Starting phenix.real_space_refine on Mon Jun 9 18:51:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b87_44334/06_2025/9b87_44334.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b87_44334/06_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_44334/06_2025/9b87_44334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b87_44334/06_2025/9b87_44334.map" model { file = "/net/cci-nas-00/data/ceres_data/9b87_44334/06_2025/9b87_44334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b87_44334/06_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-5710/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: 6.60, per 1000 atoms: 0.60 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: 2.50 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: 1.18 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: 3.09 Time building geometry restraints manager: 2.97 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.210 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.830 ------------------------------------------------------------------------------- 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 : 1.304 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: 1.3129 time to fit residues: 299.6559 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 : 1.703 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.225876 restraints weight = 11728.829| |-----------------------------------------------------------------------------| r_work (start): 0.4523 rms_B_bonded: 1.55 r_work: 0.4469 rms_B_bonded: 2.02 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 : 1.805 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: 0.6425 (OUTLIER) cc_final: 0.6085 (mttp) REVERT: D 120 TRP cc_start: 0.3782 (m100) cc_final: 0.2724 (m100) REVERT: D 254 MET cc_start: 0.3861 (mtp) cc_final: 0.3610 (mtm) REVERT: D 278 ASN cc_start: 0.5257 (OUTLIER) cc_final: 0.4881 (t160) REVERT: D 320 ARG cc_start: 0.4367 (mtp85) cc_final: 0.3999 (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: 0.7883 (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: 0.5680 (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: 1.8668 time to fit residues: 345.0529 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 : 2.054 ------------------------------------------------------------------------------- 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: 0.8980 chunk 52 optimal weight: 2.9990 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: 2.1586 ------------------------------------------------------------------------------- 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 D 189 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 = 0.4676 r_free = 0.4676 target = 0.244728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.216375 restraints weight = 11950.729| |-----------------------------------------------------------------------------| r_work (start): 0.4439 rms_B_bonded: 1.53 r_work: 0.4386 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.4302 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.4273 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= 0.223 Angle : 0.670 7.753 15244 Z= 0.365 Chirality : 0.047 0.139 1540 Planarity : 0.006 0.045 1976 Dihedral : 4.659 17.389 1480 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.80 % Allowed : 12.81 % Favored : 83.39 % 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: 0.20 (0.22), residues: 1344 helix: 0.94 (0.19), residues: 684 sheet: -0.46 (0.51), residues: 88 loop : -0.69 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 106 HIS 0.006 0.002 HIS D 346 PHE 0.017 0.003 PHE B 339 TYR 0.023 0.003 TYR C 182 ARG 0.009 0.001 ARG B 318 Details of bonding type rmsd hydrogen bonds : bond 0.05461 ( 551) hydrogen bonds : angle 5.82058 ( 1599) covalent geometry : bond 0.00522 (11232) covalent geometry : angle 0.66976 (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 176 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 1.810 Fit side-chains revert: symmetry clash REVERT: A 98 TRP cc_start: 0.7139 (t60) cc_final: 0.6903 (t60) REVERT: D 91 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6347 (mt-10) REVERT: D 120 TRP cc_start: 0.3677 (m100) cc_final: 0.2907 (m100) REVERT: D 150 ARG cc_start: 0.5952 (OUTLIER) cc_final: 0.5703 (ttm-80) REVERT: D 203 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6316 (mm-30) REVERT: D 254 MET cc_start: 0.4764 (mtp) cc_final: 0.4451 (mtm) REVERT: D 278 ASN cc_start: 0.5573 (OUTLIER) cc_final: 0.5237 (t160) REVERT: D 318 ARG cc_start: 0.5754 (OUTLIER) cc_final: 0.4391 (ttp80) REVERT: D 320 ARG cc_start: 0.4643 (mtp85) cc_final: 0.4182 (tpp80) REVERT: C 98 TRP cc_start: 0.7230 (t60) cc_final: 0.7004 (t60) REVERT: C 121 MET cc_start: 0.8501 (ttm) cc_final: 0.7974 (mtt) REVERT: C 174 ASN cc_start: 0.7497 (m110) cc_final: 0.7124 (m110) REVERT: C 293 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6708 (pt0) REVERT: B 120 TRP cc_start: 0.3955 (m100) cc_final: 0.2837 (m100) REVERT: B 147 ARG cc_start: 0.5994 (OUTLIER) cc_final: 0.5573 (ttm110) REVERT: B 161 SER cc_start: 0.4321 (OUTLIER) cc_final: 0.3945 (m) REVERT: B 291 LYS cc_start: 0.5241 (tptp) cc_final: 0.3905 (tmmt) REVERT: B 311 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6064 (mpp80) outliers start: 43 outliers final: 17 residues processed: 162 average time/residue: 2.0460 time to fit residues: 355.7985 Evaluate side-chains 143 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 1.387 ------------------------------------------------------------------------------- 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 91 GLU 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 278 ASN 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 264 MET Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 147 ARG 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: 0.0070 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.244439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.216617 restraints weight = 11863.696| |-----------------------------------------------------------------------------| r_work (start): 0.4438 rms_B_bonded: 1.51 r_work: 0.4389 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.4305 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.4737 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 : 0.593 8.191 15244 Z= 0.319 Chirality : 0.044 0.124 1540 Planarity : 0.006 0.040 1976 Dihedral : 4.404 15.481 1480 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.80 % Allowed : 14.66 % Favored : 81.54 % 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: 0.23 (0.22), residues: 1344 helix: 1.12 (0.19), residues: 676 sheet: -0.44 (0.53), residues: 88 loop : -0.88 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 106 HIS 0.004 0.001 HIS D 346 PHE 0.013 0.002 PHE D 62 TYR 0.017 0.002 TYR C 182 ARG 0.005 0.000 ARG B 318 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 551) hydrogen bonds : angle 5.58480 ( 1599) covalent geometry : bond 0.00385 (11232) covalent geometry : angle 0.59294 (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 168 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 1.442 Fit side-chains REVERT: A 98 TRP cc_start: 0.7144 (t60) cc_final: 0.6874 (t60) REVERT: A 283 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7489 (tp30) REVERT: D 34 ASP cc_start: 0.6429 (m-30) cc_final: 0.6174 (t70) REVERT: D 120 TRP cc_start: 0.3574 (m100) cc_final: 0.2780 (m100) REVERT: D 318 ARG cc_start: 0.5704 (OUTLIER) cc_final: 0.4257 (ttp80) REVERT: D 320 ARG cc_start: 0.4735 (OUTLIER) cc_final: 0.4214 (ttp80) REVERT: C 98 TRP cc_start: 0.7169 (t60) cc_final: 0.6940 (t60) REVERT: C 121 MET cc_start: 0.8484 (ttm) cc_final: 0.7934 (mtt) REVERT: C 174 ASN cc_start: 0.7699 (m110) cc_final: 0.7352 (m110) REVERT: C 177 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.6103 (ttt-90) REVERT: C 293 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6675 (pt0) REVERT: B 120 TRP cc_start: 0.3610 (m100) cc_final: 0.2770 (m100) REVERT: B 147 ARG cc_start: 0.6053 (OUTLIER) cc_final: 0.5573 (ttm110) REVERT: B 161 SER cc_start: 0.4649 (OUTLIER) cc_final: 0.4020 (p) REVERT: B 291 LYS cc_start: 0.5163 (tptp) cc_final: 0.4113 (tmmt) REVERT: B 311 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6105 (mpp80) outliers start: 43 outliers final: 17 residues processed: 156 average time/residue: 1.4743 time to fit residues: 247.6994 Evaluate side-chains 145 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 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 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 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 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 147 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 222 VAL 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 90 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 129 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 D 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.247116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.219865 restraints weight = 11796.025| |-----------------------------------------------------------------------------| r_work (start): 0.4460 rms_B_bonded: 1.51 r_work: 0.4411 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.4327 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11232 Z= 0.112 Angle : 0.523 9.581 15244 Z= 0.276 Chirality : 0.041 0.127 1540 Planarity : 0.005 0.037 1976 Dihedral : 3.939 13.616 1480 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.83 % Allowed : 16.17 % 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 (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: 1.51 (0.19), residues: 676 sheet: -0.25 (0.53), residues: 88 loop : -0.80 (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 0.010 0.001 PHE D 62 TYR 0.014 0.001 TYR C 182 ARG 0.004 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 551) hydrogen bonds : angle 5.30266 ( 1599) covalent geometry : bond 0.00243 (11232) covalent geometry : angle 0.52251 (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 159 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: A 98 TRP cc_start: 0.7154 (t60) cc_final: 0.6905 (t60) REVERT: A 177 ARG cc_start: 0.6505 (OUTLIER) cc_final: 0.6224 (ttt-90) REVERT: A 206 GLN cc_start: 0.7165 (tt0) cc_final: 0.6760 (mt0) REVERT: D 120 TRP cc_start: 0.3512 (m100) cc_final: 0.2746 (m100) REVERT: D 147 ARG cc_start: 0.6173 (ttm-80) cc_final: 0.5872 (ttm110) REVERT: D 162 MET cc_start: 0.2778 (mmm) cc_final: 0.2509 (mmm) REVERT: D 318 ARG cc_start: 0.5549 (OUTLIER) cc_final: 0.4386 (ttp80) REVERT: C 39 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6185 (mp0) REVERT: C 98 TRP cc_start: 0.7084 (t60) cc_final: 0.6861 (t60) REVERT: C 100 LYS cc_start: 0.6798 (ttmt) cc_final: 0.6532 (ttmm) REVERT: C 121 MET cc_start: 0.8475 (ttm) cc_final: 0.7971 (mtt) REVERT: C 133 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7507 (mtmt) REVERT: C 174 ASN cc_start: 0.7701 (m110) cc_final: 0.7361 (m110) REVERT: C 177 ARG cc_start: 0.6406 (OUTLIER) cc_final: 0.6166 (ttt-90) REVERT: C 293 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6652 (pt0) REVERT: B 120 TRP cc_start: 0.3615 (m100) cc_final: 0.2816 (m100) REVERT: B 161 SER cc_start: 0.4637 (OUTLIER) cc_final: 0.4023 (p) REVERT: B 291 LYS cc_start: 0.4951 (tptp) cc_final: 0.3898 (tmmt) REVERT: B 311 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.5909 (mpp80) outliers start: 32 outliers final: 11 residues processed: 152 average time/residue: 1.3876 time to fit residues: 226.0867 Evaluate side-chains 132 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 D residue 37 SER Chi-restraints excluded: chain D residue 110 ASP 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 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 293 GLN Chi-restraints excluded: chain B residue 37 SER 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 311 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 79 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 101 optimal weight: 0.0060 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 96 optimal weight: 0.0770 overall best weight: 0.4554 ------------------------------------------------------------------------------- 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 206 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 = 0.4720 r_free = 0.4720 target = 0.249331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.222152 restraints weight = 11917.506| |-----------------------------------------------------------------------------| r_work (start): 0.4469 rms_B_bonded: 1.51 r_work: 0.4418 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.4334 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.4951 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= 0.101 Angle : 0.504 10.151 15244 Z= 0.265 Chirality : 0.040 0.122 1540 Planarity : 0.004 0.036 1976 Dihedral : 3.721 13.052 1480 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.65 % Allowed : 16.70 % Favored : 80.65 % 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: 0.83 (0.23), residues: 1344 helix: 1.69 (0.20), residues: 676 sheet: -0.13 (0.53), residues: 88 loop : -0.69 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 106 HIS 0.002 0.001 HIS D 346 PHE 0.008 0.001 PHE D 73 TYR 0.012 0.001 TYR A 182 ARG 0.005 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 551) hydrogen bonds : angle 5.15271 ( 1599) covalent geometry : bond 0.00212 (11232) covalent geometry : angle 0.50432 (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 161 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.193 Fit side-chains REVERT: A 98 TRP cc_start: 0.7101 (t60) cc_final: 0.6860 (t60) REVERT: A 133 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7447 (mtmt) REVERT: A 283 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6929 (tp30) REVERT: D 101 LYS cc_start: 0.6642 (OUTLIER) cc_final: 0.6311 (mmtp) REVERT: D 120 TRP cc_start: 0.3756 (m100) cc_final: 0.2784 (m100) REVERT: D 121 MET cc_start: 0.6076 (OUTLIER) cc_final: 0.5724 (tpp) REVERT: D 318 ARG cc_start: 0.5364 (OUTLIER) cc_final: 0.4203 (ttp80) REVERT: C 39 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6166 (mp0) REVERT: C 98 TRP cc_start: 0.7145 (t60) cc_final: 0.6907 (t60) REVERT: C 100 LYS cc_start: 0.6763 (ttmt) cc_final: 0.6559 (ttmm) REVERT: C 121 MET cc_start: 0.8460 (ttm) cc_final: 0.7953 (mtt) REVERT: C 133 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7404 (mtmt) REVERT: C 174 ASN cc_start: 0.7685 (m110) cc_final: 0.7357 (m110) REVERT: C 177 ARG cc_start: 0.6448 (OUTLIER) cc_final: 0.6232 (ttt-90) REVERT: C 271 MET cc_start: 0.7071 (tpt) cc_final: 0.6806 (tpt) REVERT: C 293 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6638 (pt0) REVERT: B 102 GLU cc_start: 0.6261 (tp30) cc_final: 0.5897 (tp30) REVERT: B 120 TRP cc_start: 0.3589 (m100) cc_final: 0.2753 (m100) REVERT: B 147 ARG cc_start: 0.6011 (OUTLIER) cc_final: 0.5574 (ttm110) REVERT: B 161 SER cc_start: 0.4634 (OUTLIER) cc_final: 0.3966 (p) REVERT: B 291 LYS cc_start: 0.4866 (tptp) cc_final: 0.3983 (tmmt) REVERT: B 311 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.5901 (mpp80) outliers start: 30 outliers final: 11 residues processed: 155 average time/residue: 1.3489 time to fit residues: 224.2716 Evaluate side-chains 140 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 101 LYS Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 121 MET 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 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 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 146 LYS Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 161 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 84 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 122 optimal weight: 0.0060 chunk 39 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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 = 0.4632 r_free = 0.4632 target = 0.243576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.215356 restraints weight = 11563.058| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 1.50 r_work: 0.4302 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4205 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.5121 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= 0.128 Angle : 0.544 10.459 15244 Z= 0.287 Chirality : 0.042 0.122 1540 Planarity : 0.005 0.035 1976 Dihedral : 3.911 13.748 1480 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.45 % Allowed : 17.58 % 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: 0.65 (0.22), residues: 1344 helix: 1.54 (0.19), residues: 676 sheet: -0.25 (0.53), residues: 88 loop : -0.77 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 106 HIS 0.003 0.001 HIS D 346 PHE 0.013 0.001 PHE B 73 TYR 0.020 0.002 TYR A 182 ARG 0.005 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 551) hydrogen bonds : angle 5.22363 ( 1599) covalent geometry : bond 0.00284 (11232) covalent geometry : angle 0.54415 (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 164 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 1.283 Fit side-chains REVERT: A 98 TRP cc_start: 0.7057 (t60) cc_final: 0.6802 (t60) REVERT: A 133 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7501 (mtmt) REVERT: A 177 ARG cc_start: 0.6458 (OUTLIER) cc_final: 0.6154 (ttt-90) REVERT: A 206 GLN cc_start: 0.7201 (tt0) cc_final: 0.6759 (mt0) REVERT: A 283 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6989 (tp30) REVERT: D 101 LYS cc_start: 0.6656 (OUTLIER) cc_final: 0.6241 (mmtp) REVERT: D 105 LYS cc_start: 0.5550 (mttm) cc_final: 0.5267 (mmtt) REVERT: D 120 TRP cc_start: 0.3731 (m100) cc_final: 0.2666 (m100) REVERT: D 146 LYS cc_start: 0.6003 (OUTLIER) cc_final: 0.5742 (mptt) REVERT: D 318 ARG cc_start: 0.5778 (OUTLIER) cc_final: 0.4382 (ttp80) REVERT: C 39 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6119 (mp0) REVERT: C 98 TRP cc_start: 0.7088 (t60) cc_final: 0.6825 (t60) REVERT: C 100 LYS cc_start: 0.6814 (ttmt) cc_final: 0.6463 (ttmm) REVERT: C 121 MET cc_start: 0.8427 (ttm) cc_final: 0.7925 (mtt) REVERT: C 174 ASN cc_start: 0.7613 (m110) cc_final: 0.7265 (m110) REVERT: C 177 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.6209 (ttt-90) REVERT: C 293 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6571 (pt0) REVERT: B 102 GLU cc_start: 0.6175 (tp30) cc_final: 0.5820 (tp30) REVERT: B 120 TRP cc_start: 0.3565 (m100) cc_final: 0.2720 (m100) REVERT: B 147 ARG cc_start: 0.5797 (OUTLIER) cc_final: 0.5407 (ttm110) REVERT: B 161 SER cc_start: 0.4321 (OUTLIER) cc_final: 0.3707 (p) REVERT: B 311 ARG cc_start: 0.6896 (OUTLIER) cc_final: 0.5847 (mpp80) outliers start: 39 outliers final: 17 residues processed: 157 average time/residue: 1.4182 time to fit residues: 238.3799 Evaluate side-chains 144 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 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 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 222 VAL Chi-restraints excluded: chain B residue 311 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.5589 > 50: distance: 19 - 38: 5.401 distance: 34 - 38: 6.487 distance: 38 - 39: 6.516 distance: 39 - 40: 4.053 distance: 39 - 42: 3.460 distance: 40 - 41: 5.846 distance: 40 - 47: 4.296 distance: 42 - 43: 9.912 distance: 43 - 44: 10.834 distance: 44 - 45: 4.648 distance: 44 - 46: 3.259 distance: 47 - 48: 6.482 distance: 48 - 49: 19.154 distance: 48 - 51: 26.440 distance: 49 - 50: 13.073 distance: 49 - 54: 6.988 distance: 51 - 52: 14.258 distance: 51 - 53: 22.495 distance: 54 - 55: 15.629 distance: 54 - 107: 16.329 distance: 55 - 56: 12.322 distance: 55 - 58: 6.864 distance: 56 - 57: 3.120 distance: 56 - 61: 5.176 distance: 57 - 104: 10.371 distance: 58 - 59: 6.207 distance: 58 - 60: 10.683 distance: 61 - 62: 5.608 distance: 62 - 63: 4.380 distance: 62 - 65: 4.185 distance: 63 - 64: 4.013 distance: 63 - 68: 10.572 distance: 65 - 66: 10.117 distance: 65 - 67: 3.120 distance: 68 - 69: 8.231 distance: 68 - 97: 13.983 distance: 69 - 70: 7.531 distance: 69 - 72: 4.050 distance: 70 - 71: 8.041 distance: 70 - 75: 9.820 distance: 71 - 94: 11.773 distance: 72 - 73: 4.314 distance: 72 - 74: 10.382 distance: 75 - 76: 5.126 distance: 75 - 81: 3.005 distance: 76 - 77: 8.360 distance: 76 - 79: 5.956 distance: 77 - 78: 9.356 distance: 79 - 80: 8.488 distance: 80 - 81: 11.211 distance: 82 - 83: 4.269 distance: 83 - 84: 3.652 distance: 84 - 85: 5.451 distance: 87 - 90: 3.554 distance: 88 - 89: 8.448 distance: 88 - 94: 6.734 distance: 90 - 91: 7.485 distance: 91 - 92: 10.903 distance: 91 - 93: 18.341 distance: 95 - 96: 6.621 distance: 96 - 97: 7.661 distance: 96 - 98: 7.689 distance: 98 - 99: 3.491 distance: 99 - 100: 3.558 distance: 99 - 102: 7.761 distance: 100 - 104: 3.934 distance: 102 - 103: 5.683