Starting phenix.real_space_refine on Thu Sep 18 04:09:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eku_48137/09_2025/9eku_48137_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eku_48137/09_2025/9eku_48137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eku_48137/09_2025/9eku_48137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eku_48137/09_2025/9eku_48137.map" model { file = "/net/cci-nas-00/data/ceres_data/9eku_48137/09_2025/9eku_48137_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eku_48137/09_2025/9eku_48137_neut.cif" } resolution = 2.68 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 96 5.16 5 C 9152 2.51 5 N 2284 2.21 5 O 2424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13956 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3459 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 3 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'ZB4': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 3.34, per 1000 atoms: 0.24 Number of scatterers: 13956 At special positions: 0 Unit cell: (114.39, 114.39, 104.796, 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 96 16.00 O 2424 8.00 N 2284 7.00 C 9152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 166 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 166 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS D 253 " - pdb=" SG CYS D 284 " 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: 1.26 Conformation dependent library (CDL) restraints added in 654.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3256 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 61.9% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 66 through 106 removed outlier: 3.661A pdb=" N THR A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 138 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.636A pdb=" N LEU A 245 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 335 removed outlier: 3.548A pdb=" N VAL A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY A 332 " --> pdb=" O ASN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 377 removed outlier: 3.986A pdb=" N ILE A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 399 removed outlier: 4.097A pdb=" N CYS A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 387 " --> pdb=" O TYR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 407 removed outlier: 4.080A pdb=" N PHE A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 448 removed outlier: 3.764A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Proline residue: A 423 - end of helix removed outlier: 3.875A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 removed outlier: 4.155A pdb=" N ARG A 455 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 469 removed outlier: 3.503A pdb=" N ASN A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 482 Processing helix chain 'A' and resid 487 through 519 Processing helix chain 'B' and resid 66 through 106 removed outlier: 3.661A pdb=" N THR B 77 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 97 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 138 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.636A pdb=" N LEU B 245 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 335 removed outlier: 3.547A pdb=" N VAL B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 377 removed outlier: 3.987A pdb=" N ILE B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 399 removed outlier: 4.096A pdb=" N CYS B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 387 " --> pdb=" O TYR B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 407 removed outlier: 4.081A pdb=" N PHE B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 448 removed outlier: 3.763A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Proline residue: B 423 - end of helix removed outlier: 3.875A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 455 removed outlier: 4.155A pdb=" N ARG B 455 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 469 removed outlier: 3.503A pdb=" N ASN B 469 " --> pdb=" O PHE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 482 Processing helix chain 'B' and resid 487 through 519 Processing helix chain 'C' and resid 66 through 106 removed outlier: 3.662A pdb=" N THR C 77 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 97 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 138 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.636A pdb=" N LEU C 245 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 335 removed outlier: 3.548A pdb=" N VAL C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY C 332 " --> pdb=" O ASN C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 377 removed outlier: 3.986A pdb=" N ILE C 356 " --> pdb=" O ASN C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 399 removed outlier: 4.097A pdb=" N CYS C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER C 387 " --> pdb=" O TYR C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 407 removed outlier: 4.081A pdb=" N PHE C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 448 removed outlier: 3.764A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Proline residue: C 423 - end of helix removed outlier: 3.874A pdb=" N CYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 455 removed outlier: 4.156A pdb=" N ARG C 455 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 469 removed outlier: 3.504A pdb=" N ASN C 469 " --> pdb=" O PHE C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 482 Processing helix chain 'C' and resid 487 through 519 Processing helix chain 'D' and resid 66 through 106 removed outlier: 3.662A pdb=" N THR D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 138 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.636A pdb=" N LEU D 245 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 335 removed outlier: 3.548A pdb=" N VAL D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY D 332 " --> pdb=" O ASN D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 377 removed outlier: 3.986A pdb=" N ILE D 356 " --> pdb=" O ASN D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 399 removed outlier: 4.096A pdb=" N CYS D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 387 " --> pdb=" O TYR D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 407 removed outlier: 4.080A pdb=" N PHE D 407 " --> pdb=" O ARG D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 448 removed outlier: 3.764A pdb=" N LEU D 414 " --> pdb=" O ASN D 410 " (cutoff:3.500A) Proline residue: D 423 - end of helix removed outlier: 3.874A pdb=" N CYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 455 removed outlier: 4.155A pdb=" N ARG D 455 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 469 removed outlier: 3.503A pdb=" N ASN D 469 " --> pdb=" O PHE D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 482 Processing helix chain 'D' and resid 487 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 6.870A pdb=" N LEU A 228 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR A 170 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 173 through 176 removed outlier: 3.512A pdb=" N ASP A 183 " --> pdb=" O HIS A 174 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP A 176 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 181 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 287 removed outlier: 6.537A pdb=" N HIS A 286 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE D 184 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR D 181 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP D 176 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP D 183 " --> pdb=" O HIS D 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 119 removed outlier: 6.869A pdb=" N LEU B 228 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR B 170 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 173 through 176 removed outlier: 3.512A pdb=" N ASP B 183 " --> pdb=" O HIS B 174 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP B 176 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR B 181 " --> pdb=" O ASP B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 118 through 119 removed outlier: 6.870A pdb=" N LEU C 228 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR C 170 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 173 through 176 removed outlier: 3.511A pdb=" N ASP C 183 " --> pdb=" O HIS C 174 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP C 176 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR C 181 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 119 removed outlier: 6.870A pdb=" N LEU D 228 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR D 170 " --> pdb=" O LEU D 228 " (cutoff:3.500A) 955 hydrogen bonds defined for protein. 2781 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: 2.60 Time building geometry restraints manager: 1.65 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: 4296 1.35 - 1.48: 3804 1.48 - 1.60: 6064 1.60 - 1.73: 0 1.73 - 1.85: 136 Bond restraints: 14300 Sorted by residual: bond pdb=" C16 ZB4 B 601 " pdb=" N02 ZB4 B 601 " ideal model delta sigma weight residual 1.468 1.359 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C16 ZB4 C 601 " pdb=" N02 ZB4 C 601 " ideal model delta sigma weight residual 1.468 1.359 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C16 ZB4 D 601 " pdb=" N02 ZB4 D 601 " ideal model delta sigma weight residual 1.468 1.359 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C16 ZB4 A 601 " pdb=" N02 ZB4 A 601 " ideal model delta sigma weight residual 1.468 1.359 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C VAL C 509 " pdb=" O VAL C 509 " ideal model delta sigma weight residual 1.237 1.297 -0.061 1.13e-02 7.83e+03 2.87e+01 ... (remaining 14295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.49: 19396 7.49 - 14.98: 20 14.98 - 22.47: 4 22.47 - 29.95: 0 29.95 - 37.44: 4 Bond angle restraints: 19424 Sorted by residual: angle pdb=" C PHE D 513 " pdb=" CA PHE D 513 " pdb=" CB PHE D 513 " ideal model delta sigma weight residual 110.70 73.26 37.44 1.83e+00 2.99e-01 4.19e+02 angle pdb=" C PHE A 513 " pdb=" CA PHE A 513 " pdb=" CB PHE A 513 " ideal model delta sigma weight residual 110.70 73.29 37.41 1.83e+00 2.99e-01 4.18e+02 angle pdb=" C PHE B 513 " pdb=" CA PHE B 513 " pdb=" CB PHE B 513 " ideal model delta sigma weight residual 110.70 73.30 37.40 1.83e+00 2.99e-01 4.18e+02 angle pdb=" C PHE C 513 " pdb=" CA PHE C 513 " pdb=" CB PHE C 513 " ideal model delta sigma weight residual 110.70 73.31 37.39 1.83e+00 2.99e-01 4.17e+02 angle pdb=" CA PHE C 513 " pdb=" CB PHE C 513 " pdb=" CG PHE C 513 " ideal model delta sigma weight residual 113.80 105.29 8.51 1.00e+00 1.00e+00 7.23e+01 ... (remaining 19419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7184 17.96 - 35.91: 872 35.91 - 53.87: 216 53.87 - 71.82: 72 71.82 - 89.78: 20 Dihedral angle restraints: 8364 sinusoidal: 3312 harmonic: 5052 Sorted by residual: dihedral pdb=" C PHE D 513 " pdb=" N PHE D 513 " pdb=" CA PHE D 513 " pdb=" CB PHE D 513 " ideal model delta harmonic sigma weight residual -122.60 -83.37 -39.23 0 2.50e+00 1.60e-01 2.46e+02 dihedral pdb=" C PHE A 513 " pdb=" N PHE A 513 " pdb=" CA PHE A 513 " pdb=" CB PHE A 513 " ideal model delta harmonic sigma weight residual -122.60 -83.39 -39.21 0 2.50e+00 1.60e-01 2.46e+02 dihedral pdb=" C PHE B 513 " pdb=" N PHE B 513 " pdb=" CA PHE B 513 " pdb=" CB PHE B 513 " ideal model delta harmonic sigma weight residual -122.60 -83.43 -39.17 0 2.50e+00 1.60e-01 2.46e+02 ... (remaining 8361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1549 0.038 - 0.076: 477 0.076 - 0.114: 146 0.114 - 0.153: 56 0.153 - 0.191: 16 Chirality restraints: 2244 Sorted by residual: chirality pdb=" CA VAL C 509 " pdb=" N VAL C 509 " pdb=" C VAL C 509 " pdb=" CB VAL C 509 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" CA VAL D 509 " pdb=" N VAL D 509 " pdb=" C VAL D 509 " pdb=" CB VAL D 509 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA VAL A 509 " pdb=" N VAL A 509 " pdb=" C VAL A 509 " pdb=" CB VAL A 509 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.91e-01 ... (remaining 2241 not shown) Planarity restraints: 2384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 513 " 0.029 2.00e-02 2.50e+03 5.79e-02 3.35e+01 pdb=" C PHE C 513 " -0.100 2.00e-02 2.50e+03 pdb=" O PHE C 513 " 0.036 2.00e-02 2.50e+03 pdb=" N ILE C 514 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 513 " -0.029 2.00e-02 2.50e+03 5.77e-02 3.33e+01 pdb=" C PHE A 513 " 0.100 2.00e-02 2.50e+03 pdb=" O PHE A 513 " -0.036 2.00e-02 2.50e+03 pdb=" N ILE A 514 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 513 " 0.029 2.00e-02 2.50e+03 5.77e-02 3.33e+01 pdb=" C PHE D 513 " -0.100 2.00e-02 2.50e+03 pdb=" O PHE D 513 " 0.036 2.00e-02 2.50e+03 pdb=" N ILE D 514 " 0.035 2.00e-02 2.50e+03 ... (remaining 2381 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1995 2.76 - 3.29: 13738 3.29 - 3.83: 22934 3.83 - 4.36: 27038 4.36 - 4.90: 46582 Nonbonded interactions: 112287 Sorted by model distance: nonbonded pdb=" O LEU C 414 " pdb=" OG1 THR C 417 " model vdw 2.219 3.040 nonbonded pdb=" O LEU A 414 " pdb=" OG1 THR A 417 " model vdw 2.220 3.040 nonbonded pdb=" O LEU B 414 " pdb=" OG1 THR B 417 " model vdw 2.221 3.040 nonbonded pdb=" O LEU D 414 " pdb=" OG1 THR D 417 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR A 450 " pdb=" OD1 ASP B 384 " model vdw 2.256 3.040 ... (remaining 112282 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' 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: 4.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.250 Find NCS groups from input model: 0.140 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:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 14308 Z= 0.327 Angle : 0.994 37.443 19440 Z= 0.553 Chirality : 0.045 0.191 2244 Planarity : 0.006 0.058 2384 Dihedral : 17.582 89.781 5084 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.52 % Allowed : 25.07 % Favored : 74.41 % Cbeta Deviations : 0.25 % 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 aren not related in a simple way. whole: 0.13 (0.20), residues: 1700 helix: 1.04 (0.16), residues: 1000 sheet: -0.19 (0.35), residues: 236 loop : -1.81 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 403 TYR 0.013 0.001 TYR D 436 PHE 0.039 0.002 PHE C 513 TRP 0.008 0.001 TRP B 444 HIS 0.004 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00573 (14300) covalent geometry : angle 0.98888 (19424) SS BOND : bond 0.00121 ( 8) SS BOND : angle 3.49106 ( 16) hydrogen bonds : bond 0.13530 ( 955) hydrogen bonds : angle 6.31369 ( 2781) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 190 time to evaluate : 0.578 Fit side-chains REVERT: A 187 MET cc_start: 0.8727 (tmm) cc_final: 0.8213 (ttp) REVERT: A 247 ASN cc_start: 0.8666 (t0) cc_final: 0.8150 (t0) REVERT: B 187 MET cc_start: 0.8702 (tmm) cc_final: 0.8308 (ttp) REVERT: C 174 HIS cc_start: 0.8161 (m170) cc_final: 0.7949 (t70) REVERT: C 187 MET cc_start: 0.8696 (tmm) cc_final: 0.8208 (ttp) REVERT: D 174 HIS cc_start: 0.8166 (m170) cc_final: 0.7936 (t70) REVERT: D 187 MET cc_start: 0.8746 (tmm) cc_final: 0.8352 (ttp) outliers start: 8 outliers final: 4 residues processed: 198 average time/residue: 0.4405 time to fit residues: 98.7774 Evaluate side-chains 133 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 HIS B 247 ASN C 247 ASN D 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.108269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.081652 restraints weight = 25648.374| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.76 r_work: 0.2971 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14308 Z= 0.181 Angle : 0.625 10.044 19440 Z= 0.321 Chirality : 0.042 0.146 2244 Planarity : 0.004 0.038 2384 Dihedral : 7.990 44.680 1996 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.83 % Allowed : 23.04 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: 0.97 (0.20), residues: 1700 helix: 1.88 (0.16), residues: 1020 sheet: -0.19 (0.34), residues: 236 loop : -1.86 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 200 TYR 0.016 0.001 TYR B 497 PHE 0.015 0.001 PHE C 505 TRP 0.006 0.001 TRP A 335 HIS 0.004 0.001 HIS B 286 Details of bonding type rmsd covalent geometry : bond 0.00397 (14300) covalent geometry : angle 0.62195 (19424) SS BOND : bond 0.00120 ( 8) SS BOND : angle 2.07817 ( 16) hydrogen bonds : bond 0.06799 ( 955) hydrogen bonds : angle 4.81204 ( 2781) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 147 time to evaluate : 0.582 Fit side-chains REVERT: A 88 GLN cc_start: 0.8287 (tt0) cc_final: 0.7857 (tm-30) REVERT: A 144 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8218 (pp) REVERT: A 187 MET cc_start: 0.8674 (tmm) cc_final: 0.8000 (ttp) REVERT: A 282 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: A 334 MET cc_start: 0.2656 (OUTLIER) cc_final: 0.2115 (ttp) REVERT: B 88 GLN cc_start: 0.8266 (tt0) cc_final: 0.7830 (tm-30) REVERT: B 144 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8198 (pp) REVERT: B 187 MET cc_start: 0.8630 (tmm) cc_final: 0.8024 (ttp) REVERT: B 282 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: B 334 MET cc_start: 0.2395 (OUTLIER) cc_final: 0.2075 (ttp) REVERT: C 88 GLN cc_start: 0.8288 (tt0) cc_final: 0.7855 (tm-30) REVERT: C 144 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8136 (pp) REVERT: C 187 MET cc_start: 0.8621 (tmm) cc_final: 0.7994 (ttp) REVERT: C 282 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: C 334 MET cc_start: 0.2558 (OUTLIER) cc_final: 0.2059 (ttp) REVERT: D 88 GLN cc_start: 0.8259 (tt0) cc_final: 0.7828 (tm-30) REVERT: D 144 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8154 (pp) REVERT: D 187 MET cc_start: 0.8652 (tmm) cc_final: 0.8041 (ttp) REVERT: D 282 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: D 334 MET cc_start: 0.2567 (OUTLIER) cc_final: 0.2066 (ttp) REVERT: D 362 ASP cc_start: 0.7992 (p0) cc_final: 0.7684 (p0) outliers start: 74 outliers final: 17 residues processed: 186 average time/residue: 0.4469 time to fit residues: 94.0338 Evaluate side-chains 162 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 282 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 282 GLN Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 76 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 1 optimal weight: 0.2980 chunk 133 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.105035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.078418 restraints weight = 26191.929| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.74 r_work: 0.2932 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14308 Z= 0.207 Angle : 0.635 9.294 19440 Z= 0.330 Chirality : 0.043 0.144 2244 Planarity : 0.004 0.037 2384 Dihedral : 7.715 47.387 1996 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 7.44 % Allowed : 20.43 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 aren not related in a simple way. whole: 1.11 (0.20), residues: 1700 helix: 2.00 (0.16), residues: 1020 sheet: -0.47 (0.35), residues: 236 loop : -1.61 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 486 TYR 0.017 0.001 TYR C 497 PHE 0.017 0.001 PHE B 505 TRP 0.008 0.001 TRP A 335 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00474 (14300) covalent geometry : angle 0.63250 (19424) SS BOND : bond 0.01359 ( 8) SS BOND : angle 2.21829 ( 16) hydrogen bonds : bond 0.06918 ( 955) hydrogen bonds : angle 4.74165 ( 2781) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 136 time to evaluate : 0.562 Fit side-chains REVERT: A 88 GLN cc_start: 0.8311 (tt0) cc_final: 0.7887 (tm-30) REVERT: A 144 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8314 (pp) REVERT: A 187 MET cc_start: 0.8623 (tmm) cc_final: 0.7887 (ttp) REVERT: A 334 MET cc_start: 0.2591 (OUTLIER) cc_final: 0.1971 (ttp) REVERT: B 88 GLN cc_start: 0.8302 (tt0) cc_final: 0.7881 (tm-30) REVERT: B 144 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8267 (pp) REVERT: B 187 MET cc_start: 0.8530 (tmm) cc_final: 0.7873 (ttp) REVERT: B 334 MET cc_start: 0.2552 (OUTLIER) cc_final: 0.1968 (ttp) REVERT: C 88 GLN cc_start: 0.8288 (tt0) cc_final: 0.7874 (tm-30) REVERT: C 144 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8252 (pp) REVERT: C 187 MET cc_start: 0.8552 (tmm) cc_final: 0.7893 (ttp) REVERT: C 334 MET cc_start: 0.2550 (OUTLIER) cc_final: 0.1937 (ttp) REVERT: D 88 GLN cc_start: 0.8292 (tt0) cc_final: 0.7877 (tm-30) REVERT: D 144 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8275 (pp) REVERT: D 187 MET cc_start: 0.8625 (tmm) cc_final: 0.7978 (ttp) REVERT: D 334 MET cc_start: 0.2529 (OUTLIER) cc_final: 0.1956 (ttp) REVERT: D 362 ASP cc_start: 0.8113 (p0) cc_final: 0.7763 (p0) outliers start: 114 outliers final: 28 residues processed: 214 average time/residue: 0.3745 time to fit residues: 92.6563 Evaluate side-chains 164 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 146 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 291 GLN B 79 GLN D 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.106595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.079834 restraints weight = 25969.770| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.75 r_work: 0.2953 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14308 Z= 0.159 Angle : 0.604 9.566 19440 Z= 0.309 Chirality : 0.041 0.136 2244 Planarity : 0.004 0.041 2384 Dihedral : 7.555 46.527 1996 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.22 % Allowed : 21.28 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 aren not related in a simple way. whole: 1.29 (0.21), residues: 1700 helix: 2.21 (0.16), residues: 1012 sheet: -0.56 (0.34), residues: 244 loop : -1.55 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 403 TYR 0.015 0.001 TYR A 497 PHE 0.014 0.001 PHE D 505 TRP 0.006 0.001 TRP D 335 HIS 0.003 0.000 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00347 (14300) covalent geometry : angle 0.59969 (19424) SS BOND : bond 0.00599 ( 8) SS BOND : angle 2.46673 ( 16) hydrogen bonds : bond 0.06371 ( 955) hydrogen bonds : angle 4.59993 ( 2781) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 140 time to evaluate : 0.542 Fit side-chains REVERT: A 88 GLN cc_start: 0.8337 (tt0) cc_final: 0.7910 (tm-30) REVERT: A 144 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8231 (pp) REVERT: A 187 MET cc_start: 0.8641 (tmm) cc_final: 0.7913 (ttp) REVERT: B 88 GLN cc_start: 0.8299 (tt0) cc_final: 0.7868 (tm-30) REVERT: B 144 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8200 (pp) REVERT: B 187 MET cc_start: 0.8604 (tmm) cc_final: 0.7952 (ttp) REVERT: C 88 GLN cc_start: 0.8330 (tt0) cc_final: 0.7902 (tm-30) REVERT: C 144 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8199 (pp) REVERT: C 187 MET cc_start: 0.8611 (tmm) cc_final: 0.7959 (ttp) REVERT: D 88 GLN cc_start: 0.8342 (tt0) cc_final: 0.7914 (tm-30) REVERT: D 144 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8192 (pp) REVERT: D 187 MET cc_start: 0.8651 (tmm) cc_final: 0.8000 (ttp) REVERT: D 362 ASP cc_start: 0.8188 (p0) cc_final: 0.7813 (p0) outliers start: 80 outliers final: 33 residues processed: 192 average time/residue: 0.3373 time to fit residues: 75.9742 Evaluate side-chains 160 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 282 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 36 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS B 280 HIS C 280 HIS D 280 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.109028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.082385 restraints weight = 26041.956| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.78 r_work: 0.3004 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14308 Z= 0.129 Angle : 0.567 10.797 19440 Z= 0.288 Chirality : 0.040 0.143 2244 Planarity : 0.004 0.045 2384 Dihedral : 7.130 43.207 1996 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.68 % Allowed : 21.74 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.21), residues: 1700 helix: 2.36 (0.16), residues: 1012 sheet: -0.48 (0.34), residues: 244 loop : -1.51 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.013 0.001 TYR C 411 PHE 0.016 0.001 PHE A 290 TRP 0.006 0.001 TRP A 335 HIS 0.003 0.000 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00261 (14300) covalent geometry : angle 0.56468 (19424) SS BOND : bond 0.00622 ( 8) SS BOND : angle 1.88187 ( 16) hydrogen bonds : bond 0.05535 ( 955) hydrogen bonds : angle 4.42305 ( 2781) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 141 time to evaluate : 0.606 Fit side-chains REVERT: A 88 GLN cc_start: 0.8326 (tt0) cc_final: 0.7894 (tm-30) REVERT: A 144 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8125 (pp) REVERT: A 187 MET cc_start: 0.8652 (tmm) cc_final: 0.8000 (ttp) REVERT: B 88 GLN cc_start: 0.8320 (tt0) cc_final: 0.7893 (tm-30) REVERT: B 144 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8090 (pp) REVERT: B 187 MET cc_start: 0.8638 (tmm) cc_final: 0.8001 (ttp) REVERT: C 88 GLN cc_start: 0.8313 (tt0) cc_final: 0.7890 (tm-30) REVERT: C 144 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8100 (pp) REVERT: C 187 MET cc_start: 0.8671 (tmm) cc_final: 0.8018 (ttp) REVERT: D 88 GLN cc_start: 0.8316 (tt0) cc_final: 0.7891 (tm-30) REVERT: D 144 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8108 (pp) REVERT: D 187 MET cc_start: 0.8682 (tmm) cc_final: 0.8057 (ttp) REVERT: D 362 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7814 (p0) outliers start: 87 outliers final: 24 residues processed: 194 average time/residue: 0.3776 time to fit residues: 84.9221 Evaluate side-chains 156 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 406 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 67 optimal weight: 8.9990 chunk 171 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 0.0000 chunk 156 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.109829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.083502 restraints weight = 25877.496| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.75 r_work: 0.3022 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14308 Z= 0.122 Angle : 0.576 10.835 19440 Z= 0.284 Chirality : 0.040 0.137 2244 Planarity : 0.004 0.043 2384 Dihedral : 6.428 39.322 1988 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.52 % Allowed : 24.15 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.21), residues: 1700 helix: 2.41 (0.16), residues: 1012 sheet: -0.44 (0.33), residues: 244 loop : -1.48 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 168 TYR 0.014 0.001 TYR C 411 PHE 0.009 0.001 PHE A 505 TRP 0.005 0.001 TRP C 335 HIS 0.003 0.000 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00239 (14300) covalent geometry : angle 0.57347 (19424) SS BOND : bond 0.00501 ( 8) SS BOND : angle 1.85004 ( 16) hydrogen bonds : bond 0.05321 ( 955) hydrogen bonds : angle 4.36215 ( 2781) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 159 time to evaluate : 0.575 Fit side-chains REVERT: A 88 GLN cc_start: 0.8316 (tt0) cc_final: 0.7904 (tm-30) REVERT: A 187 MET cc_start: 0.8526 (tmm) cc_final: 0.7939 (ttp) REVERT: A 467 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8388 (mp) REVERT: B 88 GLN cc_start: 0.8302 (tt0) cc_final: 0.7875 (tm-30) REVERT: B 187 MET cc_start: 0.8534 (tmm) cc_final: 0.8000 (ttp) REVERT: B 467 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8402 (mp) REVERT: C 88 GLN cc_start: 0.8312 (tt0) cc_final: 0.7887 (tm-30) REVERT: C 187 MET cc_start: 0.8584 (tmm) cc_final: 0.7992 (ttp) REVERT: D 88 GLN cc_start: 0.8314 (tt0) cc_final: 0.7890 (tm-30) REVERT: D 187 MET cc_start: 0.8572 (tmm) cc_final: 0.8001 (ttp) REVERT: D 249 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7980 (mt-10) outliers start: 54 outliers final: 28 residues processed: 197 average time/residue: 0.3043 time to fit residues: 71.8761 Evaluate side-chains 172 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 406 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 136 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.105850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.079353 restraints weight = 25942.653| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.71 r_work: 0.2952 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14308 Z= 0.192 Angle : 0.612 10.220 19440 Z= 0.312 Chirality : 0.042 0.166 2244 Planarity : 0.004 0.040 2384 Dihedral : 6.448 37.620 1988 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.85 % Allowed : 24.02 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.21), residues: 1700 helix: 2.31 (0.16), residues: 1012 sheet: -0.52 (0.33), residues: 244 loop : -1.44 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 403 TYR 0.018 0.002 TYR A 497 PHE 0.018 0.001 PHE A 505 TRP 0.007 0.001 TRP A 335 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00444 (14300) covalent geometry : angle 0.60919 (19424) SS BOND : bond 0.00471 ( 8) SS BOND : angle 2.27400 ( 16) hydrogen bonds : bond 0.06243 ( 955) hydrogen bonds : angle 4.50851 ( 2781) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 137 time to evaluate : 0.599 Fit side-chains REVERT: A 88 GLN cc_start: 0.8341 (tt0) cc_final: 0.7932 (tm-30) REVERT: A 187 MET cc_start: 0.8510 (tmm) cc_final: 0.7924 (ttp) REVERT: A 334 MET cc_start: 0.2717 (OUTLIER) cc_final: 0.2060 (ttp) REVERT: B 88 GLN cc_start: 0.8337 (tt0) cc_final: 0.7928 (tm-30) REVERT: B 187 MET cc_start: 0.8496 (tmm) cc_final: 0.7935 (ttp) REVERT: C 88 GLN cc_start: 0.8343 (tt0) cc_final: 0.7936 (tm-30) REVERT: C 187 MET cc_start: 0.8507 (tmm) cc_final: 0.7937 (ttp) REVERT: D 88 GLN cc_start: 0.8341 (tt0) cc_final: 0.7934 (tm-30) REVERT: D 187 MET cc_start: 0.8528 (tmm) cc_final: 0.7951 (ttp) REVERT: D 334 MET cc_start: 0.2618 (OUTLIER) cc_final: 0.1927 (ttp) outliers start: 59 outliers final: 25 residues processed: 171 average time/residue: 0.3345 time to fit residues: 67.4204 Evaluate side-chains 155 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 406 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 0.0770 chunk 149 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 21 optimal weight: 0.0870 chunk 153 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 291 GLN D 291 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.107112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.080902 restraints weight = 25995.245| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.73 r_work: 0.2974 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14308 Z= 0.141 Angle : 0.587 10.475 19440 Z= 0.296 Chirality : 0.041 0.137 2244 Planarity : 0.004 0.041 2384 Dihedral : 6.357 36.775 1988 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.26 % Allowed : 25.00 % Favored : 71.74 % 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 aren not related in a simple way. whole: 1.51 (0.21), residues: 1700 helix: 2.38 (0.16), residues: 1012 sheet: -0.54 (0.33), residues: 244 loop : -1.41 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 403 TYR 0.014 0.001 TYR A 411 PHE 0.012 0.001 PHE C 505 TRP 0.005 0.001 TRP C 354 HIS 0.003 0.000 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00301 (14300) covalent geometry : angle 0.58491 (19424) SS BOND : bond 0.00437 ( 8) SS BOND : angle 1.93683 ( 16) hydrogen bonds : bond 0.05771 ( 955) hydrogen bonds : angle 4.42379 ( 2781) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 136 time to evaluate : 0.576 Fit side-chains REVERT: A 88 GLN cc_start: 0.8350 (tt0) cc_final: 0.7927 (tm-30) REVERT: A 187 MET cc_start: 0.8467 (tmm) cc_final: 0.7881 (ttp) REVERT: B 88 GLN cc_start: 0.8340 (tt0) cc_final: 0.7919 (tm-30) REVERT: B 187 MET cc_start: 0.8504 (tmm) cc_final: 0.7942 (ttp) REVERT: B 334 MET cc_start: 0.2588 (OUTLIER) cc_final: 0.1935 (ttp) REVERT: C 88 GLN cc_start: 0.8347 (tt0) cc_final: 0.7927 (tm-30) REVERT: C 187 MET cc_start: 0.8512 (tmm) cc_final: 0.7924 (ttp) REVERT: C 334 MET cc_start: 0.2603 (OUTLIER) cc_final: 0.1979 (ttp) REVERT: D 88 GLN cc_start: 0.8348 (tt0) cc_final: 0.7930 (tm-30) REVERT: D 187 MET cc_start: 0.8539 (tmm) cc_final: 0.7973 (ttp) outliers start: 50 outliers final: 35 residues processed: 174 average time/residue: 0.3273 time to fit residues: 67.4976 Evaluate side-chains 163 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 467 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 159 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.107723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.081482 restraints weight = 25921.036| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.73 r_work: 0.2991 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14308 Z= 0.131 Angle : 0.598 10.683 19440 Z= 0.300 Chirality : 0.041 0.181 2244 Planarity : 0.004 0.041 2384 Dihedral : 6.292 40.044 1988 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.13 % Allowed : 25.52 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: 1.56 (0.21), residues: 1700 helix: 2.42 (0.16), residues: 1012 sheet: -0.54 (0.33), residues: 244 loop : -1.38 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.014 0.001 TYR A 411 PHE 0.011 0.001 PHE B 505 TRP 0.005 0.001 TRP A 354 HIS 0.002 0.000 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00266 (14300) covalent geometry : angle 0.59632 (19424) SS BOND : bond 0.00821 ( 8) SS BOND : angle 1.83673 ( 16) hydrogen bonds : bond 0.05629 ( 955) hydrogen bonds : angle 4.38425 ( 2781) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 136 time to evaluate : 0.615 Fit side-chains REVERT: A 88 GLN cc_start: 0.8328 (tt0) cc_final: 0.7914 (tm-30) REVERT: A 187 MET cc_start: 0.8494 (tmm) cc_final: 0.7919 (ttp) REVERT: A 334 MET cc_start: 0.2866 (OUTLIER) cc_final: 0.2307 (ttp) REVERT: B 88 GLN cc_start: 0.8316 (tt0) cc_final: 0.7899 (tm-30) REVERT: B 187 MET cc_start: 0.8495 (tmm) cc_final: 0.7943 (ttp) REVERT: B 334 MET cc_start: 0.2609 (OUTLIER) cc_final: 0.1967 (ttp) REVERT: C 88 GLN cc_start: 0.8326 (tt0) cc_final: 0.7912 (tm-30) REVERT: C 187 MET cc_start: 0.8517 (tmm) cc_final: 0.7941 (ttp) REVERT: C 334 MET cc_start: 0.2648 (OUTLIER) cc_final: 0.2023 (ttp) REVERT: D 88 GLN cc_start: 0.8324 (tt0) cc_final: 0.7909 (tm-30) REVERT: D 187 MET cc_start: 0.8549 (tmm) cc_final: 0.7996 (ttp) REVERT: D 334 MET cc_start: 0.2700 (OUTLIER) cc_final: 0.2133 (ttp) outliers start: 48 outliers final: 33 residues processed: 166 average time/residue: 0.3192 time to fit residues: 62.8323 Evaluate side-chains 166 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 467 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 169 optimal weight: 2.9990 chunk 134 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.108898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.082711 restraints weight = 25942.306| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.74 r_work: 0.2995 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14308 Z= 0.126 Angle : 0.594 10.821 19440 Z= 0.294 Chirality : 0.040 0.144 2244 Planarity : 0.004 0.042 2384 Dihedral : 6.116 43.631 1988 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.61 % Allowed : 26.24 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: 1.65 (0.21), residues: 1700 helix: 2.48 (0.16), residues: 1020 sheet: -0.49 (0.33), residues: 244 loop : -1.36 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 318 TYR 0.014 0.001 TYR A 411 PHE 0.011 0.001 PHE A 505 TRP 0.005 0.001 TRP A 335 HIS 0.008 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00256 (14300) covalent geometry : angle 0.59168 (19424) SS BOND : bond 0.00544 ( 8) SS BOND : angle 1.75408 ( 16) hydrogen bonds : bond 0.05383 ( 955) hydrogen bonds : angle 4.31337 ( 2781) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.591 Fit side-chains REVERT: A 88 GLN cc_start: 0.8291 (tt0) cc_final: 0.7887 (tm-30) REVERT: A 187 MET cc_start: 0.8470 (tmm) cc_final: 0.7803 (ttp) REVERT: A 334 MET cc_start: 0.2882 (OUTLIER) cc_final: 0.2283 (ttp) REVERT: B 88 GLN cc_start: 0.8274 (tt0) cc_final: 0.7865 (tm-30) REVERT: B 187 MET cc_start: 0.8482 (tmm) cc_final: 0.7936 (ttp) REVERT: B 334 MET cc_start: 0.2696 (OUTLIER) cc_final: 0.2073 (ttp) REVERT: C 88 GLN cc_start: 0.8279 (tt0) cc_final: 0.7870 (tm-30) REVERT: C 187 MET cc_start: 0.8473 (tmm) cc_final: 0.7878 (ttp) REVERT: C 334 MET cc_start: 0.2761 (OUTLIER) cc_final: 0.2121 (ttp) REVERT: D 88 GLN cc_start: 0.8282 (tt0) cc_final: 0.7874 (tm-30) REVERT: D 187 MET cc_start: 0.8531 (tmm) cc_final: 0.7920 (ttp) REVERT: D 334 MET cc_start: 0.2825 (OUTLIER) cc_final: 0.2221 (ttp) outliers start: 40 outliers final: 22 residues processed: 171 average time/residue: 0.3163 time to fit residues: 64.7405 Evaluate side-chains 159 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 406 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.107490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.081074 restraints weight = 26041.035| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.74 r_work: 0.2985 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14308 Z= 0.146 Angle : 0.604 10.783 19440 Z= 0.301 Chirality : 0.041 0.146 2244 Planarity : 0.004 0.041 2384 Dihedral : 6.039 42.530 1988 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.89 % Allowed : 26.89 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: 1.57 (0.21), residues: 1700 helix: 2.39 (0.16), residues: 1020 sheet: -0.51 (0.33), residues: 244 loop : -1.37 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.014 0.001 TYR A 411 PHE 0.014 0.001 PHE B 505 TRP 0.005 0.001 TRP B 335 HIS 0.005 0.000 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00320 (14300) covalent geometry : angle 0.60175 (19424) SS BOND : bond 0.00545 ( 8) SS BOND : angle 1.84882 ( 16) hydrogen bonds : bond 0.05667 ( 955) hydrogen bonds : angle 4.35951 ( 2781) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3855.73 seconds wall clock time: 66 minutes 53.58 seconds (4013.58 seconds total)