Starting phenix.real_space_refine on Wed Feb 4 14:50:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cla_45668/02_2026/9cla_45668.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cla_45668/02_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_45668/02_2026/9cla_45668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cla_45668/02_2026/9cla_45668.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cla_45668/02_2026/9cla_45668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cla_45668/02_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-2.0-5952/lib/python3.9/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, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.69, per 1000 atoms: 0.24 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: 0.90 Conformation dependent library (CDL) restraints added in 487.0 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: 0.34 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: 1.70 Time building geometry restraints manager: 1.19 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: 2.260 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 11.450 Find NCS groups from input model: 0.180 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:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 covalent geometry : bond 0.00793 (11436) covalent geometry : angle 1.08465 (15496) hydrogen bonds : bond 0.17608 ( 660) hydrogen bonds : angle 6.43013 ( 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 : 0.440 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: 0.4388 time to fit residues: 86.3138 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 : 0.471 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.191602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.137620 restraints weight = 11395.297| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.77 r_work: 0.2967 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1210 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= 0.135 Angle : 0.544 7.149 15496 Z= 0.284 Chirality : 0.041 0.131 1728 Planarity : 0.006 0.072 1964 Dihedral : 5.869 56.397 1548 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.93 % Allowed : 17.85 % 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: 0.76 (0.23), residues: 1344 helix: 0.82 (0.17), residues: 936 sheet: -2.32 (0.61), residues: 40 loop : 0.35 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 325 TYR 0.020 0.002 TYR D 161 PHE 0.026 0.001 PHE D 140 TRP 0.014 0.002 TRP B 305 HIS 0.001 0.001 HIS D 488 Details of bonding type rmsd covalent geometry : bond 0.00318 (11436) covalent geometry : angle 0.54354 (15496) hydrogen bonds : bond 0.03933 ( 660) hydrogen bonds : angle 3.97356 ( 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 227 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 167 time to evaluate : 0.393 Fit side-chains REVERT: A 141 ASP cc_start: 0.7723 (t0) cc_final: 0.6986 (t0) REVERT: A 328 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8691 (mtt) REVERT: B 141 ASP cc_start: 0.7648 (t0) cc_final: 0.6755 (t0) REVERT: C 132 ASP cc_start: 0.6600 (t0) cc_final: 0.6386 (t0) REVERT: C 137 MET cc_start: 0.7789 (ttp) cc_final: 0.7348 (tpp) REVERT: C 141 ASP cc_start: 0.7646 (t0) cc_final: 0.6745 (t0) REVERT: C 449 ASP cc_start: 0.8404 (p0) cc_final: 0.7934 (p0) REVERT: D 132 ASP cc_start: 0.6761 (t0) cc_final: 0.6538 (t0) REVERT: D 141 ASP cc_start: 0.7594 (t0) cc_final: 0.6920 (t0) REVERT: D 145 ASN cc_start: 0.8588 (t0) cc_final: 0.8335 (t0) REVERT: D 449 ASP cc_start: 0.8428 (p0) cc_final: 0.7959 (p0) outliers start: 60 outliers final: 11 residues processed: 202 average time/residue: 0.3843 time to fit residues: 86.8562 Evaluate side-chains 153 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 B residue 405 LEU 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: 3.9990 chunk 104 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 57 optimal weight: 0.4980 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4251 r_free = 0.4251 target = 0.206012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.138141 restraints weight = 11426.902| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.58 r_work: 0.3297 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1664 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= 0.140 Angle : 0.535 7.122 15496 Z= 0.273 Chirality : 0.040 0.126 1728 Planarity : 0.006 0.061 1964 Dihedral : 5.193 57.860 1534 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 5.26 % Allowed : 18.83 % 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: 1.45 (0.23), residues: 1344 helix: 1.28 (0.17), residues: 936 sheet: -1.93 (0.61), residues: 40 loop : 0.76 (0.35), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 325 TYR 0.012 0.001 TYR D 161 PHE 0.021 0.001 PHE B 140 TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS D 488 Details of bonding type rmsd covalent geometry : bond 0.00344 (11436) covalent geometry : angle 0.53490 (15496) hydrogen bonds : bond 0.03596 ( 660) hydrogen bonds : angle 3.76857 ( 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 214 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 150 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 137 MET cc_start: 0.7858 (ttp) cc_final: 0.7481 (tpp) REVERT: B 137 MET cc_start: 0.7850 (ttp) cc_final: 0.7388 (tpp) REVERT: B 199 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7446 (mm-30) REVERT: B 332 ASP cc_start: 0.8583 (t0) cc_final: 0.8349 (t0) REVERT: C 137 MET cc_start: 0.7885 (ttp) cc_final: 0.7440 (tpp) REVERT: D 199 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7263 (mt-10) outliers start: 64 outliers final: 15 residues processed: 181 average time/residue: 0.3797 time to fit residues: 77.2673 Evaluate side-chains 145 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 C residue 117 THR 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 119 LEU Chi-restraints excluded: chain D residue 334 VAL 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: 8.9990 chunk 110 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 329 ASN B 145 ASN B 329 ASN C 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.185061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.126001 restraints weight = 11652.654| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.81 r_work: 0.2898 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 11436 Z= 0.267 Angle : 0.613 7.265 15496 Z= 0.320 Chirality : 0.046 0.152 1728 Planarity : 0.006 0.058 1964 Dihedral : 4.934 59.579 1528 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.93 % Allowed : 19.41 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.19 (0.23), residues: 1344 helix: 0.98 (0.17), residues: 940 sheet: -1.42 (0.68), residues: 40 loop : 0.92 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 325 TYR 0.016 0.002 TYR D 161 PHE 0.014 0.002 PHE A 406 TRP 0.011 0.002 TRP D 436 HIS 0.003 0.002 HIS C 488 Details of bonding type rmsd covalent geometry : bond 0.00681 (11436) covalent geometry : angle 0.61271 (15496) hydrogen bonds : bond 0.04360 ( 660) hydrogen bonds : angle 4.07518 ( 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 211 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 151 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.6044 (OUTLIER) cc_final: 0.5695 (mtt90) REVERT: A 199 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7150 (mt-10) REVERT: A 222 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7323 (tp) REVERT: B 132 ASP cc_start: 0.6693 (t0) cc_final: 0.6460 (t0) REVERT: B 141 ASP cc_start: 0.7720 (t0) cc_final: 0.7044 (t0) REVERT: B 198 ARG cc_start: 0.5761 (OUTLIER) cc_final: 0.5198 (ttt90) REVERT: B 199 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7548 (mm-30) REVERT: B 222 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7336 (tp) REVERT: C 141 ASP cc_start: 0.7702 (t0) cc_final: 0.6976 (t0) REVERT: C 170 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.8137 (mmt-90) REVERT: C 198 ARG cc_start: 0.6128 (OUTLIER) cc_final: 0.5768 (mtt90) REVERT: C 199 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7150 (mt-10) REVERT: D 132 ASP cc_start: 0.6832 (t0) cc_final: 0.6566 (t0) REVERT: D 141 ASP cc_start: 0.7697 (t0) cc_final: 0.7009 (t0) REVERT: D 198 ARG cc_start: 0.6009 (OUTLIER) cc_final: 0.5710 (mtt90) REVERT: D 222 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7331 (tp) outliers start: 60 outliers final: 15 residues processed: 183 average time/residue: 0.3668 time to fit residues: 75.0822 Evaluate side-chains 153 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU 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 119 LEU 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 119 LEU 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 416 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 80 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 329 ASN C 145 ASN D 145 ASN D 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.189287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.129462 restraints weight = 11637.286| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.83 r_work: 0.2959 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11436 Z= 0.119 Angle : 0.510 6.978 15496 Z= 0.262 Chirality : 0.040 0.129 1728 Planarity : 0.005 0.054 1964 Dihedral : 4.655 57.511 1528 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.62 % Allowed : 21.22 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.23), residues: 1344 helix: 1.32 (0.17), residues: 940 sheet: -0.81 (0.75), residues: 40 loop : 0.93 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 325 TYR 0.016 0.001 TYR D 161 PHE 0.014 0.001 PHE B 140 TRP 0.008 0.001 TRP A 436 HIS 0.001 0.000 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00283 (11436) covalent geometry : angle 0.50995 (15496) hydrogen bonds : bond 0.03381 ( 660) hydrogen bonds : angle 3.72273 ( 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 199 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASP cc_start: 0.7646 (t0) cc_final: 0.6923 (t0) REVERT: A 168 ARG cc_start: 0.7839 (ttp-110) cc_final: 0.7474 (ttp80) REVERT: B 132 ASP cc_start: 0.6509 (t0) cc_final: 0.6278 (t0) REVERT: B 141 ASP cc_start: 0.7684 (t0) cc_final: 0.6948 (t0) REVERT: B 198 ARG cc_start: 0.5766 (OUTLIER) cc_final: 0.5181 (ttt90) REVERT: B 199 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7515 (mm-30) REVERT: C 141 ASP cc_start: 0.7653 (t0) cc_final: 0.6912 (t0) REVERT: C 173 VAL cc_start: 0.8775 (t) cc_final: 0.8510 (m) REVERT: C 222 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7275 (tp) REVERT: D 132 ASP cc_start: 0.6644 (t0) cc_final: 0.6405 (t0) REVERT: D 141 ASP cc_start: 0.7648 (t0) cc_final: 0.6918 (t0) REVERT: D 198 ARG cc_start: 0.5904 (OUTLIER) cc_final: 0.5604 (mtt90) outliers start: 44 outliers final: 8 residues processed: 177 average time/residue: 0.4115 time to fit residues: 80.9576 Evaluate side-chains 147 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU 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 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 184 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 94 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 130 optimal weight: 0.3980 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN B 145 ASN C 145 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.188086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.129143 restraints weight = 11686.748| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.88 r_work: 0.2920 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11436 Z= 0.156 Angle : 0.522 7.012 15496 Z= 0.271 Chirality : 0.041 0.131 1728 Planarity : 0.005 0.053 1964 Dihedral : 3.943 57.663 1520 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.87 % Allowed : 20.07 % 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: 1.72 (0.23), residues: 1344 helix: 1.40 (0.17), residues: 940 sheet: -0.49 (0.80), residues: 40 loop : 0.93 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 170 TYR 0.013 0.002 TYR D 161 PHE 0.013 0.001 PHE A 406 TRP 0.010 0.001 TRP D 436 HIS 0.002 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00392 (11436) covalent geometry : angle 0.52226 (15496) hydrogen bonds : bond 0.03584 ( 660) hydrogen bonds : angle 3.77118 ( 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 190 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 VAL cc_start: 0.8787 (t) cc_final: 0.8534 (m) REVERT: A 198 ARG cc_start: 0.5852 (OUTLIER) cc_final: 0.5500 (mtt90) REVERT: B 132 ASP cc_start: 0.6529 (t0) cc_final: 0.6274 (t0) REVERT: B 141 ASP cc_start: 0.7697 (t0) cc_final: 0.6935 (t0) REVERT: B 173 VAL cc_start: 0.8782 (t) cc_final: 0.8527 (m) REVERT: B 198 ARG cc_start: 0.5757 (OUTLIER) cc_final: 0.5341 (ttt90) REVERT: B 199 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7507 (mm-30) REVERT: B 222 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7255 (tp) REVERT: C 141 ASP cc_start: 0.7656 (t0) cc_final: 0.6896 (t0) REVERT: C 198 ARG cc_start: 0.5908 (OUTLIER) cc_final: 0.5572 (mtt90) REVERT: C 222 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7224 (tp) REVERT: D 132 ASP cc_start: 0.6658 (t0) cc_final: 0.6401 (t0) REVERT: D 141 ASP cc_start: 0.7641 (t0) cc_final: 0.6868 (t0) REVERT: D 173 VAL cc_start: 0.8787 (t) cc_final: 0.8522 (m) REVERT: D 198 ARG cc_start: 0.5887 (OUTLIER) cc_final: 0.5535 (mtt90) REVERT: D 222 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7265 (tp) outliers start: 47 outliers final: 13 residues processed: 178 average time/residue: 0.4167 time to fit residues: 82.3883 Evaluate side-chains 166 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 119 LEU 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 405 LEU Chi-restraints excluded: chain C residue 119 LEU 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 119 LEU 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 Chi-restraints excluded: chain D residue 405 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 84 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 134 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 131 optimal weight: 0.1980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN D 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.189923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.130261 restraints weight = 11511.058| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.83 r_work: 0.2975 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11436 Z= 0.119 Angle : 0.506 8.786 15496 Z= 0.259 Chirality : 0.040 0.127 1728 Planarity : 0.005 0.051 1964 Dihedral : 3.851 58.998 1520 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.29 % Allowed : 20.64 % 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: 1.92 (0.23), residues: 1344 helix: 1.57 (0.17), residues: 940 sheet: -0.21 (0.82), residues: 40 loop : 0.93 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 170 TYR 0.021 0.001 TYR D 161 PHE 0.014 0.001 PHE D 406 TRP 0.008 0.001 TRP A 436 HIS 0.001 0.000 HIS C 488 Details of bonding type rmsd covalent geometry : bond 0.00287 (11436) covalent geometry : angle 0.50637 (15496) hydrogen bonds : bond 0.03285 ( 660) hydrogen bonds : angle 3.66033 ( 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 172 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7272 (mt-10) REVERT: A 222 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7338 (tp) REVERT: B 199 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7419 (mm-30) REVERT: C 173 VAL cc_start: 0.8795 (t) cc_final: 0.8541 (m) REVERT: C 199 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7252 (mt-10) REVERT: C 222 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7300 (tp) REVERT: D 173 VAL cc_start: 0.8796 (t) cc_final: 0.8539 (m) REVERT: D 198 ARG cc_start: 0.6002 (OUTLIER) cc_final: 0.5711 (mtt90) outliers start: 40 outliers final: 9 residues processed: 155 average time/residue: 0.4390 time to fit residues: 75.4244 Evaluate side-chains 133 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 184 ILE 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 C residue 117 THR 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 119 LEU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 198 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN B 145 ASN C 145 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.190052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 136)---------------| | r_work = 0.3269 r_free = 0.3269 target = 0.119578 restraints weight = 11475.756| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.60 r_work: 0.3006 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11436 Z= 0.124 Angle : 0.504 7.506 15496 Z= 0.259 Chirality : 0.040 0.129 1728 Planarity : 0.005 0.050 1964 Dihedral : 3.409 12.274 1516 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.80 % Allowed : 21.30 % 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: 2.03 (0.23), residues: 1344 helix: 1.66 (0.17), residues: 940 sheet: -0.13 (0.81), residues: 40 loop : 0.96 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 170 TYR 0.021 0.001 TYR D 161 PHE 0.014 0.001 PHE B 406 TRP 0.008 0.001 TRP A 436 HIS 0.001 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00304 (11436) covalent geometry : angle 0.50424 (15496) hydrogen bonds : bond 0.03304 ( 660) hydrogen bonds : angle 3.61892 ( 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 166 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.6013 (OUTLIER) cc_final: 0.5726 (mtt90) REVERT: A 222 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7247 (tp) REVERT: B 199 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7489 (mm-30) REVERT: B 222 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7250 (tp) REVERT: C 170 ARG cc_start: 0.8226 (mmt-90) cc_final: 0.8013 (mtt-85) REVERT: C 222 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7230 (tp) REVERT: D 173 VAL cc_start: 0.8774 (t) cc_final: 0.8521 (m) REVERT: D 198 ARG cc_start: 0.5953 (OUTLIER) cc_final: 0.5633 (mtt90) REVERT: D 222 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7265 (tp) outliers start: 34 outliers final: 13 residues processed: 151 average time/residue: 0.3934 time to fit residues: 66.2375 Evaluate side-chains 142 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 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 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 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 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 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: 0.5980 chunk 117 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.190235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 148)---------------| | r_work = 0.3242 r_free = 0.3242 target = 0.117257 restraints weight = 11420.296| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.89 r_work: 0.3016 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2344 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= 0.123 Angle : 0.502 7.352 15496 Z= 0.258 Chirality : 0.040 0.129 1728 Planarity : 0.005 0.049 1964 Dihedral : 3.385 12.219 1516 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.04 % Allowed : 21.46 % 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: 2.08 (0.23), residues: 1344 helix: 1.71 (0.17), residues: 940 sheet: -0.03 (0.80), residues: 40 loop : 0.91 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 170 TYR 0.020 0.001 TYR D 161 PHE 0.014 0.001 PHE D 406 TRP 0.008 0.001 TRP A 436 HIS 0.001 0.001 HIS C 488 Details of bonding type rmsd covalent geometry : bond 0.00299 (11436) covalent geometry : angle 0.50169 (15496) hydrogen bonds : bond 0.03257 ( 660) hydrogen bonds : angle 3.58840 ( 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: 37 poor density : 127 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.5954 (OUTLIER) cc_final: 0.5602 (mtt90) REVERT: A 199 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7246 (mm-30) REVERT: A 222 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7145 (tp) REVERT: B 173 VAL cc_start: 0.8738 (t) cc_final: 0.8499 (m) REVERT: B 184 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7255 (mm) REVERT: B 194 MET cc_start: 0.7394 (mmm) cc_final: 0.7004 (mmm) REVERT: B 199 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: B 222 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7178 (tp) REVERT: C 111 SER cc_start: 0.8640 (t) cc_final: 0.8429 (t) REVERT: C 170 ARG cc_start: 0.8221 (mmt-90) cc_final: 0.7983 (mmt-90) REVERT: C 173 VAL cc_start: 0.8748 (t) cc_final: 0.8509 (m) REVERT: C 198 ARG cc_start: 0.5932 (OUTLIER) cc_final: 0.5591 (mtt90) REVERT: C 199 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7220 (mm-30) REVERT: C 222 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7138 (tp) REVERT: D 173 VAL cc_start: 0.8761 (t) cc_final: 0.8514 (m) REVERT: D 198 ARG cc_start: 0.5896 (OUTLIER) cc_final: 0.5464 (mtt90) REVERT: D 222 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7187 (tp) outliers start: 37 outliers final: 12 residues processed: 151 average time/residue: 0.3762 time to fit residues: 63.6559 Evaluate side-chains 146 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 0.3980 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN B 145 ASN C 145 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.189913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.137401 restraints weight = 11433.158| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.77 r_work: 0.2974 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11436 Z= 0.147 Angle : 0.525 8.206 15496 Z= 0.272 Chirality : 0.041 0.132 1728 Planarity : 0.005 0.049 1964 Dihedral : 3.454 12.450 1516 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.06 % Allowed : 22.29 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.00 (0.23), residues: 1344 helix: 1.64 (0.17), residues: 940 sheet: -0.04 (0.79), residues: 40 loop : 0.89 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 170 TYR 0.019 0.001 TYR D 161 PHE 0.014 0.001 PHE A 406 TRP 0.009 0.001 TRP B 436 HIS 0.001 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00368 (11436) covalent geometry : angle 0.52489 (15496) hydrogen bonds : bond 0.03416 ( 660) hydrogen bonds : angle 3.64265 ( 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 150 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 198 ARG cc_start: 0.6036 (OUTLIER) cc_final: 0.5664 (mtt90) REVERT: A 199 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7255 (mm-30) REVERT: A 222 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7260 (tp) REVERT: B 199 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: B 222 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7292 (tp) REVERT: C 170 ARG cc_start: 0.8291 (mmt-90) cc_final: 0.8059 (mmt-90) REVERT: C 198 ARG cc_start: 0.5994 (OUTLIER) cc_final: 0.5616 (mtt90) REVERT: C 199 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7260 (mm-30) REVERT: C 222 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7235 (tp) REVERT: D 173 VAL cc_start: 0.8805 (t) cc_final: 0.8555 (m) REVERT: D 199 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7215 (mt-10) REVERT: D 222 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7325 (tp) outliers start: 25 outliers final: 13 residues processed: 139 average time/residue: 0.3373 time to fit residues: 53.3282 Evaluate side-chains 139 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 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 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 184 ILE 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: 1.9990 chunk 75 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.190919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.135750 restraints weight = 11474.306| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.92 r_work: 0.2971 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2384 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= 0.124 Angle : 0.508 7.500 15496 Z= 0.262 Chirality : 0.040 0.130 1728 Planarity : 0.005 0.049 1964 Dihedral : 3.388 12.412 1516 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.30 % Allowed : 22.53 % Favored : 75.16 % 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: 2.07 (0.23), residues: 1344 helix: 1.71 (0.17), residues: 940 sheet: 0.06 (0.80), residues: 40 loop : 0.88 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 170 TYR 0.019 0.001 TYR D 161 PHE 0.014 0.001 PHE D 406 TRP 0.008 0.001 TRP A 436 HIS 0.001 0.000 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00304 (11436) covalent geometry : angle 0.50835 (15496) hydrogen bonds : bond 0.03250 ( 660) hydrogen bonds : angle 3.58023 ( 1920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4185.79 seconds wall clock time: 72 minutes 1.86 seconds (4321.86 seconds total)