Starting phenix.real_space_refine on Sat Aug 23 08:30:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b87_44334/08_2025/9b87_44334.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b87_44334/08_2025/9b87_44334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b87_44334/08_2025/9b87_44334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b87_44334/08_2025/9b87_44334.map" model { file = "/net/cci-nas-00/data/ceres_data/9b87_44334/08_2025/9b87_44334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b87_44334/08_2025/9b87_44334.cif" } resolution = 2.65 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= 0.001 sd= 0.067 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 6980 2.51 5 N 1888 2.21 5 O 2004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10912 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2728 Classifications: {'peptide': 338} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 317} Chain: "D" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2728 Classifications: {'peptide': 338} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 317} Chain: "C" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2728 Classifications: {'peptide': 338} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 317} Chain: "B" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2728 Classifications: {'peptide': 338} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 317} Time building chain proxies: 2.55, per 1000 atoms: 0.23 Number of scatterers: 10912 At special positions: 0 Unit cell: (78.84, 106.92, 105.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 2004 8.00 N 1888 7.00 C 6980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 396.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2504 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 20 sheets defined 54.6% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 54 through 67 Processing helix chain 'A' and resid 69 through 85 Processing helix chain 'A' and resid 114 through 132 Processing helix chain 'A' and resid 134 through 152 removed outlier: 3.536A pdb=" N THR A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 192 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 197 through 212 removed outlier: 3.938A pdb=" N GLU A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 253 removed outlier: 3.964A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 249 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 268 removed outlier: 4.175A pdb=" N ALA A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 263 " --> pdb=" O PRO A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 279 removed outlier: 3.655A pdb=" N ALA A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 308 removed outlier: 3.526A pdb=" N SER A 301 " --> pdb=" O PRO A 297 " (cutoff:3.500A) Proline residue: A 306 - end of helix Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 330 through 345 Processing helix chain 'D' and resid 25 through 36 Processing helix chain 'D' and resid 54 through 67 Processing helix chain 'D' and resid 69 through 85 Processing helix chain 'D' and resid 114 through 133 Processing helix chain 'D' and resid 134 through 152 removed outlier: 3.542A pdb=" N THR D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 192 Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 197 through 212 removed outlier: 3.810A pdb=" N GLU D 203 " --> pdb=" O THR D 199 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 254 removed outlier: 3.963A pdb=" N TYR D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET D 249 " --> pdb=" O ILE D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 268 removed outlier: 4.491A pdb=" N ARG D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 279 removed outlier: 3.671A pdb=" N ALA D 272 " --> pdb=" O PHE D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 308 removed outlier: 3.525A pdb=" N SER D 301 " --> pdb=" O PRO D 297 " (cutoff:3.500A) Proline residue: D 306 - end of helix Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 330 through 345 Processing helix chain 'C' and resid 25 through 36 Processing helix chain 'C' and resid 54 through 67 Processing helix chain 'C' and resid 69 through 85 Processing helix chain 'C' and resid 114 through 132 Processing helix chain 'C' and resid 134 through 152 removed outlier: 3.581A pdb=" N THR C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 183 removed outlier: 4.132A pdb=" N LEU C 183 " --> pdb=" O PRO C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 192 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.986A pdb=" N GLU C 203 " --> pdb=" O THR C 199 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 253 removed outlier: 4.008A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET C 249 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 268 removed outlier: 4.478A pdb=" N ARG C 263 " --> pdb=" O PRO C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 279 removed outlier: 3.614A pdb=" N ALA C 272 " --> pdb=" O PHE C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 308 removed outlier: 3.547A pdb=" N SER C 301 " --> pdb=" O PRO C 297 " (cutoff:3.500A) Proline residue: C 306 - end of helix Processing helix chain 'C' and resid 310 through 324 Processing helix chain 'C' and resid 330 through 345 Processing helix chain 'B' and resid 25 through 36 Processing helix chain 'B' and resid 54 through 67 Processing helix chain 'B' and resid 69 through 85 Processing helix chain 'B' and resid 114 through 132 Processing helix chain 'B' and resid 134 through 152 removed outlier: 3.546A pdb=" N THR B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 192 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 197 through 212 removed outlier: 3.780A pdb=" N GLU B 203 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 253 removed outlier: 3.976A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET B 249 " --> pdb=" O ILE B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 268 removed outlier: 4.353A pdb=" N ALA B 262 " --> pdb=" O ASP B 258 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 removed outlier: 3.674A pdb=" N ALA B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 308 removed outlier: 3.520A pdb=" N SER B 301 " --> pdb=" O PRO B 297 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) Proline residue: B 306 - end of helix Processing helix chain 'B' and resid 315 through 324 Processing helix chain 'B' and resid 330 through 345 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 6.777A pdb=" N LEU A 97 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 156 Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 178 removed outlier: 4.722A pdb=" N ARG A 223 " --> pdb=" O GLN A 231 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 240 Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 350 Processing sheet with id=AA6, first strand: chain 'D' and resid 52 through 53 removed outlier: 6.879A pdb=" N LEU D 97 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 153 through 156 Processing sheet with id=AA8, first strand: chain 'D' and resid 175 through 178 removed outlier: 4.575A pdb=" N ARG D 223 " --> pdb=" O GLN D 231 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 239 through 240 removed outlier: 5.967A pdb=" N LYS D 295 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 348 through 350 Processing sheet with id=AB2, first strand: chain 'C' and resid 52 through 53 removed outlier: 6.722A pdb=" N LEU C 97 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 153 through 156 Processing sheet with id=AB4, first strand: chain 'C' and resid 175 through 178 Processing sheet with id=AB5, first strand: chain 'C' and resid 239 through 240 removed outlier: 5.972A pdb=" N LYS C 295 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 348 through 350 Processing sheet with id=AB7, first strand: chain 'B' and resid 52 through 53 removed outlier: 6.810A pdb=" N LEU B 97 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 153 through 156 Processing sheet with id=AB9, first strand: chain 'B' and resid 175 through 178 removed outlier: 4.617A pdb=" N ARG B 223 " --> pdb=" O GLN B 231 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 239 through 240 removed outlier: 5.799A pdb=" N LYS B 295 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 348 through 350 551 hydrogen bonds defined for protein. 1599 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.16 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: 2376 1.33 - 1.46: 3197 1.46 - 1.59: 5583 1.59 - 1.71: 0 1.71 - 1.84: 76 Bond restraints: 11232 Sorted by residual: bond pdb=" N LEU D 308 " pdb=" CA LEU D 308 " ideal model delta sigma weight residual 1.454 1.514 -0.060 1.27e-02 6.20e+03 2.24e+01 bond pdb=" CA ALA A 315 " pdb=" CB ALA A 315 " ideal model delta sigma weight residual 1.529 1.450 0.079 1.78e-02 3.16e+03 1.99e+01 bond pdb=" N GLN B 309 " pdb=" CA GLN B 309 " ideal model delta sigma weight residual 1.455 1.509 -0.055 1.37e-02 5.33e+03 1.60e+01 bond pdb=" N LYS B 105 " pdb=" CA LYS B 105 " ideal model delta sigma weight residual 1.453 1.500 -0.047 1.31e-02 5.83e+03 1.31e+01 bond pdb=" CA ALA B 315 " pdb=" CB ALA B 315 " ideal model delta sigma weight residual 1.536 1.484 0.052 1.53e-02 4.27e+03 1.16e+01 ... (remaining 11227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 14136 2.03 - 4.07: 980 4.07 - 6.10: 111 6.10 - 8.13: 16 8.13 - 10.17: 1 Bond angle restraints: 15244 Sorted by residual: angle pdb=" N GLN C 38 " pdb=" CA GLN C 38 " pdb=" C GLN C 38 " ideal model delta sigma weight residual 112.54 106.37 6.17 1.22e+00 6.72e-01 2.56e+01 angle pdb=" N ALA B 313 " pdb=" CA ALA B 313 " pdb=" C ALA B 313 " ideal model delta sigma weight residual 111.69 105.90 5.79 1.23e+00 6.61e-01 2.22e+01 angle pdb=" CB GLN A 314 " pdb=" CG GLN A 314 " pdb=" CD GLN A 314 " ideal model delta sigma weight residual 112.60 104.65 7.95 1.70e+00 3.46e-01 2.19e+01 angle pdb=" CA TRP C 343 " pdb=" C TRP C 343 " pdb=" O TRP C 343 " ideal model delta sigma weight residual 120.82 115.93 4.89 1.05e+00 9.07e-01 2.17e+01 angle pdb=" CB GLN C 314 " pdb=" CG GLN C 314 " pdb=" CD GLN C 314 " ideal model delta sigma weight residual 112.60 104.90 7.70 1.70e+00 3.46e-01 2.05e+01 ... (remaining 15239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 6061 17.13 - 34.27: 396 34.27 - 51.40: 76 51.40 - 68.53: 61 68.53 - 85.67: 26 Dihedral angle restraints: 6620 sinusoidal: 2720 harmonic: 3900 Sorted by residual: dihedral pdb=" C TRP C 343 " pdb=" N TRP C 343 " pdb=" CA TRP C 343 " pdb=" CB TRP C 343 " ideal model delta harmonic sigma weight residual -122.60 -134.22 11.62 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" N TRP C 343 " pdb=" C TRP C 343 " pdb=" CA TRP C 343 " pdb=" CB TRP C 343 " ideal model delta harmonic sigma weight residual 122.80 133.11 -10.31 0 2.50e+00 1.60e-01 1.70e+01 dihedral pdb=" CA ILE C 51 " pdb=" C ILE C 51 " pdb=" N THR C 52 " pdb=" CA THR C 52 " ideal model delta harmonic sigma weight residual 180.00 159.92 20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 6617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1208 0.078 - 0.155: 295 0.155 - 0.233: 33 0.233 - 0.310: 3 0.310 - 0.388: 1 Chirality restraints: 1540 Sorted by residual: chirality pdb=" CA TRP C 343 " pdb=" N TRP C 343 " pdb=" C TRP C 343 " pdb=" CB TRP C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CB ILE C 43 " pdb=" CA ILE C 43 " pdb=" CG1 ILE C 43 " pdb=" CG2 ILE C 43 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA TRP D 98 " pdb=" N TRP D 98 " pdb=" C TRP D 98 " pdb=" CB TRP D 98 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1537 not shown) Planarity restraints: 1976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 307 " -0.025 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C PHE D 307 " 0.081 2.00e-02 2.50e+03 pdb=" O PHE D 307 " -0.029 2.00e-02 2.50e+03 pdb=" N LEU D 308 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 243 " -0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" CG ASP D 243 " 0.064 2.00e-02 2.50e+03 pdb=" OD1 ASP D 243 " -0.023 2.00e-02 2.50e+03 pdb=" OD2 ASP D 243 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 202 " 0.286 9.50e-02 1.11e+02 1.28e-01 1.01e+01 pdb=" NE ARG C 202 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 202 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 202 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 202 " 0.010 2.00e-02 2.50e+03 ... (remaining 1973 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2502 2.79 - 3.32: 10364 3.32 - 3.85: 20159 3.85 - 4.37: 24401 4.37 - 4.90: 39234 Nonbonded interactions: 96660 Sorted by model distance: nonbonded pdb=" O GLN D 345 " pdb=" NE2 GLN B 319 " model vdw 2.266 3.120 nonbonded pdb=" OD2 ASP C 220 " pdb=" OG SER C 241 " model vdw 2.298 3.040 nonbonded pdb=" NZ LYS B 101 " pdb=" OE2 GLU B 107 " model vdw 2.345 3.120 nonbonded pdb=" O GLY B 158 " pdb=" NH2 ARG B 207 " model vdw 2.348 3.120 nonbonded pdb=" OD2 ASP C 34 " pdb=" OG SER C 328 " model vdw 2.361 3.040 ... (remaining 96655 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.720 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 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 : 0.009 0.079 11232 Z= 0.477 Angle : 1.100 10.169 15244 Z= 0.680 Chirality : 0.066 0.388 1540 Planarity : 0.012 0.128 1976 Dihedral : 14.681 85.669 4116 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.62 % Allowed : 4.95 % Favored : 94.43 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: -0.97 (0.20), residues: 1344 helix: -0.22 (0.17), residues: 680 sheet: -1.38 (0.51), residues: 88 loop : -0.89 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG B 320 TYR 0.037 0.007 TYR B 59 PHE 0.048 0.006 PHE B 300 TRP 0.037 0.005 TRP D 250 HIS 0.006 0.002 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00867 (11232) covalent geometry : angle 1.09975 (15244) hydrogen bonds : bond 0.12436 ( 551) hydrogen bonds : angle 7.75878 ( 1599) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 206 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.8153 (ttp) cc_final: 0.7563 (ttp) REVERT: A 254 MET cc_start: 0.7494 (mtp) cc_final: 0.7196 (mtp) REVERT: C 121 MET cc_start: 0.8135 (ttm) cc_final: 0.7848 (ttm) REVERT: C 162 MET cc_start: 0.5567 (mmm) cc_final: 0.5308 (mmm) REVERT: C 249 MET cc_start: 0.8055 (ttp) cc_final: 0.7646 (ttp) outliers start: 7 outliers final: 2 residues processed: 212 average time/residue: 0.5837 time to fit residues: 132.7770 Evaluate side-chains 120 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain B residue 311 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN A 189 GLN A 310 ASN A 314 GLN A 317 GLN C 189 GLN B 345 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.256379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.227691 restraints weight = 11758.562| |-----------------------------------------------------------------------------| r_work (start): 0.4538 rms_B_bonded: 1.55 r_work: 0.4484 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4397 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11232 Z= 0.138 Angle : 0.562 6.843 15244 Z= 0.306 Chirality : 0.042 0.119 1540 Planarity : 0.006 0.051 1976 Dihedral : 4.404 35.772 1488 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.03 % Allowed : 12.37 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.68 (0.23), residues: 1344 helix: 1.32 (0.20), residues: 676 sheet: -0.75 (0.48), residues: 88 loop : -0.31 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 41 TYR 0.012 0.002 TYR D 242 PHE 0.012 0.002 PHE D 307 TRP 0.017 0.002 TRP C 98 HIS 0.001 0.000 HIS D 346 Details of bonding type rmsd covalent geometry : bond 0.00296 (11232) covalent geometry : angle 0.56222 (15244) hydrogen bonds : bond 0.04285 ( 551) hydrogen bonds : angle 5.62730 ( 1599) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 311 ARG cc_start: 0.6940 (ttt90) cc_final: 0.6493 (ttt-90) REVERT: D 120 TRP cc_start: 0.3959 (m100) cc_final: 0.2869 (m100) REVERT: D 254 MET cc_start: 0.3767 (mtp) cc_final: 0.3525 (mtm) REVERT: D 278 ASN cc_start: 0.5266 (OUTLIER) cc_final: 0.4860 (t160) REVERT: D 320 ARG cc_start: 0.4398 (mtp85) cc_final: 0.4013 (tpp80) REVERT: C 98 TRP cc_start: 0.6874 (t60) cc_final: 0.6620 (t60) REVERT: C 121 MET cc_start: 0.8388 (ttm) cc_final: 0.7867 (mtt) REVERT: C 174 ASN cc_start: 0.7159 (m110) cc_final: 0.6736 (m110) REVERT: B 161 SER cc_start: 0.4005 (OUTLIER) cc_final: 0.3705 (m) REVERT: B 254 MET cc_start: 0.4263 (mtp) cc_final: 0.4025 (mtm) outliers start: 23 outliers final: 6 residues processed: 170 average time/residue: 0.5102 time to fit residues: 93.3495 Evaluate side-chains 123 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 161 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 45 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 110 optimal weight: 0.4980 chunk 75 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN B 345 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.248303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.219877 restraints weight = 11947.859| |-----------------------------------------------------------------------------| r_work (start): 0.4466 rms_B_bonded: 1.52 r_work: 0.4413 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.4328 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.4328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11232 Z= 0.153 Angle : 0.581 8.329 15244 Z= 0.315 Chirality : 0.044 0.128 1540 Planarity : 0.005 0.047 1976 Dihedral : 4.237 16.059 1480 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.36 % Allowed : 13.16 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.61 (0.23), residues: 1344 helix: 1.26 (0.20), residues: 684 sheet: -0.33 (0.50), residues: 88 loop : -0.45 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 318 TYR 0.011 0.002 TYR D 248 PHE 0.012 0.002 PHE C 73 TRP 0.021 0.002 TRP B 106 HIS 0.005 0.002 HIS D 346 Details of bonding type rmsd covalent geometry : bond 0.00342 (11232) covalent geometry : angle 0.58124 (15244) hydrogen bonds : bond 0.04579 ( 551) hydrogen bonds : angle 5.52272 ( 1599) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.336 Fit side-chains REVERT: A 98 TRP cc_start: 0.7102 (t60) cc_final: 0.6857 (t60) REVERT: D 90 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.6384 (mttp) REVERT: D 120 TRP cc_start: 0.3890 (m100) cc_final: 0.2907 (m100) REVERT: D 203 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6181 (mm-30) REVERT: D 254 MET cc_start: 0.4425 (mtp) cc_final: 0.4207 (mtm) REVERT: D 278 ASN cc_start: 0.5529 (OUTLIER) cc_final: 0.5186 (t160) REVERT: D 318 ARG cc_start: 0.5660 (OUTLIER) cc_final: 0.4389 (ttp80) REVERT: D 320 ARG cc_start: 0.4491 (mtp85) cc_final: 0.4049 (tpp80) REVERT: C 98 TRP cc_start: 0.7052 (t60) cc_final: 0.6822 (t60) REVERT: C 121 MET cc_start: 0.8460 (ttm) cc_final: 0.7919 (mtt) REVERT: C 174 ASN cc_start: 0.7336 (m110) cc_final: 0.6932 (m110) REVERT: C 293 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6603 (pt0) REVERT: B 120 TRP cc_start: 0.3803 (m100) cc_final: 0.2731 (m100) REVERT: B 147 ARG cc_start: 0.5782 (OUTLIER) cc_final: 0.5391 (ttm110) REVERT: B 291 LYS cc_start: 0.5167 (tptp) cc_final: 0.3859 (tmmt) REVERT: B 311 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6052 (mpp80) outliers start: 38 outliers final: 12 residues processed: 156 average time/residue: 0.6289 time to fit residues: 105.1733 Evaluate side-chains 134 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 311 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 94 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN D 346 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.245325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.217483 restraints weight = 12007.514| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 1.51 r_work: 0.4391 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.4306 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11232 Z= 0.168 Angle : 0.607 9.268 15244 Z= 0.324 Chirality : 0.044 0.123 1540 Planarity : 0.006 0.042 1976 Dihedral : 4.372 15.166 1480 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.53 % Allowed : 13.78 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.35 (0.22), residues: 1344 helix: 1.11 (0.19), residues: 684 sheet: -0.33 (0.53), residues: 88 loop : -0.69 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 267 TYR 0.012 0.002 TYR D 248 PHE 0.013 0.002 PHE B 62 TRP 0.024 0.002 TRP B 106 HIS 0.005 0.002 HIS D 346 Details of bonding type rmsd covalent geometry : bond 0.00385 (11232) covalent geometry : angle 0.60677 (15244) hydrogen bonds : bond 0.04689 ( 551) hydrogen bonds : angle 5.54010 ( 1599) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.423 Fit side-chains REVERT: A 98 TRP cc_start: 0.7098 (t60) cc_final: 0.6830 (t60) REVERT: A 206 GLN cc_start: 0.7194 (tt0) cc_final: 0.6785 (mt0) REVERT: A 283 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7576 (tp30) REVERT: D 101 LYS cc_start: 0.6736 (OUTLIER) cc_final: 0.6419 (mmtp) REVERT: D 120 TRP cc_start: 0.3915 (m100) cc_final: 0.3161 (m100) REVERT: D 140 ILE cc_start: 0.5569 (mt) cc_final: 0.5094 (mt) REVERT: D 254 MET cc_start: 0.4506 (mtp) cc_final: 0.4232 (mtm) REVERT: D 318 ARG cc_start: 0.5736 (OUTLIER) cc_final: 0.4313 (ttp80) REVERT: C 39 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6175 (mp0) REVERT: C 98 TRP cc_start: 0.7124 (t60) cc_final: 0.6887 (t60) REVERT: C 121 MET cc_start: 0.8486 (ttm) cc_final: 0.7963 (mtt) REVERT: C 133 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7449 (mtmt) REVERT: C 174 ASN cc_start: 0.7617 (m110) cc_final: 0.7264 (m110) REVERT: C 256 ASP cc_start: 0.7492 (m-30) cc_final: 0.7259 (m-30) REVERT: C 293 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6644 (pt0) REVERT: B 120 TRP cc_start: 0.3777 (m100) cc_final: 0.2928 (m100) REVERT: B 147 ARG cc_start: 0.5870 (OUTLIER) cc_final: 0.5490 (ttm110) REVERT: B 274 PHE cc_start: 0.6071 (t80) cc_final: 0.5629 (t80) REVERT: B 291 LYS cc_start: 0.5001 (tptp) cc_final: 0.4012 (tmmt) REVERT: B 311 ARG cc_start: 0.6896 (OUTLIER) cc_final: 0.6028 (mpp80) outliers start: 40 outliers final: 12 residues processed: 162 average time/residue: 0.5450 time to fit residues: 94.9680 Evaluate side-chains 139 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 311 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 105 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 48 optimal weight: 0.0670 chunk 129 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN D 319 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN B 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.245069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.217457 restraints weight = 11908.422| |-----------------------------------------------------------------------------| r_work (start): 0.4457 rms_B_bonded: 1.51 r_work: 0.4405 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.4322 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11232 Z= 0.154 Angle : 0.584 9.633 15244 Z= 0.309 Chirality : 0.043 0.123 1540 Planarity : 0.005 0.040 1976 Dihedral : 4.251 14.318 1480 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.09 % Allowed : 15.90 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.35 (0.22), residues: 1344 helix: 1.23 (0.19), residues: 676 sheet: -0.38 (0.53), residues: 88 loop : -0.84 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 318 TYR 0.013 0.002 TYR B 332 PHE 0.012 0.002 PHE D 62 TRP 0.020 0.002 TRP B 106 HIS 0.003 0.001 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00352 (11232) covalent geometry : angle 0.58382 (15244) hydrogen bonds : bond 0.04391 ( 551) hydrogen bonds : angle 5.48314 ( 1599) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 98 TRP cc_start: 0.7108 (t60) cc_final: 0.6874 (t60) REVERT: A 133 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7278 (mtmt) REVERT: A 177 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.6184 (ttt-90) REVERT: A 283 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7085 (tt0) REVERT: D 101 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6497 (mmtp) REVERT: D 120 TRP cc_start: 0.4001 (m100) cc_final: 0.3117 (m100) REVERT: D 162 MET cc_start: 0.2045 (mmm) cc_final: 0.1609 (mmm) REVERT: D 318 ARG cc_start: 0.5667 (OUTLIER) cc_final: 0.4267 (ttp80) REVERT: C 39 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6138 (mp0) REVERT: C 98 TRP cc_start: 0.7146 (t60) cc_final: 0.6903 (t60) REVERT: C 121 MET cc_start: 0.8482 (ttm) cc_final: 0.7910 (mtt) REVERT: C 133 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7454 (mtmt) REVERT: C 174 ASN cc_start: 0.7694 (m110) cc_final: 0.7358 (m110) REVERT: C 293 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6633 (pt0) REVERT: B 120 TRP cc_start: 0.3797 (m100) cc_final: 0.2867 (m100) REVERT: B 146 LYS cc_start: 0.6219 (OUTLIER) cc_final: 0.6005 (mptt) REVERT: B 147 ARG cc_start: 0.6249 (OUTLIER) cc_final: 0.5808 (ttm110) REVERT: B 274 PHE cc_start: 0.6028 (t80) cc_final: 0.5636 (t80) REVERT: B 291 LYS cc_start: 0.5096 (tptp) cc_final: 0.4053 (tmmt) REVERT: B 311 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6057 (mpp80) outliers start: 35 outliers final: 16 residues processed: 154 average time/residue: 0.5761 time to fit residues: 94.9980 Evaluate side-chains 147 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 311 ARG Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 63 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 chunk 66 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 0.0470 chunk 46 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.246225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.219063 restraints weight = 11912.485| |-----------------------------------------------------------------------------| r_work (start): 0.4453 rms_B_bonded: 1.51 r_work: 0.4403 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.4319 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11232 Z= 0.136 Angle : 0.559 9.926 15244 Z= 0.295 Chirality : 0.042 0.140 1540 Planarity : 0.005 0.038 1976 Dihedral : 4.121 14.142 1480 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.00 % Allowed : 16.43 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.41 (0.22), residues: 1344 helix: 1.33 (0.20), residues: 676 sheet: -0.45 (0.53), residues: 88 loop : -0.85 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 311 TYR 0.020 0.002 TYR A 182 PHE 0.011 0.001 PHE D 62 TRP 0.020 0.002 TRP B 106 HIS 0.002 0.001 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00303 (11232) covalent geometry : angle 0.55902 (15244) hydrogen bonds : bond 0.04145 ( 551) hydrogen bonds : angle 5.40042 ( 1599) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.343 Fit side-chains REVERT: A 98 TRP cc_start: 0.7082 (t60) cc_final: 0.6831 (t60) REVERT: A 133 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7254 (mtmt) REVERT: A 177 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.6150 (ttt-90) REVERT: A 283 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7093 (tt0) REVERT: D 101 LYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6576 (mmtp) REVERT: D 120 TRP cc_start: 0.3922 (m100) cc_final: 0.3066 (m100) REVERT: D 162 MET cc_start: 0.2132 (mmm) cc_final: 0.1703 (mmm) REVERT: D 318 ARG cc_start: 0.5772 (OUTLIER) cc_final: 0.4443 (ttp80) REVERT: C 39 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.6117 (mp0) REVERT: C 98 TRP cc_start: 0.7115 (t60) cc_final: 0.6865 (t60) REVERT: C 121 MET cc_start: 0.8470 (ttm) cc_final: 0.7923 (mtt) REVERT: C 133 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7480 (mtmt) REVERT: C 174 ASN cc_start: 0.7715 (m110) cc_final: 0.7372 (m110) REVERT: C 293 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6603 (pt0) REVERT: B 120 TRP cc_start: 0.3753 (m100) cc_final: 0.2816 (m100) REVERT: B 147 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.5775 (ttm110) REVERT: B 274 PHE cc_start: 0.5977 (t80) cc_final: 0.5538 (t80) REVERT: B 291 LYS cc_start: 0.5245 (tptp) cc_final: 0.4226 (tmmt) REVERT: B 311 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6011 (mpp80) outliers start: 34 outliers final: 19 residues processed: 149 average time/residue: 0.5769 time to fit residues: 92.1223 Evaluate side-chains 148 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 311 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 84 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 94 optimal weight: 0.0570 chunk 16 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 0.0030 chunk 6 optimal weight: 3.9990 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.246514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.218926 restraints weight = 11335.156| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 1.47 r_work: 0.4329 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.4233 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11232 Z= 0.101 Angle : 0.518 10.739 15244 Z= 0.268 Chirality : 0.040 0.127 1540 Planarity : 0.004 0.036 1976 Dihedral : 3.767 12.880 1480 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.30 % Allowed : 17.40 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.68 (0.23), residues: 1344 helix: 1.60 (0.20), residues: 676 sheet: -0.99 (0.45), residues: 128 loop : -0.61 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 311 TYR 0.012 0.001 TYR C 182 PHE 0.007 0.001 PHE B 62 TRP 0.023 0.001 TRP D 98 HIS 0.001 0.000 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00215 (11232) covalent geometry : angle 0.51820 (15244) hydrogen bonds : bond 0.03448 ( 551) hydrogen bonds : angle 5.15516 ( 1599) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.274 Fit side-chains REVERT: A 98 TRP cc_start: 0.7127 (t60) cc_final: 0.6854 (t60) REVERT: A 133 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7208 (mtmm) REVERT: A 206 GLN cc_start: 0.7075 (tt0) cc_final: 0.6675 (mt0) REVERT: A 283 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7453 (tp30) REVERT: D 52 THR cc_start: 0.7495 (OUTLIER) cc_final: 0.7280 (m) REVERT: D 101 LYS cc_start: 0.6647 (OUTLIER) cc_final: 0.6311 (mmtp) REVERT: D 120 TRP cc_start: 0.3760 (m100) cc_final: 0.2932 (m100) REVERT: D 162 MET cc_start: 0.2489 (mmm) cc_final: 0.2020 (mmm) REVERT: D 318 ARG cc_start: 0.5355 (OUTLIER) cc_final: 0.4179 (ttp80) REVERT: C 39 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6133 (mp0) REVERT: C 98 TRP cc_start: 0.7134 (t60) cc_final: 0.6899 (t60) REVERT: C 121 MET cc_start: 0.8362 (ttm) cc_final: 0.7853 (mtt) REVERT: C 174 ASN cc_start: 0.7621 (m110) cc_final: 0.7284 (m110) REVERT: C 271 MET cc_start: 0.6995 (tpt) cc_final: 0.6774 (tpt) REVERT: C 293 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6543 (pt0) REVERT: B 120 TRP cc_start: 0.3654 (m100) cc_final: 0.2707 (m100) REVERT: B 144 LEU cc_start: 0.5960 (tt) cc_final: 0.5663 (tp) REVERT: B 147 ARG cc_start: 0.5854 (OUTLIER) cc_final: 0.5449 (ttm110) REVERT: B 311 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.5863 (mpp80) outliers start: 26 outliers final: 11 residues processed: 150 average time/residue: 0.6182 time to fit residues: 99.3177 Evaluate side-chains 136 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 311 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 115 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 122 optimal weight: 0.0570 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN C 314 GLN ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.248667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.221944 restraints weight = 11836.404| |-----------------------------------------------------------------------------| r_work (start): 0.4475 rms_B_bonded: 1.52 r_work: 0.4423 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.4339 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11232 Z= 0.117 Angle : 0.543 11.020 15244 Z= 0.282 Chirality : 0.041 0.125 1540 Planarity : 0.004 0.035 1976 Dihedral : 3.822 12.987 1480 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.00 % Allowed : 18.11 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.67 (0.22), residues: 1344 helix: 1.57 (0.20), residues: 676 sheet: -0.34 (0.53), residues: 88 loop : -0.78 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 263 TYR 0.016 0.002 TYR C 182 PHE 0.012 0.001 PHE B 73 TRP 0.032 0.002 TRP D 98 HIS 0.002 0.000 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00258 (11232) covalent geometry : angle 0.54254 (15244) hydrogen bonds : bond 0.03712 ( 551) hydrogen bonds : angle 5.19855 ( 1599) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.505 Fit side-chains REVERT: A 98 TRP cc_start: 0.7150 (t60) cc_final: 0.6886 (t60) REVERT: A 133 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7335 (mtmm) REVERT: A 177 ARG cc_start: 0.6382 (OUTLIER) cc_final: 0.6112 (ttt-90) REVERT: A 283 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7061 (tt0) REVERT: D 101 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.6343 (mmtp) REVERT: D 120 TRP cc_start: 0.3802 (m100) cc_final: 0.2912 (m100) REVERT: D 146 LYS cc_start: 0.6027 (OUTLIER) cc_final: 0.5742 (mptt) REVERT: D 162 MET cc_start: 0.2426 (mmm) cc_final: 0.1994 (mmm) REVERT: D 318 ARG cc_start: 0.5492 (OUTLIER) cc_final: 0.4426 (ttp80) REVERT: D 320 ARG cc_start: 0.4768 (OUTLIER) cc_final: 0.4283 (tpp80) REVERT: C 39 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.5995 (mp0) REVERT: C 98 TRP cc_start: 0.7193 (t60) cc_final: 0.6971 (t60) REVERT: C 121 MET cc_start: 0.8418 (ttm) cc_final: 0.7914 (mtt) REVERT: C 174 ASN cc_start: 0.7740 (m110) cc_final: 0.7424 (m110) REVERT: C 293 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6513 (pt0) REVERT: B 102 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5863 (tp30) REVERT: B 120 TRP cc_start: 0.3688 (m100) cc_final: 0.2722 (m100) REVERT: B 147 ARG cc_start: 0.6166 (OUTLIER) cc_final: 0.5699 (ttm110) REVERT: B 311 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.5924 (mpp80) outliers start: 34 outliers final: 14 residues processed: 145 average time/residue: 0.6863 time to fit residues: 106.6451 Evaluate side-chains 140 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 311 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 0.0050 chunk 91 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.8174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN C 314 GLN ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.247753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.221243 restraints weight = 11821.910| |-----------------------------------------------------------------------------| r_work (start): 0.4468 rms_B_bonded: 1.51 r_work: 0.4415 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.4332 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11232 Z= 0.123 Angle : 0.562 11.558 15244 Z= 0.291 Chirality : 0.041 0.127 1540 Planarity : 0.005 0.035 1976 Dihedral : 3.882 12.963 1480 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.74 % Allowed : 18.73 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.58 (0.22), residues: 1344 helix: 1.49 (0.19), residues: 676 sheet: -0.25 (0.53), residues: 88 loop : -0.83 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 263 TYR 0.015 0.002 TYR A 182 PHE 0.008 0.001 PHE B 62 TRP 0.028 0.002 TRP B 98 HIS 0.002 0.000 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00275 (11232) covalent geometry : angle 0.56230 (15244) hydrogen bonds : bond 0.03856 ( 551) hydrogen bonds : angle 5.23588 ( 1599) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.432 Fit side-chains REVERT: A 98 TRP cc_start: 0.7063 (t60) cc_final: 0.6816 (t60) REVERT: A 133 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7422 (mtmm) REVERT: A 177 ARG cc_start: 0.6432 (OUTLIER) cc_final: 0.6164 (ttt-90) REVERT: A 206 GLN cc_start: 0.7155 (tt0) cc_final: 0.6787 (mt0) REVERT: A 283 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7082 (tt0) REVERT: A 293 GLN cc_start: 0.6856 (mt0) cc_final: 0.6648 (mt0) REVERT: D 101 LYS cc_start: 0.6689 (OUTLIER) cc_final: 0.6384 (mmtp) REVERT: D 120 TRP cc_start: 0.3937 (m100) cc_final: 0.3011 (m100) REVERT: D 162 MET cc_start: 0.2698 (mmm) cc_final: 0.2222 (mmm) REVERT: D 318 ARG cc_start: 0.5653 (OUTLIER) cc_final: 0.4492 (ttp80) REVERT: D 320 ARG cc_start: 0.4775 (OUTLIER) cc_final: 0.4278 (tpp80) REVERT: C 39 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5800 (mp0) REVERT: C 98 TRP cc_start: 0.7109 (t60) cc_final: 0.6892 (t60) REVERT: C 121 MET cc_start: 0.8429 (ttm) cc_final: 0.7933 (mtt) REVERT: C 174 ASN cc_start: 0.7743 (m110) cc_final: 0.7454 (m110) REVERT: C 293 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6504 (pt0) REVERT: B 102 GLU cc_start: 0.6098 (OUTLIER) cc_final: 0.5885 (mt-10) REVERT: B 120 TRP cc_start: 0.3714 (m100) cc_final: 0.2748 (m100) REVERT: B 147 ARG cc_start: 0.6156 (OUTLIER) cc_final: 0.5712 (ttm110) REVERT: B 311 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.5921 (mpp80) outliers start: 31 outliers final: 17 residues processed: 140 average time/residue: 0.6748 time to fit residues: 100.7653 Evaluate side-chains 143 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 311 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 89 optimal weight: 0.0980 chunk 69 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN C 314 GLN ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.248354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.221925 restraints weight = 11885.429| |-----------------------------------------------------------------------------| r_work (start): 0.4475 rms_B_bonded: 1.52 r_work: 0.4424 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.4341 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11232 Z= 0.116 Angle : 0.560 11.955 15244 Z= 0.287 Chirality : 0.041 0.140 1540 Planarity : 0.004 0.035 1976 Dihedral : 3.832 12.618 1480 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.74 % Allowed : 18.99 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.58 (0.23), residues: 1344 helix: 1.50 (0.20), residues: 676 sheet: -0.81 (0.46), residues: 128 loop : -0.70 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 150 TYR 0.013 0.001 TYR A 182 PHE 0.008 0.001 PHE D 73 TRP 0.027 0.002 TRP B 106 HIS 0.001 0.000 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00257 (11232) covalent geometry : angle 0.55951 (15244) hydrogen bonds : bond 0.03709 ( 551) hydrogen bonds : angle 5.18381 ( 1599) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.274 Fit side-chains REVERT: A 98 TRP cc_start: 0.7053 (t60) cc_final: 0.6796 (t60) REVERT: A 133 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7464 (mtmm) REVERT: A 177 ARG cc_start: 0.6377 (OUTLIER) cc_final: 0.6108 (ttt-90) REVERT: A 206 GLN cc_start: 0.7265 (tt0) cc_final: 0.6908 (mt0) REVERT: A 283 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7100 (tt0) REVERT: D 101 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.6413 (mmtp) REVERT: D 120 TRP cc_start: 0.3844 (m100) cc_final: 0.2847 (m100) REVERT: D 146 LYS cc_start: 0.6083 (OUTLIER) cc_final: 0.5839 (mptt) REVERT: D 162 MET cc_start: 0.2757 (mmm) cc_final: 0.2292 (mmm) REVERT: D 249 MET cc_start: 0.5789 (mtm) cc_final: 0.4779 (ttm) REVERT: D 318 ARG cc_start: 0.5476 (OUTLIER) cc_final: 0.4387 (ttp80) REVERT: C 39 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5833 (mp0) REVERT: C 98 TRP cc_start: 0.7200 (t60) cc_final: 0.6976 (t60) REVERT: C 121 MET cc_start: 0.8425 (ttm) cc_final: 0.7921 (mtt) REVERT: C 174 ASN cc_start: 0.7710 (m110) cc_final: 0.7437 (m110) REVERT: C 293 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6537 (pt0) REVERT: B 100 LYS cc_start: 0.6799 (tttt) cc_final: 0.6221 (tttm) REVERT: B 120 TRP cc_start: 0.3624 (m100) cc_final: 0.2664 (m100) REVERT: B 147 ARG cc_start: 0.6170 (OUTLIER) cc_final: 0.5812 (ttm110) REVERT: B 311 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.5915 (mpp80) outliers start: 31 outliers final: 15 residues processed: 138 average time/residue: 0.6058 time to fit residues: 89.1171 Evaluate side-chains 139 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 311 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.0370 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 118 optimal weight: 0.0170 chunk 89 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 40 optimal weight: 0.3980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN C 314 GLN ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.251666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.224772 restraints weight = 11888.174| |-----------------------------------------------------------------------------| r_work (start): 0.4509 rms_B_bonded: 1.58 r_work: 0.4456 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4371 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11232 Z= 0.100 Angle : 0.538 12.221 15244 Z= 0.273 Chirality : 0.040 0.142 1540 Planarity : 0.004 0.038 1976 Dihedral : 3.602 12.455 1480 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.94 % Allowed : 19.96 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.79 (0.23), residues: 1344 helix: 1.67 (0.20), residues: 676 sheet: -0.62 (0.46), residues: 128 loop : -0.61 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 150 TYR 0.009 0.001 TYR A 182 PHE 0.009 0.001 PHE D 73 TRP 0.026 0.001 TRP B 106 HIS 0.001 0.000 HIS D 346 Details of bonding type rmsd covalent geometry : bond 0.00215 (11232) covalent geometry : angle 0.53769 (15244) hydrogen bonds : bond 0.03189 ( 551) hydrogen bonds : angle 5.06312 ( 1599) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3656.05 seconds wall clock time: 63 minutes 0.89 seconds (3780.89 seconds total)