Starting phenix.real_space_refine on Tue May 13 19:05:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b87_44334/05_2025/9b87_44334.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b87_44334/05_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_44334/05_2025/9b87_44334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b87_44334/05_2025/9b87_44334.map" model { file = "/net/cci-nas-00/data/ceres_data/9b87_44334/05_2025/9b87_44334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b87_44334/05_2025/9b87_44334.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.17, per 1000 atoms: 0.66 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: 2.76 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.26 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: 3.59 Time building geometry restraints manager: 3.24 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: 0.03 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: 0.710 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.280 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.030 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (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 TRP 0.037 0.005 TRP D 250 HIS 0.006 0.002 HIS A 346 PHE 0.048 0.006 PHE B 300 TYR 0.037 0.007 TYR B 59 ARG 0.014 0.002 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.12436 ( 551) hydrogen bonds : angle 7.75878 ( 1599) covalent geometry : bond 0.00867 (11232) covalent geometry : angle 1.09975 (15244) *********************** 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 : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.8153 (ttp) cc_final: 0.7564 (ttp) REVERT: A 254 MET cc_start: 0.7494 (mtp) cc_final: 0.7198 (mtp) REVERT: C 121 MET cc_start: 0.8135 (ttm) cc_final: 0.7849 (ttm) REVERT: C 162 MET cc_start: 0.5567 (mmm) cc_final: 0.5307 (mmm) REVERT: C 249 MET cc_start: 0.8055 (ttp) cc_final: 0.7645 (ttp) outliers start: 7 outliers final: 2 residues processed: 212 average time/residue: 1.2953 time to fit residues: 295.0801 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 : 0.998 ------------------------------------------------------------------------------- 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 111 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.254785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.225882 restraints weight = 11728.829| |-----------------------------------------------------------------------------| r_work (start): 0.4524 rms_B_bonded: 1.55 r_work: 0.4469 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4381 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11232 Z= 0.149 Angle : 0.573 6.459 15244 Z= 0.315 Chirality : 0.043 0.126 1540 Planarity : 0.006 0.051 1976 Dihedral : 4.439 35.601 1488 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.39 % Allowed : 12.19 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.22), residues: 1344 helix: 1.27 (0.20), residues: 676 sheet: -0.72 (0.48), residues: 88 loop : -0.35 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 98 HIS 0.002 0.000 HIS B 346 PHE 0.014 0.002 PHE D 339 TYR 0.012 0.002 TYR D 242 ARG 0.005 0.001 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 551) hydrogen bonds : angle 5.67577 ( 1599) covalent geometry : bond 0.00314 (11232) covalent geometry : angle 0.57350 (15244) *********************** 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 179 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 311 ARG cc_start: 0.6933 (ttt90) cc_final: 0.6500 (ttt-90) REVERT: D 90 LYS cc_start: 0.6426 (OUTLIER) cc_final: 0.6086 (mttp) REVERT: D 120 TRP cc_start: 0.3780 (m100) cc_final: 0.2722 (m100) REVERT: D 254 MET cc_start: 0.3859 (mtp) cc_final: 0.3608 (mtm) REVERT: D 278 ASN cc_start: 0.5256 (OUTLIER) cc_final: 0.4880 (t160) REVERT: D 320 ARG cc_start: 0.4366 (mtp85) cc_final: 0.3998 (tpp80) REVERT: C 98 TRP cc_start: 0.6899 (t60) cc_final: 0.6675 (t60) REVERT: C 121 MET cc_start: 0.8399 (ttm) cc_final: 0.7884 (mtt) REVERT: C 174 ASN cc_start: 0.7174 (m110) cc_final: 0.6761 (m110) REVERT: C 177 ARG cc_start: 0.5962 (OUTLIER) cc_final: 0.5681 (ttt-90) REVERT: C 271 MET cc_start: 0.7051 (tpt) cc_final: 0.6833 (tpt) outliers start: 27 outliers final: 7 residues processed: 173 average time/residue: 1.2564 time to fit residues: 234.0590 Evaluate side-chains 125 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 90 LYS Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain C residue 177 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 117 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 48 optimal weight: 0.0870 chunk 52 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 314 GLN D 314 GLN B 278 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.243959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.215891 restraints weight = 11930.192| |-----------------------------------------------------------------------------| r_work (start): 0.4426 rms_B_bonded: 1.51 r_work: 0.4374 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.4291 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11232 Z= 0.226 Angle : 0.690 8.065 15244 Z= 0.376 Chirality : 0.048 0.143 1540 Planarity : 0.007 0.047 1976 Dihedral : 4.825 17.796 1480 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.71 % Allowed : 12.72 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.23), residues: 1344 helix: 0.88 (0.19), residues: 680 sheet: -0.46 (0.53), residues: 88 loop : -0.67 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 106 HIS 0.007 0.003 HIS D 346 PHE 0.019 0.003 PHE D 339 TYR 0.021 0.003 TYR C 182 ARG 0.006 0.001 ARG B 318 Details of bonding type rmsd hydrogen bonds : bond 0.05693 ( 551) hydrogen bonds : angle 5.89480 ( 1599) covalent geometry : bond 0.00524 (11232) covalent geometry : angle 0.69032 (15244) *********************** 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 174 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 1.126 Fit side-chains REVERT: A 98 TRP cc_start: 0.7187 (t60) cc_final: 0.6955 (t60) REVERT: D 120 TRP cc_start: 0.3701 (m100) cc_final: 0.2930 (m100) REVERT: D 150 ARG cc_start: 0.6050 (OUTLIER) cc_final: 0.5735 (ttm-80) REVERT: D 203 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6347 (mm-30) REVERT: D 254 MET cc_start: 0.4950 (mtp) cc_final: 0.4641 (mtm) REVERT: D 318 ARG cc_start: 0.5793 (OUTLIER) cc_final: 0.4367 (ttp80) REVERT: C 98 TRP cc_start: 0.7258 (t60) cc_final: 0.7025 (t60) REVERT: C 121 MET cc_start: 0.8483 (ttm) cc_final: 0.8032 (mtt) REVERT: C 174 ASN cc_start: 0.7572 (m110) cc_final: 0.7203 (m110) REVERT: C 271 MET cc_start: 0.7331 (tpt) cc_final: 0.7001 (tpt) REVERT: C 293 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6762 (pt0) REVERT: B 120 TRP cc_start: 0.3698 (m100) cc_final: 0.2834 (m100) REVERT: B 161 SER cc_start: 0.4428 (OUTLIER) cc_final: 0.4023 (m) REVERT: B 260 GLN cc_start: 0.5630 (OUTLIER) cc_final: 0.5392 (mt0) REVERT: B 291 LYS cc_start: 0.5136 (tptp) cc_final: 0.4007 (tmmt) REVERT: B 311 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6000 (mpp80) outliers start: 42 outliers final: 14 residues processed: 162 average time/residue: 1.3287 time to fit residues: 231.5697 Evaluate side-chains 137 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 150 ARG 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 318 ARG Chi-restraints excluded: chain D residue 336 LEU 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 293 GLN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 311 ARG Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 48 optimal weight: 0.2980 chunk 46 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.246106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.218810 restraints weight = 11736.444| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 1.49 r_work: 0.4376 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.4294 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11232 Z= 0.204 Angle : 0.641 8.467 15244 Z= 0.346 Chirality : 0.046 0.133 1540 Planarity : 0.006 0.041 1976 Dihedral : 4.652 16.428 1480 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.24 % Allowed : 14.13 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.22), residues: 1344 helix: 0.88 (0.19), residues: 676 sheet: -0.54 (0.52), residues: 88 loop : -0.99 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 106 HIS 0.004 0.002 HIS D 346 PHE 0.016 0.002 PHE D 62 TYR 0.018 0.002 TYR B 332 ARG 0.006 0.001 ARG B 318 Details of bonding type rmsd hydrogen bonds : bond 0.05093 ( 551) hydrogen bonds : angle 5.76040 ( 1599) covalent geometry : bond 0.00477 (11232) covalent geometry : angle 0.64091 (15244) *********************** 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 171 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 123 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 TRP cc_start: 0.7195 (t60) cc_final: 0.6945 (t60) REVERT: A 283 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7174 (tt0) REVERT: D 120 TRP cc_start: 0.3717 (m100) cc_final: 0.2910 (m100) REVERT: D 162 MET cc_start: 0.2785 (mmm) cc_final: 0.2570 (mmm) REVERT: D 318 ARG cc_start: 0.5769 (OUTLIER) cc_final: 0.4292 (ttp80) REVERT: C 39 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.6154 (mp0) REVERT: C 98 TRP cc_start: 0.7244 (t60) cc_final: 0.6991 (t60) REVERT: C 121 MET cc_start: 0.8511 (ttm) cc_final: 0.7998 (mtt) REVERT: C 174 ASN cc_start: 0.7728 (m110) cc_final: 0.7393 (m110) REVERT: C 177 ARG cc_start: 0.6384 (OUTLIER) cc_final: 0.6066 (ttt-90) REVERT: C 293 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6660 (pt0) REVERT: B 120 TRP cc_start: 0.3642 (m100) cc_final: 0.2854 (m100) REVERT: B 161 SER cc_start: 0.4554 (OUTLIER) cc_final: 0.3945 (p) REVERT: B 291 LYS cc_start: 0.5211 (tptp) cc_final: 0.3964 (tmmt) REVERT: B 311 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6052 (mpp80) outliers start: 48 outliers final: 26 residues processed: 152 average time/residue: 1.3253 time to fit residues: 216.4230 Evaluate side-chains 152 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 121 MET 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 A residue 351 SER Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 51 ILE 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 232 LEU Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 336 LEU 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 177 ARG 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 51 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 206 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 90 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 129 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 81 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN D 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.247356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.220227 restraints weight = 11816.804| |-----------------------------------------------------------------------------| r_work (start): 0.4467 rms_B_bonded: 1.50 r_work: 0.4418 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.4334 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11232 Z= 0.110 Angle : 0.517 8.555 15244 Z= 0.274 Chirality : 0.041 0.121 1540 Planarity : 0.005 0.039 1976 Dihedral : 3.976 13.554 1480 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.00 % Allowed : 15.81 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1344 helix: 1.44 (0.19), residues: 676 sheet: -0.36 (0.52), residues: 88 loop : -0.86 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 106 HIS 0.002 0.001 HIS D 346 PHE 0.009 0.001 PHE D 62 TYR 0.014 0.001 TYR A 182 ARG 0.004 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 551) hydrogen bonds : angle 5.32153 ( 1599) covalent geometry : bond 0.00234 (11232) covalent geometry : angle 0.51715 (15244) *********************** 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 165 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 1.402 Fit side-chains REVERT: A 98 TRP cc_start: 0.7080 (t60) cc_final: 0.6833 (t60) REVERT: A 133 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7442 (mtmt) REVERT: A 177 ARG cc_start: 0.6479 (OUTLIER) cc_final: 0.6195 (ttt-90) REVERT: D 120 TRP cc_start: 0.3450 (m100) cc_final: 0.2716 (m100) REVERT: D 162 MET cc_start: 0.2990 (mmm) cc_final: 0.2747 (mmm) REVERT: D 318 ARG cc_start: 0.5522 (OUTLIER) cc_final: 0.4327 (ttp80) REVERT: C 98 TRP cc_start: 0.7153 (t60) cc_final: 0.6911 (t60) REVERT: C 121 MET cc_start: 0.8464 (ttm) cc_final: 0.7945 (mtt) REVERT: C 133 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7463 (mtmt) REVERT: C 174 ASN cc_start: 0.7692 (m110) cc_final: 0.7365 (m110) REVERT: C 177 ARG cc_start: 0.6431 (OUTLIER) cc_final: 0.6201 (ttt-90) REVERT: C 293 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6641 (pt0) REVERT: B 120 TRP cc_start: 0.3623 (m100) cc_final: 0.2815 (m100) REVERT: B 161 SER cc_start: 0.4665 (OUTLIER) cc_final: 0.4069 (p) REVERT: B 291 LYS cc_start: 0.5034 (tptp) cc_final: 0.3895 (tmmt) outliers start: 34 outliers final: 13 residues processed: 154 average time/residue: 1.2668 time to fit residues: 210.0003 Evaluate side-chains 132 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 D residue 37 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 110 ASP 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 88 SER Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 177 ARG 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 52 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 222 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 79 optimal weight: 0.0170 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 101 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.249333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.222421 restraints weight = 11901.816| |-----------------------------------------------------------------------------| r_work (start): 0.4480 rms_B_bonded: 1.51 r_work: 0.4430 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.4346 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11232 Z= 0.103 Angle : 0.510 10.369 15244 Z= 0.268 Chirality : 0.040 0.118 1540 Planarity : 0.004 0.037 1976 Dihedral : 3.733 13.049 1480 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.56 % Allowed : 17.31 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1344 helix: 1.63 (0.19), residues: 676 sheet: -0.89 (0.45), residues: 128 loop : -0.61 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 98 HIS 0.002 0.001 HIS D 346 PHE 0.009 0.001 PHE D 73 TYR 0.021 0.001 TYR A 182 ARG 0.005 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 551) hydrogen bonds : angle 5.14365 ( 1599) covalent geometry : bond 0.00217 (11232) covalent geometry : angle 0.51013 (15244) *********************** 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 159 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.251 Fit side-chains REVERT: A 98 TRP cc_start: 0.7116 (t60) cc_final: 0.6834 (t60) REVERT: A 133 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7436 (mtmt) REVERT: A 177 ARG cc_start: 0.6415 (OUTLIER) cc_final: 0.6116 (ttt-90) REVERT: A 206 GLN cc_start: 0.7154 (tt0) cc_final: 0.6734 (mt0) REVERT: A 283 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7001 (tp30) REVERT: D 120 TRP cc_start: 0.3619 (m100) cc_final: 0.2884 (m100) REVERT: D 162 MET cc_start: 0.2981 (mmm) cc_final: 0.2728 (mmm) REVERT: D 318 ARG cc_start: 0.5372 (OUTLIER) cc_final: 0.4311 (ttp80) REVERT: C 98 TRP cc_start: 0.7231 (t60) cc_final: 0.7014 (t60) REVERT: C 100 LYS cc_start: 0.6726 (ttmt) cc_final: 0.6496 (ttmm) REVERT: C 121 MET cc_start: 0.8450 (ttm) cc_final: 0.8013 (mtt) REVERT: C 133 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7398 (mtmt) REVERT: C 174 ASN cc_start: 0.7723 (m110) cc_final: 0.7392 (m110) REVERT: C 177 ARG cc_start: 0.6432 (OUTLIER) cc_final: 0.6221 (ttt-90) REVERT: C 293 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6580 (pt0) REVERT: B 120 TRP cc_start: 0.3537 (m100) cc_final: 0.2736 (m100) REVERT: B 161 SER cc_start: 0.4566 (OUTLIER) cc_final: 0.3904 (p) REVERT: B 291 LYS cc_start: 0.5140 (tptp) cc_final: 0.4117 (tmmt) outliers start: 29 outliers final: 14 residues processed: 156 average time/residue: 1.3181 time to fit residues: 221.2850 Evaluate side-chains 143 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 283 GLU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 52 THR 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 88 SER Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 177 ARG 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 52 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 84 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 38 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.242125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.213759 restraints weight = 11592.166| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 1.51 r_work: 0.4286 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4191 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11232 Z= 0.146 Angle : 0.570 10.315 15244 Z= 0.302 Chirality : 0.043 0.136 1540 Planarity : 0.005 0.036 1976 Dihedral : 4.072 14.073 1480 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.27 % Allowed : 17.31 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1344 helix: 1.39 (0.19), residues: 676 sheet: -0.28 (0.53), residues: 88 loop : -0.88 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 106 HIS 0.003 0.001 HIS D 346 PHE 0.012 0.002 PHE D 62 TYR 0.018 0.002 TYR A 182 ARG 0.005 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 551) hydrogen bonds : angle 5.32832 ( 1599) covalent geometry : bond 0.00331 (11232) covalent geometry : angle 0.56996 (15244) *********************** 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 161 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 1.210 Fit side-chains REVERT: A 98 TRP cc_start: 0.7108 (t60) cc_final: 0.6868 (t60) REVERT: A 133 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7460 (mtmt) REVERT: A 177 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.6264 (ttt-90) REVERT: A 283 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7000 (tp30) REVERT: D 120 TRP cc_start: 0.3670 (m100) cc_final: 0.2852 (m100) REVERT: D 162 MET cc_start: 0.2894 (mmm) cc_final: 0.2625 (mmm) REVERT: D 318 ARG cc_start: 0.5760 (OUTLIER) cc_final: 0.4314 (ttp80) REVERT: C 39 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.6081 (mp0) REVERT: C 98 TRP cc_start: 0.7151 (t60) cc_final: 0.6905 (t60) REVERT: C 100 LYS cc_start: 0.6849 (ttmt) cc_final: 0.6505 (ttmm) REVERT: C 121 MET cc_start: 0.8444 (ttm) cc_final: 0.7929 (mtt) REVERT: C 133 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7452 (mtmt) REVERT: C 174 ASN cc_start: 0.7635 (m110) cc_final: 0.7298 (m110) REVERT: C 177 ARG cc_start: 0.6435 (OUTLIER) cc_final: 0.6171 (ttt-90) REVERT: C 293 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6595 (pt0) REVERT: B 120 TRP cc_start: 0.3636 (m100) cc_final: 0.2781 (m100) REVERT: B 121 MET cc_start: 0.6569 (tmm) cc_final: 0.6259 (tmt) REVERT: B 161 SER cc_start: 0.4222 (OUTLIER) cc_final: 0.3678 (p) REVERT: B 277 LYS cc_start: 0.5994 (OUTLIER) cc_final: 0.5395 (tmtp) outliers start: 37 outliers final: 18 residues processed: 156 average time/residue: 1.3327 time to fit residues: 223.1415 Evaluate side-chains 144 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 52 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 237 THR 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 177 ARG Chi-restraints excluded: chain C residue 192 THR 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 52 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 chunk 105 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.243936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.216119 restraints weight = 11304.635| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 1.47 r_work: 0.4308 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.4213 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.5278 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 : 0.533 11.108 15244 Z= 0.280 Chirality : 0.041 0.123 1540 Planarity : 0.004 0.036 1976 Dihedral : 3.859 13.535 1480 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.45 % Allowed : 17.23 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1344 helix: 1.49 (0.19), residues: 676 sheet: -0.22 (0.53), residues: 88 loop : -0.86 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 106 HIS 0.002 0.001 HIS D 346 PHE 0.010 0.001 PHE D 62 TYR 0.013 0.001 TYR A 182 ARG 0.005 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 551) hydrogen bonds : angle 5.20293 ( 1599) covalent geometry : bond 0.00255 (11232) covalent geometry : angle 0.53271 (15244) *********************** 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 157 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 98 TRP cc_start: 0.7057 (t60) cc_final: 0.6818 (t60) REVERT: A 133 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7531 (mtmt) REVERT: A 177 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.6224 (ttt-90) REVERT: A 206 GLN cc_start: 0.7105 (tt0) cc_final: 0.6722 (mt0) REVERT: A 283 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6958 (tp30) REVERT: D 105 LYS cc_start: 0.5628 (mttm) cc_final: 0.5341 (mmtt) REVERT: D 120 TRP cc_start: 0.3623 (m100) cc_final: 0.2796 (m100) REVERT: D 146 LYS cc_start: 0.5874 (OUTLIER) cc_final: 0.5584 (mptt) REVERT: D 162 MET cc_start: 0.2935 (mmm) cc_final: 0.2674 (mmm) REVERT: D 318 ARG cc_start: 0.5614 (OUTLIER) cc_final: 0.4335 (ttp80) REVERT: C 39 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.6053 (mp0) REVERT: C 98 TRP cc_start: 0.7161 (t60) cc_final: 0.6924 (t60) REVERT: C 100 LYS cc_start: 0.6809 (ttmt) cc_final: 0.6483 (ttmm) REVERT: C 121 MET cc_start: 0.8411 (ttm) cc_final: 0.7906 (mtt) REVERT: C 174 ASN cc_start: 0.7610 (m110) cc_final: 0.7265 (m110) REVERT: C 177 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.6192 (ttt-90) REVERT: C 293 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6617 (pt0) REVERT: B 120 TRP cc_start: 0.3645 (m100) cc_final: 0.2780 (m100) REVERT: B 161 SER cc_start: 0.4339 (OUTLIER) cc_final: 0.3732 (p) REVERT: B 189 GLN cc_start: 0.5559 (tp40) cc_final: 0.5019 (tt0) REVERT: B 277 LYS cc_start: 0.6003 (OUTLIER) cc_final: 0.5394 (tmtp) outliers start: 39 outliers final: 21 residues processed: 147 average time/residue: 1.3954 time to fit residues: 219.6455 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 : 1.162 ------------------------------------------------------------------------------- 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 D residue 37 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 65 LEU 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 177 ARG Chi-restraints excluded: chain C residue 192 THR 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 52 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 104 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 314 GLN C 314 GLN ** C 317 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 = 0.4635 r_free = 0.4635 target = 0.243836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.215889 restraints weight = 11483.547| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 1.50 r_work: 0.4307 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.4211 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.5348 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= 0.119 Angle : 0.539 11.426 15244 Z= 0.283 Chirality : 0.041 0.131 1540 Planarity : 0.004 0.036 1976 Dihedral : 3.852 13.274 1480 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.18 % Allowed : 17.40 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.22), residues: 1344 helix: 1.47 (0.19), residues: 676 sheet: -0.17 (0.53), residues: 88 loop : -0.89 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 106 HIS 0.002 0.001 HIS D 346 PHE 0.010 0.001 PHE D 62 TYR 0.013 0.001 TYR A 182 ARG 0.005 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 551) hydrogen bonds : angle 5.18301 ( 1599) covalent geometry : bond 0.00261 (11232) covalent geometry : angle 0.53887 (15244) *********************** 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 156 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 1.309 Fit side-chains revert: symmetry clash REVERT: A 98 TRP cc_start: 0.7057 (t60) cc_final: 0.6809 (t60) REVERT: A 177 ARG cc_start: 0.6517 (OUTLIER) cc_final: 0.6226 (ttt-90) REVERT: A 283 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6970 (tp30) REVERT: D 120 TRP cc_start: 0.3626 (m100) cc_final: 0.2795 (m100) REVERT: D 146 LYS cc_start: 0.5897 (OUTLIER) cc_final: 0.5595 (mptt) REVERT: D 162 MET cc_start: 0.2880 (mmm) cc_final: 0.2629 (mmm) REVERT: D 318 ARG cc_start: 0.5666 (OUTLIER) cc_final: 0.4382 (ttp80) REVERT: C 39 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.5930 (mp0) REVERT: C 98 TRP cc_start: 0.7119 (t60) cc_final: 0.6880 (t60) REVERT: C 100 LYS cc_start: 0.6797 (ttmt) cc_final: 0.6500 (ttmm) REVERT: C 121 MET cc_start: 0.8417 (ttm) cc_final: 0.7926 (mtt) REVERT: C 174 ASN cc_start: 0.7597 (m110) cc_final: 0.7296 (m110) REVERT: C 177 ARG cc_start: 0.6468 (OUTLIER) cc_final: 0.6235 (ttt-90) REVERT: C 293 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6605 (pt0) REVERT: B 120 TRP cc_start: 0.3611 (m100) cc_final: 0.2705 (m100) REVERT: B 146 LYS cc_start: 0.5954 (OUTLIER) cc_final: 0.5711 (mptt) REVERT: B 147 ARG cc_start: 0.5609 (OUTLIER) cc_final: 0.5173 (ttm110) REVERT: B 161 SER cc_start: 0.4186 (OUTLIER) cc_final: 0.3639 (p) REVERT: B 189 GLN cc_start: 0.5564 (tp40) cc_final: 0.5069 (tt0) REVERT: B 277 LYS cc_start: 0.6020 (OUTLIER) cc_final: 0.5410 (tmtp) outliers start: 36 outliers final: 21 residues processed: 151 average time/residue: 1.3190 time to fit residues: 213.7985 Evaluate side-chains 144 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 177 ARG Chi-restraints excluded: chain A residue 243 ASP 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 65 LEU 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 237 THR 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 177 ARG Chi-restraints excluded: chain C residue 192 THR 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 52 THR 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 161 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 29 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 14 optimal weight: 0.0370 chunk 27 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 overall best weight: 1.0260 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.242271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.214239 restraints weight = 11454.441| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 1.50 r_work: 0.4292 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4196 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.5420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11232 Z= 0.137 Angle : 0.569 11.606 15244 Z= 0.299 Chirality : 0.042 0.136 1540 Planarity : 0.005 0.036 1976 Dihedral : 4.007 13.263 1480 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.09 % Allowed : 17.93 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.22), residues: 1344 helix: 1.33 (0.19), residues: 676 sheet: -0.28 (0.52), residues: 88 loop : -0.93 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 98 HIS 0.002 0.001 HIS D 346 PHE 0.012 0.002 PHE D 62 TYR 0.013 0.002 TYR A 182 ARG 0.005 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 551) hydrogen bonds : angle 5.27964 ( 1599) covalent geometry : bond 0.00307 (11232) covalent geometry : angle 0.56880 (15244) ********************** 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 155 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 98 TRP cc_start: 0.7089 (t60) cc_final: 0.6857 (t60) REVERT: A 177 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.6279 (ttt-90) REVERT: A 283 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: A 293 GLN cc_start: 0.7061 (mt0) cc_final: 0.6831 (mt0) REVERT: D 120 TRP cc_start: 0.3556 (m100) cc_final: 0.2723 (m100) REVERT: D 146 LYS cc_start: 0.5896 (OUTLIER) cc_final: 0.5598 (mptt) REVERT: D 162 MET cc_start: 0.2971 (mmm) cc_final: 0.2705 (mmm) REVERT: D 249 MET cc_start: 0.5742 (mtm) cc_final: 0.4653 (ttm) REVERT: D 318 ARG cc_start: 0.5792 (OUTLIER) cc_final: 0.4382 (ttp80) REVERT: C 39 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.5735 (mp0) REVERT: C 98 TRP cc_start: 0.7150 (t60) cc_final: 0.6920 (t60) REVERT: C 100 LYS cc_start: 0.6842 (ttmt) cc_final: 0.6488 (ttmm) REVERT: C 121 MET cc_start: 0.8430 (ttm) cc_final: 0.7926 (mtt) REVERT: C 174 ASN cc_start: 0.7605 (m110) cc_final: 0.7299 (m110) REVERT: C 177 ARG cc_start: 0.6474 (OUTLIER) cc_final: 0.6223 (ttt-90) REVERT: C 293 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6629 (pt0) REVERT: B 120 TRP cc_start: 0.3655 (m100) cc_final: 0.2737 (m100) REVERT: B 146 LYS cc_start: 0.6036 (OUTLIER) cc_final: 0.5805 (mptt) REVERT: B 147 ARG cc_start: 0.5657 (OUTLIER) cc_final: 0.5226 (ttm110) REVERT: B 161 SER cc_start: 0.4193 (OUTLIER) cc_final: 0.3662 (p) REVERT: B 277 LYS cc_start: 0.5938 (OUTLIER) cc_final: 0.5349 (tmtp) outliers start: 35 outliers final: 21 residues processed: 148 average time/residue: 1.4042 time to fit residues: 222.7039 Evaluate side-chains 150 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 177 ARG Chi-restraints excluded: chain A residue 243 ASP 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 65 LEU 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 237 THR 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 177 ARG Chi-restraints excluded: chain C residue 192 THR 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 52 THR 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 161 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 277 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 67 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN A 314 GLN C 314 GLN ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.243349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.215544 restraints weight = 11323.645| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 1.49 r_work: 0.4305 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.4210 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11232 Z= 0.124 Angle : 0.557 11.770 15244 Z= 0.291 Chirality : 0.041 0.162 1540 Planarity : 0.005 0.036 1976 Dihedral : 3.923 13.198 1480 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.18 % Allowed : 17.84 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.22), residues: 1344 helix: 1.39 (0.19), residues: 676 sheet: -0.25 (0.52), residues: 88 loop : -0.92 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 106 HIS 0.002 0.001 HIS D 346 PHE 0.010 0.001 PHE D 62 TYR 0.012 0.001 TYR C 182 ARG 0.005 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 551) hydrogen bonds : angle 5.25370 ( 1599) covalent geometry : bond 0.00276 (11232) covalent geometry : angle 0.55730 (15244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8167.45 seconds wall clock time: 141 minutes 1.11 seconds (8461.11 seconds total)