Starting phenix.real_space_refine on Wed Aug 5 18:47:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e4b_47504/08_2026/9e4b_47504.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e4b_47504/08_2026/9e4b_47504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e4b_47504/08_2026/9e4b_47504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e4b_47504/08_2026/9e4b_47504.map" model { file = "/net/cci-nas-00/data/ceres_data/9e4b_47504/08_2026/9e4b_47504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e4b_47504/08_2026/9e4b_47504.cif" } resolution = 3.09 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= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 6945 2.51 5 N 1782 2.21 5 O 2028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10842 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3614 Classifications: {'peptide': 451} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 432} Restraints were copied for chains: B, C Time building chain proxies: 2.75, per 1000 atoms: 0.25 Number of scatterers: 10842 At special positions: 0 Unit cell: (97.904, 98.748, 131.664, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2028 8.00 N 1782 7.00 C 6945 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 314 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 314 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 314 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 337 " distance=2.03 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: 0.81 Conformation dependent library (CDL) restraints added in 346.2 milliseconds 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 12 sheets defined 41.7% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.833A pdb=" N ILE A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 29 through 34' Processing helix chain 'A' and resid 40 through 70 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 338 through 345 removed outlier: 4.110A pdb=" N LYS A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 397 through 404 removed outlier: 3.605A pdb=" N GLY A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 443 Processing helix chain 'A' and resid 446 through 465 Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.834A pdb=" N ILE B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'B' and resid 40 through 70 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 338 through 345 removed outlier: 4.110A pdb=" N LYS B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 356 Processing helix chain 'B' and resid 386 through 394 Processing helix chain 'B' and resid 397 through 404 removed outlier: 3.606A pdb=" N GLY B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 443 Processing helix chain 'B' and resid 446 through 465 Processing helix chain 'C' and resid 17 through 25 Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.833A pdb=" N ILE C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 29 through 34' Processing helix chain 'C' and resid 40 through 70 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 338 through 345 removed outlier: 4.109A pdb=" N LYS C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 356 Processing helix chain 'C' and resid 386 through 394 Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.605A pdb=" N GLY C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 443 Processing helix chain 'C' and resid 446 through 465 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 81 removed outlier: 13.118A pdb=" N ASN A 416 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N CYS A 275 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N GLU A 418 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU A 277 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE A 420 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG A 279 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLN A 422 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE A 281 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N LYS A 424 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 178 removed outlier: 6.248A pdb=" N LEU A 169 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASP A 223 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE A 269 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 189 removed outlier: 6.607A pdb=" N LYS A 193 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASN A 94 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 245 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 81 removed outlier: 13.118A pdb=" N ASN B 416 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N CYS B 275 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N GLU B 418 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLU B 277 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE B 420 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG B 279 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLN B 422 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE B 281 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N LYS B 424 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 177 through 178 removed outlier: 6.247A pdb=" N LEU B 169 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASP B 223 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE B 269 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'B' and resid 184 through 189 removed outlier: 6.608A pdb=" N LYS B 193 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASN B 94 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 245 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 81 removed outlier: 13.118A pdb=" N ASN C 416 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N CYS C 275 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N GLU C 418 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU C 277 " --> pdb=" O GLU C 418 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE C 420 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG C 279 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLN C 422 " --> pdb=" O ARG C 279 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE C 281 " --> pdb=" O GLN C 422 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N LYS C 424 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 177 through 178 removed outlier: 6.248A pdb=" N LEU C 169 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASP C 223 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE C 269 " --> pdb=" O ILE C 405 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB3, first strand: chain 'C' and resid 184 through 189 removed outlier: 6.608A pdb=" N LYS C 193 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASN C 94 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE C 245 " --> pdb=" O VAL C 265 " (cutoff:3.500A) 525 hydrogen bonds defined for protein. 1476 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: 1.90 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3516 1.35 - 1.46: 2639 1.46 - 1.58: 4825 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 11100 Sorted by residual: bond pdb=" CA ILE C 381 " pdb=" CB ILE C 381 " ideal model delta sigma weight residual 1.547 1.538 0.009 1.10e-02 8.26e+03 6.46e-01 bond pdb=" CA ILE A 381 " pdb=" CB ILE A 381 " ideal model delta sigma weight residual 1.547 1.538 0.009 1.10e-02 8.26e+03 6.11e-01 bond pdb=" CA ILE B 381 " pdb=" CB ILE B 381 " ideal model delta sigma weight residual 1.547 1.539 0.008 1.10e-02 8.26e+03 5.31e-01 bond pdb=" CA VAL B 273 " pdb=" CB VAL B 273 " ideal model delta sigma weight residual 1.540 1.531 0.009 1.36e-02 5.41e+03 4.55e-01 bond pdb=" CA VAL C 273 " pdb=" CB VAL C 273 " ideal model delta sigma weight residual 1.540 1.531 0.009 1.36e-02 5.41e+03 4.54e-01 ... (remaining 11095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 14597 0.93 - 1.87: 301 1.87 - 2.80: 72 2.80 - 3.74: 27 3.74 - 4.67: 12 Bond angle restraints: 15009 Sorted by residual: angle pdb=" N ILE A 443 " pdb=" CA ILE A 443 " pdb=" C ILE A 443 " ideal model delta sigma weight residual 113.47 110.26 3.21 1.01e+00 9.80e-01 1.01e+01 angle pdb=" N ILE C 443 " pdb=" CA ILE C 443 " pdb=" C ILE C 443 " ideal model delta sigma weight residual 113.47 110.26 3.21 1.01e+00 9.80e-01 1.01e+01 angle pdb=" N ILE B 443 " pdb=" CA ILE B 443 " pdb=" C ILE B 443 " ideal model delta sigma weight residual 113.47 110.30 3.17 1.01e+00 9.80e-01 9.83e+00 angle pdb=" CA ILE B 381 " pdb=" C ILE B 381 " pdb=" N PRO B 382 " ideal model delta sigma weight residual 117.33 119.34 -2.01 1.01e+00 9.80e-01 3.97e+00 angle pdb=" CA ILE C 381 " pdb=" C ILE C 381 " pdb=" N PRO C 382 " ideal model delta sigma weight residual 117.33 119.32 -1.99 1.01e+00 9.80e-01 3.90e+00 ... (remaining 15004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6133 17.88 - 35.76: 431 35.76 - 53.64: 102 53.64 - 71.52: 30 71.52 - 89.41: 9 Dihedral angle restraints: 6705 sinusoidal: 2742 harmonic: 3963 Sorted by residual: dihedral pdb=" CB CYS A 290 " pdb=" SG CYS A 290 " pdb=" SG CYS A 367 " pdb=" CB CYS A 367 " ideal model delta sinusoidal sigma weight residual -86.00 -149.45 63.45 1 1.00e+01 1.00e-02 5.31e+01 dihedral pdb=" CB CYS C 290 " pdb=" SG CYS C 290 " pdb=" SG CYS C 367 " pdb=" CB CYS C 367 " ideal model delta sinusoidal sigma weight residual -86.00 -149.45 63.45 1 1.00e+01 1.00e-02 5.31e+01 dihedral pdb=" CB CYS B 290 " pdb=" SG CYS B 290 " pdb=" SG CYS B 367 " pdb=" CB CYS B 367 " ideal model delta sinusoidal sigma weight residual -86.00 -149.43 63.43 1 1.00e+01 1.00e-02 5.31e+01 ... (remaining 6702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 999 0.027 - 0.054: 426 0.054 - 0.081: 115 0.081 - 0.108: 54 0.108 - 0.135: 26 Chirality restraints: 1620 Sorted by residual: chirality pdb=" CA ILE B 124 " pdb=" N ILE B 124 " pdb=" C ILE B 124 " pdb=" CB ILE B 124 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE C 124 " pdb=" N ILE C 124 " pdb=" C ILE C 124 " pdb=" CB ILE C 124 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 1617 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 284 " -0.014 5.00e-02 4.00e+02 2.18e-02 7.61e-01 pdb=" N PRO B 285 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO B 285 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 285 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 284 " 0.014 5.00e-02 4.00e+02 2.18e-02 7.59e-01 pdb=" N PRO A 285 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 284 " -0.014 5.00e-02 4.00e+02 2.17e-02 7.55e-01 pdb=" N PRO C 285 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO C 285 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 285 " -0.012 5.00e-02 4.00e+02 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2619 2.79 - 3.32: 10174 3.32 - 3.85: 17785 3.85 - 4.37: 21543 4.37 - 4.90: 36715 Nonbonded interactions: 88836 Sorted by model distance: nonbonded pdb=" OE1 GLU A 235 " pdb=" OH TYR B 389 " model vdw 2.265 3.040 nonbonded pdb=" OE1 GLU B 235 " pdb=" OH TYR C 389 " model vdw 2.281 3.040 nonbonded pdb=" O THR A 236 " pdb=" OG1 THR A 239 " model vdw 2.306 3.040 nonbonded pdb=" O THR C 236 " pdb=" OG1 THR C 239 " model vdw 2.307 3.040 nonbonded pdb=" O THR B 236 " pdb=" OG1 THR B 239 " model vdw 2.307 3.040 ... (remaining 88831 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.730 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.130 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 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 : 0.001 0.024 11121 Z= 0.072 Angle : 0.397 4.674 15051 Z= 0.212 Chirality : 0.036 0.135 1620 Planarity : 0.002 0.022 1944 Dihedral : 13.848 89.406 4098 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.31 (0.23), residues: 1347 helix: 1.49 (0.25), residues: 459 sheet: -0.18 (0.30), residues: 288 loop : 1.18 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 326 TYR 0.009 0.001 TYR B 426 PHE 0.005 0.001 PHE C 263 TRP 0.002 0.000 TRP A 233 HIS 0.002 0.000 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00144 / 0.07 (11100) covalent geometry : angle 0.39470 / 0.21 (15009) SS BOND : bond 0.00121 / 0.06 ( 21) SS BOND : angle 0.88144 / 0.59 ( 42) hydrogen bonds : bond 0.23402 / 16.03 ( 525) hydrogen bonds : angle 8.47271 / 5.96 ( 1476) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9086 (tt) cc_final: 0.8816 (mm) REVERT: A 136 GLU cc_start: 0.8965 (tt0) cc_final: 0.8689 (tm-30) REVERT: A 210 MET cc_start: 0.8493 (mpp) cc_final: 0.8293 (mpp) REVERT: A 375 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8275 (mt-10) REVERT: A 451 LEU cc_start: 0.8913 (tt) cc_final: 0.8548 (mt) REVERT: A 458 TYR cc_start: 0.8371 (t80) cc_final: 0.7875 (t80) REVERT: B 48 LEU cc_start: 0.9222 (tt) cc_final: 0.9015 (tp) REVERT: B 136 GLU cc_start: 0.8968 (tt0) cc_final: 0.8678 (tm-30) REVERT: B 210 MET cc_start: 0.8462 (mpp) cc_final: 0.8253 (mpp) REVERT: B 375 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8299 (mt-10) REVERT: B 451 LEU cc_start: 0.8893 (tt) cc_final: 0.8628 (mt) REVERT: C 41 LEU cc_start: 0.9149 (tp) cc_final: 0.8934 (tp) REVERT: C 136 GLU cc_start: 0.8958 (tt0) cc_final: 0.8707 (tm-30) REVERT: C 330 MET cc_start: 0.9172 (mtt) cc_final: 0.8958 (mtt) REVERT: C 375 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8222 (mt-10) REVERT: C 451 LEU cc_start: 0.8936 (tt) cc_final: 0.8696 (mt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1215 time to fit residues: 23.2176 Evaluate side-chains 82 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 chunk 55 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3228 r_free = 0.3228 target = 0.084282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.060774 restraints weight = 20486.103| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.08 r_work: 0.2605 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11121 Z= 0.170 Angle : 0.509 4.915 15051 Z= 0.276 Chirality : 0.041 0.149 1620 Planarity : 0.003 0.022 1944 Dihedral : 3.872 15.574 1476 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.51 % Allowed : 5.75 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.55 (0.23), residues: 1347 helix: 1.97 (0.24), residues: 471 sheet: -0.04 (0.28), residues: 282 loop : 1.01 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 121 TYR 0.013 0.001 TYR A 282 PHE 0.007 0.001 PHE C 257 TRP 0.007 0.001 TRP B 233 HIS 0.003 0.001 HIS C 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (11100) covalent geometry : angle 0.50691 / 0.27 (15009) SS BOND : bond 0.00350 / 0.17 ( 21) SS BOND : angle 1.03679 / 0.69 ( 42) hydrogen bonds : bond 0.04120 / 2.90 ( 525) hydrogen bonds : angle 5.73665 / 4.03 ( 1476) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.339 Fit side-chains REVERT: A 48 LEU cc_start: 0.8948 (tt) cc_final: 0.8700 (mm) REVERT: A 136 GLU cc_start: 0.9075 (tt0) cc_final: 0.8820 (tm-30) REVERT: A 330 MET cc_start: 0.9344 (mtt) cc_final: 0.9082 (mtt) REVERT: A 364 GLU cc_start: 0.8137 (pm20) cc_final: 0.7813 (pm20) REVERT: A 375 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8029 (mt-10) REVERT: A 409 ASP cc_start: 0.8672 (t0) cc_final: 0.8239 (t0) REVERT: A 451 LEU cc_start: 0.8566 (tt) cc_final: 0.8313 (mp) REVERT: A 458 TYR cc_start: 0.8343 (t80) cc_final: 0.7847 (t80) REVERT: B 136 GLU cc_start: 0.9100 (tt0) cc_final: 0.8833 (tm-30) REVERT: B 330 MET cc_start: 0.9273 (mtt) cc_final: 0.9071 (mtt) REVERT: B 375 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7883 (mt-10) REVERT: B 409 ASP cc_start: 0.8639 (t0) cc_final: 0.8097 (t0) REVERT: B 451 LEU cc_start: 0.8554 (tt) cc_final: 0.8255 (mp) REVERT: B 458 TYR cc_start: 0.8293 (t80) cc_final: 0.7872 (t80) REVERT: C 136 GLU cc_start: 0.9094 (tt0) cc_final: 0.8849 (tm-30) REVERT: C 201 ARG cc_start: 0.8550 (mtm180) cc_final: 0.8309 (ttp-110) REVERT: C 330 MET cc_start: 0.9224 (mtt) cc_final: 0.8936 (mtt) REVERT: C 375 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7855 (mt-10) REVERT: C 409 ASP cc_start: 0.8660 (t0) cc_final: 0.8279 (t0) REVERT: C 451 LEU cc_start: 0.8615 (tt) cc_final: 0.8317 (mp) outliers start: 6 outliers final: 1 residues processed: 93 average time/residue: 0.1199 time to fit residues: 15.5177 Evaluate side-chains 79 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 365 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 67 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3190 r_free = 0.3190 target = 0.082136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.059053 restraints weight = 20557.359| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.03 r_work: 0.2574 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 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 : 0.004 0.039 11121 Z= 0.176 Angle : 0.485 4.870 15051 Z= 0.259 Chirality : 0.040 0.141 1620 Planarity : 0.003 0.022 1944 Dihedral : 3.941 15.340 1476 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.59 % Allowed : 8.71 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.51 (0.23), residues: 1347 helix: 2.44 (0.24), residues: 453 sheet: -0.41 (0.27), residues: 288 loop : 0.77 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.010 0.001 TYR B 195 PHE 0.007 0.001 PHE A 21 TRP 0.003 0.001 TRP C 46 HIS 0.003 0.001 HIS C 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (11100) covalent geometry : angle 0.48253 / 0.26 (15009) SS BOND : bond 0.00381 / 0.21 ( 21) SS BOND : angle 0.96619 / 0.64 ( 42) hydrogen bonds : bond 0.03634 / 2.54 ( 525) hydrogen bonds : angle 5.34482 / 3.75 ( 1476) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.433 Fit side-chains REVERT: A 48 LEU cc_start: 0.8897 (tt) cc_final: 0.8668 (mm) REVERT: A 136 GLU cc_start: 0.9136 (tt0) cc_final: 0.8876 (tm-30) REVERT: A 330 MET cc_start: 0.9368 (mtt) cc_final: 0.9118 (mtt) REVERT: A 375 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8107 (mt-10) REVERT: A 409 ASP cc_start: 0.8718 (t0) cc_final: 0.8337 (t0) REVERT: A 451 LEU cc_start: 0.8581 (tt) cc_final: 0.8318 (mt) REVERT: A 458 TYR cc_start: 0.8402 (t80) cc_final: 0.7892 (t80) REVERT: B 136 GLU cc_start: 0.9167 (tt0) cc_final: 0.8881 (tm-30) REVERT: B 330 MET cc_start: 0.9380 (mtt) cc_final: 0.9064 (mtt) REVERT: B 375 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7969 (mt-10) REVERT: B 409 ASP cc_start: 0.8649 (t0) cc_final: 0.8121 (t0) REVERT: B 451 LEU cc_start: 0.8581 (tt) cc_final: 0.8278 (mp) REVERT: B 458 TYR cc_start: 0.8356 (t80) cc_final: 0.7928 (t80) REVERT: C 41 LEU cc_start: 0.8861 (tp) cc_final: 0.8638 (tp) REVERT: C 136 GLU cc_start: 0.9122 (tt0) cc_final: 0.8862 (tm-30) REVERT: C 330 MET cc_start: 0.9254 (mtt) cc_final: 0.8914 (mtt) REVERT: C 375 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7905 (mt-10) REVERT: C 409 ASP cc_start: 0.8756 (t0) cc_final: 0.8296 (t0) REVERT: C 451 LEU cc_start: 0.8626 (tt) cc_final: 0.8304 (mp) REVERT: C 458 TYR cc_start: 0.8398 (t80) cc_final: 0.7907 (t80) outliers start: 7 outliers final: 3 residues processed: 81 average time/residue: 0.1116 time to fit residues: 12.8278 Evaluate side-chains 76 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 452 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 88 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.3186 r_free = 0.3186 target = 0.081967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.058345 restraints weight = 20625.114| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 3.07 r_work: 0.2551 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11121 Z= 0.186 Angle : 0.481 4.845 15051 Z= 0.256 Chirality : 0.040 0.140 1620 Planarity : 0.003 0.024 1944 Dihedral : 3.996 15.173 1476 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.18 % Allowed : 10.15 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.41 (0.23), residues: 1347 helix: 2.51 (0.24), residues: 453 sheet: -0.59 (0.26), residues: 297 loop : 0.68 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 201 TYR 0.010 0.001 TYR A 195 PHE 0.007 0.001 PHE C 21 TRP 0.003 0.001 TRP A 233 HIS 0.003 0.001 HIS C 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (11100) covalent geometry : angle 0.47878 / 0.25 (15009) SS BOND : bond 0.00387 / 0.21 ( 21) SS BOND : angle 0.95708 / 0.64 ( 42) hydrogen bonds : bond 0.03304 / 2.30 ( 525) hydrogen bonds : angle 5.17630 / 3.63 ( 1476) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8882 (tt) REVERT: A 48 LEU cc_start: 0.8879 (tt) cc_final: 0.8646 (mm) REVERT: A 330 MET cc_start: 0.9408 (mtt) cc_final: 0.8987 (mtm) REVERT: A 354 VAL cc_start: 0.9188 (t) cc_final: 0.8954 (p) REVERT: A 375 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8173 (mt-10) REVERT: A 409 ASP cc_start: 0.8839 (t0) cc_final: 0.8156 (t0) REVERT: A 451 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8310 (mt) REVERT: A 458 TYR cc_start: 0.8424 (t80) cc_final: 0.7898 (t80) REVERT: B 136 GLU cc_start: 0.9194 (tt0) cc_final: 0.8897 (tm-30) REVERT: B 330 MET cc_start: 0.9392 (mtt) cc_final: 0.9066 (mtt) REVERT: B 354 VAL cc_start: 0.9218 (t) cc_final: 0.8968 (p) REVERT: B 375 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8118 (mt-10) REVERT: B 409 ASP cc_start: 0.8758 (t0) cc_final: 0.8062 (t0) REVERT: B 451 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8239 (mp) REVERT: B 458 TYR cc_start: 0.8389 (t80) cc_final: 0.7925 (t80) REVERT: C 41 LEU cc_start: 0.8833 (tp) cc_final: 0.8607 (tp) REVERT: C 136 GLU cc_start: 0.9161 (tt0) cc_final: 0.8891 (tm-30) REVERT: C 330 MET cc_start: 0.9276 (mtt) cc_final: 0.8932 (mtt) REVERT: C 375 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8005 (mt-10) REVERT: C 409 ASP cc_start: 0.8823 (t0) cc_final: 0.8341 (t0) REVERT: C 451 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8261 (mp) REVERT: C 458 TYR cc_start: 0.8427 (t80) cc_final: 0.7917 (t80) outliers start: 14 outliers final: 5 residues processed: 84 average time/residue: 0.1206 time to fit residues: 14.0782 Evaluate side-chains 85 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3242 r_free = 0.3242 target = 0.083514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.059208 restraints weight = 20854.278| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.28 r_work: 0.2573 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11121 Z= 0.137 Angle : 0.467 6.285 15051 Z= 0.247 Chirality : 0.039 0.137 1620 Planarity : 0.003 0.023 1944 Dihedral : 3.963 19.157 1476 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.44 % Allowed : 10.49 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.48 (0.23), residues: 1347 helix: 2.66 (0.24), residues: 453 sheet: -0.66 (0.26), residues: 297 loop : 0.70 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 121 TYR 0.009 0.001 TYR A 195 PHE 0.006 0.001 PHE C 442 TRP 0.003 0.001 TRP B 233 HIS 0.004 0.001 HIS C 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (11100) covalent geometry : angle 0.46038 / 0.24 (15009) SS BOND : bond 0.00313 / 0.16 ( 21) SS BOND : angle 1.52882 / 1.02 ( 42) hydrogen bonds : bond 0.03102 / 2.16 ( 525) hydrogen bonds : angle 5.05721 / 3.54 ( 1476) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8936 (tt) REVERT: A 48 LEU cc_start: 0.8924 (tt) cc_final: 0.8689 (mm) REVERT: A 330 MET cc_start: 0.9471 (mtt) cc_final: 0.9134 (mtt) REVERT: A 354 VAL cc_start: 0.9242 (t) cc_final: 0.9009 (p) REVERT: A 364 GLU cc_start: 0.8249 (pm20) cc_final: 0.7791 (pm20) REVERT: A 375 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8234 (mt-10) REVERT: A 409 ASP cc_start: 0.8859 (t0) cc_final: 0.8236 (t0) REVERT: A 451 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8419 (mt) REVERT: A 458 TYR cc_start: 0.8474 (t80) cc_final: 0.7960 (t80) REVERT: B 330 MET cc_start: 0.9432 (mtt) cc_final: 0.9121 (mtt) REVERT: B 354 VAL cc_start: 0.9259 (t) cc_final: 0.9017 (p) REVERT: B 375 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8228 (mt-10) REVERT: B 409 ASP cc_start: 0.8815 (t0) cc_final: 0.8151 (t0) REVERT: B 451 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8377 (mp) REVERT: B 458 TYR cc_start: 0.8425 (t80) cc_final: 0.7955 (t80) REVERT: C 41 LEU cc_start: 0.8876 (tp) cc_final: 0.8658 (tp) REVERT: C 330 MET cc_start: 0.9354 (mtt) cc_final: 0.9040 (mtt) REVERT: C 375 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8113 (mt-10) REVERT: C 409 ASP cc_start: 0.8819 (t0) cc_final: 0.8399 (t0) REVERT: C 451 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8473 (mt) REVERT: C 458 TYR cc_start: 0.8486 (t80) cc_final: 0.7980 (t80) outliers start: 17 outliers final: 6 residues processed: 86 average time/residue: 0.1099 time to fit residues: 13.1602 Evaluate side-chains 85 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 10 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3253 r_free = 0.3253 target = 0.084138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.059965 restraints weight = 20979.413| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.27 r_work: 0.2592 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11121 Z= 0.114 Angle : 0.452 6.837 15051 Z= 0.235 Chirality : 0.039 0.138 1620 Planarity : 0.003 0.024 1944 Dihedral : 3.825 15.178 1476 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.18 % Allowed : 10.58 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.57 (0.23), residues: 1347 helix: 2.80 (0.24), residues: 453 sheet: -0.68 (0.26), residues: 297 loop : 0.74 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 121 TYR 0.008 0.001 TYR A 195 PHE 0.005 0.001 PHE B 442 TRP 0.002 0.001 TRP C 233 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (11100) covalent geometry : angle 0.44791 / 0.23 (15009) SS BOND : bond 0.00279 / 0.14 ( 21) SS BOND : angle 1.19210 / 0.80 ( 42) hydrogen bonds : bond 0.02877 / 1.99 ( 525) hydrogen bonds : angle 4.96053 / 3.47 ( 1476) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.252 Fit side-chains REVERT: A 30 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8929 (tt) REVERT: A 38 ARG cc_start: 0.8483 (ppt170) cc_final: 0.8244 (ptm160) REVERT: A 48 LEU cc_start: 0.8889 (tt) cc_final: 0.8667 (mm) REVERT: A 330 MET cc_start: 0.9442 (mtt) cc_final: 0.9104 (mtt) REVERT: A 354 VAL cc_start: 0.9248 (t) cc_final: 0.9034 (p) REVERT: A 364 GLU cc_start: 0.8245 (pm20) cc_final: 0.8035 (pm20) REVERT: A 375 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8274 (mt-10) REVERT: A 409 ASP cc_start: 0.8854 (t0) cc_final: 0.8163 (t0) REVERT: A 451 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8441 (mt) REVERT: A 458 TYR cc_start: 0.8471 (t80) cc_final: 0.7962 (t80) REVERT: B 210 MET cc_start: 0.8731 (mpp) cc_final: 0.8494 (mpp) REVERT: B 330 MET cc_start: 0.9403 (mtt) cc_final: 0.9090 (mtt) REVERT: B 354 VAL cc_start: 0.9264 (t) cc_final: 0.9028 (p) REVERT: B 375 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8278 (mt-10) REVERT: B 409 ASP cc_start: 0.8783 (t0) cc_final: 0.8041 (t0) REVERT: B 451 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8377 (mp) REVERT: B 458 TYR cc_start: 0.8468 (t80) cc_final: 0.7978 (t80) REVERT: C 330 MET cc_start: 0.9321 (mtt) cc_final: 0.8999 (mtt) REVERT: C 354 VAL cc_start: 0.9249 (t) cc_final: 0.9025 (p) REVERT: C 375 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8161 (mt-10) REVERT: C 409 ASP cc_start: 0.8816 (t0) cc_final: 0.8379 (t0) REVERT: C 451 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8376 (mp) REVERT: C 458 TYR cc_start: 0.8474 (t80) cc_final: 0.7963 (t80) outliers start: 14 outliers final: 7 residues processed: 85 average time/residue: 0.1220 time to fit residues: 14.0290 Evaluate side-chains 87 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 76 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.4126 > 50:) chunk 127 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3206 r_free = 0.3206 target = 0.082235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.058500 restraints weight = 20806.648| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 3.22 r_work: 0.2525 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11121 Z= 0.260 Angle : 0.533 6.349 15051 Z= 0.277 Chirality : 0.041 0.140 1620 Planarity : 0.003 0.024 1944 Dihedral : 4.137 16.060 1476 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.69 % Allowed : 11.17 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1347 helix: 2.63 (0.24), residues: 453 sheet: -0.73 (0.26), residues: 297 loop : 0.72 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 121 TYR 0.012 0.001 TYR A 195 PHE 0.009 0.001 PHE A 21 TRP 0.007 0.001 TRP C 46 HIS 0.005 0.001 HIS C 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.26 (11100) covalent geometry : angle 0.52983 / 0.28 (15009) SS BOND : bond 0.00438 / 0.23 ( 21) SS BOND : angle 1.26320 / 0.83 ( 42) hydrogen bonds : bond 0.03318 / 2.31 ( 525) hydrogen bonds : angle 5.11255 / 3.58 ( 1476) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8930 (tt) REVERT: A 48 LEU cc_start: 0.8999 (tt) cc_final: 0.8766 (mm) REVERT: A 330 MET cc_start: 0.9471 (mtt) cc_final: 0.9126 (mtt) REVERT: A 354 VAL cc_start: 0.9302 (t) cc_final: 0.9092 (p) REVERT: A 364 GLU cc_start: 0.8335 (pm20) cc_final: 0.7876 (pm20) REVERT: A 375 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8369 (mt-10) REVERT: A 409 ASP cc_start: 0.8985 (t0) cc_final: 0.8455 (t0) REVERT: A 451 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8514 (mt) REVERT: A 458 TYR cc_start: 0.8545 (t80) cc_final: 0.8005 (t80) REVERT: B 129 MET cc_start: 0.7383 (pmm) cc_final: 0.7179 (pmm) REVERT: B 330 MET cc_start: 0.9443 (mtt) cc_final: 0.9100 (mtt) REVERT: B 354 VAL cc_start: 0.9321 (t) cc_final: 0.9085 (p) REVERT: B 375 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8287 (mt-10) REVERT: B 409 ASP cc_start: 0.8905 (t0) cc_final: 0.8129 (t0) REVERT: B 451 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8502 (mt) REVERT: B 458 TYR cc_start: 0.8535 (t80) cc_final: 0.8015 (t80) REVERT: C 354 VAL cc_start: 0.9316 (t) cc_final: 0.9107 (p) REVERT: C 375 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8138 (mt-10) REVERT: C 409 ASP cc_start: 0.8909 (t0) cc_final: 0.8404 (t0) REVERT: C 451 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8487 (mt) REVERT: C 458 TYR cc_start: 0.8553 (t80) cc_final: 0.8009 (t80) outliers start: 20 outliers final: 7 residues processed: 81 average time/residue: 0.0913 time to fit residues: 10.3167 Evaluate side-chains 82 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 61 optimal weight: 0.0980 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3207 r_free = 0.3207 target = 0.082797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.058757 restraints weight = 20623.140| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.15 r_work: 0.2569 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11121 Z= 0.124 Angle : 0.470 9.640 15051 Z= 0.243 Chirality : 0.039 0.136 1620 Planarity : 0.003 0.024 1944 Dihedral : 3.917 14.395 1476 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.52 % Allowed : 11.00 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.48 (0.23), residues: 1347 helix: 2.76 (0.24), residues: 453 sheet: -0.79 (0.26), residues: 297 loop : 0.68 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 121 TYR 0.008 0.001 TYR A 195 PHE 0.008 0.001 PHE B 442 TRP 0.007 0.001 TRP C 46 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (11100) covalent geometry : angle 0.46740 / 0.24 (15009) SS BOND : bond 0.00316 / 0.17 ( 21) SS BOND : angle 1.02658 / 0.68 ( 42) hydrogen bonds : bond 0.02927 / 2.03 ( 525) hydrogen bonds : angle 4.99932 / 3.50 ( 1476) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8782 (tt) REVERT: A 38 ARG cc_start: 0.8550 (ppt170) cc_final: 0.8281 (ptm160) REVERT: A 48 LEU cc_start: 0.8890 (tt) cc_final: 0.8660 (mm) REVERT: A 201 ARG cc_start: 0.8082 (ptm-80) cc_final: 0.7719 (ppt170) REVERT: A 330 MET cc_start: 0.9431 (mtt) cc_final: 0.9059 (mtt) REVERT: A 354 VAL cc_start: 0.9227 (t) cc_final: 0.9016 (p) REVERT: A 364 GLU cc_start: 0.8287 (pm20) cc_final: 0.7784 (pm20) REVERT: A 375 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8237 (mt-10) REVERT: A 409 ASP cc_start: 0.8864 (t0) cc_final: 0.8307 (t0) REVERT: A 451 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8318 (mt) REVERT: A 458 TYR cc_start: 0.8438 (t80) cc_final: 0.7922 (t80) REVERT: B 330 MET cc_start: 0.9369 (mtt) cc_final: 0.9005 (mtt) REVERT: B 354 VAL cc_start: 0.9240 (t) cc_final: 0.9012 (p) REVERT: B 375 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8251 (mt-10) REVERT: B 409 ASP cc_start: 0.8779 (t0) cc_final: 0.7987 (t0) REVERT: B 451 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8272 (mp) REVERT: B 458 TYR cc_start: 0.8428 (t80) cc_final: 0.7894 (t80) REVERT: C 354 VAL cc_start: 0.9245 (t) cc_final: 0.9034 (p) REVERT: C 375 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8054 (mt-10) REVERT: C 409 ASP cc_start: 0.8803 (t0) cc_final: 0.8289 (t0) REVERT: C 451 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8264 (mp) REVERT: C 458 TYR cc_start: 0.8439 (t80) cc_final: 0.7908 (t80) outliers start: 18 outliers final: 7 residues processed: 81 average time/residue: 0.1127 time to fit residues: 12.7802 Evaluate side-chains 85 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 123 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3206 r_free = 0.3206 target = 0.082735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.058569 restraints weight = 20756.564| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.17 r_work: 0.2566 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11121 Z= 0.141 Angle : 0.494 12.636 15051 Z= 0.250 Chirality : 0.039 0.147 1620 Planarity : 0.003 0.024 1944 Dihedral : 3.898 14.167 1476 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.52 % Allowed : 11.34 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.32 (0.23), residues: 1347 helix: 2.44 (0.24), residues: 471 sheet: -0.77 (0.28), residues: 279 loop : 0.59 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 121 TYR 0.009 0.001 TYR A 195 PHE 0.006 0.001 PHE B 442 TRP 0.007 0.001 TRP C 46 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (11100) covalent geometry : angle 0.49140 / 0.25 (15009) SS BOND : bond 0.00321 / 0.17 ( 21) SS BOND : angle 1.00916 / 0.67 ( 42) hydrogen bonds : bond 0.02951 / 2.05 ( 525) hydrogen bonds : angle 4.99077 / 3.49 ( 1476) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8799 (tt) REVERT: A 48 LEU cc_start: 0.8891 (tt) cc_final: 0.8657 (mm) REVERT: A 330 MET cc_start: 0.9425 (mtt) cc_final: 0.9061 (mtt) REVERT: A 354 VAL cc_start: 0.9236 (t) cc_final: 0.9026 (p) REVERT: A 364 GLU cc_start: 0.8309 (pm20) cc_final: 0.7801 (pm20) REVERT: A 375 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8267 (mt-10) REVERT: A 409 ASP cc_start: 0.8869 (t0) cc_final: 0.8302 (t0) REVERT: A 451 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8323 (mt) REVERT: A 458 TYR cc_start: 0.8451 (t80) cc_final: 0.7933 (t80) REVERT: B 330 MET cc_start: 0.9356 (mtt) cc_final: 0.8992 (mtt) REVERT: B 354 VAL cc_start: 0.9241 (t) cc_final: 0.9013 (p) REVERT: B 375 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8279 (mt-10) REVERT: B 409 ASP cc_start: 0.8803 (t0) cc_final: 0.8213 (t0) REVERT: B 451 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8286 (mp) REVERT: B 458 TYR cc_start: 0.8434 (t80) cc_final: 0.7899 (t80) REVERT: C 354 VAL cc_start: 0.9239 (t) cc_final: 0.9030 (p) REVERT: C 375 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8108 (mt-10) REVERT: C 409 ASP cc_start: 0.8807 (t0) cc_final: 0.8276 (t0) REVERT: C 451 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8272 (mp) REVERT: C 458 TYR cc_start: 0.8456 (t80) cc_final: 0.7924 (t80) outliers start: 18 outliers final: 10 residues processed: 83 average time/residue: 0.1261 time to fit residues: 14.6909 Evaluate side-chains 87 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 78 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 0.0060 chunk 95 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.083028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.059035 restraints weight = 20604.849| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.15 r_work: 0.2572 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11121 Z= 0.129 Angle : 0.495 11.459 15051 Z= 0.247 Chirality : 0.040 0.285 1620 Planarity : 0.003 0.024 1944 Dihedral : 3.845 14.050 1476 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.44 % Allowed : 11.68 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.30 (0.23), residues: 1347 helix: 2.42 (0.24), residues: 471 sheet: -0.78 (0.27), residues: 279 loop : 0.57 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 121 TYR 0.008 0.001 TYR A 195 PHE 0.005 0.001 PHE C 442 TRP 0.005 0.001 TRP B 46 HIS 0.002 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (11100) covalent geometry : angle 0.49291 / 0.25 (15009) SS BOND : bond 0.00305 / 0.16 ( 21) SS BOND : angle 0.96565 / 0.64 ( 42) hydrogen bonds : bond 0.02884 / 1.99 ( 525) hydrogen bonds : angle 4.96267 / 3.47 ( 1476) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8805 (tt) REVERT: A 48 LEU cc_start: 0.8889 (tt) cc_final: 0.8656 (mm) REVERT: A 201 ARG cc_start: 0.8056 (ptm-80) cc_final: 0.7678 (ppt170) REVERT: A 330 MET cc_start: 0.9420 (mtt) cc_final: 0.9017 (mtt) REVERT: A 354 VAL cc_start: 0.9232 (t) cc_final: 0.9021 (p) REVERT: A 364 GLU cc_start: 0.8342 (pm20) cc_final: 0.7801 (pm20) REVERT: A 375 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8274 (mt-10) REVERT: A 409 ASP cc_start: 0.8867 (t0) cc_final: 0.8300 (t0) REVERT: A 451 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8369 (mt) REVERT: A 458 TYR cc_start: 0.8446 (t80) cc_final: 0.7927 (t80) REVERT: B 330 MET cc_start: 0.9362 (mtt) cc_final: 0.9005 (mtt) REVERT: B 354 VAL cc_start: 0.9245 (t) cc_final: 0.9018 (p) REVERT: B 375 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8288 (mt-10) REVERT: B 409 ASP cc_start: 0.8761 (t0) cc_final: 0.8175 (t0) REVERT: B 451 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8234 (mp) REVERT: B 458 TYR cc_start: 0.8437 (t80) cc_final: 0.7902 (t80) REVERT: C 354 VAL cc_start: 0.9247 (t) cc_final: 0.9035 (p) REVERT: C 375 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8117 (mt-10) REVERT: C 409 ASP cc_start: 0.8794 (t0) cc_final: 0.8274 (t0) REVERT: C 451 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8276 (mp) REVERT: C 458 TYR cc_start: 0.8444 (t80) cc_final: 0.7917 (t80) outliers start: 17 outliers final: 10 residues processed: 81 average time/residue: 0.1208 time to fit residues: 13.8534 Evaluate side-chains 86 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3207 r_free = 0.3207 target = 0.082782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.058752 restraints weight = 20671.813| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 3.15 r_work: 0.2565 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11121 Z= 0.143 Angle : 0.509 12.134 15051 Z= 0.252 Chirality : 0.039 0.220 1620 Planarity : 0.003 0.024 1944 Dihedral : 3.870 14.078 1476 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.27 % Allowed : 12.01 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.29 (0.23), residues: 1347 helix: 2.42 (0.24), residues: 471 sheet: -0.80 (0.27), residues: 279 loop : 0.57 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 121 TYR 0.009 0.001 TYR A 195 PHE 0.006 0.001 PHE C 21 TRP 0.007 0.001 TRP C 46 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (11100) covalent geometry : angle 0.50746 / 0.25 (15009) SS BOND : bond 0.00320 / 0.17 ( 21) SS BOND : angle 0.99124 / 0.66 ( 42) hydrogen bonds : bond 0.02941 / 2.03 ( 525) hydrogen bonds : angle 4.97363 / 3.49 ( 1476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1898.59 seconds wall clock time: 33 minutes 31.48 seconds (2011.48 seconds total)