Starting phenix.real_space_refine on Tue Nov 18 14:19:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5onv_3835/11_2025/5onv_3835.cif Found real_map, /net/cci-nas-00/data/ceres_data/5onv_3835/11_2025/5onv_3835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5onv_3835/11_2025/5onv_3835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5onv_3835/11_2025/5onv_3835.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5onv_3835/11_2025/5onv_3835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5onv_3835/11_2025/5onv_3835.map" } resolution = 4.1 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9235 2.51 5 N 2470 2.21 5 O 2815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14640 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.76, per 1000 atoms: 0.19 Number of scatterers: 14640 At special positions: 0 Unit cell: (98.04, 85.5, 192.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 10 15.00 Mg 5 11.99 O 2815 8.00 N 2470 7.00 C 9235 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: 1.31 Conformation dependent library (CDL) restraints added in 593.3 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 25 sheets defined 52.3% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 93 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 295 removed outlier: 4.685A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 181 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 295 removed outlier: 4.686A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 374 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 93 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 113 through 124 Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 181 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 295 removed outlier: 4.686A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 93 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 181 through 197 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.684A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 355 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 93 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 181 through 197 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 295 removed outlier: 4.685A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.926A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.926A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 178 Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.926A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 176 through 178 Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.925A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'D' and resid 176 through 178 Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.925A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC6, first strand: chain 'E' and resid 176 through 178 Processing sheet with id=AC7, first strand: chain 'E' and resid 238 through 241 780 hydrogen bonds defined for protein. 2025 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3568 1.33 - 1.45: 3352 1.45 - 1.57: 7844 1.57 - 1.69: 11 1.69 - 1.81: 185 Bond restraints: 14960 Sorted by residual: bond pdb=" CA ILE B 151 " pdb=" C ILE B 151 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.21e-02 6.83e+03 1.16e+01 bond pdb=" CA ILE A 151 " pdb=" C ILE A 151 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.21e-02 6.83e+03 1.14e+01 bond pdb=" CA ILE E 151 " pdb=" C ILE E 151 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.21e-02 6.83e+03 1.13e+01 bond pdb=" CA ILE D 151 " pdb=" C ILE D 151 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.21e-02 6.83e+03 1.12e+01 bond pdb=" CA ILE C 151 " pdb=" C ILE C 151 " ideal model delta sigma weight residual 1.522 1.482 0.040 1.21e-02 6.83e+03 1.11e+01 ... (remaining 14955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 18932 2.76 - 5.52: 1197 5.52 - 8.27: 114 8.27 - 11.03: 47 11.03 - 13.79: 15 Bond angle restraints: 20305 Sorted by residual: angle pdb=" C VAL B 129 " pdb=" N PRO B 130 " pdb=" CA PRO B 130 " ideal model delta sigma weight residual 119.24 127.99 -8.75 1.04e+00 9.25e-01 7.08e+01 angle pdb=" C VAL E 129 " pdb=" N PRO E 130 " pdb=" CA PRO E 130 " ideal model delta sigma weight residual 119.24 127.98 -8.74 1.04e+00 9.25e-01 7.06e+01 angle pdb=" C VAL D 129 " pdb=" N PRO D 130 " pdb=" CA PRO D 130 " ideal model delta sigma weight residual 119.24 127.95 -8.71 1.04e+00 9.25e-01 7.01e+01 angle pdb=" C VAL A 129 " pdb=" N PRO A 130 " pdb=" CA PRO A 130 " ideal model delta sigma weight residual 119.24 127.95 -8.71 1.04e+00 9.25e-01 7.01e+01 angle pdb=" C VAL C 129 " pdb=" N PRO C 130 " pdb=" CA PRO C 130 " ideal model delta sigma weight residual 119.24 127.94 -8.70 1.04e+00 9.25e-01 7.00e+01 ... (remaining 20300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.98: 8735 24.98 - 49.97: 195 49.97 - 74.95: 55 74.95 - 99.94: 5 99.94 - 124.92: 5 Dihedral angle restraints: 8995 sinusoidal: 3635 harmonic: 5360 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 64.92 -124.92 1 2.00e+01 2.50e-03 3.77e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 64.92 -124.91 1 2.00e+01 2.50e-03 3.77e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 64.91 -124.91 1 2.00e+01 2.50e-03 3.77e+01 ... (remaining 8992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1159 0.047 - 0.093: 794 0.093 - 0.139: 229 0.139 - 0.186: 68 0.186 - 0.232: 5 Chirality restraints: 2255 Sorted by residual: chirality pdb=" CA PRO E 32 " pdb=" N PRO E 32 " pdb=" C PRO E 32 " pdb=" CB PRO E 32 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PRO A 32 " pdb=" N PRO A 32 " pdb=" C PRO A 32 " pdb=" CB PRO A 32 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PRO B 32 " pdb=" N PRO B 32 " pdb=" C PRO B 32 " pdb=" CB PRO B 32 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2252 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 375 " -0.031 2.00e-02 2.50e+03 6.30e-02 3.97e+01 pdb=" C PHE A 375 " 0.109 2.00e-02 2.50e+03 pdb=" O PHE A 375 " -0.039 2.00e-02 2.50e+03 pdb=" OXT PHE A 375 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 375 " -0.031 2.00e-02 2.50e+03 6.30e-02 3.96e+01 pdb=" C PHE C 375 " 0.109 2.00e-02 2.50e+03 pdb=" O PHE C 375 " -0.039 2.00e-02 2.50e+03 pdb=" OXT PHE C 375 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 375 " -0.031 2.00e-02 2.50e+03 6.30e-02 3.96e+01 pdb=" C PHE D 375 " 0.109 2.00e-02 2.50e+03 pdb=" O PHE D 375 " -0.039 2.00e-02 2.50e+03 pdb=" OXT PHE D 375 " -0.039 2.00e-02 2.50e+03 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 73 2.58 - 3.16: 13822 3.16 - 3.74: 23147 3.74 - 4.32: 35259 4.32 - 4.90: 53364 Nonbonded interactions: 125665 Sorted by model distance: nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 1.996 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 1.996 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 1.996 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.996 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 1.996 2.170 ... (remaining 125660 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' selection = chain 'E' } 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.130 Find NCS groups from input model: 0.120 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 : 0.013 0.059 14960 Z= 0.822 Angle : 1.559 13.788 20305 Z= 1.007 Chirality : 0.065 0.232 2255 Planarity : 0.018 0.148 2595 Dihedral : 11.903 124.921 5565 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 3.55 % Allowed : 6.28 % Favored : 90.16 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -2.61 (0.18), residues: 1830 helix: -1.67 (0.14), residues: 840 sheet: -1.16 (0.29), residues: 325 loop : -1.83 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 177 TYR 0.048 0.006 TYR C 306 PHE 0.024 0.004 PHE D 375 TRP 0.036 0.008 TRP C 340 HIS 0.007 0.002 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.01324 (14960) covalent geometry : angle 1.55902 (20305) hydrogen bonds : bond 0.14660 ( 780) hydrogen bonds : angle 7.95550 ( 2025) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 729 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.6781 (m-30) cc_final: 0.6244 (t0) REVERT: A 34 ILE cc_start: 0.9600 (mt) cc_final: 0.9176 (tp) REVERT: A 78 ASN cc_start: 0.8024 (t0) cc_final: 0.6175 (t0) REVERT: A 81 ASP cc_start: 0.8614 (m-30) cc_final: 0.7836 (m-30) REVERT: A 86 TRP cc_start: 0.9000 (m-10) cc_final: 0.8463 (m-10) REVERT: A 101 HIS cc_start: 0.8657 (p-80) cc_final: 0.8381 (p-80) REVERT: A 103 THR cc_start: 0.9150 (m) cc_final: 0.8925 (t) REVERT: A 205 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7334 (mt-10) REVERT: A 212 ILE cc_start: 0.9101 (mt) cc_final: 0.8797 (mt) REVERT: A 217 CYS cc_start: 0.8849 (m) cc_final: 0.8641 (m) REVERT: A 287 ILE cc_start: 0.8526 (pt) cc_final: 0.8218 (tt) REVERT: A 291 LYS cc_start: 0.8939 (tmmt) cc_final: 0.8398 (mptt) REVERT: B 39 ARG cc_start: 0.7648 (ttp-170) cc_final: 0.7329 (ttp-170) REVERT: B 153 LEU cc_start: 0.9277 (tp) cc_final: 0.8852 (mt) REVERT: B 192 ILE cc_start: 0.8894 (pt) cc_final: 0.8645 (mm) REVERT: B 280 ASN cc_start: 0.8454 (m-40) cc_final: 0.8097 (m-40) REVERT: B 305 MET cc_start: 0.9134 (mmm) cc_final: 0.8281 (mmt) REVERT: B 352 PHE cc_start: 0.8985 (t80) cc_final: 0.8538 (t80) REVERT: B 370 VAL cc_start: 0.9205 (t) cc_final: 0.8988 (t) REVERT: C 21 PHE cc_start: 0.6982 (m-80) cc_final: 0.6697 (m-80) REVERT: C 47 MET cc_start: 0.5790 (mtm) cc_final: 0.5476 (ptp) REVERT: C 78 ASN cc_start: 0.7367 (t0) cc_final: 0.5629 (t0) REVERT: C 81 ASP cc_start: 0.8543 (m-30) cc_final: 0.7803 (m-30) REVERT: C 87 HIS cc_start: 0.8818 (t70) cc_final: 0.8517 (t-170) REVERT: C 161 HIS cc_start: 0.9368 (p90) cc_final: 0.9015 (p90) REVERT: C 165 ILE cc_start: 0.9235 (mt) cc_final: 0.8849 (tp) REVERT: C 176 MET cc_start: 0.7815 (mtt) cc_final: 0.7493 (mtp) REVERT: C 227 MET cc_start: 0.8793 (tmm) cc_final: 0.8509 (tmm) REVERT: C 267 ILE cc_start: 0.9221 (pt) cc_final: 0.8943 (mp) REVERT: C 280 ASN cc_start: 0.8636 (m-40) cc_final: 0.8430 (m-40) REVERT: C 292 ASP cc_start: 0.8383 (m-30) cc_final: 0.7877 (t0) REVERT: C 305 MET cc_start: 0.8730 (mmm) cc_final: 0.8473 (mmt) REVERT: C 340 TRP cc_start: 0.9034 (t60) cc_final: 0.8513 (t60) REVERT: D 43 VAL cc_start: 0.8558 (t) cc_final: 0.7244 (t) REVERT: D 47 MET cc_start: 0.6272 (mtm) cc_final: 0.5205 (ptp) REVERT: D 106 THR cc_start: 0.7793 (t) cc_final: 0.7508 (t) REVERT: D 127 PHE cc_start: 0.8855 (m-80) cc_final: 0.8611 (m-10) REVERT: D 137 GLN cc_start: 0.8093 (mt0) cc_final: 0.7369 (mm-40) REVERT: D 142 LEU cc_start: 0.9277 (mt) cc_final: 0.8956 (mt) REVERT: D 155 SER cc_start: 0.8418 (t) cc_final: 0.8207 (t) REVERT: D 157 ASP cc_start: 0.6757 (t70) cc_final: 0.6547 (t70) REVERT: D 162 ASN cc_start: 0.8722 (t0) cc_final: 0.8289 (p0) REVERT: D 165 ILE cc_start: 0.9133 (mt) cc_final: 0.8685 (tp) REVERT: D 214 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7863 (mt-10) REVERT: D 244 ASP cc_start: 0.9017 (p0) cc_final: 0.8808 (p0) REVERT: D 270 GLU cc_start: 0.7542 (tt0) cc_final: 0.7241 (pt0) REVERT: D 280 ASN cc_start: 0.9029 (m-40) cc_final: 0.7997 (m-40) REVERT: D 288 ASP cc_start: 0.7521 (t70) cc_final: 0.7135 (t0) REVERT: D 299 MET cc_start: 0.8340 (mtp) cc_final: 0.8129 (mtt) REVERT: D 305 MET cc_start: 0.8509 (mmm) cc_final: 0.8294 (tpp) REVERT: D 311 ASP cc_start: 0.8585 (m-30) cc_final: 0.8128 (t70) REVERT: D 358 THR cc_start: 0.8877 (p) cc_final: 0.8602 (t) REVERT: E 11 ASP cc_start: 0.8631 (t0) cc_final: 0.8362 (t0) REVERT: E 21 PHE cc_start: 0.7218 (m-80) cc_final: 0.6829 (m-80) REVERT: E 30 VAL cc_start: 0.9277 (t) cc_final: 0.9027 (m) REVERT: E 43 VAL cc_start: 0.8529 (t) cc_final: 0.7362 (t) REVERT: E 47 MET cc_start: 0.6952 (mtm) cc_final: 0.5810 (ttt) REVERT: E 78 ASN cc_start: 0.8135 (t0) cc_final: 0.7279 (t0) REVERT: E 87 HIS cc_start: 0.8871 (t70) cc_final: 0.8636 (t-170) REVERT: E 104 LEU cc_start: 0.9137 (tp) cc_final: 0.8876 (tp) REVERT: E 137 GLN cc_start: 0.8192 (mt0) cc_final: 0.7965 (mm-40) REVERT: E 205 GLU cc_start: 0.7870 (mt-10) cc_final: 0.6965 (mt-10) REVERT: E 211 ASP cc_start: 0.7563 (t70) cc_final: 0.7012 (t70) REVERT: E 280 ASN cc_start: 0.9023 (m-40) cc_final: 0.7973 (m110) REVERT: E 292 ASP cc_start: 0.8502 (m-30) cc_final: 0.8090 (t70) outliers start: 0 outliers final: 0 residues processed: 729 average time/residue: 0.1314 time to fit residues: 139.1791 Evaluate side-chains 371 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 263 GLN A 280 ASN B 87 HIS ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN D 12 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.094181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.082418 restraints weight = 35398.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.085406 restraints weight = 18786.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.087445 restraints weight = 11508.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.088823 restraints weight = 7667.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.089782 restraints weight = 5468.629| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14960 Z= 0.159 Angle : 0.715 7.005 20305 Z= 0.372 Chirality : 0.046 0.165 2255 Planarity : 0.007 0.055 2595 Dihedral : 7.289 91.221 2085 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.86 % Favored : 94.59 % Rotamer: Outliers : 0.06 % Allowed : 2.17 % Favored : 97.76 % 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: -0.82 (0.19), residues: 1830 helix: 0.24 (0.17), residues: 820 sheet: -0.71 (0.29), residues: 325 loop : -1.29 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 39 TYR 0.018 0.001 TYR C 166 PHE 0.013 0.001 PHE A 127 TRP 0.017 0.002 TRP B 86 HIS 0.012 0.002 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00350 (14960) covalent geometry : angle 0.71452 (20305) hydrogen bonds : bond 0.04464 ( 780) hydrogen bonds : angle 5.68644 ( 2025) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 550 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8970 (t0) cc_final: 0.8442 (t0) REVERT: A 24 ASP cc_start: 0.7156 (m-30) cc_final: 0.6475 (t70) REVERT: A 34 ILE cc_start: 0.9569 (mt) cc_final: 0.9221 (tp) REVERT: A 41 GLN cc_start: 0.7377 (tm-30) cc_final: 0.7032 (tm-30) REVERT: A 43 VAL cc_start: 0.8077 (t) cc_final: 0.7712 (t) REVERT: A 47 MET cc_start: 0.5222 (ptt) cc_final: 0.4946 (ptt) REVERT: A 78 ASN cc_start: 0.7835 (t0) cc_final: 0.7631 (t0) REVERT: A 82 MET cc_start: 0.8738 (tmm) cc_final: 0.8530 (tpt) REVERT: A 118 LYS cc_start: 0.9105 (mmtt) cc_final: 0.8902 (mmtt) REVERT: A 154 ASP cc_start: 0.8001 (t70) cc_final: 0.7155 (t0) REVERT: A 161 HIS cc_start: 0.8348 (p90) cc_final: 0.7846 (p90) REVERT: A 217 CYS cc_start: 0.8627 (m) cc_final: 0.8270 (m) REVERT: A 252 ASN cc_start: 0.8912 (p0) cc_final: 0.8671 (p0) REVERT: A 291 LYS cc_start: 0.8616 (tmmt) cc_final: 0.8386 (mptt) REVERT: A 292 ASP cc_start: 0.7702 (m-30) cc_final: 0.7018 (t0) REVERT: A 293 LEU cc_start: 0.9391 (mt) cc_final: 0.9188 (mp) REVERT: B 31 PHE cc_start: 0.8891 (p90) cc_final: 0.8625 (p90) REVERT: B 41 GLN cc_start: 0.7527 (tm-30) cc_final: 0.7228 (tm-30) REVERT: B 47 MET cc_start: 0.5480 (mtm) cc_final: 0.4123 (tmm) REVERT: B 105 LEU cc_start: 0.9385 (mp) cc_final: 0.9080 (mp) REVERT: B 106 THR cc_start: 0.8440 (t) cc_final: 0.8043 (p) REVERT: B 113 LYS cc_start: 0.8725 (ptmt) cc_final: 0.8494 (ptmt) REVERT: B 117 GLU cc_start: 0.8388 (pt0) cc_final: 0.8180 (pp20) REVERT: B 123 MET cc_start: 0.8721 (mmp) cc_final: 0.8464 (mmp) REVERT: B 153 LEU cc_start: 0.9132 (tp) cc_final: 0.8541 (mt) REVERT: B 192 ILE cc_start: 0.8621 (pt) cc_final: 0.8408 (pt) REVERT: B 252 ASN cc_start: 0.8971 (p0) cc_final: 0.8771 (p0) REVERT: B 253 GLU cc_start: 0.7826 (mp0) cc_final: 0.7357 (mp0) REVERT: B 362 TYR cc_start: 0.8331 (t80) cc_final: 0.8052 (t80) REVERT: C 31 PHE cc_start: 0.8977 (p90) cc_final: 0.8720 (p90) REVERT: C 80 ASP cc_start: 0.7703 (p0) cc_final: 0.7204 (p0) REVERT: C 82 MET cc_start: 0.8177 (tmm) cc_final: 0.7895 (tmm) REVERT: C 113 LYS cc_start: 0.8827 (ptmt) cc_final: 0.8352 (ttpt) REVERT: C 161 HIS cc_start: 0.9028 (p90) cc_final: 0.8725 (p-80) REVERT: C 227 MET cc_start: 0.8528 (tmm) cc_final: 0.8310 (tmm) REVERT: C 246 GLN cc_start: 0.8367 (tp40) cc_final: 0.8086 (tp-100) REVERT: C 252 ASN cc_start: 0.8719 (p0) cc_final: 0.8493 (p0) REVERT: C 292 ASP cc_start: 0.8092 (m-30) cc_final: 0.7607 (t0) REVERT: C 340 TRP cc_start: 0.8955 (t60) cc_final: 0.8338 (t60) REVERT: D 47 MET cc_start: 0.5551 (mtm) cc_final: 0.4709 (ttt) REVERT: D 121 GLN cc_start: 0.8738 (tp40) cc_final: 0.8387 (tp40) REVERT: D 154 ASP cc_start: 0.8297 (t0) cc_final: 0.8022 (t0) REVERT: D 162 ASN cc_start: 0.8190 (t0) cc_final: 0.7917 (p0) REVERT: D 184 ASP cc_start: 0.8152 (t70) cc_final: 0.7916 (t70) REVERT: D 217 CYS cc_start: 0.8081 (m) cc_final: 0.7733 (m) REVERT: D 226 GLU cc_start: 0.7736 (tt0) cc_final: 0.7473 (tt0) REVERT: D 305 MET cc_start: 0.8413 (mmm) cc_final: 0.7888 (tpp) REVERT: D 314 GLN cc_start: 0.8494 (tt0) cc_final: 0.8196 (tm-30) REVERT: D 316 GLU cc_start: 0.8193 (tp30) cc_final: 0.7702 (tp30) REVERT: D 318 THR cc_start: 0.8941 (m) cc_final: 0.8587 (p) REVERT: D 330 ILE cc_start: 0.9306 (mm) cc_final: 0.9081 (mm) REVERT: D 355 MET cc_start: 0.8802 (mmm) cc_final: 0.8571 (mmm) REVERT: D 356 TRP cc_start: 0.8472 (m100) cc_final: 0.8183 (m100) REVERT: D 369 ILE cc_start: 0.9018 (tp) cc_final: 0.8806 (tp) REVERT: E 47 MET cc_start: 0.6802 (mtm) cc_final: 0.6474 (ttt) REVERT: E 51 ASP cc_start: 0.7625 (p0) cc_final: 0.7331 (p0) REVERT: E 56 ASP cc_start: 0.8481 (p0) cc_final: 0.8249 (p0) REVERT: E 121 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8188 (mm-40) REVERT: E 154 ASP cc_start: 0.8479 (t0) cc_final: 0.8157 (t0) REVERT: E 190 MET cc_start: 0.8353 (mtm) cc_final: 0.8045 (mtm) REVERT: E 283 MET cc_start: 0.8587 (mmp) cc_final: 0.8318 (tpp) outliers start: 1 outliers final: 0 residues processed: 551 average time/residue: 0.1127 time to fit residues: 94.5095 Evaluate side-chains 345 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS A 280 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS B 360 GLN B 371 HIS ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 87 HIS E 137 GLN E 371 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.092556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.081002 restraints weight = 35853.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.083998 restraints weight = 18740.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.085979 restraints weight = 11256.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.087317 restraints weight = 7440.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.088215 restraints weight = 5266.664| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14960 Z= 0.134 Angle : 0.663 6.020 20305 Z= 0.335 Chirality : 0.045 0.180 2255 Planarity : 0.005 0.047 2595 Dihedral : 6.572 73.254 2085 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.04 % Favored : 95.41 % Rotamer: Outliers : 0.13 % Allowed : 2.17 % Favored : 97.70 % 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: -0.22 (0.19), residues: 1830 helix: 0.71 (0.18), residues: 820 sheet: -0.77 (0.28), residues: 325 loop : -0.73 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 147 TYR 0.032 0.001 TYR A 279 PHE 0.013 0.001 PHE E 255 TRP 0.009 0.002 TRP B 86 HIS 0.012 0.002 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00285 (14960) covalent geometry : angle 0.66289 (20305) hydrogen bonds : bond 0.03901 ( 780) hydrogen bonds : angle 5.32132 ( 2025) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 445 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7132 (m-30) cc_final: 0.6537 (t0) REVERT: A 34 ILE cc_start: 0.9624 (mt) cc_final: 0.9226 (tp) REVERT: A 86 TRP cc_start: 0.8958 (m-10) cc_final: 0.8705 (m-10) REVERT: A 121 GLN cc_start: 0.8964 (pp30) cc_final: 0.8695 (pp30) REVERT: A 154 ASP cc_start: 0.7888 (t70) cc_final: 0.6844 (t70) REVERT: A 161 HIS cc_start: 0.8271 (p90) cc_final: 0.7647 (p90) REVERT: A 217 CYS cc_start: 0.8541 (m) cc_final: 0.8154 (m) REVERT: B 43 VAL cc_start: 0.8579 (t) cc_final: 0.8227 (t) REVERT: B 47 MET cc_start: 0.5480 (mtm) cc_final: 0.4946 (tpp) REVERT: B 83 GLU cc_start: 0.8924 (pp20) cc_final: 0.8422 (pt0) REVERT: B 117 GLU cc_start: 0.8439 (pt0) cc_final: 0.8223 (pp20) REVERT: B 153 LEU cc_start: 0.9144 (tp) cc_final: 0.8519 (mt) REVERT: B 253 GLU cc_start: 0.7748 (mp0) cc_final: 0.7489 (mp0) REVERT: B 269 MET cc_start: 0.7942 (tpp) cc_final: 0.7612 (tmm) REVERT: C 81 ASP cc_start: 0.8390 (m-30) cc_final: 0.8161 (m-30) REVERT: C 82 MET cc_start: 0.8406 (tmm) cc_final: 0.7945 (tmm) REVERT: C 113 LYS cc_start: 0.8937 (ptmt) cc_final: 0.8591 (ttpt) REVERT: C 119 MET cc_start: 0.9362 (ttp) cc_final: 0.9118 (ttp) REVERT: C 161 HIS cc_start: 0.9082 (p90) cc_final: 0.8241 (p90) REVERT: C 227 MET cc_start: 0.8533 (tmm) cc_final: 0.8315 (tmm) REVERT: C 276 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7459 (tm-30) REVERT: C 292 ASP cc_start: 0.7965 (m-30) cc_final: 0.7705 (t0) REVERT: C 340 TRP cc_start: 0.8953 (t60) cc_final: 0.8164 (t60) REVERT: D 47 MET cc_start: 0.5335 (mtm) cc_final: 0.4262 (ttt) REVERT: D 72 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7748 (tm-30) REVERT: D 75 ILE cc_start: 0.9190 (mt) cc_final: 0.8682 (pt) REVERT: D 113 LYS cc_start: 0.8596 (ptmt) cc_final: 0.7877 (ttmt) REVERT: D 117 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8313 (mt-10) REVERT: D 121 GLN cc_start: 0.8547 (tp40) cc_final: 0.8218 (tp40) REVERT: D 137 GLN cc_start: 0.8158 (mt0) cc_final: 0.7712 (mm-40) REVERT: D 184 ASP cc_start: 0.8129 (t70) cc_final: 0.7845 (t70) REVERT: D 226 GLU cc_start: 0.7693 (tt0) cc_final: 0.7354 (tt0) REVERT: D 269 MET cc_start: 0.7898 (tpp) cc_final: 0.7682 (tpp) REVERT: D 299 MET cc_start: 0.7956 (mtt) cc_final: 0.7350 (mtt) REVERT: D 305 MET cc_start: 0.8321 (mmm) cc_final: 0.7843 (tpp) REVERT: D 356 TRP cc_start: 0.8453 (m100) cc_final: 0.8012 (m100) REVERT: D 369 ILE cc_start: 0.8923 (tp) cc_final: 0.8646 (tp) REVERT: E 43 VAL cc_start: 0.8246 (t) cc_final: 0.7853 (t) REVERT: E 47 MET cc_start: 0.6515 (mtm) cc_final: 0.5357 (ttt) REVERT: E 72 GLU cc_start: 0.8523 (pp20) cc_final: 0.8085 (pp20) REVERT: E 80 ASP cc_start: 0.8240 (t70) cc_final: 0.7649 (t0) REVERT: E 137 GLN cc_start: 0.8274 (mt0) cc_final: 0.8035 (mt0) REVERT: E 283 MET cc_start: 0.8646 (mmp) cc_final: 0.8356 (tpp) REVERT: E 371 HIS cc_start: 0.7472 (t70) cc_final: 0.7040 (t70) outliers start: 2 outliers final: 0 residues processed: 447 average time/residue: 0.1103 time to fit residues: 75.4343 Evaluate side-chains 297 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 178 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS B 12 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS C 87 HIS ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 40 HIS ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.085859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.074552 restraints weight = 36591.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.077318 restraints weight = 19418.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.079171 restraints weight = 11844.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.080440 restraints weight = 7939.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.081265 restraints weight = 5696.817| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14960 Z= 0.221 Angle : 0.727 7.957 20305 Z= 0.370 Chirality : 0.047 0.157 2255 Planarity : 0.005 0.037 2595 Dihedral : 6.575 60.813 2085 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.30 % Favored : 94.21 % Rotamer: Outliers : 0.19 % Allowed : 3.39 % 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: -0.23 (0.20), residues: 1830 helix: 0.56 (0.17), residues: 825 sheet: -0.78 (0.28), residues: 325 loop : -0.52 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 290 TYR 0.029 0.002 TYR A 279 PHE 0.020 0.002 PHE C 31 TRP 0.017 0.002 TRP C 79 HIS 0.008 0.002 HIS E 371 Details of bonding type rmsd covalent geometry : bond 0.00493 (14960) covalent geometry : angle 0.72740 (20305) hydrogen bonds : bond 0.04311 ( 780) hydrogen bonds : angle 5.26699 ( 2025) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 371 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7468 (m-30) cc_final: 0.7000 (t0) REVERT: A 34 ILE cc_start: 0.9689 (mt) cc_final: 0.9343 (tp) REVERT: A 67 LEU cc_start: 0.9450 (mp) cc_final: 0.9245 (mp) REVERT: A 78 ASN cc_start: 0.7967 (t0) cc_final: 0.7761 (t0) REVERT: A 101 HIS cc_start: 0.8431 (p-80) cc_final: 0.8077 (p-80) REVERT: A 154 ASP cc_start: 0.8280 (t70) cc_final: 0.7696 (t70) REVERT: A 166 TYR cc_start: 0.8034 (t80) cc_final: 0.7712 (t80) REVERT: A 167 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7697 (tm-30) REVERT: A 217 CYS cc_start: 0.8501 (m) cc_final: 0.8138 (m) REVERT: A 246 GLN cc_start: 0.8699 (mm110) cc_final: 0.8392 (mm-40) REVERT: A 292 ASP cc_start: 0.8015 (m-30) cc_final: 0.7427 (t0) REVERT: A 305 MET cc_start: 0.8707 (mmm) cc_final: 0.8498 (mmm) REVERT: B 47 MET cc_start: 0.6098 (mtm) cc_final: 0.5029 (tpp) REVERT: B 83 GLU cc_start: 0.8978 (pp20) cc_final: 0.8600 (pt0) REVERT: B 91 TYR cc_start: 0.9034 (m-80) cc_final: 0.8680 (m-10) REVERT: B 113 LYS cc_start: 0.8848 (ptmt) cc_final: 0.8593 (pttt) REVERT: B 117 GLU cc_start: 0.8522 (pt0) cc_final: 0.8308 (pp20) REVERT: B 246 GLN cc_start: 0.8862 (mt0) cc_final: 0.8358 (mt0) REVERT: C 80 ASP cc_start: 0.7946 (p0) cc_final: 0.7551 (p0) REVERT: C 82 MET cc_start: 0.8634 (tmm) cc_final: 0.8130 (tmm) REVERT: C 113 LYS cc_start: 0.9000 (ptmt) cc_final: 0.8658 (ttpt) REVERT: C 161 HIS cc_start: 0.9270 (p90) cc_final: 0.8847 (p90) REVERT: C 176 MET cc_start: 0.7445 (mtp) cc_final: 0.7072 (mtt) REVERT: C 222 ASP cc_start: 0.7200 (p0) cc_final: 0.6697 (p0) REVERT: C 227 MET cc_start: 0.8653 (tmm) cc_final: 0.8298 (tmm) REVERT: C 269 MET cc_start: 0.8111 (mmm) cc_final: 0.7736 (tpp) REVERT: C 276 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7602 (tm-30) REVERT: C 288 ASP cc_start: 0.7082 (t70) cc_final: 0.6829 (t70) REVERT: C 292 ASP cc_start: 0.8180 (m-30) cc_final: 0.7745 (t0) REVERT: C 299 MET cc_start: 0.8596 (ttm) cc_final: 0.8318 (mtp) REVERT: D 72 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8054 (tm-30) REVERT: D 75 ILE cc_start: 0.9353 (mt) cc_final: 0.9012 (pt) REVERT: D 184 ASP cc_start: 0.8397 (t70) cc_final: 0.8168 (t70) REVERT: D 305 MET cc_start: 0.8468 (mmm) cc_final: 0.8211 (tpp) REVERT: D 316 GLU cc_start: 0.8400 (tp30) cc_final: 0.7916 (tp30) REVERT: E 72 GLU cc_start: 0.8962 (pp20) cc_final: 0.8474 (pp20) REVERT: E 80 ASP cc_start: 0.8396 (t70) cc_final: 0.8095 (t0) REVERT: E 86 TRP cc_start: 0.9129 (m-10) cc_final: 0.8891 (m-10) REVERT: E 87 HIS cc_start: 0.8668 (t-90) cc_final: 0.8392 (t-90) REVERT: E 119 MET cc_start: 0.8710 (ptp) cc_final: 0.8510 (ptt) REVERT: E 140 LEU cc_start: 0.8894 (mt) cc_final: 0.8507 (mp) REVERT: E 154 ASP cc_start: 0.8366 (t0) cc_final: 0.8094 (t0) REVERT: E 283 MET cc_start: 0.8707 (mmp) cc_final: 0.8362 (tpp) REVERT: E 305 MET cc_start: 0.7848 (mmt) cc_final: 0.7389 (mmt) outliers start: 3 outliers final: 0 residues processed: 373 average time/residue: 0.1032 time to fit residues: 60.4919 Evaluate side-chains 271 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 117 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 90 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 chunk 160 optimal weight: 0.0670 chunk 101 optimal weight: 4.9990 overall best weight: 1.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS E 12 ASN E 40 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.084525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.073090 restraints weight = 36833.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.075903 restraints weight = 19251.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.077768 restraints weight = 11603.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.079044 restraints weight = 7704.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.079928 restraints weight = 5503.497| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14960 Z= 0.144 Angle : 0.657 7.111 20305 Z= 0.330 Chirality : 0.045 0.186 2255 Planarity : 0.004 0.039 2595 Dihedral : 6.297 63.814 2085 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.75 % Favored : 94.97 % Rotamer: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.01 (0.20), residues: 1830 helix: 0.77 (0.18), residues: 820 sheet: -0.79 (0.28), residues: 325 loop : -0.38 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 206 TYR 0.022 0.001 TYR A 279 PHE 0.014 0.001 PHE B 124 TRP 0.012 0.002 TRP B 86 HIS 0.005 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00318 (14960) covalent geometry : angle 0.65651 (20305) hydrogen bonds : bond 0.03775 ( 780) hydrogen bonds : angle 5.06623 ( 2025) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 388 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7618 (m-30) cc_final: 0.7217 (t0) REVERT: A 34 ILE cc_start: 0.9686 (mt) cc_final: 0.9329 (tp) REVERT: A 43 VAL cc_start: 0.8320 (t) cc_final: 0.7978 (p) REVERT: A 78 ASN cc_start: 0.7952 (t0) cc_final: 0.7667 (t0) REVERT: A 121 GLN cc_start: 0.9248 (pp30) cc_final: 0.8933 (pp30) REVERT: A 154 ASP cc_start: 0.8046 (t70) cc_final: 0.7345 (t70) REVERT: A 217 CYS cc_start: 0.8533 (m) cc_final: 0.8138 (m) REVERT: A 292 ASP cc_start: 0.8105 (m-30) cc_final: 0.7442 (t0) REVERT: A 305 MET cc_start: 0.8644 (mmm) cc_final: 0.8364 (mmm) REVERT: B 82 MET cc_start: 0.8508 (mmm) cc_final: 0.8208 (tpt) REVERT: B 83 GLU cc_start: 0.8961 (pp20) cc_final: 0.8694 (pt0) REVERT: B 91 TYR cc_start: 0.9115 (m-80) cc_final: 0.8711 (m-10) REVERT: B 113 LYS cc_start: 0.8992 (ptmt) cc_final: 0.8228 (pttt) REVERT: B 200 PHE cc_start: 0.9009 (m-80) cc_final: 0.8572 (m-80) REVERT: B 246 GLN cc_start: 0.8964 (mt0) cc_final: 0.8399 (mt0) REVERT: B 305 MET cc_start: 0.9047 (mmm) cc_final: 0.8202 (mmt) REVERT: C 82 MET cc_start: 0.8595 (tmm) cc_final: 0.8196 (tmm) REVERT: C 113 LYS cc_start: 0.8966 (ptmt) cc_final: 0.8663 (ttpt) REVERT: C 222 ASP cc_start: 0.7197 (p0) cc_final: 0.6723 (p0) REVERT: C 227 MET cc_start: 0.8646 (tmm) cc_final: 0.8374 (tmm) REVERT: C 269 MET cc_start: 0.7835 (mmm) cc_final: 0.7541 (tpp) REVERT: C 276 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7510 (tm-30) REVERT: C 288 ASP cc_start: 0.7021 (t70) cc_final: 0.6791 (t70) REVERT: C 292 ASP cc_start: 0.8202 (m-30) cc_final: 0.7821 (t0) REVERT: D 72 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7956 (tm-30) REVERT: D 75 ILE cc_start: 0.9257 (mt) cc_final: 0.8847 (pt) REVERT: D 113 LYS cc_start: 0.8621 (ptmt) cc_final: 0.8419 (ptpt) REVERT: D 180 LEU cc_start: 0.8891 (tp) cc_final: 0.8659 (tp) REVERT: D 184 ASP cc_start: 0.8252 (t70) cc_final: 0.7969 (t70) REVERT: D 316 GLU cc_start: 0.8448 (tp30) cc_final: 0.7872 (tp30) REVERT: E 39 ARG cc_start: 0.8754 (ttp-170) cc_final: 0.8233 (ttt90) REVERT: E 72 GLU cc_start: 0.8890 (pp20) cc_final: 0.8400 (pp20) REVERT: E 80 ASP cc_start: 0.8369 (t70) cc_final: 0.8073 (t0) REVERT: E 87 HIS cc_start: 0.8485 (t-90) cc_final: 0.8273 (t-90) REVERT: E 113 LYS cc_start: 0.9301 (ttmm) cc_final: 0.9089 (mttm) REVERT: E 119 MET cc_start: 0.8459 (ptp) cc_final: 0.8222 (ptt) REVERT: E 137 GLN cc_start: 0.8860 (mt0) cc_final: 0.8626 (mt0) REVERT: E 154 ASP cc_start: 0.8510 (t0) cc_final: 0.8236 (t0) REVERT: E 157 ASP cc_start: 0.7191 (t70) cc_final: 0.6603 (t70) REVERT: E 283 MET cc_start: 0.8581 (mmp) cc_final: 0.8377 (tpp) REVERT: E 305 MET cc_start: 0.7995 (mmt) cc_final: 0.7483 (tpp) outliers start: 1 outliers final: 0 residues processed: 389 average time/residue: 0.1021 time to fit residues: 62.3196 Evaluate side-chains 267 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 168 optimal weight: 0.0470 chunk 35 optimal weight: 8.9990 chunk 169 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 12 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 40 HIS E 173 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.083874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.072683 restraints weight = 36693.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.075345 restraints weight = 19145.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.077202 restraints weight = 11701.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.078435 restraints weight = 7724.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.079321 restraints weight = 5518.792| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.6174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14960 Z= 0.157 Angle : 0.660 8.263 20305 Z= 0.332 Chirality : 0.045 0.193 2255 Planarity : 0.004 0.042 2595 Dihedral : 6.232 63.613 2085 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.25 % Favored : 94.54 % Rotamer: Outliers : 0.06 % Allowed : 1.92 % Favored : 98.02 % 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: 0.09 (0.20), residues: 1830 helix: 1.00 (0.18), residues: 790 sheet: -0.83 (0.29), residues: 325 loop : -0.43 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 62 TYR 0.018 0.001 TYR B 166 PHE 0.013 0.001 PHE B 124 TRP 0.015 0.002 TRP B 86 HIS 0.010 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00354 (14960) covalent geometry : angle 0.65953 (20305) hydrogen bonds : bond 0.03874 ( 780) hydrogen bonds : angle 5.03305 ( 2025) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7853 (m-30) cc_final: 0.7302 (t0) REVERT: A 34 ILE cc_start: 0.9687 (mt) cc_final: 0.9298 (tp) REVERT: A 78 ASN cc_start: 0.7939 (t0) cc_final: 0.7640 (t0) REVERT: A 154 ASP cc_start: 0.8038 (t70) cc_final: 0.7320 (t70) REVERT: A 246 GLN cc_start: 0.8615 (mm110) cc_final: 0.8414 (mm-40) REVERT: A 283 MET cc_start: 0.8679 (mmm) cc_final: 0.8332 (mmp) REVERT: A 305 MET cc_start: 0.8644 (mmm) cc_final: 0.8270 (mmm) REVERT: B 83 GLU cc_start: 0.8990 (pp20) cc_final: 0.8692 (pt0) REVERT: B 91 TYR cc_start: 0.9104 (m-80) cc_final: 0.8700 (m-10) REVERT: B 113 LYS cc_start: 0.8976 (ptmt) cc_final: 0.8277 (pttt) REVERT: B 305 MET cc_start: 0.9052 (mmm) cc_final: 0.8219 (mmt) REVERT: C 82 MET cc_start: 0.8578 (tmm) cc_final: 0.8204 (tmm) REVERT: C 113 LYS cc_start: 0.8964 (ptmt) cc_final: 0.8701 (ttpt) REVERT: C 190 MET cc_start: 0.8102 (mtm) cc_final: 0.7841 (mtt) REVERT: C 227 MET cc_start: 0.8685 (tmm) cc_final: 0.8391 (tmm) REVERT: C 269 MET cc_start: 0.7882 (mmm) cc_final: 0.7645 (tpp) REVERT: C 276 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7542 (tm-30) REVERT: C 288 ASP cc_start: 0.7071 (t70) cc_final: 0.6799 (t70) REVERT: C 292 ASP cc_start: 0.8165 (m-30) cc_final: 0.7692 (t0) REVERT: C 299 MET cc_start: 0.8602 (ttm) cc_final: 0.8336 (mtp) REVERT: D 72 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7851 (tm-30) REVERT: D 75 ILE cc_start: 0.9273 (mt) cc_final: 0.8941 (pt) REVERT: D 113 LYS cc_start: 0.8696 (ptmt) cc_final: 0.8431 (ptpt) REVERT: D 184 ASP cc_start: 0.8258 (t70) cc_final: 0.8006 (t70) REVERT: D 217 CYS cc_start: 0.8158 (m) cc_final: 0.7572 (m) REVERT: D 283 MET cc_start: 0.8422 (mmt) cc_final: 0.7940 (mmt) REVERT: D 316 GLU cc_start: 0.8440 (tp30) cc_final: 0.7930 (tp30) REVERT: E 72 GLU cc_start: 0.8981 (pp20) cc_final: 0.8521 (pp20) REVERT: E 80 ASP cc_start: 0.8340 (t70) cc_final: 0.8020 (t0) REVERT: E 119 MET cc_start: 0.8513 (ptp) cc_final: 0.8273 (ptt) REVERT: E 140 LEU cc_start: 0.8873 (mt) cc_final: 0.8510 (mp) REVERT: E 154 ASP cc_start: 0.8671 (t0) cc_final: 0.8235 (t0) REVERT: E 283 MET cc_start: 0.8566 (mmp) cc_final: 0.8301 (mmm) REVERT: E 368 SER cc_start: 0.9115 (p) cc_final: 0.8750 (t) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.1060 time to fit residues: 61.2831 Evaluate side-chains 261 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 96 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 141 optimal weight: 0.5980 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS E 12 ASN E 40 HIS E 111 ASN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.080292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.069369 restraints weight = 37749.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.071965 restraints weight = 19963.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.073675 restraints weight = 12131.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.074811 restraints weight = 8120.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.075672 restraints weight = 5888.529| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.6510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14960 Z= 0.249 Angle : 0.751 10.534 20305 Z= 0.382 Chirality : 0.048 0.202 2255 Planarity : 0.005 0.053 2595 Dihedral : 6.598 63.816 2085 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.41 % Favored : 94.32 % Rotamer: Outliers : 0.13 % Allowed : 1.73 % Favored : 98.15 % 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: -0.27 (0.19), residues: 1830 helix: 0.57 (0.18), residues: 825 sheet: -0.84 (0.30), residues: 315 loop : -0.59 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 147 TYR 0.025 0.002 TYR B 198 PHE 0.018 0.002 PHE B 255 TRP 0.023 0.003 TRP B 356 HIS 0.007 0.002 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00563 (14960) covalent geometry : angle 0.75104 (20305) hydrogen bonds : bond 0.04510 ( 780) hydrogen bonds : angle 5.29155 ( 2025) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 332 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.9746 (mt) cc_final: 0.9343 (tp) REVERT: A 43 VAL cc_start: 0.8578 (t) cc_final: 0.7896 (t) REVERT: A 78 ASN cc_start: 0.8010 (t0) cc_final: 0.7717 (t0) REVERT: A 154 ASP cc_start: 0.8090 (t70) cc_final: 0.7498 (t70) REVERT: A 217 CYS cc_start: 0.8460 (m) cc_final: 0.8213 (m) REVERT: A 246 GLN cc_start: 0.8630 (mm110) cc_final: 0.8370 (mm-40) REVERT: A 283 MET cc_start: 0.8730 (mmm) cc_final: 0.8337 (mmp) REVERT: A 305 MET cc_start: 0.8651 (mmm) cc_final: 0.8381 (mmm) REVERT: B 83 GLU cc_start: 0.8911 (pp20) cc_final: 0.8702 (pt0) REVERT: B 91 TYR cc_start: 0.9089 (m-80) cc_final: 0.8620 (m-10) REVERT: B 113 LYS cc_start: 0.8970 (ptmt) cc_final: 0.8720 (pttt) REVERT: B 199 SER cc_start: 0.8294 (m) cc_final: 0.7805 (p) REVERT: B 305 MET cc_start: 0.9091 (mmm) cc_final: 0.8309 (mmt) REVERT: C 80 ASP cc_start: 0.8127 (p0) cc_final: 0.7753 (p0) REVERT: C 82 MET cc_start: 0.8481 (tmm) cc_final: 0.7994 (tmm) REVERT: C 121 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8541 (tm-30) REVERT: C 154 ASP cc_start: 0.8852 (t0) cc_final: 0.8601 (t0) REVERT: C 227 MET cc_start: 0.8661 (tmm) cc_final: 0.8360 (tmm) REVERT: C 246 GLN cc_start: 0.8508 (tp-100) cc_final: 0.8305 (tp-100) REVERT: C 276 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7639 (tm-30) REVERT: C 288 ASP cc_start: 0.7005 (t70) cc_final: 0.6690 (t70) REVERT: C 292 ASP cc_start: 0.8126 (m-30) cc_final: 0.7662 (t0) REVERT: C 299 MET cc_start: 0.8692 (ttm) cc_final: 0.8344 (mtp) REVERT: C 336 LYS cc_start: 0.8857 (mtpt) cc_final: 0.8525 (mmmt) REVERT: D 75 ILE cc_start: 0.9368 (mt) cc_final: 0.9026 (pt) REVERT: D 113 LYS cc_start: 0.8749 (ptmt) cc_final: 0.8476 (ptpt) REVERT: D 153 LEU cc_start: 0.9105 (tp) cc_final: 0.8896 (tp) REVERT: D 180 LEU cc_start: 0.8845 (tp) cc_final: 0.8633 (tp) REVERT: D 184 ASP cc_start: 0.8325 (t70) cc_final: 0.8037 (t70) REVERT: D 316 GLU cc_start: 0.8590 (tp30) cc_final: 0.8013 (tp30) REVERT: D 325 MET cc_start: 0.8012 (mmp) cc_final: 0.7791 (mmm) REVERT: D 352 PHE cc_start: 0.8976 (t80) cc_final: 0.8727 (t80) REVERT: E 72 GLU cc_start: 0.9119 (pp20) cc_final: 0.8589 (pp20) REVERT: E 80 ASP cc_start: 0.8384 (t70) cc_final: 0.8122 (t0) REVERT: E 100 GLU cc_start: 0.7687 (tt0) cc_final: 0.7163 (tt0) REVERT: E 101 HIS cc_start: 0.7998 (p-80) cc_final: 0.6997 (p-80) REVERT: E 103 THR cc_start: 0.9108 (t) cc_final: 0.8883 (t) REVERT: E 154 ASP cc_start: 0.8643 (t0) cc_final: 0.8209 (t0) REVERT: E 305 MET cc_start: 0.8073 (mmt) cc_final: 0.7382 (tpt) outliers start: 2 outliers final: 1 residues processed: 334 average time/residue: 0.0988 time to fit residues: 53.0706 Evaluate side-chains 255 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 52 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 165 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN E 40 HIS E 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.082191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.071111 restraints weight = 37239.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.073755 restraints weight = 19500.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.075528 restraints weight = 11822.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.076779 restraints weight = 7872.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.077641 restraints weight = 5632.158| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.6675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14960 Z= 0.186 Angle : 0.709 9.088 20305 Z= 0.356 Chirality : 0.046 0.201 2255 Planarity : 0.005 0.047 2595 Dihedral : 6.549 63.152 2085 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.92 % Favored : 94.81 % Rotamer: Outliers : 0.06 % Allowed : 0.89 % Favored : 99.04 % 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: -0.21 (0.19), residues: 1830 helix: 0.63 (0.18), residues: 825 sheet: -0.81 (0.30), residues: 315 loop : -0.58 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 147 TYR 0.021 0.002 TYR A 166 PHE 0.013 0.001 PHE E 255 TRP 0.037 0.002 TRP E 86 HIS 0.008 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00425 (14960) covalent geometry : angle 0.70934 (20305) hydrogen bonds : bond 0.04082 ( 780) hydrogen bonds : angle 5.18285 ( 2025) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 332 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.9685 (mt) cc_final: 0.9426 (tp) REVERT: A 78 ASN cc_start: 0.7940 (t0) cc_final: 0.7643 (t0) REVERT: A 121 GLN cc_start: 0.9218 (pp30) cc_final: 0.8967 (pp30) REVERT: A 154 ASP cc_start: 0.8046 (t70) cc_final: 0.7449 (t70) REVERT: A 176 MET cc_start: 0.7812 (mpp) cc_final: 0.7498 (mpp) REVERT: A 217 CYS cc_start: 0.8543 (m) cc_final: 0.8260 (m) REVERT: A 246 GLN cc_start: 0.8637 (mm110) cc_final: 0.8416 (mm-40) REVERT: A 283 MET cc_start: 0.9002 (mmm) cc_final: 0.8541 (mmm) REVERT: A 305 MET cc_start: 0.8664 (mmm) cc_final: 0.8311 (mmm) REVERT: A 360 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8640 (tm-30) REVERT: B 91 TYR cc_start: 0.9112 (m-80) cc_final: 0.8693 (m-10) REVERT: B 113 LYS cc_start: 0.9014 (ptmt) cc_final: 0.8752 (pttt) REVERT: B 176 MET cc_start: 0.7919 (mtt) cc_final: 0.7659 (mtt) REVERT: B 199 SER cc_start: 0.8180 (m) cc_final: 0.7716 (p) REVERT: B 305 MET cc_start: 0.9033 (mmm) cc_final: 0.8316 (mmt) REVERT: C 82 MET cc_start: 0.8419 (tmm) cc_final: 0.8113 (tmm) REVERT: C 121 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8564 (tm-30) REVERT: C 190 MET cc_start: 0.8208 (mtm) cc_final: 0.7953 (mtt) REVERT: C 227 MET cc_start: 0.8632 (tmm) cc_final: 0.8330 (tmm) REVERT: C 246 GLN cc_start: 0.8618 (tp-100) cc_final: 0.8402 (tp-100) REVERT: C 276 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7499 (tm-30) REVERT: C 288 ASP cc_start: 0.7033 (t70) cc_final: 0.6718 (t70) REVERT: C 292 ASP cc_start: 0.8165 (m-30) cc_final: 0.7676 (t0) REVERT: C 299 MET cc_start: 0.8579 (ttm) cc_final: 0.8304 (mtp) REVERT: D 72 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8211 (tm-30) REVERT: D 75 ILE cc_start: 0.9359 (mt) cc_final: 0.8994 (pt) REVERT: D 113 LYS cc_start: 0.8713 (ptmt) cc_final: 0.8457 (ptpt) REVERT: D 184 ASP cc_start: 0.8297 (t70) cc_final: 0.8008 (t70) REVERT: D 217 CYS cc_start: 0.8004 (m) cc_final: 0.7582 (m) REVERT: D 292 ASP cc_start: 0.8260 (m-30) cc_final: 0.7721 (t0) REVERT: D 316 GLU cc_start: 0.8575 (tp30) cc_final: 0.8004 (tp30) REVERT: D 352 PHE cc_start: 0.8889 (t80) cc_final: 0.8551 (t80) REVERT: E 72 GLU cc_start: 0.9147 (pp20) cc_final: 0.8606 (pp20) REVERT: E 80 ASP cc_start: 0.8536 (t70) cc_final: 0.8167 (t0) REVERT: E 140 LEU cc_start: 0.8888 (mt) cc_final: 0.8529 (mp) REVERT: E 154 ASP cc_start: 0.8668 (t0) cc_final: 0.8156 (t0) REVERT: E 305 MET cc_start: 0.8101 (mmt) cc_final: 0.7433 (tpt) REVERT: E 325 MET cc_start: 0.8498 (mmm) cc_final: 0.7841 (mmm) outliers start: 1 outliers final: 0 residues processed: 333 average time/residue: 0.0974 time to fit residues: 52.1077 Evaluate side-chains 243 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 39 optimal weight: 0.4980 chunk 136 optimal weight: 0.0270 chunk 25 optimal weight: 0.2980 chunk 179 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 41 GLN C 87 HIS C 371 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS E 40 HIS ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.086318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.075102 restraints weight = 35812.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.077873 restraints weight = 18459.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.079715 restraints weight = 10998.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.080952 restraints weight = 7234.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.081800 restraints weight = 5157.242| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.6840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14960 Z= 0.124 Angle : 0.675 8.650 20305 Z= 0.337 Chirality : 0.045 0.197 2255 Planarity : 0.004 0.046 2595 Dihedral : 6.254 62.860 2085 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.25 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: 0.01 (0.20), residues: 1830 helix: 0.86 (0.18), residues: 790 sheet: -0.64 (0.31), residues: 310 loop : -0.51 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 147 TYR 0.021 0.001 TYR A 279 PHE 0.011 0.001 PHE E 255 TRP 0.040 0.003 TRP E 86 HIS 0.013 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00275 (14960) covalent geometry : angle 0.67546 (20305) hydrogen bonds : bond 0.03626 ( 780) hydrogen bonds : angle 5.06462 ( 2025) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.9575 (mt) cc_final: 0.9325 (tp) REVERT: A 78 ASN cc_start: 0.7913 (t0) cc_final: 0.7609 (t0) REVERT: A 154 ASP cc_start: 0.8057 (t70) cc_final: 0.7490 (t70) REVERT: A 176 MET cc_start: 0.7838 (mpp) cc_final: 0.7564 (mpp) REVERT: A 217 CYS cc_start: 0.8355 (m) cc_final: 0.8022 (m) REVERT: A 305 MET cc_start: 0.8567 (mmm) cc_final: 0.8286 (mmm) REVERT: A 340 TRP cc_start: 0.9053 (t60) cc_final: 0.8456 (t60) REVERT: B 91 TYR cc_start: 0.9122 (m-80) cc_final: 0.8681 (m-10) REVERT: B 115 ASN cc_start: 0.8896 (m-40) cc_final: 0.8449 (t0) REVERT: B 176 MET cc_start: 0.7911 (mtt) cc_final: 0.7654 (mtt) REVERT: B 199 SER cc_start: 0.8081 (m) cc_final: 0.7802 (p) REVERT: B 280 ASN cc_start: 0.7951 (m110) cc_final: 0.7566 (m110) REVERT: B 305 MET cc_start: 0.8968 (mmm) cc_final: 0.8578 (tpp) REVERT: C 121 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8550 (tm-30) REVERT: C 190 MET cc_start: 0.8123 (mtm) cc_final: 0.7906 (mtt) REVERT: C 227 MET cc_start: 0.8602 (tmm) cc_final: 0.8388 (tmm) REVERT: C 246 GLN cc_start: 0.8586 (tp-100) cc_final: 0.8338 (tp-100) REVERT: C 276 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7489 (tm-30) REVERT: C 288 ASP cc_start: 0.6760 (t70) cc_final: 0.6474 (t70) REVERT: C 292 ASP cc_start: 0.8150 (m-30) cc_final: 0.7738 (t0) REVERT: D 113 LYS cc_start: 0.8844 (ptmt) cc_final: 0.8634 (ptpt) REVERT: D 180 LEU cc_start: 0.8975 (tp) cc_final: 0.8764 (tp) REVERT: D 184 ASP cc_start: 0.8065 (t70) cc_final: 0.7822 (t70) REVERT: D 283 MET cc_start: 0.8403 (mmt) cc_final: 0.8073 (mmp) REVERT: D 316 GLU cc_start: 0.8473 (tp30) cc_final: 0.7938 (tp30) REVERT: D 356 TRP cc_start: 0.8395 (m100) cc_final: 0.7937 (m100) REVERT: E 72 GLU cc_start: 0.9083 (pp20) cc_final: 0.8634 (pp20) REVERT: E 80 ASP cc_start: 0.8450 (t70) cc_final: 0.8094 (t0) REVERT: E 154 ASP cc_start: 0.8567 (t0) cc_final: 0.8028 (t0) REVERT: E 283 MET cc_start: 0.8519 (mmt) cc_final: 0.8168 (mmm) REVERT: E 305 MET cc_start: 0.7989 (mmt) cc_final: 0.7570 (tpp) REVERT: E 371 HIS cc_start: 0.7657 (t-90) cc_final: 0.7195 (t-90) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.1019 time to fit residues: 58.1127 Evaluate side-chains 269 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 134 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 129 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 280 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 371 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS E 40 HIS ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS E 371 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.085594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.074316 restraints weight = 36141.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.077065 restraints weight = 18902.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.078904 restraints weight = 11358.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.080166 restraints weight = 7539.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.081068 restraints weight = 5386.380| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.6963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14960 Z= 0.143 Angle : 0.692 8.623 20305 Z= 0.346 Chirality : 0.045 0.222 2255 Planarity : 0.004 0.042 2595 Dihedral : 6.208 60.586 2085 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.03 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -0.01 (0.20), residues: 1830 helix: 0.83 (0.18), residues: 790 sheet: -0.68 (0.30), residues: 310 loop : -0.49 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 147 TYR 0.024 0.001 TYR A 166 PHE 0.012 0.001 PHE D 200 TRP 0.042 0.002 TRP E 86 HIS 0.007 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00326 (14960) covalent geometry : angle 0.69161 (20305) hydrogen bonds : bond 0.03788 ( 780) hydrogen bonds : angle 5.09159 ( 2025) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.9582 (mt) cc_final: 0.9318 (tp) REVERT: A 78 ASN cc_start: 0.7845 (t0) cc_final: 0.7494 (t0) REVERT: A 154 ASP cc_start: 0.7987 (t70) cc_final: 0.7358 (t70) REVERT: A 176 MET cc_start: 0.7838 (mpp) cc_final: 0.7545 (mpp) REVERT: A 217 CYS cc_start: 0.8649 (m) cc_final: 0.8337 (m) REVERT: A 279 TYR cc_start: 0.8889 (t80) cc_final: 0.8680 (t80) REVERT: A 297 ASN cc_start: 0.8875 (t0) cc_final: 0.8636 (t0) REVERT: A 305 MET cc_start: 0.8692 (mmm) cc_final: 0.8345 (mmm) REVERT: A 340 TRP cc_start: 0.9047 (t60) cc_final: 0.8304 (t60) REVERT: B 43 VAL cc_start: 0.8668 (t) cc_final: 0.8409 (t) REVERT: B 91 TYR cc_start: 0.9101 (m-80) cc_final: 0.8634 (m-10) REVERT: B 115 ASN cc_start: 0.9013 (m-40) cc_final: 0.8117 (t0) REVERT: B 176 MET cc_start: 0.7936 (mtt) cc_final: 0.7638 (mtt) REVERT: B 199 SER cc_start: 0.8195 (m) cc_final: 0.7902 (p) REVERT: B 257 CYS cc_start: 0.9311 (t) cc_final: 0.9101 (t) REVERT: B 305 MET cc_start: 0.9022 (mmm) cc_final: 0.8557 (tpp) REVERT: C 121 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8129 (tm-30) REVERT: C 227 MET cc_start: 0.8584 (tmm) cc_final: 0.8296 (tmm) REVERT: C 276 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7515 (tm-30) REVERT: C 288 ASP cc_start: 0.6812 (t70) cc_final: 0.6472 (t70) REVERT: C 292 ASP cc_start: 0.8174 (m-30) cc_final: 0.7664 (t0) REVERT: D 113 LYS cc_start: 0.8826 (ptmt) cc_final: 0.8615 (ptpt) REVERT: D 180 LEU cc_start: 0.8880 (tp) cc_final: 0.8599 (tp) REVERT: D 184 ASP cc_start: 0.8129 (t70) cc_final: 0.7860 (t70) REVERT: D 283 MET cc_start: 0.8548 (mmt) cc_final: 0.8210 (mmp) REVERT: D 316 GLU cc_start: 0.8467 (tp30) cc_final: 0.7948 (tp30) REVERT: D 356 TRP cc_start: 0.8420 (m100) cc_final: 0.7950 (m100) REVERT: E 72 GLU cc_start: 0.9088 (pp20) cc_final: 0.8671 (pp20) REVERT: E 80 ASP cc_start: 0.8458 (t70) cc_final: 0.8076 (t0) REVERT: E 140 LEU cc_start: 0.8860 (mt) cc_final: 0.8491 (mp) REVERT: E 154 ASP cc_start: 0.8614 (t0) cc_final: 0.7964 (t0) REVERT: E 155 SER cc_start: 0.8950 (t) cc_final: 0.8688 (p) REVERT: E 190 MET cc_start: 0.8428 (mmt) cc_final: 0.8044 (mmt) REVERT: E 283 MET cc_start: 0.8611 (mmt) cc_final: 0.8208 (mpp) REVERT: E 305 MET cc_start: 0.7901 (mmt) cc_final: 0.7482 (tpp) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.1002 time to fit residues: 55.0852 Evaluate side-chains 268 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 62 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 0.0370 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 168 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 108 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS C 371 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS E 40 HIS ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.086625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.075262 restraints weight = 36272.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.078060 restraints weight = 18968.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.079919 restraints weight = 11381.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.081124 restraints weight = 7549.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.082041 restraints weight = 5454.856| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.7099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14960 Z= 0.133 Angle : 0.685 8.757 20305 Z= 0.343 Chirality : 0.045 0.207 2255 Planarity : 0.004 0.043 2595 Dihedral : 6.132 60.550 2085 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.46 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.05 (0.20), residues: 1830 helix: 0.82 (0.19), residues: 785 sheet: -0.48 (0.31), residues: 300 loop : -0.45 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 147 TYR 0.021 0.001 TYR A 166 PHE 0.014 0.001 PHE D 200 TRP 0.030 0.002 TRP E 86 HIS 0.006 0.001 HIS E 371 Details of bonding type rmsd covalent geometry : bond 0.00301 (14960) covalent geometry : angle 0.68539 (20305) hydrogen bonds : bond 0.03697 ( 780) hydrogen bonds : angle 5.16102 ( 2025) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2286.26 seconds wall clock time: 40 minutes 34.31 seconds (2434.31 seconds total)