Starting phenix.real_space_refine on Tue Dec 31 10:02:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d1m_27135/12_2024/8d1m_27135.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1m_27135/12_2024/8d1m_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_27135/12_2024/8d1m_27135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1m_27135/12_2024/8d1m_27135.map" model { file = "/net/cci-nas-00/data/ceres_data/8d1m_27135/12_2024/8d1m_27135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1m_27135/12_2024/8d1m_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 7.19, per 1000 atoms: 0.46 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: 4.22 Conformation dependent library (CDL) restraints added in 2.0 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: 1.56 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: 4.12 Time building geometry restraints manager: 4.80 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.670 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: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 32.980 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 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= 0.382 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 *********************** 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 : 1.865 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: 0.3235 time to fit residues: 153.8786 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 : 2.108 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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= 0.214 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 *********************** 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 : 1.752 Fit side-chains revert: symmetry clash REVERT: A 209 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8455 (p) REVERT: E 209 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8400 (p) REVERT: B 62 PHE cc_start: 0.8160 (t80) cc_final: 0.7957 (t80) REVERT: B 209 SER cc_start: 0.8613 (OUTLIER) cc_final: 0.8411 (p) REVERT: B 331 ARG cc_start: 0.7511 (ttp80) cc_final: 0.7260 (ttp80) REVERT: D 302 ASP cc_start: 0.8334 (m-30) cc_final: 0.8016 (m-30) REVERT: C 360 MET cc_start: 0.8202 (mmt) cc_final: 0.7653 (mmt) outliers start: 32 outliers final: 19 residues processed: 265 average time/residue: 0.3602 time to fit residues: 132.9494 Evaluate side-chains 233 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 211 time to evaluate : 2.048 ------------------------------------------------------------------------------- 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 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 93 optimal weight: 6.9990 chunk 52 optimal weight: 0.0270 chunk 139 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.7442 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16065 Z= 0.262 Angle : 0.522 6.673 21885 Z= 0.275 Chirality : 0.038 0.151 2375 Planarity : 0.004 0.035 2750 Dihedral : 3.940 17.158 2090 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.18 % Allowed : 10.74 % Favored : 87.08 % 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: 1.49 (0.19), residues: 1870 helix: 1.55 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 0.09 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 93 HIS 0.004 0.001 HIS D 178 PHE 0.021 0.002 PHE B 248 TYR 0.019 0.002 TYR E 236 ARG 0.006 0.001 ARG A 331 *********************** 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 249 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 1.875 Fit side-chains REVERT: A 209 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.8424 (p) REVERT: A 356 ARG cc_start: 0.7350 (mmt180) cc_final: 0.7020 (mmt90) REVERT: E 209 SER cc_start: 0.8590 (OUTLIER) cc_final: 0.8377 (p) REVERT: B 331 ARG cc_start: 0.7533 (ttp80) cc_final: 0.7324 (ttp80) REVERT: B 344 GLN cc_start: 0.7803 (mt0) cc_final: 0.7533 (mm-40) REVERT: D 344 GLN cc_start: 0.7905 (mt0) cc_final: 0.7581 (mm-40) REVERT: C 344 GLN cc_start: 0.7841 (mt0) cc_final: 0.7532 (mm-40) REVERT: C 360 MET cc_start: 0.8175 (mmt) cc_final: 0.7649 (mmt) outliers start: 37 outliers final: 26 residues processed: 242 average time/residue: 0.3798 time to fit residues: 125.9953 Evaluate side-chains 233 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 2.023 ------------------------------------------------------------------------------- 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 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 328 ASP 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 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 166 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1703 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= 0.206 Angle : 0.498 6.670 21885 Z= 0.261 Chirality : 0.037 0.147 2375 Planarity : 0.004 0.047 2750 Dihedral : 3.805 16.592 2090 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.53 % Allowed : 12.63 % Favored : 85.84 % 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: 1.55 (0.19), residues: 1870 helix: 1.54 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.23 (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 0.016 0.001 TYR E 97 ARG 0.008 0.001 ARG C 356 *********************** 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 258 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 2.007 Fit side-chains REVERT: A 68 TYR cc_start: 0.5116 (t80) cc_final: 0.4880 (t80) REVERT: A 331 ARG cc_start: 0.7602 (ttp80) cc_final: 0.7323 (ttp80) REVERT: B 262 LYS cc_start: 0.8403 (mptt) cc_final: 0.8161 (mmtp) REVERT: B 331 ARG cc_start: 0.7520 (ttp80) cc_final: 0.7314 (ttp80) REVERT: B 344 GLN cc_start: 0.7767 (mt0) cc_final: 0.7503 (mm-40) REVERT: D 344 GLN cc_start: 0.7921 (mt0) cc_final: 0.7596 (mm-40) REVERT: C 68 TYR cc_start: 0.5316 (t80) cc_final: 0.4986 (t80) REVERT: C 344 GLN cc_start: 0.7850 (mt0) cc_final: 0.7489 (mm-40) REVERT: C 360 MET cc_start: 0.8159 (mmt) cc_final: 0.7637 (mmt) outliers start: 26 outliers final: 20 residues processed: 254 average time/residue: 0.3644 time to fit residues: 127.7480 Evaluate side-chains 228 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 1.901 ------------------------------------------------------------------------------- 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 336 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 171 LEU 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 75 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 148 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 chunk 133 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1886 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= 0.160 Angle : 0.472 6.666 21885 Z= 0.246 Chirality : 0.035 0.145 2375 Planarity : 0.004 0.051 2750 Dihedral : 3.665 15.937 2090 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.71 % Allowed : 13.45 % Favored : 84.84 % 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: 1.65 (0.19), residues: 1870 helix: 1.62 (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 B 93 HIS 0.002 0.001 HIS D 178 PHE 0.013 0.001 PHE B 248 TYR 0.012 0.001 TYR D 68 ARG 0.009 0.001 ARG E 331 *********************** 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 240 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 1.828 Fit side-chains REVERT: A 340 LYS cc_start: 0.8054 (mttp) cc_final: 0.7538 (mtpp) REVERT: B 209 SER cc_start: 0.8559 (OUTLIER) cc_final: 0.8352 (p) REVERT: B 262 LYS cc_start: 0.8394 (mptt) cc_final: 0.8188 (mmtp) REVERT: B 344 GLN cc_start: 0.7752 (mt0) cc_final: 0.7493 (mm-40) REVERT: D 344 GLN cc_start: 0.7884 (mt0) cc_final: 0.7564 (mm-40) REVERT: C 344 GLN cc_start: 0.7839 (mt0) cc_final: 0.7523 (mm-40) REVERT: C 360 MET cc_start: 0.8147 (mmt) cc_final: 0.7610 (mmt) outliers start: 29 outliers final: 19 residues processed: 236 average time/residue: 0.3773 time to fit residues: 122.6915 Evaluate side-chains 218 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 1.860 ------------------------------------------------------------------------------- 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 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 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 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 60 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 148 optimal weight: 0.0060 chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16065 Z= 0.265 Angle : 0.514 6.778 21885 Z= 0.268 Chirality : 0.038 0.150 2375 Planarity : 0.005 0.050 2750 Dihedral : 3.798 16.827 2090 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.95 % Allowed : 14.75 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.56 (0.19), residues: 1870 helix: 1.54 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.23 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.004 0.001 HIS D 178 PHE 0.021 0.001 PHE B 248 TYR 0.016 0.001 TYR E 236 ARG 0.011 0.001 ARG B 331 *********************** 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 245 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 1.929 Fit side-chains REVERT: A 300 GLU cc_start: 0.7044 (pm20) cc_final: 0.6764 (pm20) REVERT: A 331 ARG cc_start: 0.7603 (ttp80) cc_final: 0.7362 (ttp80) REVERT: B 262 LYS cc_start: 0.8404 (mptt) cc_final: 0.8157 (mmtp) REVERT: B 344 GLN cc_start: 0.7775 (mt0) cc_final: 0.7543 (mm-40) REVERT: D 62 PHE cc_start: 0.8171 (t80) cc_final: 0.7964 (t80) REVERT: D 344 GLN cc_start: 0.7880 (mt0) cc_final: 0.7550 (mm-40) REVERT: C 344 GLN cc_start: 0.7881 (mt0) cc_final: 0.7551 (mm-40) REVERT: C 360 MET cc_start: 0.8148 (mmt) cc_final: 0.7593 (mmt) outliers start: 33 outliers final: 28 residues processed: 239 average time/residue: 0.3759 time to fit residues: 125.1349 Evaluate side-chains 238 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 1.767 ------------------------------------------------------------------------------- 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 228 ASP 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 336 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 145 THR 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 75 LEU Chi-restraints excluded: chain D residue 164 THR 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 145 THR 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 172 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN D 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16065 Z= 0.237 Angle : 0.500 6.738 21885 Z= 0.261 Chirality : 0.037 0.147 2375 Planarity : 0.005 0.050 2750 Dihedral : 3.783 16.778 2090 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.95 % Allowed : 15.04 % Favored : 83.01 % 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: 1.58 (0.19), residues: 1870 helix: 1.57 (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 0.001 TRP E 93 HIS 0.003 0.001 HIS D 178 PHE 0.020 0.001 PHE B 248 TYR 0.017 0.001 TYR E 97 ARG 0.012 0.001 ARG B 331 *********************** 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 238 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 1.996 Fit side-chains REVERT: A 331 ARG cc_start: 0.7607 (ttp80) cc_final: 0.7322 (ttp80) REVERT: E 331 ARG cc_start: 0.7637 (ttp80) cc_final: 0.7366 (ttp80) REVERT: B 262 LYS cc_start: 0.8403 (mptt) cc_final: 0.8203 (mmtp) REVERT: B 344 GLN cc_start: 0.7781 (mt0) cc_final: 0.7544 (mm-40) REVERT: D 62 PHE cc_start: 0.8187 (t80) cc_final: 0.7983 (t80) REVERT: D 331 ARG cc_start: 0.7638 (ttp-110) cc_final: 0.7331 (ttp80) REVERT: D 344 GLN cc_start: 0.7855 (mt0) cc_final: 0.7522 (mm-40) REVERT: C 344 GLN cc_start: 0.7883 (mt0) cc_final: 0.7545 (mm-40) REVERT: C 360 MET cc_start: 0.8104 (mmt) cc_final: 0.7541 (mmt) outliers start: 33 outliers final: 28 residues processed: 233 average time/residue: 0.3770 time to fit residues: 120.6030 Evaluate side-chains 227 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 1.881 ------------------------------------------------------------------------------- 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 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 336 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 145 THR 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 75 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 164 THR 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 145 THR 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 71 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16065 Z= 0.162 Angle : 0.475 6.722 21885 Z= 0.248 Chirality : 0.035 0.145 2375 Planarity : 0.004 0.053 2750 Dihedral : 3.656 16.139 2090 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.15 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 (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: 1.68 (0.19), residues: 1870 helix: 1.67 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.21 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 93 HIS 0.002 0.001 HIS C 178 PHE 0.017 0.001 PHE E 80 TYR 0.013 0.001 TYR E 97 ARG 0.011 0.001 ARG B 331 *********************** 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 244 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 1.788 Fit side-chains REVERT: A 331 ARG cc_start: 0.7548 (ttp80) cc_final: 0.7288 (ttp80) REVERT: E 331 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7364 (ttp80) REVERT: B 262 LYS cc_start: 0.8401 (mptt) cc_final: 0.8198 (mmtp) REVERT: B 344 GLN cc_start: 0.7777 (mt0) cc_final: 0.7543 (mm-40) REVERT: D 331 ARG cc_start: 0.7593 (ttp-110) cc_final: 0.7378 (ttp80) REVERT: D 340 LYS cc_start: 0.8215 (mttp) cc_final: 0.7685 (mtpp) REVERT: D 344 GLN cc_start: 0.7839 (mt0) cc_final: 0.7514 (mm-40) REVERT: C 344 GLN cc_start: 0.7876 (mt0) cc_final: 0.7549 (mm-40) outliers start: 29 outliers final: 24 residues processed: 239 average time/residue: 0.3730 time to fit residues: 122.1279 Evaluate side-chains 229 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 1.947 ------------------------------------------------------------------------------- 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 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 336 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 145 THR 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 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 145 THR 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 170 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 72 optimal weight: 0.4980 chunk 130 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 165 optimal weight: 0.2980 chunk 109 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16065 Z= 0.157 Angle : 0.468 6.778 21885 Z= 0.244 Chirality : 0.035 0.145 2375 Planarity : 0.005 0.056 2750 Dihedral : 3.612 15.924 2090 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.71 % Allowed : 15.46 % Favored : 82.83 % 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: 1.69 (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 A 93 HIS 0.002 0.001 HIS D 178 PHE 0.017 0.001 PHE D 113 TYR 0.020 0.001 TYR C 97 ARG 0.010 0.001 ARG D 25 *********************** 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 242 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 1.745 Fit side-chains REVERT: B 60 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7802 (tt) REVERT: D 331 ARG cc_start: 0.7600 (ttp-110) cc_final: 0.7394 (ttp80) REVERT: D 340 LYS cc_start: 0.8218 (mttp) cc_final: 0.7686 (mtpp) REVERT: D 344 GLN cc_start: 0.7855 (mt0) cc_final: 0.7529 (mm-40) REVERT: C 344 GLN cc_start: 0.7885 (mt0) cc_final: 0.7575 (mm-40) outliers start: 29 outliers final: 26 residues processed: 237 average time/residue: 0.3702 time to fit residues: 120.6088 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 : 1.815 ------------------------------------------------------------------------------- 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 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 336 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 145 THR 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 145 THR Chi-restraints excluded: chain D residue 164 THR 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 145 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 242 VAL 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 175 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 184 optimal weight: 6.9990 chunk 169 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN D 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16065 Z= 0.194 Angle : 0.486 6.810 21885 Z= 0.253 Chirality : 0.036 0.146 2375 Planarity : 0.005 0.056 2750 Dihedral : 3.640 16.481 2090 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.65 % Allowed : 15.69 % 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: 1.53 (0.19), residues: 1870 helix: 1.55 (0.15), residues: 1230 sheet: None (None), residues: 0 loop : 0.09 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 93 HIS 0.003 0.001 HIS D 178 PHE 0.017 0.001 PHE D 248 TYR 0.026 0.001 TYR A 97 ARG 0.009 0.001 ARG B 25 ********************** 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 234 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 2.052 Fit side-chains REVERT: E 331 ARG cc_start: 0.7636 (ttp80) cc_final: 0.7234 (ttp80) REVERT: B 331 ARG cc_start: 0.7548 (ttp80) cc_final: 0.7276 (ptm-80) REVERT: D 331 ARG cc_start: 0.7617 (ttp-110) cc_final: 0.7401 (ttp80) REVERT: D 340 LYS cc_start: 0.8232 (mttp) cc_final: 0.7702 (mtpp) REVERT: D 344 GLN cc_start: 0.7810 (mt0) cc_final: 0.7510 (mm-40) REVERT: C 344 GLN cc_start: 0.7886 (mt0) cc_final: 0.7596 (mm-40) outliers start: 28 outliers final: 24 residues processed: 229 average time/residue: 0.3909 time to fit residues: 122.0895 Evaluate side-chains 229 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 1.918 ------------------------------------------------------------------------------- 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 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 336 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 145 THR 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 332 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 242 VAL 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 156 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 150 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.138270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.106306 restraints weight = 18351.302| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.00 r_work: 0.3069 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2206 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= 0.170 Angle : 0.474 6.779 21885 Z= 0.247 Chirality : 0.035 0.145 2375 Planarity : 0.005 0.056 2750 Dihedral : 3.590 15.589 2090 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.65 % Allowed : 15.81 % Favored : 82.54 % 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: 1.57 (0.19), residues: 1870 helix: 1.58 (0.15), residues: 1230 sheet: None (None), residues: 0 loop : 0.11 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 93 HIS 0.002 0.001 HIS C 178 PHE 0.016 0.001 PHE E 80 TYR 0.026 0.001 TYR B 97 ARG 0.009 0.001 ARG D 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3369.78 seconds wall clock time: 62 minutes 37.86 seconds (3757.86 seconds total)