Starting phenix.real_space_refine on Wed Mar 4 18:05:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d1m_27135/03_2026/8d1m_27135.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1m_27135/03_2026/8d1m_27135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d1m_27135/03_2026/8d1m_27135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1m_27135/03_2026/8d1m_27135.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d1m_27135/03_2026/8d1m_27135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1m_27135/03_2026/8d1m_27135.map" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.095 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 80 5.16 5 C 10260 2.51 5 N 2550 2.21 5 O 2700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15590 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Restraints were copied for chains: E, B, D, C Time building chain proxies: 2.40, per 1000 atoms: 0.15 Number of scatterers: 15590 At special positions: 0 Unit cell: (109.56, 106.24, 110.39, 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 80 16.00 O 2700 8.00 N 2550 7.00 C 10260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 661.3 milliseconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 5 sheets defined 68.0% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 17 through 23 Processing helix chain 'A' and resid 27 through 53 removed outlier: 3.553A pdb=" N LEU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLY A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 73 removed outlier: 3.510A pdb=" N TYR A 72 " --> pdb=" O TYR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.571A pdb=" N VAL A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.713A pdb=" N ALA A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.567A pdb=" N LYS A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.640A pdb=" N LEU A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.700A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 3.741A pdb=" N LEU A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.923A pdb=" N VAL A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.766A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 removed outlier: 3.550A pdb=" N ASP A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'E' and resid 17 through 23 Processing helix chain 'E' and resid 27 through 53 removed outlier: 3.554A pdb=" N LEU E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLY E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 removed outlier: 3.511A pdb=" N TYR E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 99 Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.572A pdb=" N VAL E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.713A pdb=" N ALA E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 149 removed outlier: 3.567A pdb=" N LYS E 149 " --> pdb=" O THR E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 160 removed outlier: 3.640A pdb=" N LEU E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.699A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 removed outlier: 3.741A pdb=" N LEU E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU E 217 " --> pdb=" O GLU E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.922A pdb=" N VAL E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.765A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 324 removed outlier: 3.550A pdb=" N ASP E 323 " --> pdb=" O LEU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'B' and resid 17 through 23 Processing helix chain 'B' and resid 27 through 52 removed outlier: 3.552A pdb=" N LEU B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLY B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 73 removed outlier: 3.510A pdb=" N TYR B 72 " --> pdb=" O TYR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 99 Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.571A pdb=" N VAL B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.713A pdb=" N ALA B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 removed outlier: 3.566A pdb=" N LYS B 149 " --> pdb=" O THR B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.640A pdb=" N LEU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.699A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 removed outlier: 3.741A pdb=" N LEU B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.923A pdb=" N VAL B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.765A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 removed outlier: 3.550A pdb=" N ASP B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 27 through 53 removed outlier: 3.553A pdb=" N LEU D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLY D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 removed outlier: 3.510A pdb=" N TYR D 72 " --> pdb=" O TYR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 99 Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.572A pdb=" N VAL D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.713A pdb=" N ALA D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 removed outlier: 3.567A pdb=" N LYS D 149 " --> pdb=" O THR D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.640A pdb=" N LEU D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.699A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 removed outlier: 3.741A pdb=" N LEU D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.922A pdb=" N VAL D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.766A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 324 removed outlier: 3.551A pdb=" N ASP D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 52 removed outlier: 3.554A pdb=" N LEU C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLY C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 73 removed outlier: 3.511A pdb=" N TYR C 72 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 99 Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.571A pdb=" N VAL C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.713A pdb=" N ALA C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.567A pdb=" N LYS C 149 " --> pdb=" O THR C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.640A pdb=" N LEU C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.699A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 removed outlier: 3.741A pdb=" N LEU C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.923A pdb=" N VAL C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.765A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 removed outlier: 3.550A pdb=" N ASP C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 348 removed outlier: 4.202A pdb=" N TYR A 347 " --> pdb=" O GLN E 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 375 through 376 removed outlier: 4.213A pdb=" N TYR B 347 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 347 through 348 removed outlier: 4.220A pdb=" N TYR E 347 " --> pdb=" O GLN D 376 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 375 through 376 removed outlier: 4.223A pdb=" N TYR C 347 " --> pdb=" O GLN B 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 347 through 348 removed outlier: 4.204A pdb=" N TYR D 347 " --> pdb=" O GLN C 376 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2664 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3103 1.33 - 1.45: 4143 1.45 - 1.57: 8679 1.57 - 1.69: 5 1.69 - 1.81: 135 Bond restraints: 16065 Sorted by residual: bond pdb=" CA LEU A 75 " pdb=" C LEU A 75 " ideal model delta sigma weight residual 1.523 1.574 -0.050 1.34e-02 5.57e+03 1.41e+01 bond pdb=" CA LEU B 75 " pdb=" C LEU B 75 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.34e-02 5.57e+03 1.41e+01 bond pdb=" CA LEU C 75 " pdb=" C LEU C 75 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.34e-02 5.57e+03 1.38e+01 bond pdb=" CA LEU E 75 " pdb=" C LEU E 75 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.34e-02 5.57e+03 1.37e+01 bond pdb=" CA LEU D 75 " pdb=" C LEU D 75 " ideal model delta sigma weight residual 1.523 1.573 -0.049 1.34e-02 5.57e+03 1.36e+01 ... (remaining 16060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 21175 2.39 - 4.79: 645 4.79 - 7.18: 55 7.18 - 9.57: 5 9.57 - 11.97: 5 Bond angle restraints: 21885 Sorted by residual: angle pdb=" N ASP D 301 " pdb=" CA ASP D 301 " pdb=" C ASP D 301 " ideal model delta sigma weight residual 109.79 97.82 11.97 1.56e+00 4.11e-01 5.88e+01 angle pdb=" N ASP C 301 " pdb=" CA ASP C 301 " pdb=" C ASP C 301 " ideal model delta sigma weight residual 109.79 97.83 11.96 1.56e+00 4.11e-01 5.88e+01 angle pdb=" N ASP B 301 " pdb=" CA ASP B 301 " pdb=" C ASP B 301 " ideal model delta sigma weight residual 109.79 97.84 11.95 1.56e+00 4.11e-01 5.87e+01 angle pdb=" N ASP A 301 " pdb=" CA ASP A 301 " pdb=" C ASP A 301 " ideal model delta sigma weight residual 109.79 97.84 11.95 1.56e+00 4.11e-01 5.87e+01 angle pdb=" N ASP E 301 " pdb=" CA ASP E 301 " pdb=" C ASP E 301 " ideal model delta sigma weight residual 109.79 97.85 11.94 1.56e+00 4.11e-01 5.86e+01 ... (remaining 21880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 8370 17.76 - 35.52: 780 35.52 - 53.28: 170 53.28 - 71.04: 25 71.04 - 88.80: 30 Dihedral angle restraints: 9375 sinusoidal: 3810 harmonic: 5565 Sorted by residual: dihedral pdb=" CA ARG C 313 " pdb=" CB ARG C 313 " pdb=" CG ARG C 313 " pdb=" CD ARG C 313 " ideal model delta sinusoidal sigma weight residual -180.00 -122.62 -57.38 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CA ARG A 313 " pdb=" CB ARG A 313 " pdb=" CG ARG A 313 " pdb=" CD ARG A 313 " ideal model delta sinusoidal sigma weight residual -180.00 -122.62 -57.38 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CA ARG D 313 " pdb=" CB ARG D 313 " pdb=" CG ARG D 313 " pdb=" CD ARG D 313 " ideal model delta sinusoidal sigma weight residual -180.00 -122.65 -57.35 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 9372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1746 0.050 - 0.100: 429 0.100 - 0.150: 128 0.150 - 0.200: 47 0.200 - 0.250: 25 Chirality restraints: 2375 Sorted by residual: chirality pdb=" CA ILE C 28 " pdb=" N ILE C 28 " pdb=" C ILE C 28 " pdb=" CB ILE C 28 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ILE B 28 " pdb=" N ILE B 28 " pdb=" C ILE B 28 " pdb=" CB ILE B 28 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ILE E 28 " pdb=" N ILE E 28 " pdb=" C ILE E 28 " pdb=" CB ILE E 28 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 2372 not shown) Planarity restraints: 2750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 29 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C TYR E 29 " 0.036 2.00e-02 2.50e+03 pdb=" O TYR E 29 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS E 30 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 29 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C TYR C 29 " -0.036 2.00e-02 2.50e+03 pdb=" O TYR C 29 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS C 30 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 29 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C TYR A 29 " 0.036 2.00e-02 2.50e+03 pdb=" O TYR A 29 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS A 30 " -0.012 2.00e-02 2.50e+03 ... (remaining 2747 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 6141 2.90 - 3.40: 16376 3.40 - 3.90: 27431 3.90 - 4.40: 31976 4.40 - 4.90: 53230 Nonbonded interactions: 135154 Sorted by model distance: nonbonded pdb=" N ASP B 301 " pdb=" O ASP B 301 " model vdw 2.396 2.496 nonbonded pdb=" N ASP A 301 " pdb=" O ASP A 301 " model vdw 2.397 2.496 nonbonded pdb=" N ASP C 301 " pdb=" O ASP C 301 " model vdw 2.397 2.496 nonbonded pdb=" N ASP D 301 " pdb=" O ASP D 301 " model vdw 2.397 2.496 nonbonded pdb=" N ASP E 301 " pdb=" O ASP E 301 " model vdw 2.397 2.496 ... (remaining 135149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'B' selection = chain 'D' selection = chain 'C' } 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: 1.750 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.040 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.006 0.050 16065 Z= 0.372 Angle : 0.865 11.965 21885 Z= 0.584 Chirality : 0.057 0.250 2375 Planarity : 0.005 0.040 2750 Dihedral : 15.342 88.804 5785 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.67 % Favored : 97.06 % Rotamer: Outliers : 1.18 % Allowed : 2.36 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.18), residues: 1870 helix: 1.48 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -0.17 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 122 TYR 0.032 0.002 TYR B 236 PHE 0.021 0.002 PHE C 248 TRP 0.014 0.002 TRP E 93 HIS 0.005 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00593 (16065) covalent geometry : angle 0.86516 (21885) hydrogen bonds : bond 0.15254 ( 918) hydrogen bonds : angle 5.14974 ( 2664) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 316 time to evaluate : 0.528 Fit side-chains REVERT: A 331 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7245 (ttp80) REVERT: E 262 LYS cc_start: 0.8124 (mmtp) cc_final: 0.7898 (mmtm) REVERT: B 331 ARG cc_start: 0.7519 (ttp80) cc_final: 0.7174 (ttp80) REVERT: B 344 GLN cc_start: 0.7810 (mt0) cc_final: 0.7569 (mm-40) REVERT: C 173 LYS cc_start: 0.8744 (tmmt) cc_final: 0.8516 (tttm) REVERT: C 331 ARG cc_start: 0.7555 (ttp80) cc_final: 0.7185 (ttp80) REVERT: C 360 MET cc_start: 0.8182 (mmt) cc_final: 0.7716 (mmt) outliers start: 20 outliers final: 10 residues processed: 334 average time/residue: 0.1370 time to fit residues: 65.8447 Evaluate side-chains 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 221 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 296 ASN E 256 GLN E 296 ASN B 256 GLN B 296 ASN D 256 GLN D 296 ASN C 256 GLN C 296 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.110064 restraints weight = 18228.290| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.96 r_work: 0.3046 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16065 Z= 0.140 Angle : 0.525 8.132 21885 Z= 0.278 Chirality : 0.037 0.149 2375 Planarity : 0.004 0.028 2750 Dihedral : 3.984 16.879 2095 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.89 % Allowed : 8.85 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.19), residues: 1870 helix: 1.74 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : 0.00 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 25 TYR 0.016 0.002 TYR C 236 PHE 0.017 0.001 PHE B 248 TRP 0.013 0.001 TRP B 93 HIS 0.003 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00318 (16065) covalent geometry : angle 0.52545 (21885) hydrogen bonds : bond 0.05264 ( 918) hydrogen bonds : angle 4.06098 ( 2664) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 0.517 Fit side-chains REVERT: A 209 SER cc_start: 0.8864 (OUTLIER) cc_final: 0.8475 (p) REVERT: E 209 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8461 (p) REVERT: E 262 LYS cc_start: 0.7932 (mmtp) cc_final: 0.7718 (mmtm) REVERT: E 331 ARG cc_start: 0.8188 (ttp80) cc_final: 0.7900 (ttp80) REVERT: B 209 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8490 (p) REVERT: B 300 GLU cc_start: 0.6994 (pm20) cc_final: 0.6742 (pm20) REVERT: B 331 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7743 (ttp80) REVERT: D 209 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8490 (p) REVERT: D 300 GLU cc_start: 0.7030 (pm20) cc_final: 0.6803 (pm20) REVERT: D 302 ASP cc_start: 0.8387 (m-30) cc_final: 0.8022 (m-30) REVERT: C 360 MET cc_start: 0.8511 (mmt) cc_final: 0.8005 (mmt) outliers start: 32 outliers final: 19 residues processed: 263 average time/residue: 0.1596 time to fit residues: 58.6149 Evaluate side-chains 234 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 16 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 137 optimal weight: 0.0020 chunk 133 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.133101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.100438 restraints weight = 18727.443| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.04 r_work: 0.2984 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16065 Z= 0.162 Angle : 0.514 6.678 21885 Z= 0.271 Chirality : 0.038 0.151 2375 Planarity : 0.004 0.035 2750 Dihedral : 3.905 16.882 2090 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.12 % Allowed : 11.27 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.19), residues: 1870 helix: 1.54 (0.14), residues: 1195 sheet: None (None), residues: 0 loop : 0.19 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 331 TYR 0.018 0.001 TYR E 236 PHE 0.020 0.001 PHE B 248 TRP 0.012 0.001 TRP E 93 HIS 0.004 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00381 (16065) covalent geometry : angle 0.51434 (21885) hydrogen bonds : bond 0.05168 ( 918) hydrogen bonds : angle 3.91417 ( 2664) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 0.633 Fit side-chains REVERT: A 209 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8476 (p) REVERT: A 356 ARG cc_start: 0.7197 (mmt180) cc_final: 0.6719 (mmt90) REVERT: E 209 SER cc_start: 0.8826 (OUTLIER) cc_final: 0.8462 (p) REVERT: E 262 LYS cc_start: 0.8062 (mmtp) cc_final: 0.7857 (mmtm) REVERT: E 300 GLU cc_start: 0.7068 (pm20) cc_final: 0.6759 (pm20) REVERT: B 300 GLU cc_start: 0.7059 (pm20) cc_final: 0.6765 (pm20) REVERT: B 331 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7751 (ttp80) REVERT: B 344 GLN cc_start: 0.7768 (mt0) cc_final: 0.7386 (mm-40) REVERT: D 209 SER cc_start: 0.8820 (OUTLIER) cc_final: 0.8498 (p) REVERT: D 300 GLU cc_start: 0.7140 (pm20) cc_final: 0.6880 (pm20) REVERT: D 344 GLN cc_start: 0.7823 (mt0) cc_final: 0.7363 (mm-40) REVERT: C 344 GLN cc_start: 0.7736 (mt0) cc_final: 0.7344 (mm-40) REVERT: C 360 MET cc_start: 0.8518 (mmt) cc_final: 0.8021 (mmt) outliers start: 36 outliers final: 24 residues processed: 245 average time/residue: 0.1739 time to fit residues: 58.7585 Evaluate side-chains 232 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 36 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 153 optimal weight: 0.0770 chunk 161 optimal weight: 3.9990 overall best weight: 1.1144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.135851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.103662 restraints weight = 18620.534| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.02 r_work: 0.3065 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16065 Z= 0.131 Angle : 0.488 6.710 21885 Z= 0.255 Chirality : 0.036 0.147 2375 Planarity : 0.004 0.048 2750 Dihedral : 3.765 16.513 2090 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.71 % Allowed : 12.33 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.19), residues: 1870 helix: 1.56 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.25 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 356 TYR 0.012 0.001 TYR B 236 PHE 0.016 0.001 PHE B 248 TRP 0.012 0.001 TRP E 93 HIS 0.003 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00300 (16065) covalent geometry : angle 0.48754 (21885) hydrogen bonds : bond 0.04747 ( 918) hydrogen bonds : angle 3.83881 ( 2664) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 0.572 Fit side-chains REVERT: A 68 TYR cc_start: 0.4829 (t80) cc_final: 0.4513 (t80) REVERT: A 209 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8455 (p) REVERT: E 209 SER cc_start: 0.8809 (OUTLIER) cc_final: 0.8440 (p) REVERT: E 300 GLU cc_start: 0.7027 (pm20) cc_final: 0.6744 (pm20) REVERT: B 262 LYS cc_start: 0.8191 (mptt) cc_final: 0.7879 (mmtp) REVERT: B 300 GLU cc_start: 0.7067 (pm20) cc_final: 0.6763 (pm20) REVERT: B 331 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7763 (ttp80) REVERT: B 344 GLN cc_start: 0.7714 (mt0) cc_final: 0.7337 (mm-40) REVERT: D 68 TYR cc_start: 0.4916 (t80) cc_final: 0.4659 (t80) REVERT: D 209 SER cc_start: 0.8795 (OUTLIER) cc_final: 0.8439 (p) REVERT: D 300 GLU cc_start: 0.7117 (pm20) cc_final: 0.6881 (pm20) REVERT: D 344 GLN cc_start: 0.7837 (mt0) cc_final: 0.7375 (mm-40) REVERT: C 68 TYR cc_start: 0.4850 (t80) cc_final: 0.4493 (t80) REVERT: C 300 GLU cc_start: 0.7190 (pm20) cc_final: 0.6914 (pm20) REVERT: C 344 GLN cc_start: 0.7688 (mt0) cc_final: 0.7256 (mm-40) REVERT: C 360 MET cc_start: 0.8474 (mmt) cc_final: 0.7981 (mmt) outliers start: 29 outliers final: 20 residues processed: 258 average time/residue: 0.1705 time to fit residues: 61.0417 Evaluate side-chains 236 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 140 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.110546 restraints weight = 18325.730| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.94 r_work: 0.3069 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16065 Z= 0.120 Angle : 0.473 6.688 21885 Z= 0.246 Chirality : 0.036 0.145 2375 Planarity : 0.004 0.050 2750 Dihedral : 3.670 15.701 2090 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.83 % Allowed : 13.39 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.19), residues: 1870 helix: 1.62 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.24 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 356 TYR 0.010 0.001 TYR B 68 PHE 0.014 0.001 PHE B 248 TRP 0.012 0.001 TRP B 93 HIS 0.002 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00269 (16065) covalent geometry : angle 0.47324 (21885) hydrogen bonds : bond 0.04542 ( 918) hydrogen bonds : angle 3.77058 ( 2664) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 209 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8434 (p) REVERT: A 331 ARG cc_start: 0.8357 (ttp80) cc_final: 0.7775 (ttp80) REVERT: E 209 SER cc_start: 0.8812 (OUTLIER) cc_final: 0.8447 (p) REVERT: E 300 GLU cc_start: 0.7025 (pm20) cc_final: 0.6774 (pm20) REVERT: B 300 GLU cc_start: 0.7073 (pm20) cc_final: 0.6795 (pm20) REVERT: B 331 ARG cc_start: 0.8183 (ttp80) cc_final: 0.7739 (ttp80) REVERT: B 344 GLN cc_start: 0.7730 (mt0) cc_final: 0.7356 (mm-40) REVERT: D 300 GLU cc_start: 0.7195 (pm20) cc_final: 0.6938 (pm20) REVERT: D 344 GLN cc_start: 0.7823 (mt0) cc_final: 0.7371 (mm-40) REVERT: C 300 GLU cc_start: 0.7195 (pm20) cc_final: 0.6951 (pm20) REVERT: C 344 GLN cc_start: 0.7735 (mt0) cc_final: 0.7316 (mm-40) REVERT: C 360 MET cc_start: 0.8495 (mmt) cc_final: 0.7991 (mmt) outliers start: 31 outliers final: 23 residues processed: 241 average time/residue: 0.1717 time to fit residues: 57.2480 Evaluate side-chains 230 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 103 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 159 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 153 optimal weight: 0.3980 chunk 109 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 120 GLN B 120 GLN D 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.142071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.110645 restraints weight = 18303.074| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.96 r_work: 0.3078 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16065 Z= 0.124 Angle : 0.473 6.738 21885 Z= 0.246 Chirality : 0.036 0.146 2375 Planarity : 0.004 0.051 2750 Dihedral : 3.627 15.633 2090 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.95 % Allowed : 14.45 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.19), residues: 1870 helix: 1.65 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.26 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 331 TYR 0.010 0.001 TYR D 236 PHE 0.015 0.001 PHE B 248 TRP 0.012 0.001 TRP A 93 HIS 0.003 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00284 (16065) covalent geometry : angle 0.47326 (21885) hydrogen bonds : bond 0.04565 ( 918) hydrogen bonds : angle 3.75177 ( 2664) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 0.607 Fit side-chains REVERT: A 209 SER cc_start: 0.8827 (OUTLIER) cc_final: 0.8443 (p) REVERT: A 331 ARG cc_start: 0.8364 (ttp80) cc_final: 0.7785 (ttp80) REVERT: E 209 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8480 (p) REVERT: E 300 GLU cc_start: 0.7089 (pm20) cc_final: 0.6822 (pm20) REVERT: E 331 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7823 (ttp80) REVERT: B 300 GLU cc_start: 0.7074 (pm20) cc_final: 0.6800 (pm20) REVERT: B 331 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7782 (ttp80) REVERT: B 344 GLN cc_start: 0.7761 (mt0) cc_final: 0.7419 (mm-40) REVERT: D 209 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8469 (p) REVERT: D 300 GLU cc_start: 0.7197 (pm20) cc_final: 0.6966 (pm20) REVERT: D 331 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7470 (ttp80) REVERT: D 344 GLN cc_start: 0.7805 (mt0) cc_final: 0.7358 (mm-40) REVERT: C 344 GLN cc_start: 0.7769 (mt0) cc_final: 0.7341 (mm-40) REVERT: C 360 MET cc_start: 0.8505 (mmt) cc_final: 0.8015 (mmt) outliers start: 33 outliers final: 25 residues processed: 241 average time/residue: 0.1679 time to fit residues: 56.4208 Evaluate side-chains 232 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 116 optimal weight: 0.0980 chunk 114 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 168 optimal weight: 0.0060 chunk 127 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 107 optimal weight: 0.0970 chunk 81 optimal weight: 5.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN E 120 GLN B 215 ASN D 215 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.114133 restraints weight = 18128.951| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.92 r_work: 0.3123 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16065 Z= 0.098 Angle : 0.449 6.704 21885 Z= 0.233 Chirality : 0.034 0.143 2375 Planarity : 0.004 0.049 2750 Dihedral : 3.454 14.963 2090 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.71 % Allowed : 15.16 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.19), residues: 1870 helix: 1.77 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : 0.28 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 25 TYR 0.010 0.001 TYR B 68 PHE 0.012 0.001 PHE C 80 TRP 0.011 0.001 TRP D 93 HIS 0.002 0.000 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00203 (16065) covalent geometry : angle 0.44919 (21885) hydrogen bonds : bond 0.04077 ( 918) hydrogen bonds : angle 3.67492 ( 2664) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 0.641 Fit side-chains REVERT: A 209 SER cc_start: 0.8694 (OUTLIER) cc_final: 0.8387 (p) REVERT: E 209 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8468 (p) REVERT: E 300 GLU cc_start: 0.7145 (pm20) cc_final: 0.6891 (pm20) REVERT: B 209 SER cc_start: 0.8690 (OUTLIER) cc_final: 0.8369 (p) REVERT: B 300 GLU cc_start: 0.6951 (pm20) cc_final: 0.6734 (pm20) REVERT: B 331 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7723 (ttp80) REVERT: B 344 GLN cc_start: 0.7616 (mt0) cc_final: 0.7319 (mm-40) REVERT: D 87 THR cc_start: 0.9033 (m) cc_final: 0.8827 (m) REVERT: D 209 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8449 (p) REVERT: D 331 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7296 (ttp80) REVERT: D 344 GLN cc_start: 0.7800 (mt0) cc_final: 0.7339 (mm-40) REVERT: C 344 GLN cc_start: 0.7767 (mt0) cc_final: 0.7343 (mm-40) outliers start: 29 outliers final: 19 residues processed: 254 average time/residue: 0.1614 time to fit residues: 57.3040 Evaluate side-chains 237 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 3.9990 chunk 178 optimal weight: 0.4980 chunk 171 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 120 GLN D 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.142897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.111329 restraints weight = 18452.542| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.99 r_work: 0.3072 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16065 Z= 0.112 Angle : 0.478 9.425 21885 Z= 0.243 Chirality : 0.035 0.145 2375 Planarity : 0.004 0.053 2750 Dihedral : 3.471 15.625 2090 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.77 % Allowed : 16.05 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.19), residues: 1870 helix: 1.79 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : 0.33 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 356 TYR 0.014 0.001 TYR E 97 PHE 0.019 0.001 PHE B 248 TRP 0.011 0.001 TRP D 93 HIS 0.002 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00250 (16065) covalent geometry : angle 0.47840 (21885) hydrogen bonds : bond 0.04282 ( 918) hydrogen bonds : angle 3.66079 ( 2664) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 0.583 Fit side-chains REVERT: A 209 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8476 (p) REVERT: A 331 ARG cc_start: 0.8283 (ttp80) cc_final: 0.8060 (ttp80) REVERT: E 209 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8481 (p) REVERT: E 300 GLU cc_start: 0.7130 (pm20) cc_final: 0.6843 (pm20) REVERT: E 331 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7796 (ttp80) REVERT: B 180 MET cc_start: 0.9066 (mmm) cc_final: 0.8683 (mmp) REVERT: B 300 GLU cc_start: 0.6995 (pm20) cc_final: 0.6755 (pm20) REVERT: B 331 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7687 (ttp80) REVERT: B 344 GLN cc_start: 0.7573 (mt0) cc_final: 0.7322 (mm-40) REVERT: D 209 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8429 (p) REVERT: D 331 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7306 (ttp80) REVERT: D 344 GLN cc_start: 0.7719 (mt0) cc_final: 0.7282 (mm-40) REVERT: C 344 GLN cc_start: 0.7763 (mt0) cc_final: 0.7375 (mm-40) outliers start: 30 outliers final: 23 residues processed: 236 average time/residue: 0.1691 time to fit residues: 55.2368 Evaluate side-chains 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 56 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.109536 restraints weight = 18406.552| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.96 r_work: 0.3075 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16065 Z= 0.140 Angle : 0.498 9.039 21885 Z= 0.255 Chirality : 0.036 0.146 2375 Planarity : 0.005 0.057 2750 Dihedral : 3.573 16.015 2090 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.77 % Allowed : 16.05 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.19), residues: 1870 helix: 1.71 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.32 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 356 TYR 0.021 0.001 TYR D 97 PHE 0.022 0.001 PHE C 248 TRP 0.012 0.001 TRP E 93 HIS 0.003 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00329 (16065) covalent geometry : angle 0.49763 (21885) hydrogen bonds : bond 0.04660 ( 918) hydrogen bonds : angle 3.73008 ( 2664) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 0.508 Fit side-chains REVERT: A 209 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8500 (p) REVERT: E 209 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8521 (p) REVERT: E 300 GLU cc_start: 0.7112 (pm20) cc_final: 0.6856 (pm20) REVERT: B 180 MET cc_start: 0.9080 (mmm) cc_final: 0.8698 (mmp) REVERT: B 300 GLU cc_start: 0.7023 (pm20) cc_final: 0.6790 (pm20) REVERT: B 331 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7721 (ttp80) REVERT: B 344 GLN cc_start: 0.7650 (mt0) cc_final: 0.7392 (mm-40) REVERT: D 209 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8467 (p) REVERT: D 331 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7344 (ttp80) REVERT: D 340 LYS cc_start: 0.8046 (mttp) cc_final: 0.7387 (mtpp) REVERT: D 344 GLN cc_start: 0.7764 (mt0) cc_final: 0.7328 (mm-40) REVERT: C 331 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7552 (ttp80) REVERT: C 344 GLN cc_start: 0.7863 (mt0) cc_final: 0.7489 (mm-40) outliers start: 30 outliers final: 23 residues processed: 233 average time/residue: 0.1677 time to fit residues: 53.9233 Evaluate side-chains 232 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 28 optimal weight: 0.7980 chunk 177 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.142548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.111036 restraints weight = 18286.407| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.97 r_work: 0.3074 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16065 Z= 0.119 Angle : 0.482 9.340 21885 Z= 0.247 Chirality : 0.036 0.144 2375 Planarity : 0.005 0.062 2750 Dihedral : 3.540 15.592 2090 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.53 % Allowed : 16.17 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.19), residues: 1870 helix: 1.74 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.31 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 356 TYR 0.026 0.001 TYR B 97 PHE 0.019 0.001 PHE C 248 TRP 0.012 0.001 TRP D 93 HIS 0.002 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00268 (16065) covalent geometry : angle 0.48200 (21885) hydrogen bonds : bond 0.04444 ( 918) hydrogen bonds : angle 3.71404 ( 2664) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.579 Fit side-chains REVERT: A 209 SER cc_start: 0.8890 (OUTLIER) cc_final: 0.8525 (p) REVERT: A 340 LYS cc_start: 0.7855 (mttp) cc_final: 0.7242 (mtpp) REVERT: E 209 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8552 (p) REVERT: E 300 GLU cc_start: 0.7132 (pm20) cc_final: 0.6877 (pm20) REVERT: E 331 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7563 (ttp80) REVERT: B 331 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7736 (ttp80) REVERT: B 344 GLN cc_start: 0.7646 (mt0) cc_final: 0.7392 (mm-40) REVERT: D 209 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8500 (p) REVERT: D 331 ARG cc_start: 0.8029 (ttp80) cc_final: 0.7361 (ttp80) REVERT: D 340 LYS cc_start: 0.8054 (mttp) cc_final: 0.7396 (mtpp) REVERT: D 344 GLN cc_start: 0.7779 (mt0) cc_final: 0.7348 (mm-40) REVERT: C 331 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7527 (ttp80) REVERT: C 344 GLN cc_start: 0.7869 (mt0) cc_final: 0.7495 (mm-40) outliers start: 26 outliers final: 21 residues processed: 230 average time/residue: 0.1558 time to fit residues: 49.3070 Evaluate side-chains 227 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 46 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.139347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.107198 restraints weight = 18315.444| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.05 r_work: 0.3063 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16065 Z= 0.119 Angle : 0.485 9.556 21885 Z= 0.248 Chirality : 0.036 0.144 2375 Planarity : 0.005 0.065 2750 Dihedral : 3.523 15.639 2090 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.53 % Allowed : 16.40 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.19), residues: 1870 helix: 1.74 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.31 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 25 TYR 0.024 0.001 TYR B 97 PHE 0.018 0.001 PHE C 248 TRP 0.012 0.001 TRP B 93 HIS 0.002 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00271 (16065) covalent geometry : angle 0.48480 (21885) hydrogen bonds : bond 0.04434 ( 918) hydrogen bonds : angle 3.70363 ( 2664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3876.88 seconds wall clock time: 67 minutes 4.78 seconds (4024.78 seconds total)