Starting phenix.real_space_refine on Thu Jul 31 22:52:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eku_48137/07_2025/9eku_48137_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eku_48137/07_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_48137/07_2025/9eku_48137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eku_48137/07_2025/9eku_48137.map" model { file = "/net/cci-nas-00/data/ceres_data/9eku_48137/07_2025/9eku_48137_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eku_48137/07_2025/9eku_48137_neut.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, D Time building chain proxies: 7.18, per 1000 atoms: 0.51 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 C 166 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 166 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 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: 3.05 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.18 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: 3.84 Time building geometry restraints manager: 3.65 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 29.280 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:10.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.380 ------------------------------------------------------------------------------- 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 : 8.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.008 0.001 TRP B 444 HIS 0.004 0.001 HIS C 286 PHE 0.039 0.002 PHE C 513 TYR 0.013 0.001 TYR D 436 ARG 0.005 0.001 ARG B 403 Details of bonding type rmsd hydrogen bonds : bond 0.13530 ( 955) hydrogen bonds : angle 6.31369 ( 2781) SS BOND : bond 0.00121 ( 8) SS BOND : angle 3.49106 ( 16) covalent geometry : bond 0.00573 (14300) covalent geometry : angle 0.98888 (19424) *********************** 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 : 1.558 Fit side-chains REVERT: A 187 MET cc_start: 0.8727 (tmm) cc_final: 0.8212 (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: 0.9002 time to fit residues: 203.1744 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 : 1.940 ------------------------------------------------------------------------------- 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 145 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 134 optimal weight: 0.4980 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.109925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.083563 restraints weight = 25605.700| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.75 r_work: 0.3023 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1437 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= 0.152 Angle : 0.606 10.077 19440 Z= 0.310 Chirality : 0.041 0.133 2244 Planarity : 0.004 0.039 2384 Dihedral : 8.001 46.017 1996 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.50 % Allowed : 23.43 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.20), residues: 1700 helix: 1.93 (0.16), residues: 1020 sheet: -0.12 (0.34), residues: 236 loop : -1.83 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 354 HIS 0.004 0.001 HIS C 286 PHE 0.013 0.001 PHE A 513 TYR 0.015 0.001 TYR D 436 ARG 0.009 0.001 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.06441 ( 955) hydrogen bonds : angle 4.77522 ( 2781) SS BOND : bond 0.00268 ( 8) SS BOND : angle 1.88113 ( 16) covalent geometry : bond 0.00303 (14300) covalent geometry : angle 0.60385 (19424) *********************** 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 222 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 153 time to evaluate : 1.539 Fit side-chains REVERT: A 88 GLN cc_start: 0.8283 (tt0) cc_final: 0.7847 (tm-30) REVERT: A 144 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8094 (pp) REVERT: A 187 MET cc_start: 0.8693 (tmm) cc_final: 0.8014 (ttp) REVERT: A 282 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: B 88 GLN cc_start: 0.8239 (tt0) cc_final: 0.7806 (tm-30) REVERT: B 144 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8075 (pp) REVERT: B 187 MET cc_start: 0.8625 (tmm) cc_final: 0.8033 (ttp) REVERT: B 282 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: B 334 MET cc_start: 0.2347 (OUTLIER) cc_final: 0.2096 (ttp) REVERT: C 88 GLN cc_start: 0.8268 (tt0) cc_final: 0.7834 (tm-30) REVERT: C 144 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8064 (pp) REVERT: C 174 HIS cc_start: 0.8258 (m170) cc_final: 0.7482 (t70) REVERT: C 187 MET cc_start: 0.8637 (tmm) cc_final: 0.8009 (ttp) REVERT: C 282 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: C 334 MET cc_start: 0.2525 (OUTLIER) cc_final: 0.2099 (ttp) REVERT: D 88 GLN cc_start: 0.8269 (tt0) cc_final: 0.7839 (tm-30) REVERT: D 144 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8072 (pp) REVERT: D 187 MET cc_start: 0.8669 (tmm) cc_final: 0.8075 (ttp) REVERT: D 282 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7951 (tt0) outliers start: 69 outliers final: 16 residues processed: 190 average time/residue: 0.9578 time to fit residues: 205.0235 Evaluate side-chains 167 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 445 ILE Chi-restraints excluded: chain A residue 510 LEU 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 285 LYS 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 510 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 39 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.103945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.077347 restraints weight = 26155.471| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.73 r_work: 0.2902 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 14308 Z= 0.255 Angle : 0.668 9.094 19440 Z= 0.348 Chirality : 0.044 0.169 2244 Planarity : 0.004 0.036 2384 Dihedral : 7.758 44.754 1996 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.72 % Allowed : 20.89 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.20), residues: 1700 helix: 1.95 (0.16), residues: 1020 sheet: -0.27 (0.36), residues: 228 loop : -1.68 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 335 HIS 0.005 0.001 HIS A 234 PHE 0.017 0.002 PHE A 505 TYR 0.020 0.002 TYR D 497 ARG 0.003 0.001 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.07328 ( 955) hydrogen bonds : angle 4.82541 ( 2781) SS BOND : bond 0.00344 ( 8) SS BOND : angle 2.34861 ( 16) covalent geometry : bond 0.00598 (14300) covalent geometry : angle 0.66489 (19424) *********************** 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 240 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 137 time to evaluate : 1.715 Fit side-chains REVERT: A 88 GLN cc_start: 0.8362 (tt0) cc_final: 0.7943 (tm-30) REVERT: A 144 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8383 (pp) REVERT: A 187 MET cc_start: 0.8607 (tmm) cc_final: 0.7872 (ttp) REVERT: A 334 MET cc_start: 0.2633 (OUTLIER) cc_final: 0.1972 (ttp) REVERT: B 88 GLN cc_start: 0.8344 (tt0) cc_final: 0.7938 (tm-30) REVERT: B 144 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8370 (pp) REVERT: B 187 MET cc_start: 0.8568 (tmm) cc_final: 0.7889 (ttp) REVERT: B 334 MET cc_start: 0.2604 (OUTLIER) cc_final: 0.1962 (ttp) REVERT: C 88 GLN cc_start: 0.8330 (tt0) cc_final: 0.7921 (tm-30) REVERT: C 144 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8350 (pp) REVERT: C 187 MET cc_start: 0.8548 (tmm) cc_final: 0.7865 (ttp) REVERT: C 334 MET cc_start: 0.2575 (OUTLIER) cc_final: 0.1920 (ttp) REVERT: D 88 GLN cc_start: 0.8329 (tt0) cc_final: 0.7922 (tm-30) REVERT: D 144 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8359 (pp) REVERT: D 187 MET cc_start: 0.8598 (tmm) cc_final: 0.7889 (ttp) REVERT: D 334 MET cc_start: 0.2583 (OUTLIER) cc_final: 0.1964 (ttp) outliers start: 103 outliers final: 27 residues processed: 205 average time/residue: 0.7266 time to fit residues: 173.2755 Evaluate side-chains 158 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 393 SER Chi-restraints excluded: chain A residue 425 VAL 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 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 393 SER Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 115 ASP 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 393 SER Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 115 ASP 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 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 59 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 0.0270 chunk 50 optimal weight: 0.9980 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN B 79 GLN C 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 = 0.3546 r_free = 0.3546 target = 0.107852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.081268 restraints weight = 25694.744| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.73 r_work: 0.2981 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14308 Z= 0.135 Angle : 0.589 9.615 19440 Z= 0.301 Chirality : 0.040 0.140 2244 Planarity : 0.004 0.041 2384 Dihedral : 7.533 46.744 1996 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.96 % Allowed : 21.93 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.21), residues: 1700 helix: 2.24 (0.16), residues: 1012 sheet: -0.51 (0.34), residues: 244 loop : -1.49 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 354 HIS 0.002 0.000 HIS A 234 PHE 0.011 0.001 PHE D 505 TYR 0.013 0.001 TYR D 436 ARG 0.002 0.000 ARG D 486 Details of bonding type rmsd hydrogen bonds : bond 0.06079 ( 955) hydrogen bonds : angle 4.57063 ( 2781) SS BOND : bond 0.00365 ( 8) SS BOND : angle 2.15630 ( 16) covalent geometry : bond 0.00263 (14300) covalent geometry : angle 0.58623 (19424) *********************** 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 219 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 143 time to evaluate : 1.555 Fit side-chains REVERT: A 88 GLN cc_start: 0.8301 (tt0) cc_final: 0.7872 (tm-30) REVERT: A 144 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8134 (pp) REVERT: A 187 MET cc_start: 0.8677 (tmm) cc_final: 0.7958 (ttp) REVERT: B 88 GLN cc_start: 0.8298 (tt0) cc_final: 0.7867 (tm-30) REVERT: B 144 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8137 (pp) REVERT: B 187 MET cc_start: 0.8624 (tmm) cc_final: 0.7933 (ttp) REVERT: C 88 GLN cc_start: 0.8307 (tt0) cc_final: 0.7877 (tm-30) REVERT: C 144 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8115 (pp) REVERT: C 187 MET cc_start: 0.8638 (tmm) cc_final: 0.7943 (ttp) REVERT: D 88 GLN cc_start: 0.8313 (tt0) cc_final: 0.7880 (tm-30) REVERT: D 144 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8119 (pp) REVERT: D 187 MET cc_start: 0.8673 (tmm) cc_final: 0.7985 (ttp) outliers start: 76 outliers final: 29 residues processed: 193 average time/residue: 0.6695 time to fit residues: 152.7854 Evaluate side-chains 158 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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 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 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 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 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 D residue 95 GLU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 282 GLN 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 42 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 142 optimal weight: 0.2980 chunk 99 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS B 291 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.108015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.081520 restraints weight = 25879.028| |-----------------------------------------------------------------------------| r_work (start): 0.3114 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: 0.8093 moved from start: 0.2421 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= 0.136 Angle : 0.590 10.921 19440 Z= 0.295 Chirality : 0.040 0.144 2244 Planarity : 0.004 0.042 2384 Dihedral : 6.829 42.667 1990 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.55 % Allowed : 21.93 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.21), residues: 1700 helix: 2.32 (0.16), residues: 1012 sheet: -0.43 (0.34), residues: 244 loop : -1.52 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 335 HIS 0.003 0.000 HIS A 234 PHE 0.018 0.001 PHE A 290 TYR 0.013 0.001 TYR A 436 ARG 0.003 0.000 ARG C 403 Details of bonding type rmsd hydrogen bonds : bond 0.05793 ( 955) hydrogen bonds : angle 4.46677 ( 2781) SS BOND : bond 0.00538 ( 8) SS BOND : angle 2.04373 ( 16) covalent geometry : bond 0.00283 (14300) covalent geometry : angle 0.58689 (19424) *********************** 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 219 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 134 time to evaluate : 1.456 Fit side-chains REVERT: A 88 GLN cc_start: 0.8312 (tt0) cc_final: 0.7883 (tm-30) REVERT: A 144 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8081 (pp) REVERT: A 187 MET cc_start: 0.8641 (tmm) cc_final: 0.7942 (ttp) REVERT: B 88 GLN cc_start: 0.8276 (tt0) cc_final: 0.7865 (tm-30) REVERT: B 144 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8053 (pp) REVERT: B 187 MET cc_start: 0.8607 (tmm) cc_final: 0.7929 (ttp) REVERT: C 88 GLN cc_start: 0.8302 (tt0) cc_final: 0.7893 (tm-30) REVERT: C 144 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8050 (pp) REVERT: C 187 MET cc_start: 0.8635 (tmm) cc_final: 0.7947 (ttp) REVERT: D 88 GLN cc_start: 0.8311 (tt0) cc_final: 0.7901 (tm-30) REVERT: D 144 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8048 (pp) REVERT: D 187 MET cc_start: 0.8650 (tmm) cc_final: 0.7972 (ttp) outliers start: 85 outliers final: 32 residues processed: 190 average time/residue: 0.6484 time to fit residues: 145.9409 Evaluate side-chains 162 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 115 ASP 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 314 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 314 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain C residue 74 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 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 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 326 LEU 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 117 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 HIS C 280 HIS D 280 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.107695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.081101 restraints weight = 26069.701| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.76 r_work: 0.2970 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2565 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= 0.145 Angle : 0.579 10.214 19440 Z= 0.293 Chirality : 0.040 0.134 2244 Planarity : 0.004 0.040 2384 Dihedral : 6.645 38.903 1988 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.37 % Allowed : 22.98 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.21), residues: 1700 helix: 2.32 (0.16), residues: 1012 sheet: -0.46 (0.33), residues: 244 loop : -1.45 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 335 HIS 0.003 0.000 HIS A 234 PHE 0.012 0.001 PHE A 505 TYR 0.014 0.001 TYR B 497 ARG 0.002 0.000 ARG B 403 Details of bonding type rmsd hydrogen bonds : bond 0.05841 ( 955) hydrogen bonds : angle 4.45657 ( 2781) SS BOND : bond 0.00427 ( 8) SS BOND : angle 2.01289 ( 16) covalent geometry : bond 0.00314 (14300) covalent geometry : angle 0.57635 (19424) *********************** 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 198 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 131 time to evaluate : 1.447 Fit side-chains REVERT: A 88 GLN cc_start: 0.8352 (tt0) cc_final: 0.7931 (tm-30) REVERT: A 144 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8095 (pp) REVERT: A 187 MET cc_start: 0.8599 (tmm) cc_final: 0.7969 (ttp) REVERT: B 88 GLN cc_start: 0.8308 (tt0) cc_final: 0.7901 (tm-30) REVERT: B 144 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8071 (pp) REVERT: B 187 MET cc_start: 0.8600 (tmm) cc_final: 0.7976 (ttp) REVERT: C 88 GLN cc_start: 0.8332 (tt0) cc_final: 0.7932 (tm-30) REVERT: C 144 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8075 (pp) REVERT: C 187 MET cc_start: 0.8588 (tmm) cc_final: 0.7943 (ttp) REVERT: D 88 GLN cc_start: 0.8305 (tt0) cc_final: 0.7905 (tm-30) REVERT: D 144 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8080 (pp) REVERT: D 187 MET cc_start: 0.8619 (tmm) cc_final: 0.7999 (ttp) outliers start: 67 outliers final: 37 residues processed: 177 average time/residue: 0.6495 time to fit residues: 136.2256 Evaluate side-chains 168 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 1.559 ------------------------------------------------------------------------------- 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 299 LEU Chi-restraints excluded: chain A residue 314 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 496 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 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 C residue 95 GLU Chi-restraints excluded: chain C residue 115 ASP 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 359 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 115 ASP 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 359 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 496 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 53 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.105912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.079131 restraints weight = 26224.784| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.75 r_work: 0.2945 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14308 Z= 0.185 Angle : 0.604 10.230 19440 Z= 0.307 Chirality : 0.041 0.150 2244 Planarity : 0.004 0.039 2384 Dihedral : 6.629 38.050 1988 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.50 % Allowed : 23.04 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.21), residues: 1700 helix: 2.27 (0.16), residues: 1012 sheet: -0.50 (0.33), residues: 244 loop : -1.47 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 335 HIS 0.003 0.000 HIS D 234 PHE 0.015 0.001 PHE A 505 TYR 0.017 0.001 TYR B 497 ARG 0.002 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.06223 ( 955) hydrogen bonds : angle 4.50314 ( 2781) SS BOND : bond 0.00417 ( 8) SS BOND : angle 2.18534 ( 16) covalent geometry : bond 0.00425 (14300) covalent geometry : angle 0.60053 (19424) *********************** 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 202 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 133 time to evaluate : 1.592 Fit side-chains REVERT: A 88 GLN cc_start: 0.8322 (tt0) cc_final: 0.7919 (tm-30) REVERT: A 144 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8157 (pp) REVERT: A 187 MET cc_start: 0.8534 (tmm) cc_final: 0.7913 (ttp) REVERT: B 88 GLN cc_start: 0.8317 (tt0) cc_final: 0.7911 (tm-30) REVERT: B 144 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8153 (pp) REVERT: B 187 MET cc_start: 0.8499 (tmm) cc_final: 0.7817 (ttp) REVERT: C 88 GLN cc_start: 0.8313 (tt0) cc_final: 0.7918 (tm-30) REVERT: C 144 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8129 (pp) REVERT: C 187 MET cc_start: 0.8525 (tmm) cc_final: 0.7830 (ttp) REVERT: D 88 GLN cc_start: 0.8321 (tt0) cc_final: 0.7923 (tm-30) REVERT: D 144 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8142 (pp) REVERT: D 187 MET cc_start: 0.8511 (tmm) cc_final: 0.7830 (ttp) outliers start: 69 outliers final: 35 residues processed: 178 average time/residue: 0.6508 time to fit residues: 136.8409 Evaluate side-chains 168 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 1.675 ------------------------------------------------------------------------------- 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 299 LEU 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 A residue 496 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 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 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 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 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 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 326 LEU Chi-restraints excluded: chain D residue 359 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.105293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.078843 restraints weight = 25838.237| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.72 r_work: 0.2942 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14308 Z= 0.179 Angle : 0.623 10.433 19440 Z= 0.314 Chirality : 0.042 0.174 2244 Planarity : 0.004 0.038 2384 Dihedral : 6.663 42.735 1988 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.11 % Allowed : 23.30 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.21), residues: 1700 helix: 2.26 (0.16), residues: 1012 sheet: -0.56 (0.33), residues: 244 loop : -1.44 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 335 HIS 0.003 0.000 HIS A 234 PHE 0.015 0.001 PHE A 505 TYR 0.016 0.001 TYR A 497 ARG 0.002 0.000 ARG B 403 Details of bonding type rmsd hydrogen bonds : bond 0.06297 ( 955) hydrogen bonds : angle 4.49935 ( 2781) SS BOND : bond 0.00635 ( 8) SS BOND : angle 2.17935 ( 16) covalent geometry : bond 0.00408 (14300) covalent geometry : angle 0.61984 (19424) *********************** 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 196 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 133 time to evaluate : 1.619 Fit side-chains REVERT: A 88 GLN cc_start: 0.8328 (tt0) cc_final: 0.7929 (tm-30) REVERT: A 144 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8165 (pp) REVERT: A 187 MET cc_start: 0.8484 (tmm) cc_final: 0.7814 (ttp) REVERT: B 88 GLN cc_start: 0.8311 (tt0) cc_final: 0.7918 (tm-30) REVERT: B 144 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8189 (pp) REVERT: B 187 MET cc_start: 0.8466 (tmm) cc_final: 0.7880 (ttp) REVERT: C 88 GLN cc_start: 0.8317 (tt0) cc_final: 0.7919 (tm-30) REVERT: C 144 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8176 (pp) REVERT: C 187 MET cc_start: 0.8481 (tmm) cc_final: 0.7875 (ttp) REVERT: D 88 GLN cc_start: 0.8325 (tt0) cc_final: 0.7925 (tm-30) REVERT: D 144 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8183 (pp) REVERT: D 187 MET cc_start: 0.8482 (tmm) cc_final: 0.7887 (ttp) outliers start: 63 outliers final: 29 residues processed: 176 average time/residue: 0.9700 time to fit residues: 198.6369 Evaluate side-chains 159 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 1.706 ------------------------------------------------------------------------------- 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 299 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 496 LEU 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 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 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 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 359 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 406 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 65 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 134 optimal weight: 0.0030 chunk 52 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 291 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.107991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.081640 restraints weight = 25798.179| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.73 r_work: 0.2989 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14308 Z= 0.133 Angle : 0.601 10.664 19440 Z= 0.299 Chirality : 0.041 0.143 2244 Planarity : 0.004 0.040 2384 Dihedral : 6.472 43.214 1988 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.33 % Allowed : 24.28 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.21), residues: 1700 helix: 2.37 (0.16), residues: 1012 sheet: -0.53 (0.33), residues: 244 loop : -1.42 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 354 HIS 0.007 0.001 HIS B 292 PHE 0.010 0.001 PHE A 235 TYR 0.014 0.001 TYR A 411 ARG 0.002 0.000 ARG B 403 Details of bonding type rmsd hydrogen bonds : bond 0.05589 ( 955) hydrogen bonds : angle 4.36229 ( 2781) SS BOND : bond 0.00585 ( 8) SS BOND : angle 1.72273 ( 16) covalent geometry : bond 0.00277 (14300) covalent geometry : angle 0.59931 (19424) *********************** 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 194 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 1.566 Fit side-chains REVERT: A 88 GLN cc_start: 0.8310 (tt0) cc_final: 0.7893 (tm-30) REVERT: A 144 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8060 (pp) REVERT: A 187 MET cc_start: 0.8501 (tmm) cc_final: 0.7817 (ttp) REVERT: A 334 MET cc_start: 0.2792 (OUTLIER) cc_final: 0.2238 (ttp) REVERT: B 88 GLN cc_start: 0.8305 (tt0) cc_final: 0.7892 (tm-30) REVERT: B 144 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8048 (pp) REVERT: B 187 MET cc_start: 0.8493 (tmm) cc_final: 0.7849 (ttp) REVERT: B 334 MET cc_start: 0.2603 (OUTLIER) cc_final: 0.2020 (ttp) REVERT: C 88 GLN cc_start: 0.8299 (tt0) cc_final: 0.7892 (tm-30) REVERT: C 144 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8071 (pp) REVERT: C 187 MET cc_start: 0.8490 (tmm) cc_final: 0.7809 (ttp) REVERT: C 334 MET cc_start: 0.2646 (OUTLIER) cc_final: 0.2061 (ttp) REVERT: D 88 GLN cc_start: 0.8299 (tt0) cc_final: 0.7890 (tm-30) REVERT: D 144 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8075 (pp) REVERT: D 187 MET cc_start: 0.8503 (tmm) cc_final: 0.7877 (ttp) outliers start: 51 outliers final: 28 residues processed: 175 average time/residue: 0.6543 time to fit residues: 136.1735 Evaluate side-chains 169 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 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 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 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 95 GLU 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 359 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 406 THR 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 359 VAL 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 149 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 138 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.107712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.081383 restraints weight = 25831.477| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.74 r_work: 0.2988 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2921 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= 0.136 Angle : 0.606 10.810 19440 Z= 0.300 Chirality : 0.041 0.139 2244 Planarity : 0.004 0.040 2384 Dihedral : 6.309 41.177 1988 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.55 % Allowed : 25.39 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.21), residues: 1700 helix: 2.40 (0.16), residues: 1012 sheet: -0.52 (0.33), residues: 244 loop : -1.41 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 335 HIS 0.003 0.000 HIS D 234 PHE 0.012 0.001 PHE A 505 TYR 0.014 0.001 TYR D 411 ARG 0.002 0.000 ARG C 403 Details of bonding type rmsd hydrogen bonds : bond 0.05619 ( 955) hydrogen bonds : angle 4.34188 ( 2781) SS BOND : bond 0.00547 ( 8) SS BOND : angle 1.80437 ( 16) covalent geometry : bond 0.00287 (14300) covalent geometry : angle 0.60371 (19424) ********************** 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 179 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 2.058 Fit side-chains REVERT: A 88 GLN cc_start: 0.8332 (tt0) cc_final: 0.7915 (tm-30) REVERT: A 144 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8035 (pp) REVERT: A 187 MET cc_start: 0.8502 (tmm) cc_final: 0.7858 (ttp) REVERT: A 334 MET cc_start: 0.2896 (OUTLIER) cc_final: 0.2311 (ttp) REVERT: B 88 GLN cc_start: 0.8334 (tt0) cc_final: 0.7919 (tm-30) REVERT: B 144 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8083 (pp) REVERT: B 187 MET cc_start: 0.8500 (tmm) cc_final: 0.7887 (ttp) REVERT: B 334 MET cc_start: 0.2645 (OUTLIER) cc_final: 0.2032 (ttp) REVERT: C 88 GLN cc_start: 0.8333 (tt0) cc_final: 0.7922 (tm-30) REVERT: C 144 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8082 (pp) REVERT: C 187 MET cc_start: 0.8504 (tmm) cc_final: 0.7855 (ttp) REVERT: C 334 MET cc_start: 0.2750 (OUTLIER) cc_final: 0.2134 (ttp) REVERT: D 88 GLN cc_start: 0.8325 (tt0) cc_final: 0.7911 (tm-30) REVERT: D 144 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8091 (pp) REVERT: D 187 MET cc_start: 0.8518 (tmm) cc_final: 0.7904 (ttp) outliers start: 39 outliers final: 27 residues processed: 168 average time/residue: 1.0775 time to fit residues: 214.8348 Evaluate side-chains 168 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 3.050 ------------------------------------------------------------------------------- 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 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 A residue 467 LEU 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 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 95 GLU 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 359 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 406 THR 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 359 VAL 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 63 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.106190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.079676 restraints weight = 26152.893| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.74 r_work: 0.2957 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14308 Z= 0.167 Angle : 0.625 10.803 19440 Z= 0.311 Chirality : 0.041 0.141 2244 Planarity : 0.004 0.039 2384 Dihedral : 6.291 42.626 1988 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.35 % Allowed : 26.11 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.21), residues: 1700 helix: 2.33 (0.16), residues: 1020 sheet: -0.55 (0.33), residues: 244 loop : -1.43 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 335 HIS 0.003 0.000 HIS B 234 PHE 0.014 0.001 PHE A 350 TYR 0.015 0.001 TYR C 497 ARG 0.002 0.000 ARG B 403 Details of bonding type rmsd hydrogen bonds : bond 0.05990 ( 955) hydrogen bonds : angle 4.40308 ( 2781) SS BOND : bond 0.00522 ( 8) SS BOND : angle 1.94706 ( 16) covalent geometry : bond 0.00378 (14300) covalent geometry : angle 0.62267 (19424) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8016.12 seconds wall clock time: 145 minutes 41.81 seconds (8741.81 seconds total)