Starting phenix.real_space_refine on Fri Jul 3 01:38:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cla_45668/07_2026/9cla_45668.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cla_45668/07_2026/9cla_45668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cla_45668/07_2026/9cla_45668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cla_45668/07_2026/9cla_45668.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cla_45668/07_2026/9cla_45668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cla_45668/07_2026/9cla_45668.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.040 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: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 44 5.16 5 C 7348 2.51 5 N 1832 2.21 5 O 1924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11152 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Chain: "B" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Chain: "C" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Chain: "D" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' K': 4} Chain breaks: 4 Time building chain proxies: 2.07, per 1000 atoms: 0.19 Number of scatterers: 11152 At special positions: 0 Unit cell: (109.725, 109.725, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 44 16.00 O 1924 8.00 N 1832 7.00 C 7348 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: 0.97 Conformation dependent library (CDL) restraints added in 384.1 milliseconds 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2568 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 4 sheets defined 70.8% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 132 through 138 removed outlier: 3.839A pdb=" N ARG A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 166 removed outlier: 3.606A pdb=" N ILE A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 removed outlier: 4.128A pdb=" N GLU A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 202 Processing helix chain 'A' and resid 214 through 226 Processing helix chain 'A' and resid 230 through 254 Processing helix chain 'A' and resid 293 through 316 Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 336 through 348 removed outlier: 3.714A pdb=" N PHE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 371 through 379 removed outlier: 3.558A pdb=" N LEU A 377 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 394 Processing helix chain 'A' and resid 394 through 420 Processing helix chain 'A' and resid 430 through 443 removed outlier: 4.412A pdb=" N TRP A 436 " --> pdb=" O PRO A 432 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TRP A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 474 removed outlier: 3.704A pdb=" N ILE A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.562A pdb=" N ILE A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 132 through 138 removed outlier: 3.839A pdb=" N ARG B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.606A pdb=" N ILE B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.127A pdb=" N GLU B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 214 through 226 Processing helix chain 'B' and resid 230 through 254 Processing helix chain 'B' and resid 293 through 316 Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 336 through 348 removed outlier: 3.714A pdb=" N PHE B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 371 through 379 removed outlier: 3.558A pdb=" N LEU B 377 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 379 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 394 Processing helix chain 'B' and resid 394 through 420 Processing helix chain 'B' and resid 430 through 443 removed outlier: 4.412A pdb=" N TRP B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TRP B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 474 removed outlier: 3.704A pdb=" N ILE B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.562A pdb=" N ILE B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 132 through 138 removed outlier: 3.839A pdb=" N ARG C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 166 removed outlier: 3.606A pdb=" N ILE C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 187 removed outlier: 4.128A pdb=" N GLU C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 202 Processing helix chain 'C' and resid 214 through 226 Processing helix chain 'C' and resid 230 through 254 Processing helix chain 'C' and resid 293 through 316 Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 336 through 348 removed outlier: 3.714A pdb=" N PHE C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 371 through 379 removed outlier: 3.558A pdb=" N LEU C 377 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG C 379 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 394 Processing helix chain 'C' and resid 394 through 420 Processing helix chain 'C' and resid 430 through 443 removed outlier: 4.412A pdb=" N TRP C 436 " --> pdb=" O PRO C 432 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TRP C 437 " --> pdb=" O ASP C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 474 removed outlier: 3.705A pdb=" N ILE C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.562A pdb=" N ILE C 479 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 132 through 138 removed outlier: 3.839A pdb=" N ARG D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 166 removed outlier: 3.607A pdb=" N ILE D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 187 removed outlier: 4.127A pdb=" N GLU D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 202 Processing helix chain 'D' and resid 214 through 226 Processing helix chain 'D' and resid 230 through 254 Processing helix chain 'D' and resid 293 through 316 Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 336 through 348 removed outlier: 3.714A pdb=" N PHE D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 370 Processing helix chain 'D' and resid 371 through 379 removed outlier: 3.558A pdb=" N LEU D 377 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG D 379 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 394 Processing helix chain 'D' and resid 394 through 420 Processing helix chain 'D' and resid 430 through 443 removed outlier: 4.413A pdb=" N TRP D 436 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TRP D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 474 removed outlier: 3.704A pdb=" N ILE D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.562A pdb=" N ILE D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 removed outlier: 3.670A pdb=" N THR A 117 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N TYR A 147 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL A 107 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE A 149 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASN A 109 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 113 through 118 removed outlier: 3.671A pdb=" N THR B 117 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N TYR B 147 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL B 107 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE B 149 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN B 109 " --> pdb=" O PHE B 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 113 through 118 removed outlier: 3.670A pdb=" N THR C 117 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N TYR C 147 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL C 107 " --> pdb=" O TYR C 147 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE C 149 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASN C 109 " --> pdb=" O PHE C 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 113 through 118 removed outlier: 3.669A pdb=" N THR D 117 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N TYR D 147 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL D 107 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE D 149 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN D 109 " --> pdb=" O PHE D 149 " (cutoff:3.500A) 660 hydrogen bonds defined for protein. 1920 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: 1.76 Time building geometry restraints manager: 1.23 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: 2128 1.33 - 1.45: 2865 1.45 - 1.57: 6375 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 11436 Sorted by residual: bond pdb=" N VAL B 453 " pdb=" CA VAL B 453 " ideal model delta sigma weight residual 1.459 1.504 -0.045 9.10e-03 1.21e+04 2.44e+01 bond pdb=" N VAL A 453 " pdb=" CA VAL A 453 " ideal model delta sigma weight residual 1.459 1.503 -0.044 9.10e-03 1.21e+04 2.37e+01 bond pdb=" N VAL D 453 " pdb=" CA VAL D 453 " ideal model delta sigma weight residual 1.459 1.503 -0.044 9.10e-03 1.21e+04 2.36e+01 bond pdb=" N VAL C 453 " pdb=" CA VAL C 453 " ideal model delta sigma weight residual 1.459 1.502 -0.044 9.10e-03 1.21e+04 2.29e+01 bond pdb=" CA SER B 430 " pdb=" CB SER B 430 " ideal model delta sigma weight residual 1.531 1.460 0.071 1.67e-02 3.59e+03 1.81e+01 ... (remaining 11431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 14144 1.90 - 3.81: 1142 3.81 - 5.71: 182 5.71 - 7.62: 16 7.62 - 9.52: 12 Bond angle restraints: 15496 Sorted by residual: angle pdb=" CA PHE B 295 " pdb=" C PHE B 295 " pdb=" O PHE B 295 " ideal model delta sigma weight residual 120.55 115.50 5.05 1.06e+00 8.90e-01 2.27e+01 angle pdb=" CA ASP C 449 " pdb=" CB ASP C 449 " pdb=" CG ASP C 449 " ideal model delta sigma weight residual 112.60 117.34 -4.74 1.00e+00 1.00e+00 2.24e+01 angle pdb=" C ASP B 449 " pdb=" CA ASP B 449 " pdb=" CB ASP B 449 " ideal model delta sigma weight residual 110.79 118.65 -7.86 1.66e+00 3.63e-01 2.24e+01 angle pdb=" CA PHE A 295 " pdb=" C PHE A 295 " pdb=" O PHE A 295 " ideal model delta sigma weight residual 120.55 115.53 5.02 1.06e+00 8.90e-01 2.24e+01 angle pdb=" C ASP C 449 " pdb=" CA ASP C 449 " pdb=" CB ASP C 449 " ideal model delta sigma weight residual 110.79 118.62 -7.83 1.66e+00 3.63e-01 2.23e+01 ... (remaining 15491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 5832 16.65 - 33.29: 660 33.29 - 49.94: 160 49.94 - 66.58: 92 66.58 - 83.23: 8 Dihedral angle restraints: 6752 sinusoidal: 2780 harmonic: 3972 Sorted by residual: dihedral pdb=" N TYR B 147 " pdb=" C TYR B 147 " pdb=" CA TYR B 147 " pdb=" CB TYR B 147 " ideal model delta harmonic sigma weight residual 122.80 113.86 8.94 0 2.50e+00 1.60e-01 1.28e+01 dihedral pdb=" N TYR A 147 " pdb=" C TYR A 147 " pdb=" CA TYR A 147 " pdb=" CB TYR A 147 " ideal model delta harmonic sigma weight residual 122.80 113.90 8.90 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" N TYR D 147 " pdb=" C TYR D 147 " pdb=" CA TYR D 147 " pdb=" CB TYR D 147 " ideal model delta harmonic sigma weight residual 122.80 113.93 8.87 0 2.50e+00 1.60e-01 1.26e+01 ... (remaining 6749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1246 0.059 - 0.117: 323 0.117 - 0.176: 124 0.176 - 0.234: 23 0.234 - 0.293: 12 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA VAL B 451 " pdb=" N VAL B 451 " pdb=" C VAL B 451 " pdb=" CB VAL B 451 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA VAL D 451 " pdb=" N VAL D 451 " pdb=" C VAL D 451 " pdb=" CB VAL D 451 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA VAL C 451 " pdb=" N VAL C 451 " pdb=" C VAL C 451 " pdb=" CB VAL C 451 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 1725 not shown) Planarity restraints: 1964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 317 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO B 318 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO B 318 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 318 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 317 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO C 318 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO C 318 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 318 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 317 " -0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO A 318 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 318 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 318 " -0.055 5.00e-02 4.00e+02 ... (remaining 1961 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 3250 2.81 - 3.40: 12659 3.40 - 3.98: 22035 3.98 - 4.56: 31589 4.56 - 5.14: 45319 Nonbonded interactions: 114852 Sorted by model distance: nonbonded pdb=" OG1 THR D 128 " pdb=" OH TYR D 163 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR A 128 " pdb=" OH TYR A 163 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR C 128 " pdb=" OH TYR C 163 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" OH TYR B 163 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR A 447 " pdb=" OG1 THR D 441 " model vdw 2.339 3.040 ... (remaining 114847 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' and resid 103 through 490) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.770 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 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 : 0.008 0.071 11436 Z= 0.528 Angle : 1.085 9.520 15496 Z= 0.770 Chirality : 0.066 0.293 1728 Planarity : 0.011 0.119 1964 Dihedral : 16.563 83.228 4184 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.97 % Allowed : 18.83 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.22), residues: 1344 helix: -0.35 (0.17), residues: 932 sheet: -3.13 (0.44), residues: 68 loop : -0.20 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 325 TYR 0.007 0.002 TYR C 447 PHE 0.014 0.002 PHE C 406 TRP 0.015 0.003 TRP C 436 HIS 0.002 0.001 HIS D 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00793 / 0.53 (11436) covalent geometry : angle 1.08465 / 0.77 (15496) hydrogen bonds : bond 0.17608 / 11.44 ( 660) hydrogen bonds : angle 6.43013 / 4.56 ( 1920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.431 Fit side-chains REVERT: A 137 MET cc_start: 0.7942 (tpp) cc_final: 0.7737 (ttp) REVERT: A 141 ASP cc_start: 0.7691 (t0) cc_final: 0.7051 (t0) REVERT: A 151 ARG cc_start: 0.8788 (mmm160) cc_final: 0.8582 (mmm160) REVERT: A 449 ASP cc_start: 0.8678 (p0) cc_final: 0.8388 (p0) REVERT: B 145 ASN cc_start: 0.8586 (t0) cc_final: 0.8299 (t0) REVERT: B 195 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7598 (mm-30) REVERT: C 145 ASN cc_start: 0.8588 (t0) cc_final: 0.8334 (t0) REVERT: C 195 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7642 (mm-30) REVERT: D 137 MET cc_start: 0.7980 (tpp) cc_final: 0.7772 (ttp) REVERT: D 145 ASN cc_start: 0.8563 (t0) cc_final: 0.8217 (t0) REVERT: D 330 LEU cc_start: 0.8200 (mm) cc_final: 0.7747 (mt) outliers start: 24 outliers final: 16 residues processed: 178 average time/residue: 0.4068 time to fit residues: 80.2034 Evaluate side-chains 148 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 478 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.190926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.121733 restraints weight = 11502.368| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.88 r_work: 0.2982 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11436 Z= 0.139 Angle : 0.551 7.161 15496 Z= 0.287 Chirality : 0.041 0.131 1728 Planarity : 0.006 0.072 1964 Dihedral : 5.894 56.467 1548 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.10 % Allowed : 17.68 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.23), residues: 1344 helix: 0.83 (0.17), residues: 936 sheet: -2.31 (0.61), residues: 40 loop : 0.60 (0.35), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 325 TYR 0.022 0.001 TYR D 161 PHE 0.025 0.002 PHE C 140 TRP 0.012 0.002 TRP B 305 HIS 0.001 0.001 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (11436) covalent geometry : angle 0.55095 / 0.29 (15496) hydrogen bonds : bond 0.03784 / 2.48 ( 660) hydrogen bonds : angle 3.95498 / 2.80 ( 1920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 161 time to evaluate : 0.531 Fit side-chains REVERT: A 328 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8636 (mtt) REVERT: B 141 ASP cc_start: 0.7627 (t0) cc_final: 0.6706 (t0) REVERT: C 132 ASP cc_start: 0.6569 (t0) cc_final: 0.6344 (t0) REVERT: C 137 MET cc_start: 0.7794 (ttp) cc_final: 0.7360 (tpp) REVERT: C 141 ASP cc_start: 0.7582 (t0) cc_final: 0.6677 (t0) REVERT: C 449 ASP cc_start: 0.8402 (p0) cc_final: 0.7956 (p0) REVERT: D 132 ASP cc_start: 0.6748 (t0) cc_final: 0.6522 (t0) REVERT: D 141 ASP cc_start: 0.7540 (t0) cc_final: 0.6863 (t0) REVERT: D 145 ASN cc_start: 0.8576 (t0) cc_final: 0.8336 (t0) REVERT: D 449 ASP cc_start: 0.8421 (p0) cc_final: 0.7969 (p0) outliers start: 62 outliers final: 10 residues processed: 196 average time/residue: 0.3866 time to fit residues: 84.6686 Evaluate side-chains 154 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 198 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN A 329 ASN B 329 ASN C 145 ASN C 329 ASN D 329 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.205524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.138278 restraints weight = 11509.332| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.42 r_work: 0.3273 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11436 Z= 0.153 Angle : 0.547 7.147 15496 Z= 0.280 Chirality : 0.041 0.127 1728 Planarity : 0.006 0.061 1964 Dihedral : 5.124 58.437 1532 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.18 % Allowed : 18.50 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.24), residues: 1344 helix: 1.24 (0.17), residues: 936 sheet: -1.99 (0.61), residues: 40 loop : 0.83 (0.35), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 325 TYR 0.014 0.002 TYR A 163 PHE 0.022 0.001 PHE C 140 TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS D 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.15 (11436) covalent geometry : angle 0.54745 / 0.28 (15496) hydrogen bonds : bond 0.03673 / 2.41 ( 660) hydrogen bonds : angle 3.80867 / 2.71 ( 1920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 160 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 137 MET cc_start: 0.7839 (ttp) cc_final: 0.7538 (tpp) REVERT: A 141 ASP cc_start: 0.7506 (t0) cc_final: 0.6810 (t0) REVERT: B 137 MET cc_start: 0.7830 (ttp) cc_final: 0.7411 (tpp) REVERT: B 199 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7549 (mm-30) REVERT: B 332 ASP cc_start: 0.8463 (t0) cc_final: 0.8253 (t0) REVERT: B 450 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8605 (ttm) REVERT: C 132 ASP cc_start: 0.6596 (t0) cc_final: 0.6359 (t0) REVERT: C 141 ASP cc_start: 0.7601 (t0) cc_final: 0.6945 (t0) REVERT: C 449 ASP cc_start: 0.8431 (p0) cc_final: 0.7724 (p0) REVERT: C 450 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8504 (ttm) REVERT: D 141 ASP cc_start: 0.7518 (t0) cc_final: 0.6666 (t0) REVERT: D 199 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7249 (mt-10) REVERT: D 449 ASP cc_start: 0.8472 (p0) cc_final: 0.7752 (p0) REVERT: D 450 MET cc_start: 0.8849 (mtp) cc_final: 0.8477 (ttm) outliers start: 63 outliers final: 13 residues processed: 191 average time/residue: 0.3503 time to fit residues: 75.9009 Evaluate side-chains 153 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 405 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN A 329 ASN B 145 ASN B 329 ASN C 329 ASN D 329 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.189037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.117963 restraints weight = 11688.196| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.94 r_work: 0.2976 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11436 Z= 0.152 Angle : 0.543 7.074 15496 Z= 0.279 Chirality : 0.041 0.127 1728 Planarity : 0.005 0.056 1964 Dihedral : 4.725 57.814 1528 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.11 % Allowed : 20.39 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.23), residues: 1344 helix: 1.28 (0.17), residues: 940 sheet: -1.45 (0.65), residues: 40 loop : 1.04 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 325 TYR 0.017 0.002 TYR D 161 PHE 0.013 0.001 PHE B 406 TRP 0.009 0.001 TRP A 436 HIS 0.001 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.15 (11436) covalent geometry : angle 0.54320 / 0.28 (15496) hydrogen bonds : bond 0.03554 / 2.34 ( 660) hydrogen bonds : angle 3.76563 / 2.67 ( 1920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.7922 (ttp) cc_final: 0.7607 (tpp) REVERT: A 199 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7163 (mt-10) REVERT: B 132 ASP cc_start: 0.6516 (t0) cc_final: 0.6308 (t0) REVERT: B 141 ASP cc_start: 0.7644 (t0) cc_final: 0.6978 (t0) REVERT: B 199 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: B 450 MET cc_start: 0.8936 (mtp) cc_final: 0.8669 (ttm) REVERT: C 141 ASP cc_start: 0.7586 (t0) cc_final: 0.6943 (t0) REVERT: C 170 ARG cc_start: 0.8314 (mmm-85) cc_final: 0.7976 (mmt-90) REVERT: C 199 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7145 (mt-10) REVERT: C 433 ASP cc_start: 0.8591 (t0) cc_final: 0.8315 (t0) REVERT: C 450 MET cc_start: 0.8925 (mtp) cc_final: 0.8679 (ttm) REVERT: D 141 ASP cc_start: 0.7599 (t0) cc_final: 0.6860 (t0) REVERT: D 198 ARG cc_start: 0.5808 (OUTLIER) cc_final: 0.5551 (mtt90) REVERT: D 199 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7112 (mt-10) REVERT: D 433 ASP cc_start: 0.8590 (t0) cc_final: 0.8318 (t0) REVERT: D 450 MET cc_start: 0.8925 (mtp) cc_final: 0.8626 (ttm) outliers start: 50 outliers final: 13 residues processed: 178 average time/residue: 0.3744 time to fit residues: 74.8741 Evaluate side-chains 155 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 405 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 80 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN A 329 ASN B 145 ASN B 329 ASN C 145 ASN C 329 ASN D 145 ASN D 329 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.189609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.130186 restraints weight = 11643.904| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.66 r_work: 0.2979 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11436 Z= 0.149 Angle : 0.528 7.014 15496 Z= 0.271 Chirality : 0.041 0.132 1728 Planarity : 0.005 0.054 1964 Dihedral : 3.949 57.508 1520 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 5.02 % Allowed : 18.67 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.23), residues: 1344 helix: 1.38 (0.17), residues: 940 sheet: -0.73 (0.75), residues: 40 loop : 1.06 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 325 TYR 0.015 0.002 TYR D 161 PHE 0.014 0.001 PHE A 140 TRP 0.009 0.001 TRP C 436 HIS 0.002 0.001 HIS D 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (11436) covalent geometry : angle 0.52768 / 0.27 (15496) hydrogen bonds : bond 0.03511 / 2.31 ( 660) hydrogen bonds : angle 3.69740 / 2.63 ( 1920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 159 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.7849 (ttp) cc_final: 0.7600 (tpp) REVERT: A 141 ASP cc_start: 0.7589 (t0) cc_final: 0.6873 (t0) REVERT: A 198 ARG cc_start: 0.6007 (OUTLIER) cc_final: 0.5724 (mtt90) REVERT: A 222 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7271 (tp) REVERT: B 132 ASP cc_start: 0.6522 (t0) cc_final: 0.6284 (t0) REVERT: B 141 ASP cc_start: 0.7677 (t0) cc_final: 0.6927 (t0) REVERT: B 198 ARG cc_start: 0.5762 (OUTLIER) cc_final: 0.5254 (ttt90) REVERT: B 199 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7475 (mm-30) REVERT: B 222 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7243 (tp) REVERT: B 450 MET cc_start: 0.8923 (mtp) cc_final: 0.8712 (ttm) REVERT: C 137 MET cc_start: 0.7805 (ttp) cc_final: 0.7405 (tpp) REVERT: C 141 ASP cc_start: 0.7634 (t0) cc_final: 0.6896 (t0) REVERT: C 170 ARG cc_start: 0.8335 (mmm-85) cc_final: 0.7992 (mmt-90) REVERT: C 198 ARG cc_start: 0.5925 (OUTLIER) cc_final: 0.5633 (mtt90) REVERT: C 222 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7240 (tp) REVERT: C 449 ASP cc_start: 0.8657 (p0) cc_final: 0.7812 (p0) REVERT: C 450 MET cc_start: 0.8910 (mtp) cc_final: 0.8576 (ttm) REVERT: D 132 ASP cc_start: 0.6595 (t0) cc_final: 0.6335 (t0) REVERT: D 141 ASP cc_start: 0.7645 (t0) cc_final: 0.6905 (t0) REVERT: D 198 ARG cc_start: 0.5977 (OUTLIER) cc_final: 0.5692 (mtt90) REVERT: D 222 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7293 (tp) REVERT: D 449 ASP cc_start: 0.8642 (p0) cc_final: 0.7984 (p0) REVERT: D 450 MET cc_start: 0.8914 (mtp) cc_final: 0.8567 (ttm) outliers start: 61 outliers final: 19 residues processed: 191 average time/residue: 0.3526 time to fit residues: 76.1794 Evaluate side-chains 170 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 94 optimal weight: 0.6980 chunk 132 optimal weight: 0.0050 chunk 98 optimal weight: 0.1980 chunk 130 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 128 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.192495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.132414 restraints weight = 11753.043| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.86 r_work: 0.3007 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11436 Z= 0.103 Angle : 0.494 6.905 15496 Z= 0.253 Chirality : 0.039 0.125 1728 Planarity : 0.005 0.051 1964 Dihedral : 3.796 59.597 1520 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.29 % Allowed : 20.56 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.23), residues: 1344 helix: 1.64 (0.17), residues: 940 sheet: -0.26 (0.81), residues: 40 loop : 0.99 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 325 TYR 0.014 0.001 TYR D 161 PHE 0.014 0.001 PHE A 406 TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (11436) covalent geometry : angle 0.49424 / 0.25 (15496) hydrogen bonds : bond 0.03072 / 2.02 ( 660) hydrogen bonds : angle 3.54180 / 2.51 ( 1920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.7913 (ttp) cc_final: 0.7615 (tpp) REVERT: A 198 ARG cc_start: 0.5921 (OUTLIER) cc_final: 0.5572 (mtt90) REVERT: A 222 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7292 (tp) REVERT: B 141 ASP cc_start: 0.7700 (t0) cc_final: 0.6998 (t0) REVERT: B 199 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7488 (mm-30) REVERT: B 222 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7293 (tp) REVERT: C 137 MET cc_start: 0.7786 (ttp) cc_final: 0.7409 (tpp) REVERT: C 141 ASP cc_start: 0.7672 (t0) cc_final: 0.6976 (t0) REVERT: C 198 ARG cc_start: 0.5938 (OUTLIER) cc_final: 0.5588 (mtt90) REVERT: C 199 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7263 (mm-30) REVERT: C 222 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7276 (tp) REVERT: D 132 ASP cc_start: 0.6571 (t0) cc_final: 0.6276 (t0) REVERT: D 137 MET cc_start: 0.7782 (ttp) cc_final: 0.7390 (tpp) REVERT: D 141 ASP cc_start: 0.7608 (t0) cc_final: 0.6910 (t0) REVERT: D 198 ARG cc_start: 0.5915 (OUTLIER) cc_final: 0.5604 (mtt90) REVERT: D 222 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7302 (tp) REVERT: D 332 ASP cc_start: 0.8435 (t0) cc_final: 0.7685 (m-30) REVERT: D 449 ASP cc_start: 0.8570 (p0) cc_final: 0.7944 (p0) REVERT: D 450 MET cc_start: 0.8820 (mtp) cc_final: 0.8484 (ttm) outliers start: 40 outliers final: 7 residues processed: 178 average time/residue: 0.3785 time to fit residues: 75.7703 Evaluate side-chains 158 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 334 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 84 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 90 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN B 145 ASN C 145 ASN D 145 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.191066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.130330 restraints weight = 11598.477| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.80 r_work: 0.2988 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11436 Z= 0.121 Angle : 0.503 6.941 15496 Z= 0.259 Chirality : 0.039 0.128 1728 Planarity : 0.005 0.049 1964 Dihedral : 3.372 11.293 1516 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.78 % Allowed : 20.15 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.23), residues: 1344 helix: 1.70 (0.17), residues: 940 sheet: -0.06 (0.80), residues: 40 loop : 1.02 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 325 TYR 0.019 0.001 TYR D 161 PHE 0.013 0.001 PHE A 406 TRP 0.007 0.001 TRP A 436 HIS 0.001 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (11436) covalent geometry : angle 0.50318 / 0.26 (15496) hydrogen bonds : bond 0.03198 / 2.10 ( 660) hydrogen bonds : angle 3.55637 / 2.52 ( 1920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.7888 (ttp) cc_final: 0.7580 (tpp) REVERT: A 141 ASP cc_start: 0.7730 (t0) cc_final: 0.7065 (t0) REVERT: A 198 ARG cc_start: 0.5943 (OUTLIER) cc_final: 0.5664 (mtt90) REVERT: A 222 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7215 (tp) REVERT: B 141 ASP cc_start: 0.7675 (t0) cc_final: 0.6983 (t0) REVERT: B 199 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7492 (mm-30) REVERT: B 222 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7237 (tp) REVERT: C 137 MET cc_start: 0.7770 (ttp) cc_final: 0.7362 (tpp) REVERT: C 141 ASP cc_start: 0.7662 (t0) cc_final: 0.7001 (t0) REVERT: C 198 ARG cc_start: 0.5824 (OUTLIER) cc_final: 0.5376 (mtt90) REVERT: C 199 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7195 (mm-30) REVERT: C 222 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7192 (tp) REVERT: D 198 ARG cc_start: 0.5857 (OUTLIER) cc_final: 0.5489 (mtt90) REVERT: D 222 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7219 (tp) REVERT: D 449 ASP cc_start: 0.8545 (p0) cc_final: 0.7721 (p0) REVERT: D 450 MET cc_start: 0.8847 (mtp) cc_final: 0.8538 (ttm) outliers start: 46 outliers final: 13 residues processed: 176 average time/residue: 0.3583 time to fit residues: 70.5101 Evaluate side-chains 158 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 405 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.192432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3297 r_free = 0.3297 target = 0.122949 restraints weight = 11629.431| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.81 r_work: 0.3035 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11436 Z= 0.112 Angle : 0.502 8.975 15496 Z= 0.256 Chirality : 0.039 0.126 1728 Planarity : 0.005 0.048 1964 Dihedral : 3.325 11.329 1516 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.88 % Allowed : 21.22 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.23), residues: 1344 helix: 1.80 (0.17), residues: 940 sheet: 0.01 (0.80), residues: 40 loop : 0.97 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 170 TYR 0.019 0.001 TYR D 161 PHE 0.014 0.001 PHE A 406 TRP 0.007 0.001 TRP C 436 HIS 0.001 0.000 HIS D 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (11436) covalent geometry : angle 0.50173 / 0.26 (15496) hydrogen bonds : bond 0.03085 / 2.03 ( 660) hydrogen bonds : angle 3.50483 / 2.48 ( 1920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.7873 (ttp) cc_final: 0.7519 (tpp) REVERT: A 170 ARG cc_start: 0.8268 (mmt-90) cc_final: 0.8045 (mmt-90) REVERT: A 198 ARG cc_start: 0.5929 (OUTLIER) cc_final: 0.5532 (mtt90) REVERT: A 199 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7115 (mm-30) REVERT: A 222 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7198 (tp) REVERT: B 199 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7366 (mm-30) REVERT: B 222 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7227 (tp) REVERT: C 137 MET cc_start: 0.7784 (ttp) cc_final: 0.7335 (tpp) REVERT: C 198 ARG cc_start: 0.5806 (OUTLIER) cc_final: 0.5370 (mtt90) REVERT: C 199 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7145 (mm-30) REVERT: C 222 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7181 (tp) REVERT: D 137 MET cc_start: 0.7758 (ttp) cc_final: 0.7382 (tpp) REVERT: D 198 ARG cc_start: 0.5905 (OUTLIER) cc_final: 0.5638 (mtt90) REVERT: D 222 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7240 (tp) REVERT: D 449 ASP cc_start: 0.8497 (p0) cc_final: 0.7702 (p0) REVERT: D 450 MET cc_start: 0.8801 (mtp) cc_final: 0.8490 (ttm) outliers start: 35 outliers final: 11 residues processed: 151 average time/residue: 0.3633 time to fit residues: 62.0434 Evaluate side-chains 144 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 405 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 107 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 113 optimal weight: 0.0050 chunk 88 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN B 145 ASN C 145 ASN D 145 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.191784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.126105 restraints weight = 11578.424| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.64 r_work: 0.3021 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11436 Z= 0.119 Angle : 0.504 7.899 15496 Z= 0.258 Chirality : 0.040 0.129 1728 Planarity : 0.005 0.048 1964 Dihedral : 3.318 11.838 1516 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.63 % Allowed : 21.79 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.23), residues: 1344 helix: 1.84 (0.17), residues: 940 sheet: 0.05 (0.78), residues: 40 loop : 0.95 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 170 TYR 0.018 0.001 TYR D 161 PHE 0.013 0.001 PHE B 406 TRP 0.008 0.001 TRP A 436 HIS 0.001 0.000 HIS C 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (11436) covalent geometry : angle 0.50359 / 0.26 (15496) hydrogen bonds : bond 0.03136 / 2.07 ( 660) hydrogen bonds : angle 3.50879 / 2.48 ( 1920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.7968 (ttp) cc_final: 0.7652 (tpp) REVERT: A 198 ARG cc_start: 0.6004 (OUTLIER) cc_final: 0.5612 (mtt90) REVERT: A 222 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7305 (tp) REVERT: B 199 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7495 (mm-30) REVERT: B 222 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7293 (tp) REVERT: C 137 MET cc_start: 0.7817 (ttp) cc_final: 0.7390 (tpp) REVERT: C 198 ARG cc_start: 0.5818 (OUTLIER) cc_final: 0.5340 (ttt90) REVERT: C 222 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7263 (tp) REVERT: D 137 MET cc_start: 0.7806 (ttp) cc_final: 0.7433 (tpp) REVERT: D 198 ARG cc_start: 0.6011 (OUTLIER) cc_final: 0.5615 (mtt90) REVERT: D 199 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7119 (mm-30) REVERT: D 222 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7311 (tp) REVERT: D 449 ASP cc_start: 0.8573 (p0) cc_final: 0.7743 (p0) REVERT: D 450 MET cc_start: 0.8875 (mtp) cc_final: 0.8569 (ttm) outliers start: 32 outliers final: 11 residues processed: 149 average time/residue: 0.3923 time to fit residues: 65.4397 Evaluate side-chains 147 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 405 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.189432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.129457 restraints weight = 11572.594| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.81 r_work: 0.2961 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11436 Z= 0.166 Angle : 0.542 8.098 15496 Z= 0.281 Chirality : 0.041 0.133 1728 Planarity : 0.005 0.048 1964 Dihedral : 3.498 12.780 1516 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.14 % Allowed : 22.29 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.23), residues: 1344 helix: 1.63 (0.17), residues: 940 sheet: -0.11 (0.75), residues: 40 loop : 0.94 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 170 TYR 0.017 0.002 TYR D 161 PHE 0.013 0.001 PHE A 406 TRP 0.010 0.001 TRP C 436 HIS 0.002 0.001 HIS C 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (11436) covalent geometry : angle 0.54230 / 0.28 (15496) hydrogen bonds : bond 0.03544 / 2.34 ( 660) hydrogen bonds : angle 3.66470 / 2.59 ( 1920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.7823 (ttp) cc_final: 0.7473 (tpp) REVERT: A 170 ARG cc_start: 0.8325 (mmt-90) cc_final: 0.7978 (mmt90) REVERT: A 198 ARG cc_start: 0.6080 (OUTLIER) cc_final: 0.5743 (mtt90) REVERT: A 222 LEU cc_start: 0.7584 (mp) cc_final: 0.7207 (tp) REVERT: B 173 VAL cc_start: 0.8783 (t) cc_final: 0.8533 (m) REVERT: B 199 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7471 (mm-30) REVERT: B 222 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7274 (tp) REVERT: C 198 ARG cc_start: 0.5822 (OUTLIER) cc_final: 0.5408 (ttt90) REVERT: C 222 LEU cc_start: 0.7570 (mp) cc_final: 0.7182 (tp) REVERT: D 198 ARG cc_start: 0.6012 (OUTLIER) cc_final: 0.5601 (mtt90) REVERT: D 222 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7300 (tp) REVERT: D 449 ASP cc_start: 0.8705 (p0) cc_final: 0.7826 (p0) REVERT: D 450 MET cc_start: 0.8969 (mtp) cc_final: 0.8626 (ttm) outliers start: 26 outliers final: 10 residues processed: 148 average time/residue: 0.3094 time to fit residues: 51.7049 Evaluate side-chains 139 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 405 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 65 optimal weight: 0.9990 chunk 75 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN B 145 ASN C 145 ASN D 145 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.190473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.130524 restraints weight = 11631.885| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.83 r_work: 0.3111 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11436 Z= 0.136 Angle : 0.530 8.903 15496 Z= 0.272 Chirality : 0.040 0.128 1728 Planarity : 0.005 0.047 1964 Dihedral : 3.438 13.012 1516 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.89 % Allowed : 23.19 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.23), residues: 1344 helix: 1.68 (0.17), residues: 940 sheet: -0.12 (0.76), residues: 40 loop : 0.89 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 170 TYR 0.017 0.001 TYR D 161 PHE 0.013 0.001 PHE B 406 TRP 0.009 0.001 TRP D 436 HIS 0.001 0.001 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (11436) covalent geometry : angle 0.53019 / 0.27 (15496) hydrogen bonds : bond 0.03295 / 2.17 ( 660) hydrogen bonds : angle 3.57900 / 2.53 ( 1920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4121.29 seconds wall clock time: 70 minutes 59.85 seconds (4259.85 seconds total)