Starting phenix.real_space_refine on Fri Jun 13 20:19:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d1m_27135/06_2025/8d1m_27135.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1m_27135/06_2025/8d1m_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d1m_27135/06_2025/8d1m_27135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1m_27135/06_2025/8d1m_27135.map" model { file = "/net/cci-nas-00/data/ceres_data/8d1m_27135/06_2025/8d1m_27135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1m_27135/06_2025/8d1m_27135.cif" } resolution = 3.11 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= 0.005 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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D Time building chain proxies: 6.83, per 1000 atoms: 0.44 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: 4.05 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.51 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: 4.14 Time building geometry restraints manager: 4.74 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' 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: 1.650 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: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 32.980 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.860 ------------------------------------------------------------------------------- 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 (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: 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 TRP 0.014 0.002 TRP E 93 HIS 0.005 0.001 HIS B 178 PHE 0.021 0.002 PHE C 248 TYR 0.032 0.002 TYR B 236 ARG 0.009 0.001 ARG E 122 Details of bonding type rmsd hydrogen bonds : bond 0.15254 ( 918) hydrogen bonds : angle 5.14974 ( 2664) covalent geometry : bond 0.00593 (16065) covalent geometry : angle 0.86516 (21885) *********************** 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 : 1.911 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: 0.3352 time to fit residues: 160.8804 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 : 1.600 ------------------------------------------------------------------------------- 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 156 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.141270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.109777 restraints weight = 18225.966| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.97 r_work: 0.3056 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16065 Z= 0.146 Angle : 0.529 8.052 21885 Z= 0.280 Chirality : 0.038 0.150 2375 Planarity : 0.004 0.028 2750 Dihedral : 4.009 16.950 2095 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.89 % Allowed : 8.73 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.19), residues: 1870 helix: 1.72 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -0.00 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 93 HIS 0.003 0.001 HIS D 178 PHE 0.018 0.002 PHE B 248 TYR 0.016 0.002 TYR C 236 ARG 0.006 0.001 ARG D 331 Details of bonding type rmsd hydrogen bonds : bond 0.05313 ( 918) hydrogen bonds : angle 4.07135 ( 2664) covalent geometry : bond 0.00336 (16065) covalent geometry : angle 0.52910 (21885) *********************** 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 273 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 1.665 Fit side-chains revert: symmetry clash REVERT: A 209 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8540 (p) REVERT: E 209 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8532 (p) REVERT: E 262 LYS cc_start: 0.7975 (mmtp) cc_final: 0.7766 (mmtm) REVERT: B 209 SER cc_start: 0.8893 (OUTLIER) cc_final: 0.8589 (p) REVERT: B 300 GLU cc_start: 0.7003 (pm20) cc_final: 0.6786 (pm20) REVERT: B 331 ARG cc_start: 0.8269 (ttp80) cc_final: 0.7776 (ttp80) REVERT: D 209 SER cc_start: 0.8837 (OUTLIER) cc_final: 0.8534 (p) REVERT: D 300 GLU cc_start: 0.7027 (pm20) cc_final: 0.6814 (pm20) REVERT: D 302 ASP cc_start: 0.8413 (m-30) cc_final: 0.8044 (m-30) REVERT: C 360 MET cc_start: 0.8542 (mmt) cc_final: 0.8030 (mmt) outliers start: 32 outliers final: 19 residues processed: 265 average time/residue: 0.3613 time to fit residues: 134.0938 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 : 1.781 ------------------------------------------------------------------------------- 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 148 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.134766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.102500 restraints weight = 18490.258| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.02 r_work: 0.3061 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16065 Z= 0.141 Angle : 0.498 6.655 21885 Z= 0.262 Chirality : 0.037 0.148 2375 Planarity : 0.004 0.032 2750 Dihedral : 3.845 16.781 2090 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.01 % Allowed : 11.27 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.19), residues: 1870 helix: 1.55 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.27 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 93 HIS 0.003 0.001 HIS D 178 PHE 0.017 0.001 PHE B 248 TYR 0.017 0.001 TYR C 236 ARG 0.006 0.001 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.04926 ( 918) hydrogen bonds : angle 3.87068 ( 2664) covalent geometry : bond 0.00325 (16065) covalent geometry : angle 0.49758 (21885) *********************** 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 261 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 1.644 Fit side-chains REVERT: A 209 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8452 (p) REVERT: A 331 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7834 (ttp80) REVERT: E 209 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8428 (p) REVERT: E 262 LYS cc_start: 0.8042 (mmtp) cc_final: 0.7834 (mmtm) REVERT: E 300 GLU cc_start: 0.7077 (pm20) cc_final: 0.6774 (pm20) REVERT: B 209 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8492 (p) REVERT: B 300 GLU cc_start: 0.7074 (pm20) cc_final: 0.6786 (pm20) REVERT: B 344 GLN cc_start: 0.7731 (mt0) cc_final: 0.7354 (mm-40) REVERT: D 68 TYR cc_start: 0.4888 (t80) cc_final: 0.4497 (t80) REVERT: D 209 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8462 (p) REVERT: D 300 GLU cc_start: 0.7117 (pm20) cc_final: 0.6875 (pm20) REVERT: D 344 GLN cc_start: 0.7818 (mt0) cc_final: 0.7337 (mm-40) REVERT: C 68 TYR cc_start: 0.5046 (t80) cc_final: 0.4583 (t80) REVERT: C 344 GLN cc_start: 0.7665 (mt0) cc_final: 0.7241 (mm-40) REVERT: C 360 MET cc_start: 0.8473 (mmt) cc_final: 0.7975 (mmt) outliers start: 34 outliers final: 21 residues processed: 254 average time/residue: 0.3582 time to fit residues: 125.2042 Evaluate side-chains 232 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 1.619 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 5.9990 chunk 134 optimal weight: 0.0020 chunk 123 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.142544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.111585 restraints weight = 18244.815| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.94 r_work: 0.3102 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16065 Z= 0.113 Angle : 0.471 6.674 21885 Z= 0.246 Chirality : 0.035 0.144 2375 Planarity : 0.004 0.047 2750 Dihedral : 3.667 15.872 2090 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.59 % Allowed : 12.74 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.66 (0.19), residues: 1870 helix: 1.63 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.26 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 185 HIS 0.002 0.001 HIS D 178 PHE 0.013 0.001 PHE B 248 TYR 0.010 0.001 TYR C 97 ARG 0.010 0.001 ARG C 356 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 918) hydrogen bonds : angle 3.77723 ( 2664) covalent geometry : bond 0.00249 (16065) covalent geometry : angle 0.47140 (21885) *********************** 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 276 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 1.594 Fit side-chains REVERT: A 68 TYR cc_start: 0.4913 (t80) cc_final: 0.4641 (t80) REVERT: A 209 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8532 (p) REVERT: E 209 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8546 (p) REVERT: E 300 GLU cc_start: 0.7052 (pm20) cc_final: 0.6782 (pm20) REVERT: B 209 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8521 (p) REVERT: B 262 LYS cc_start: 0.8285 (mptt) cc_final: 0.8031 (mmtp) REVERT: B 300 GLU cc_start: 0.7059 (pm20) cc_final: 0.6776 (pm20) REVERT: B 331 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7694 (ttp80) REVERT: B 344 GLN cc_start: 0.7790 (mt0) cc_final: 0.7435 (mm-40) REVERT: D 300 GLU cc_start: 0.7153 (pm20) cc_final: 0.6915 (pm20) REVERT: D 344 GLN cc_start: 0.7858 (mt0) cc_final: 0.7399 (mm-40) REVERT: C 300 GLU cc_start: 0.7203 (pm20) cc_final: 0.6935 (pm20) REVERT: C 344 GLN cc_start: 0.7779 (mt0) cc_final: 0.7373 (mm-40) REVERT: C 360 MET cc_start: 0.8503 (mmt) cc_final: 0.7984 (mmt) outliers start: 27 outliers final: 18 residues processed: 271 average time/residue: 0.3283 time to fit residues: 124.2668 Evaluate side-chains 229 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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 171 LEU Chi-restraints excluded: chain A residue 209 SER 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 164 THR 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 181 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 165 optimal weight: 0.0980 chunk 158 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.141804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.110077 restraints weight = 18405.011| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.05 r_work: 0.3059 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16065 Z= 0.112 Angle : 0.467 6.693 21885 Z= 0.242 Chirality : 0.035 0.144 2375 Planarity : 0.004 0.048 2750 Dihedral : 3.588 15.300 2090 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.71 % Allowed : 13.86 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.72 (0.19), residues: 1870 helix: 1.68 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.28 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 93 HIS 0.002 0.001 HIS D 178 PHE 0.014 0.001 PHE D 113 TYR 0.009 0.001 TYR B 236 ARG 0.009 0.001 ARG E 331 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 918) hydrogen bonds : angle 3.72937 ( 2664) covalent geometry : bond 0.00247 (16065) covalent geometry : angle 0.46694 (21885) *********************** 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 251 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 1.645 Fit side-chains REVERT: A 209 SER cc_start: 0.8738 (OUTLIER) cc_final: 0.8364 (p) REVERT: A 331 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7758 (ttp80) REVERT: A 340 LYS cc_start: 0.7785 (mttp) cc_final: 0.7166 (mtpp) REVERT: E 209 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8392 (p) REVERT: E 300 GLU cc_start: 0.7047 (pm20) cc_final: 0.6767 (pm20) REVERT: E 331 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7825 (ttp80) REVERT: B 300 GLU cc_start: 0.7059 (pm20) cc_final: 0.6758 (pm20) REVERT: B 331 ARG cc_start: 0.8180 (ttp80) cc_final: 0.7628 (ttp80) REVERT: B 344 GLN cc_start: 0.7623 (mt0) cc_final: 0.7256 (mm-40) REVERT: D 209 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8374 (p) REVERT: D 300 GLU cc_start: 0.7164 (pm20) cc_final: 0.6889 (pm20) REVERT: D 302 ASP cc_start: 0.8353 (m-30) cc_final: 0.8066 (m-30) REVERT: D 344 GLN cc_start: 0.7789 (mt0) cc_final: 0.7321 (mm-40) REVERT: C 300 GLU cc_start: 0.7202 (pm20) cc_final: 0.6956 (pm20) REVERT: C 344 GLN cc_start: 0.7702 (mt0) cc_final: 0.7271 (mm-40) REVERT: C 360 MET cc_start: 0.8491 (mmt) cc_final: 0.7986 (mmt) outliers start: 29 outliers final: 18 residues processed: 247 average time/residue: 0.3739 time to fit residues: 128.6242 Evaluate side-chains 236 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 1.694 ------------------------------------------------------------------------------- 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 335 ASP Chi-restraints excluded: chain E residue 28 ILE 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 209 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 145 optimal weight: 4.9990 chunk 171 optimal weight: 0.0570 chunk 6 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 126 optimal weight: 0.0770 overall best weight: 0.4856 ------------------------------------------------------------------------------- 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 120 GLN B 215 ASN D 120 GLN D 215 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.145429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.114369 restraints weight = 18275.049| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.97 r_work: 0.3060 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16065 Z= 0.099 Angle : 0.449 6.697 21885 Z= 0.232 Chirality : 0.035 0.142 2375 Planarity : 0.004 0.048 2750 Dihedral : 3.460 14.668 2090 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.77 % Allowed : 14.99 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.70 (0.19), residues: 1870 helix: 1.70 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : 0.15 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 185 HIS 0.002 0.001 HIS A 267 PHE 0.010 0.001 PHE E 248 TYR 0.010 0.001 TYR C 68 ARG 0.008 0.001 ARG D 25 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 918) hydrogen bonds : angle 3.66958 ( 2664) covalent geometry : bond 0.00210 (16065) covalent geometry : angle 0.44945 (21885) *********************** 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 271 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 2.106 Fit side-chains REVERT: A 209 SER cc_start: 0.8654 (OUTLIER) cc_final: 0.8342 (p) REVERT: A 340 LYS cc_start: 0.7809 (mttp) cc_final: 0.7148 (mtpp) REVERT: E 209 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8441 (p) REVERT: E 300 GLU cc_start: 0.7110 (pm20) cc_final: 0.6826 (pm20) REVERT: B 209 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8357 (p) REVERT: B 300 GLU cc_start: 0.7026 (pm20) cc_final: 0.6740 (pm20) REVERT: B 331 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7663 (ttp80) REVERT: B 344 GLN cc_start: 0.7592 (mt0) cc_final: 0.7329 (mm-40) REVERT: D 209 SER cc_start: 0.8728 (OUTLIER) cc_final: 0.8423 (p) REVERT: D 300 GLU cc_start: 0.7211 (pm20) cc_final: 0.6998 (pm20) REVERT: D 331 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7500 (ttp80) REVERT: D 344 GLN cc_start: 0.7767 (mt0) cc_final: 0.7318 (mm-40) REVERT: C 300 GLU cc_start: 0.7183 (pm20) cc_final: 0.6967 (pm20) REVERT: C 344 GLN cc_start: 0.7728 (mt0) cc_final: 0.7306 (mm-40) outliers start: 30 outliers final: 15 residues processed: 267 average time/residue: 0.3611 time to fit residues: 135.6181 Evaluate side-chains 236 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 217 time to evaluate : 2.017 ------------------------------------------------------------------------------- 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 335 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.132070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.099164 restraints weight = 18794.411| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.08 r_work: 0.2987 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16065 Z= 0.251 Angle : 0.584 8.610 21885 Z= 0.301 Chirality : 0.041 0.152 2375 Planarity : 0.005 0.050 2750 Dihedral : 3.885 17.216 2088 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.83 % Allowed : 15.52 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.48 (0.19), residues: 1870 helix: 1.48 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.20 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 93 HIS 0.005 0.001 HIS B 178 PHE 0.036 0.002 PHE B 248 TYR 0.023 0.002 TYR D 236 ARG 0.009 0.001 ARG C 356 Details of bonding type rmsd hydrogen bonds : bond 0.05730 ( 918) hydrogen bonds : angle 3.94012 ( 2664) covalent geometry : bond 0.00614 (16065) covalent geometry : angle 0.58362 (21885) *********************** 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 256 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 1.852 Fit side-chains REVERT: A 340 LYS cc_start: 0.7938 (mttp) cc_final: 0.7248 (mtpp) REVERT: A 344 GLN cc_start: 0.7830 (mt0) cc_final: 0.7465 (mm-40) REVERT: E 300 GLU cc_start: 0.7172 (pm20) cc_final: 0.6850 (pm20) REVERT: E 344 GLN cc_start: 0.7775 (mt0) cc_final: 0.7296 (mm-40) REVERT: B 207 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8440 (tp) REVERT: B 300 GLU cc_start: 0.7168 (pm20) cc_final: 0.6833 (pm20) REVERT: B 331 ARG cc_start: 0.8223 (ttp80) cc_final: 0.7686 (ttp80) REVERT: B 344 GLN cc_start: 0.7789 (mt0) cc_final: 0.7426 (mm-40) REVERT: D 62 PHE cc_start: 0.8228 (t80) cc_final: 0.7989 (t80) REVERT: D 300 GLU cc_start: 0.7259 (pm20) cc_final: 0.6944 (pm20) REVERT: D 331 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7537 (ttp80) REVERT: D 344 GLN cc_start: 0.7800 (mt0) cc_final: 0.7354 (mm-40) REVERT: C 300 GLU cc_start: 0.7294 (pm20) cc_final: 0.7045 (pm20) REVERT: C 344 GLN cc_start: 0.7823 (mt0) cc_final: 0.7400 (mm-40) REVERT: C 360 MET cc_start: 0.8467 (mmt) cc_final: 0.7942 (mmt) outliers start: 31 outliers final: 25 residues processed: 252 average time/residue: 0.3533 time to fit residues: 123.5089 Evaluate side-chains 243 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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 E residue 28 ILE Chi-restraints excluded: chain E residue 164 THR 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 207 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 88 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 65 LEU 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 42 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.2980 chunk 99 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.141469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.110310 restraints weight = 18199.328| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.94 r_work: 0.3051 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16065 Z= 0.114 Angle : 0.479 9.294 21885 Z= 0.247 Chirality : 0.035 0.141 2375 Planarity : 0.004 0.052 2750 Dihedral : 3.622 16.572 2088 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.47 % Allowed : 16.40 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.66 (0.19), residues: 1870 helix: 1.65 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.22 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.002 0.001 HIS C 178 PHE 0.019 0.001 PHE B 248 TYR 0.013 0.001 TYR E 97 ARG 0.009 0.001 ARG C 356 Details of bonding type rmsd hydrogen bonds : bond 0.04472 ( 918) hydrogen bonds : angle 3.78004 ( 2664) covalent geometry : bond 0.00248 (16065) covalent geometry : angle 0.47899 (21885) *********************** 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 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 1.665 Fit side-chains REVERT: A 209 SER cc_start: 0.8811 (OUTLIER) cc_final: 0.8473 (p) REVERT: A 331 ARG cc_start: 0.8318 (ttp80) cc_final: 0.7609 (ttp80) REVERT: A 340 LYS cc_start: 0.7862 (mttp) cc_final: 0.7205 (mtpp) REVERT: E 209 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8469 (p) REVERT: E 300 GLU cc_start: 0.7102 (pm20) cc_final: 0.6845 (pm20) REVERT: E 331 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7556 (ttp80) REVERT: B 207 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8249 (tt) REVERT: B 300 GLU cc_start: 0.6941 (pm20) cc_final: 0.6719 (pm20) REVERT: B 331 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7629 (ttp80) REVERT: B 344 GLN cc_start: 0.7704 (mt0) cc_final: 0.7357 (mm-40) REVERT: D 209 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8436 (p) REVERT: D 331 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7506 (ttp80) REVERT: D 340 LYS cc_start: 0.7972 (mttp) cc_final: 0.7315 (mtpp) REVERT: D 344 GLN cc_start: 0.7797 (mt0) cc_final: 0.7359 (mm-40) REVERT: C 344 GLN cc_start: 0.7777 (mt0) cc_final: 0.7367 (mm-40) REVERT: C 360 MET cc_start: 0.8459 (mmt) cc_final: 0.7890 (mmt) outliers start: 25 outliers final: 19 residues processed: 227 average time/residue: 0.3666 time to fit residues: 114.5227 Evaluate side-chains 227 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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 E residue 28 ILE Chi-restraints excluded: chain E residue 209 SER 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 207 LEU Chi-restraints excluded: chain B residue 209 SER 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 171 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 91 optimal weight: 0.0170 chunk 109 optimal weight: 8.9990 chunk 142 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.139258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.106763 restraints weight = 18462.173| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.08 r_work: 0.3055 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16065 Z= 0.118 Angle : 0.481 9.040 21885 Z= 0.247 Chirality : 0.036 0.145 2375 Planarity : 0.004 0.057 2750 Dihedral : 3.566 16.866 2088 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.42 % Allowed : 16.58 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.71 (0.19), residues: 1870 helix: 1.68 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.24 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 93 HIS 0.002 0.001 HIS D 178 PHE 0.022 0.001 PHE D 80 TYR 0.019 0.001 TYR B 97 ARG 0.009 0.001 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 918) hydrogen bonds : angle 3.73808 ( 2664) covalent geometry : bond 0.00266 (16065) covalent geometry : angle 0.48126 (21885) *********************** 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 235 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 1.733 Fit side-chains REVERT: A 209 SER cc_start: 0.8819 (OUTLIER) cc_final: 0.8471 (p) REVERT: A 340 LYS cc_start: 0.7863 (mttp) cc_final: 0.7204 (mtpp) REVERT: E 209 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8483 (p) REVERT: E 300 GLU cc_start: 0.7111 (pm20) cc_final: 0.6840 (pm20) REVERT: E 331 ARG cc_start: 0.8144 (ttp80) cc_final: 0.7495 (ttp80) REVERT: B 300 GLU cc_start: 0.6999 (pm20) cc_final: 0.6758 (pm20) REVERT: B 331 ARG cc_start: 0.8176 (ttp80) cc_final: 0.7681 (ttp80) REVERT: B 344 GLN cc_start: 0.7632 (mt0) cc_final: 0.7353 (mm-40) REVERT: D 209 SER cc_start: 0.8826 (OUTLIER) cc_final: 0.8469 (p) REVERT: D 331 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7601 (ttp80) REVERT: D 340 LYS cc_start: 0.7989 (mttp) cc_final: 0.7322 (mtpp) REVERT: D 344 GLN cc_start: 0.7718 (mt0) cc_final: 0.7287 (mm-40) REVERT: C 344 GLN cc_start: 0.7786 (mt0) cc_final: 0.7376 (mm-40) outliers start: 24 outliers final: 17 residues processed: 232 average time/residue: 0.3616 time to fit residues: 115.6183 Evaluate side-chains 222 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 E residue 28 ILE 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 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 83 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 173 optimal weight: 0.0970 chunk 78 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.140416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.109112 restraints weight = 18518.175| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.95 r_work: 0.3083 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 : 0.003 0.042 16065 Z= 0.125 Angle : 0.489 8.992 21885 Z= 0.251 Chirality : 0.036 0.145 2375 Planarity : 0.004 0.059 2750 Dihedral : 3.567 16.750 2088 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.42 % Allowed : 16.52 % 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 (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: 1.70 (0.19), residues: 1870 helix: 1.68 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.24 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 93 HIS 0.002 0.001 HIS D 178 PHE 0.022 0.001 PHE D 80 TYR 0.028 0.001 TYR B 97 ARG 0.009 0.001 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 918) hydrogen bonds : angle 3.74490 ( 2664) covalent geometry : bond 0.00287 (16065) covalent geometry : angle 0.48939 (21885) ********************** 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 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 1.829 Fit side-chains REVERT: A 209 SER cc_start: 0.8865 (OUTLIER) cc_final: 0.8519 (p) REVERT: A 340 LYS cc_start: 0.7922 (mttp) cc_final: 0.7270 (mtpp) REVERT: E 209 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8561 (p) REVERT: E 300 GLU cc_start: 0.7070 (pm20) cc_final: 0.6834 (pm20) REVERT: E 331 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7651 (ttp80) REVERT: B 300 GLU cc_start: 0.6977 (pm20) cc_final: 0.6757 (pm20) REVERT: B 331 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7683 (ttp80) REVERT: B 344 GLN cc_start: 0.7663 (mt0) cc_final: 0.7392 (mm-40) REVERT: D 209 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8523 (p) REVERT: D 331 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7627 (ttp80) REVERT: D 340 LYS cc_start: 0.8058 (mttp) cc_final: 0.7394 (mtpp) REVERT: D 344 GLN cc_start: 0.7784 (mt0) cc_final: 0.7365 (mm-40) REVERT: C 344 GLN cc_start: 0.7886 (mt0) cc_final: 0.7493 (mm-40) outliers start: 24 outliers final: 20 residues processed: 228 average time/residue: 0.3620 time to fit residues: 113.6600 Evaluate side-chains 230 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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 332 MET 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 B residue 28 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 209 SER 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 65 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 59 optimal weight: 5.9990 chunk 149 optimal weight: 0.0770 chunk 150 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.144475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.113060 restraints weight = 18286.594| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.97 r_work: 0.3107 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16065 Z= 0.106 Angle : 0.471 9.079 21885 Z= 0.241 Chirality : 0.035 0.144 2375 Planarity : 0.004 0.060 2750 Dihedral : 3.489 16.386 2088 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.36 % Allowed : 16.46 % 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 (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: 1.76 (0.19), residues: 1870 helix: 1.73 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.26 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 93 HIS 0.002 0.001 HIS D 178 PHE 0.020 0.001 PHE D 80 TYR 0.023 0.001 TYR B 97 ARG 0.009 0.001 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 918) hydrogen bonds : angle 3.69743 ( 2664) covalent geometry : bond 0.00230 (16065) covalent geometry : angle 0.47066 (21885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8017.09 seconds wall clock time: 140 minutes 52.45 seconds (8452.45 seconds total)