3961 (t80) REVERT: B 357 TYR cc_start: 0.5906 (m-80) cc_final: 0.5621 (m-80) REVERT: B 369 MET cc_start: 0.3829 (mtt) cc_final: 0.3626 (mtm) REVERT: C 235 ARG cc_start: 0.5852 (mtp180) cc_final: 0.5401 (mpt180) REVERT: C 261 ASP cc_start: 0.7268 (m-30) cc_final: 0.7006 (m-30) REVERT: C 270 TYR cc_start: 0.3947 (t80) cc_final: 0.3404 (t80) REVERT: C 340 PHE cc_start: 0.7454 (m-10) cc_final: 0.7187 (m-10) REVERT: C 366 PHE cc_start: 0.6831 (p90) cc_final: 0.6398 (p90) REVERT: C 377 ARG cc_start: 0.7831 (tpm170) cc_final: 0.7249 (mpt180) REVERT: D 91 LEU cc_start: 0.8039 (tp) cc_final: 0.7785 (mt) REVERT: D 261 ASP cc_start: 0.7256 (m-30) cc_final: 0.6933 (m-30) REVERT: D 340 PHE cc_start: 0.7865 (m-10) cc_final: 0.7304 (m-10) REVERT: D 357 TYR cc_start: 0.6285 (m-80) cc_final: 0.5934 (m-80) REVERT: D 391 ARG cc_start: 0.6353 (tpt-90) cc_final: 0.5985 (tpp80) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2109 time to fit residues: 65.6260 Evaluate side-chains 182 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 125 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 217 ASN C 217 ASN D 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5038 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12568 Z= 0.251 Angle : 0.803 8.490 17140 Z= 0.379 Chirality : 0.045 0.157 2052 Planarity : 0.005 0.064 2100 Dihedral : 10.498 165.684 1752 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.22), residues: 1512 helix: 0.19 (0.18), residues: 860 sheet: 0.29 (0.55), residues: 88 loop : -2.42 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 264 HIS 0.008 0.001 HIS C 232 PHE 0.017 0.001 PHE A 366 TYR 0.017 0.001 TYR A 186 ARG 0.007 0.000 ARG D 377 *********************** 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 fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8519 (mt) cc_final: 0.8081 (mt) REVERT: A 104 LEU cc_start: 0.8055 (pp) cc_final: 0.7386 (mm) REVERT: A 261 ASP cc_start: 0.7484 (m-30) cc_final: 0.7171 (m-30) REVERT: A 334 MET cc_start: 0.6310 (tpt) cc_final: 0.5623 (mpp) REVERT: A 340 PHE cc_start: 0.7448 (m-10) cc_final: 0.7191 (m-10) REVERT: A 366 PHE cc_start: 0.6788 (p90) cc_final: 0.6337 (p90) REVERT: A 368 GLU cc_start: 0.6288 (pm20) cc_final: 0.6087 (pm20) REVERT: A 413 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8283 (mm-30) REVERT: B 329 ILE cc_start: 0.5658 (pt) cc_final: 0.5299 (pt) REVERT: B 339 TYR cc_start: 0.4694 (m-80) cc_final: 0.4298 (m-80) REVERT: B 340 PHE cc_start: 0.7160 (m-80) cc_final: 0.6949 (m-80) REVERT: B 357 TYR cc_start: 0.5856 (m-80) cc_final: 0.5433 (m-80) REVERT: C 235 ARG cc_start: 0.5567 (mtp180) cc_final: 0.5163 (mpt180) REVERT: C 366 PHE cc_start: 0.6550 (p90) cc_final: 0.6021 (p90) REVERT: D 261 ASP cc_start: 0.7237 (m-30) cc_final: 0.6913 (m-30) REVERT: D 339 TYR cc_start: 0.3970 (m-80) cc_final: 0.3388 (m-80) REVERT: D 340 PHE cc_start: 0.7859 (m-10) cc_final: 0.7431 (m-80) REVERT: D 366 PHE cc_start: 0.6594 (p90) cc_final: 0.6248 (p90) REVERT: D 391 ARG cc_start: 0.5766 (tpt-90) cc_final: 0.5475 (tpp80) outliers start: 1 outliers final: 1 residues processed: 208 average time/residue: 0.2014 time to fit residues: 63.2935 Evaluate side-chains 185 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.5980 chunk 132 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN A 232 HIS 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5033 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12568 Z= 0.211 Angle : 0.783 9.206 17140 Z= 0.368 Chirality : 0.044 0.167 2052 Planarity : 0.006 0.066 2100 Dihedral : 9.261 147.865 1752 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.99 (0.22), residues: 1512 helix: 0.36 (0.18), residues: 860 sheet: 0.34 (0.57), residues: 88 loop : -2.46 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 264 HIS 0.005 0.001 HIS C 232 PHE 0.018 0.001 PHE B 366 TYR 0.021 0.001 TYR A 270 ARG 0.004 0.000 ARG A 235 *********************** 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 204 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8512 (mt) cc_final: 0.8060 (mt) REVERT: A 104 LEU cc_start: 0.8080 (pp) cc_final: 0.7401 (mm) REVERT: A 235 ARG cc_start: 0.6721 (ttp-170) cc_final: 0.6076 (mmt180) REVERT: A 251 GLU cc_start: 0.6781 (tp30) cc_final: 0.6446 (tp30) REVERT: A 261 ASP cc_start: 0.7586 (m-30) cc_final: 0.7269 (m-30) REVERT: A 334 MET cc_start: 0.6236 (tpt) cc_final: 0.5440 (mpp) REVERT: A 357 TYR cc_start: 0.6355 (m-80) cc_final: 0.5851 (m-80) REVERT: A 366 PHE cc_start: 0.6629 (p90) cc_final: 0.6411 (p90) REVERT: A 390 TYR cc_start: 0.6459 (m-80) cc_final: 0.6016 (m-80) REVERT: A 413 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8259 (mm-30) REVERT: B 261 ASP cc_start: 0.7271 (m-30) cc_final: 0.6893 (m-30) REVERT: B 296 ILE cc_start: 0.6544 (mm) cc_final: 0.6237 (mt) REVERT: B 339 TYR cc_start: 0.4497 (m-80) cc_final: 0.4122 (m-80) REVERT: B 340 PHE cc_start: 0.7199 (m-80) cc_final: 0.6929 (m-80) REVERT: B 366 PHE cc_start: 0.7162 (p90) cc_final: 0.6645 (p90) REVERT: C 366 PHE cc_start: 0.6666 (p90) cc_final: 0.6144 (p90) REVERT: C 377 ARG cc_start: 0.7886 (tpm170) cc_final: 0.7384 (tpp-160) REVERT: D 339 TYR cc_start: 0.4063 (m-80) cc_final: 0.3351 (m-80) REVERT: D 340 PHE cc_start: 0.8035 (m-10) cc_final: 0.7587 (m-80) REVERT: D 366 PHE cc_start: 0.6522 (p90) cc_final: 0.6143 (p90) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1995 time to fit residues: 61.8410 Evaluate side-chains 182 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 146 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 67 optimal weight: 0.0070 chunk 90 optimal weight: 0.6980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5041 moved from start: 0.5929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12568 Z= 0.205 Angle : 0.782 9.208 17140 Z= 0.367 Chirality : 0.044 0.152 2052 Planarity : 0.006 0.072 2100 Dihedral : 8.810 139.505 1752 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.99 (0.22), residues: 1512 helix: 0.29 (0.18), residues: 892 sheet: 0.37 (0.58), residues: 88 loop : -2.48 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 176 HIS 0.004 0.001 HIS C 232 PHE 0.019 0.001 PHE D 366 TYR 0.017 0.001 TYR A 270 ARG 0.008 0.000 ARG B 377 *********************** 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 209 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8511 (mt) cc_final: 0.8047 (mt) REVERT: A 104 LEU cc_start: 0.8148 (pp) cc_final: 0.7368 (mm) REVERT: A 235 ARG cc_start: 0.6754 (ttp-170) cc_final: 0.6090 (mmt180) REVERT: A 251 GLU cc_start: 0.6874 (tp30) cc_final: 0.6470 (tp30) REVERT: A 261 ASP cc_start: 0.7686 (m-30) cc_final: 0.7351 (m-30) REVERT: A 334 MET cc_start: 0.6211 (tpt) cc_final: 0.5595 (mpp) REVERT: A 357 TYR cc_start: 0.6408 (m-80) cc_final: 0.5879 (m-80) REVERT: A 366 PHE cc_start: 0.6452 (p90) cc_final: 0.6122 (p90) REVERT: A 413 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8326 (mm-30) REVERT: B 261 ASP cc_start: 0.7181 (m-30) cc_final: 0.6786 (m-30) REVERT: B 296 ILE cc_start: 0.6505 (mm) cc_final: 0.6195 (mt) REVERT: B 339 TYR cc_start: 0.4582 (m-80) cc_final: 0.4055 (m-80) REVERT: B 340 PHE cc_start: 0.7240 (m-80) cc_final: 0.6939 (m-80) REVERT: B 366 PHE cc_start: 0.7038 (p90) cc_final: 0.6599 (p90) REVERT: B 377 ARG cc_start: 0.7793 (tpm170) cc_final: 0.7263 (tpp-160) REVERT: C 235 ARG cc_start: 0.6461 (ttp-170) cc_final: 0.5846 (mmt180) REVERT: C 366 PHE cc_start: 0.6745 (p90) cc_final: 0.6283 (p90) REVERT: D 339 TYR cc_start: 0.4355 (m-80) cc_final: 0.3528 (m-80) REVERT: D 340 PHE cc_start: 0.8074 (m-10) cc_final: 0.7621 (m-80) REVERT: D 366 PHE cc_start: 0.6616 (p90) cc_final: 0.6244 (p90) REVERT: D 369 MET cc_start: 0.6652 (tpp) cc_final: 0.5198 (tmm) REVERT: D 371 LEU cc_start: 0.7156 (pp) cc_final: 0.6730 (tp) REVERT: D 390 TYR cc_start: 0.6770 (m-80) cc_final: 0.6420 (m-80) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1902 time to fit residues: 61.1831 Evaluate side-chains 179 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 217 ASN C 217 ASN C 410 GLN D 217 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5063 moved from start: 0.6296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12568 Z= 0.218 Angle : 0.791 11.621 17140 Z= 0.370 Chirality : 0.045 0.149 2052 Planarity : 0.006 0.058 2100 Dihedral : 8.562 132.971 1752 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.95 (0.22), residues: 1512 helix: 0.33 (0.18), residues: 892 sheet: 0.35 (0.57), residues: 88 loop : -2.47 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 176 HIS 0.004 0.001 HIS C 232 PHE 0.015 0.001 PHE A 96 TYR 0.017 0.001 TYR A 270 ARG 0.005 0.000 ARG D 111 *********************** 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 200 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.343 Fit side-chains REVERT: A 100 LEU cc_start: 0.8510 (mt) cc_final: 0.8033 (mt) REVERT: A 104 LEU cc_start: 0.8163 (pp) cc_final: 0.7380 (mm) REVERT: A 235 ARG cc_start: 0.6792 (ttp-170) cc_final: 0.6120 (mmt180) REVERT: A 261 ASP cc_start: 0.7637 (m-30) cc_final: 0.7292 (m-30) REVERT: A 334 MET cc_start: 0.6503 (tpt) cc_final: 0.5833 (mpp) REVERT: A 339 TYR cc_start: 0.4594 (m-10) cc_final: 0.3728 (m-80) REVERT: A 357 TYR cc_start: 0.6445 (m-80) cc_final: 0.5874 (m-80) REVERT: A 366 PHE cc_start: 0.6458 (p90) cc_final: 0.6047 (p90) REVERT: A 413 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8348 (mm-30) REVERT: B 261 ASP cc_start: 0.7217 (m-30) cc_final: 0.6812 (m-30) REVERT: B 337 ASP cc_start: 0.4498 (t0) cc_final: 0.3872 (t70) REVERT: B 339 TYR cc_start: 0.4483 (m-80) cc_final: 0.3970 (m-80) REVERT: B 340 PHE cc_start: 0.7458 (m-80) cc_final: 0.7086 (m-80) REVERT: B 366 PHE cc_start: 0.7076 (p90) cc_final: 0.6569 (p90) REVERT: C 235 ARG cc_start: 0.6296 (ttp-170) cc_final: 0.5702 (mpt180) REVERT: C 339 TYR cc_start: 0.3646 (m-80) cc_final: 0.2823 (m-80) REVERT: C 366 PHE cc_start: 0.6815 (p90) cc_final: 0.6263 (p90) REVERT: C 377 ARG cc_start: 0.8084 (tpm170) cc_final: 0.7575 (tpp-160) REVERT: C 389 LEU cc_start: 0.7187 (mp) cc_final: 0.6747 (tp) REVERT: C 390 TYR cc_start: 0.6545 (m-80) cc_final: 0.5740 (m-80) REVERT: D 339 TYR cc_start: 0.4383 (m-80) cc_final: 0.3535 (m-80) REVERT: D 340 PHE cc_start: 0.8009 (m-10) cc_final: 0.7650 (m-80) REVERT: D 357 TYR cc_start: 0.6284 (m-80) cc_final: 0.6001 (m-80) REVERT: D 366 PHE cc_start: 0.6465 (p90) cc_final: 0.6204 (p90) REVERT: D 369 MET cc_start: 0.6641 (tpp) cc_final: 0.5145 (tmm) REVERT: D 371 LEU cc_start: 0.7154 (pp) cc_final: 0.6745 (tp) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1915 time to fit residues: 58.7529 Evaluate side-chains 175 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.0980 chunk 136 optimal weight: 0.9980 chunk 140 optimal weight: 0.0770 chunk 82 optimal weight: 0.0970 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 89 optimal weight: 0.0040 chunk 144 optimal weight: 0.0170 overall best weight: 0.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5019 moved from start: 0.6388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12568 Z= 0.187 Angle : 0.781 11.131 17140 Z= 0.366 Chirality : 0.044 0.154 2052 Planarity : 0.005 0.053 2100 Dihedral : 8.448 131.802 1752 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.83 (0.22), residues: 1512 helix: 0.44 (0.18), residues: 880 sheet: 1.25 (0.62), residues: 68 loop : -2.44 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 176 HIS 0.004 0.001 HIS B 232 PHE 0.013 0.001 PHE A 96 TYR 0.012 0.001 TYR A 270 ARG 0.006 0.000 ARG B 235 *********************** 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 fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8581 (mt) cc_final: 0.8137 (mt) REVERT: A 104 LEU cc_start: 0.8172 (pp) cc_final: 0.7378 (mm) REVERT: A 235 ARG cc_start: 0.6796 (ttp-170) cc_final: 0.6151 (mmt180) REVERT: A 261 ASP cc_start: 0.7628 (m-30) cc_final: 0.7283 (m-30) REVERT: A 334 MET cc_start: 0.6507 (tpt) cc_final: 0.5681 (mpp) REVERT: A 357 TYR cc_start: 0.6308 (m-80) cc_final: 0.5750 (m-80) REVERT: A 366 PHE cc_start: 0.6556 (p90) cc_final: 0.6184 (p90) REVERT: B 261 ASP cc_start: 0.7104 (m-30) cc_final: 0.6698 (m-30) REVERT: B 337 ASP cc_start: 0.4712 (t0) cc_final: 0.4143 (t70) REVERT: B 339 TYR cc_start: 0.4594 (m-80) cc_final: 0.4068 (m-80) REVERT: B 340 PHE cc_start: 0.7421 (m-80) cc_final: 0.6912 (m-80) REVERT: B 366 PHE cc_start: 0.6974 (p90) cc_final: 0.6492 (p90) REVERT: B 369 MET cc_start: 0.4599 (mtt) cc_final: 0.3856 (tmm) REVERT: C 235 ARG cc_start: 0.6422 (ttp-170) cc_final: 0.5782 (mpt180) REVERT: C 339 TYR cc_start: 0.3622 (m-80) cc_final: 0.2774 (m-80) REVERT: C 366 PHE cc_start: 0.6737 (p90) cc_final: 0.6204 (p90) REVERT: C 389 LEU cc_start: 0.7232 (mp) cc_final: 0.6770 (tp) REVERT: C 390 TYR cc_start: 0.6590 (m-80) cc_final: 0.5771 (m-80) REVERT: D 339 TYR cc_start: 0.4258 (m-80) cc_final: 0.3393 (m-80) REVERT: D 340 PHE cc_start: 0.8035 (m-10) cc_final: 0.7698 (m-80) REVERT: D 366 PHE cc_start: 0.6457 (p90) cc_final: 0.6042 (p90) REVERT: D 369 MET cc_start: 0.6594 (tpp) cc_final: 0.5128 (tmm) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1760 time to fit residues: 56.6127 Evaluate side-chains 174 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.3980 chunk 68 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 12 optimal weight: 0.0040 chunk 93 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 95 optimal weight: 0.0970 chunk 128 optimal weight: 0.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 217 ASN C 217 ASN C 410 GLN D 217 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5043 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12568 Z= 0.194 Angle : 0.788 11.260 17140 Z= 0.369 Chirality : 0.045 0.153 2052 Planarity : 0.005 0.050 2100 Dihedral : 8.419 131.678 1752 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.81 (0.22), residues: 1512 helix: 0.44 (0.18), residues: 884 sheet: 1.30 (0.62), residues: 68 loop : -2.41 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 176 HIS 0.003 0.001 HIS C 232 PHE 0.014 0.001 PHE A 96 TYR 0.015 0.001 TYR C 259 ARG 0.003 0.000 ARG D 356 ********************** 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 fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.268 Fit side-chains REVERT: A 100 LEU cc_start: 0.8550 (mt) cc_final: 0.8115 (mt) REVERT: A 104 LEU cc_start: 0.8008 (pp) cc_final: 0.7245 (mm) REVERT: A 235 ARG cc_start: 0.6779 (ttp-170) cc_final: 0.6135 (mmt180) REVERT: A 261 ASP cc_start: 0.7484 (m-30) cc_final: 0.7160 (m-30) REVERT: A 334 MET cc_start: 0.6560 (tpt) cc_final: 0.5670 (mpp) REVERT: A 357 TYR cc_start: 0.6401 (m-80) cc_final: 0.5800 (m-80) REVERT: A 366 PHE cc_start: 0.6602 (p90) cc_final: 0.6226 (p90) REVERT: A 369 MET cc_start: 0.5908 (mmp) cc_final: 0.3993 (tmm) REVERT: A 413 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8084 (mm-30) REVERT: B 261 ASP cc_start: 0.7029 (m-30) cc_final: 0.6614 (m-30) REVERT: B 337 ASP cc_start: 0.4628 (t0) cc_final: 0.4084 (t70) REVERT: B 339 TYR cc_start: 0.4521 (m-80) cc_final: 0.3982 (m-80) REVERT: B 340 PHE cc_start: 0.7496 (m-80) cc_final: 0.6998 (m-80) REVERT: B 366 PHE cc_start: 0.7042 (p90) cc_final: 0.6552 (p90) REVERT: B 369 MET cc_start: 0.4988 (mtt) cc_final: 0.4120 (tmm) REVERT: C 235 ARG cc_start: 0.6355 (ttp-170) cc_final: 0.5725 (mpt180) REVERT: C 339 TYR cc_start: 0.3677 (m-80) cc_final: 0.2836 (m-80) REVERT: C 366 PHE cc_start: 0.6733 (p90) cc_final: 0.6154 (p90) REVERT: C 369 MET cc_start: 0.6399 (mmt) cc_final: 0.4595 (tmm) REVERT: C 377 ARG cc_start: 0.8065 (tpm170) cc_final: 0.7586 (tpp-160) REVERT: C 389 LEU cc_start: 0.7227 (mp) cc_final: 0.6756 (tp) REVERT: C 390 TYR cc_start: 0.6574 (m-80) cc_final: 0.5800 (m-80) REVERT: D 339 TYR cc_start: 0.4213 (m-80) cc_final: 0.3404 (m-80) REVERT: D 340 PHE cc_start: 0.8027 (m-10) cc_final: 0.7667 (m-80) REVERT: D 366 PHE cc_start: 0.6440 (p90) cc_final: 0.6093 (p90) REVERT: D 369 MET cc_start: 0.6646 (tpp) cc_final: 0.5468 (tmm) REVERT: D 371 LEU cc_start: 0.7214 (pp) cc_final: 0.6835 (tp) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1883 time to fit residues: 58.5096 Evaluate side-chains 169 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 120 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 124 optimal weight: 0.0370 chunk 15 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 217 ASN C 217 ASN D 217 ASN D 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.249766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.222596 restraints weight = 139267.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.227715 restraints weight = 73441.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.227257 restraints weight = 58200.810| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 0.6737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12568 Z= 0.195 Angle : 0.794 11.289 17140 Z= 0.371 Chirality : 0.045 0.150 2052 Planarity : 0.005 0.050 2100 Dihedral : 8.385 131.551 1752 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.75 (0.22), residues: 1512 helix: 0.48 (0.18), residues: 884 sheet: 1.36 (0.63), residues: 68 loop : -2.38 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 176 HIS 0.003 0.001 HIS C 232 PHE 0.014 0.001 PHE A 96 TYR 0.013 0.001 TYR A 270 ARG 0.004 0.000 ARG B 235 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2344.89 seconds wall clock time: 42 minutes 40.42 seconds (2560.42 seconds total)