Starting phenix.real_space_refine on Tue Mar 3 11:43:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qk1_14028/03_2026/7qk1_14028.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qk1_14028/03_2026/7qk1_14028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qk1_14028/03_2026/7qk1_14028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qk1_14028/03_2026/7qk1_14028.map" model { file = "/net/cci-nas-00/data/ceres_data/7qk1_14028/03_2026/7qk1_14028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qk1_14028/03_2026/7qk1_14028.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 6 5.16 5 C 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3444 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 0.91, per 1000 atoms: 0.26 Number of scatterers: 3444 At special positions: 0 Unit cell: (127.952, 116.32, 36.35, 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 6 16.00 O 642 8.00 N 636 7.00 C 2160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 153.8 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 50.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 306 through 310 removed outlier: 6.409A pdb=" N GLN C 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N TYR E 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL C 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.651A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 317 through 323 Processing sheet with id=AA4, first strand: chain 'E' and resid 333 through 334 removed outlier: 6.980A pdb=" N GLY C 333 " --> pdb=" O GLY E 334 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 337 through 342 Processing sheet with id=AA6, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.438A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 350 through 354 removed outlier: 6.463A pdb=" N GLN C 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ILE E 354 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS C 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 350 through 354 removed outlier: 6.463A pdb=" N GLN C 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ILE E 354 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS C 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 356 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU F 357 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP C 358 " --> pdb=" O LEU F 357 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.637A pdb=" N THR C 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 368 through 378 removed outlier: 6.556A pdb=" N LYS C 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N GLU E 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE C 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N HIS E 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR C 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LEU E 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS C 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N PHE E 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR C 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN C 368 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ILE F 371 " --> pdb=" O ASN C 368 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LYS C 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N THR F 373 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU C 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N LYS F 375 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N HIS C 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N THR F 377 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU C 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.624A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.894A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 317 through 318 Processing sheet with id=AB5, first strand: chain 'B' and resid 325 through 329 removed outlier: 6.632A pdb=" N GLY A 326 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N HIS B 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 333 through 334 removed outlier: 6.560A pdb=" N GLY A 333 " --> pdb=" O GLY B 334 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 337 through 342 removed outlier: 6.545A pdb=" N GLU A 338 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N SER B 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS A 340 " --> pdb=" O SER B 341 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.507A pdb=" N ASP A 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 350 through 351 removed outlier: 6.247A pdb=" N VAL A 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 354 through 362 removed outlier: 6.819A pdb=" N GLY B 355 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER A 356 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 369 through 378 removed outlier: 6.653A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LYS A 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N THR D 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU A 372 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N LYS D 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N HIS A 374 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR D 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU A 376 " --> pdb=" O THR D 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 70 hydrogen bonds defined for protein. 207 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: 0.45 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 922 1.33 - 1.45: 484 1.45 - 1.57: 2086 1.57 - 1.68: 0 1.68 - 1.80: 6 Bond restraints: 3498 Sorted by residual: bond pdb=" CZ ARG B 379 " pdb=" NH2 ARG B 379 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 8.79e+00 bond pdb=" CZ ARG A 379 " pdb=" NH2 ARG A 379 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.60e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.59e+00 bond pdb=" CZ ARG D 379 " pdb=" NH2 ARG D 379 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.07e+00 bond pdb=" CZ ARG B 349 " pdb=" NH2 ARG B 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.65e+00 ... (remaining 3493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 3062 1.81 - 3.62: 1317 3.62 - 5.43: 261 5.43 - 7.24: 35 7.24 - 9.05: 5 Bond angle restraints: 4680 Sorted by residual: angle pdb=" CA HIS A 330 " pdb=" C HIS A 330 " pdb=" N LYS A 331 " ideal model delta sigma weight residual 115.27 124.32 -9.05 1.47e+00 4.63e-01 3.79e+01 angle pdb=" CA GLY D 355 " pdb=" C GLY D 355 " pdb=" N SER D 356 " ideal model delta sigma weight residual 114.58 118.94 -4.36 8.60e-01 1.35e+00 2.57e+01 angle pdb=" C VAL B 318 " pdb=" CA VAL B 318 " pdb=" CB VAL B 318 " ideal model delta sigma weight residual 110.42 117.19 -6.77 1.35e+00 5.49e-01 2.52e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 117.56 -4.96 1.00e+00 1.00e+00 2.46e+01 angle pdb=" C VAL A 318 " pdb=" CA VAL A 318 " pdb=" CB VAL A 318 " ideal model delta sigma weight residual 110.77 117.70 -6.93 1.42e+00 4.96e-01 2.38e+01 ... (remaining 4675 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.79: 1966 16.79 - 33.58: 142 33.58 - 50.36: 17 50.36 - 67.15: 2 67.15 - 83.93: 9 Dihedral angle restraints: 2136 sinusoidal: 894 harmonic: 1242 Sorted by residual: dihedral pdb=" CA HIS A 330 " pdb=" C HIS A 330 " pdb=" N LYS A 331 " pdb=" CA LYS A 331 " ideal model delta harmonic sigma weight residual -180.00 -148.96 -31.04 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA HIS D 330 " pdb=" C HIS D 330 " pdb=" N LYS D 331 " pdb=" CA LYS D 331 " ideal model delta harmonic sigma weight residual -180.00 -150.17 -29.83 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA HIS B 330 " pdb=" C HIS B 330 " pdb=" N LYS B 331 " pdb=" CA LYS B 331 " ideal model delta harmonic sigma weight residual 180.00 -150.80 -29.20 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 2133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 305 0.076 - 0.152: 152 0.152 - 0.228: 41 0.228 - 0.305: 23 0.305 - 0.381: 7 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA ARG A 349 " pdb=" N ARG A 349 " pdb=" C ARG A 349 " pdb=" CB ARG A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA GLU A 372 " pdb=" N GLU A 372 " pdb=" C GLU A 372 " pdb=" CB GLU A 372 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA ARG D 349 " pdb=" N ARG D 349 " pdb=" C ARG D 349 " pdb=" CB ARG D 349 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 525 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 346 " 0.066 2.00e-02 2.50e+03 4.09e-02 2.92e+01 pdb=" CG PHE A 346 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 346 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 PHE A 346 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE A 346 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 346 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 346 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 346 " 0.060 2.00e-02 2.50e+03 3.73e-02 2.43e+01 pdb=" CG PHE B 346 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 346 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE B 346 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE B 346 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 346 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 346 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " -0.062 2.00e-02 2.50e+03 3.28e-02 2.16e+01 pdb=" CG TYR D 310 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " -0.047 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1614 2.98 - 3.46: 2765 3.46 - 3.94: 5256 3.94 - 4.42: 5505 4.42 - 4.90: 10767 Nonbonded interactions: 25907 Sorted by model distance: nonbonded pdb=" N HIS A 330 " pdb=" O HIS A 330 " model vdw 2.502 2.496 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.510 3.040 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.554 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.565 3.040 nonbonded pdb=" N HIS B 330 " pdb=" O HIS B 330 " model vdw 2.570 2.496 ... (remaining 25902 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.630 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.011 0.040 3498 Z= 0.703 Angle : 1.965 9.054 4680 Z= 1.293 Chirality : 0.108 0.381 528 Planarity : 0.011 0.053 594 Dihedral : 12.976 83.931 1344 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 349 TYR 0.062 0.016 TYR D 310 PHE 0.066 0.013 PHE A 346 HIS 0.019 0.005 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.01074 ( 3498) covalent geometry : angle 1.96516 ( 4680) hydrogen bonds : bond 0.09217 ( 70) hydrogen bonds : angle 7.15928 ( 207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: E 321 LYS cc_start: 0.8565 (mttt) cc_final: 0.8338 (mttt) REVERT: E 343 LYS cc_start: 0.9338 (mttt) cc_final: 0.8014 (pptt) REVERT: E 348 ASP cc_start: 0.9112 (t70) cc_final: 0.8885 (t0) REVERT: E 349 ARG cc_start: 0.8398 (ttm170) cc_final: 0.6034 (pmt-80) REVERT: F 359 ASN cc_start: 0.9004 (t0) cc_final: 0.8764 (t0) REVERT: F 369 LYS cc_start: 0.8094 (pttt) cc_final: 0.7601 (tptp) REVERT: B 321 LYS cc_start: 0.8578 (mmtp) cc_final: 0.7919 (pttt) REVERT: B 347 LYS cc_start: 0.9049 (mttt) cc_final: 0.7810 (pttm) REVERT: D 331 LYS cc_start: 0.7993 (mtpt) cc_final: 0.7016 (mmtm) REVERT: D 342 GLU cc_start: 0.8098 (tt0) cc_final: 0.7821 (tt0) REVERT: D 347 LYS cc_start: 0.8753 (mttt) cc_final: 0.8434 (mmmt) REVERT: D 349 ARG cc_start: 0.8783 (pmm-80) cc_final: 0.6310 (mmp80) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1134 time to fit residues: 23.1094 Evaluate side-chains 139 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 ASN E 368 ASN F 329 HIS F 330 HIS A 362 HIS A 374 HIS D 362 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.114433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.103659 restraints weight = 5775.572| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.49 r_work: 0.3447 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3498 Z= 0.166 Angle : 0.680 6.934 4680 Z= 0.344 Chirality : 0.051 0.145 528 Planarity : 0.004 0.032 594 Dihedral : 6.993 29.703 462 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.27 % Allowed : 15.15 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 379 TYR 0.019 0.002 TYR C 310 PHE 0.010 0.002 PHE B 378 HIS 0.003 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 3498) covalent geometry : angle 0.68047 ( 4680) hydrogen bonds : bond 0.02150 ( 70) hydrogen bonds : angle 5.11949 ( 207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.141 Fit side-chains REVERT: C 310 TYR cc_start: 0.9415 (t80) cc_final: 0.9022 (t80) REVERT: C 315 LEU cc_start: 0.9376 (mt) cc_final: 0.9171 (mt) REVERT: E 314 ASP cc_start: 0.8724 (t0) cc_final: 0.8436 (t0) REVERT: E 338 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7293 (tm-30) REVERT: E 340 LYS cc_start: 0.7782 (mtmt) cc_final: 0.7432 (mptt) REVERT: E 368 ASN cc_start: 0.8669 (m110) cc_final: 0.8367 (m-40) REVERT: F 331 LYS cc_start: 0.7653 (mmmt) cc_final: 0.6422 (ttmt) REVERT: F 340 LYS cc_start: 0.8409 (mmtp) cc_final: 0.8112 (mmtp) REVERT: F 359 ASN cc_start: 0.9342 (t0) cc_final: 0.9032 (t0) REVERT: F 369 LYS cc_start: 0.8365 (pttt) cc_final: 0.7065 (tppt) REVERT: A 317 LYS cc_start: 0.8294 (mtmt) cc_final: 0.7648 (mttm) REVERT: A 338 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8278 (tm-30) REVERT: A 340 LYS cc_start: 0.8407 (mttm) cc_final: 0.8093 (mtpt) REVERT: A 349 ARG cc_start: 0.8038 (ptp-170) cc_final: 0.7761 (ptm160) REVERT: A 351 GLN cc_start: 0.8565 (tt0) cc_final: 0.8126 (mt0) REVERT: B 319 THR cc_start: 0.9144 (m) cc_final: 0.8765 (p) REVERT: B 321 LYS cc_start: 0.8660 (mmtp) cc_final: 0.7207 (pttt) REVERT: B 327 ASN cc_start: 0.8929 (t0) cc_final: 0.8525 (t0) REVERT: B 338 GLU cc_start: 0.8729 (tt0) cc_final: 0.8246 (tm-30) REVERT: B 340 LYS cc_start: 0.8984 (mtpt) cc_final: 0.8400 (mttm) REVERT: B 347 LYS cc_start: 0.8980 (mttt) cc_final: 0.7732 (pttm) REVERT: B 348 ASP cc_start: 0.8642 (t0) cc_final: 0.7410 (p0) REVERT: B 349 ARG cc_start: 0.8543 (ptp-170) cc_final: 0.6327 (pmt-80) REVERT: D 331 LYS cc_start: 0.8099 (mtpt) cc_final: 0.6438 (mmpt) REVERT: D 347 LYS cc_start: 0.8742 (mttt) cc_final: 0.8364 (mmmt) REVERT: D 349 ARG cc_start: 0.8344 (pmm-80) cc_final: 0.5587 (mmp80) REVERT: D 351 GLN cc_start: 0.8455 (tt0) cc_final: 0.7848 (mt0) REVERT: D 370 LYS cc_start: 0.8984 (tttm) cc_final: 0.8679 (tptm) outliers start: 9 outliers final: 4 residues processed: 149 average time/residue: 0.1027 time to fit residues: 17.3770 Evaluate side-chains 139 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 ASN F 327 ASN A 327 ASN A 359 ASN B 327 ASN B 359 ASN B 368 ASN B 374 HIS D 327 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.107831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.097018 restraints weight = 5592.080| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.40 r_work: 0.3398 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3498 Z= 0.271 Angle : 0.705 7.222 4680 Z= 0.354 Chirality : 0.053 0.138 528 Planarity : 0.004 0.041 594 Dihedral : 6.691 30.572 462 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.55 % Allowed : 15.66 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 379 TYR 0.014 0.002 TYR C 310 PHE 0.017 0.003 PHE B 378 HIS 0.006 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00617 ( 3498) covalent geometry : angle 0.70519 ( 4680) hydrogen bonds : bond 0.02141 ( 70) hydrogen bonds : angle 4.66606 ( 207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.148 Fit side-chains REVERT: C 310 TYR cc_start: 0.9406 (t80) cc_final: 0.9100 (t80) REVERT: E 314 ASP cc_start: 0.8601 (t0) cc_final: 0.8305 (t0) REVERT: F 331 LYS cc_start: 0.6703 (mmmt) cc_final: 0.5423 (ttmt) REVERT: F 338 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7078 (tm-30) REVERT: F 359 ASN cc_start: 0.9334 (t0) cc_final: 0.9042 (t0) REVERT: F 369 LYS cc_start: 0.8548 (pttt) cc_final: 0.7108 (tptt) REVERT: A 308 ILE cc_start: 0.8769 (mt) cc_final: 0.8565 (mt) REVERT: A 338 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8217 (tm-30) REVERT: A 340 LYS cc_start: 0.8412 (mttm) cc_final: 0.8084 (mtpt) REVERT: A 349 ARG cc_start: 0.8236 (ptp-170) cc_final: 0.7929 (ptm160) REVERT: A 351 GLN cc_start: 0.8600 (tt0) cc_final: 0.8159 (mt0) REVERT: A 372 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: B 321 LYS cc_start: 0.8789 (mmtp) cc_final: 0.7121 (pttm) REVERT: B 338 GLU cc_start: 0.8743 (tt0) cc_final: 0.8221 (tm-30) REVERT: B 340 LYS cc_start: 0.8907 (mtpt) cc_final: 0.8538 (mtpp) REVERT: B 347 LYS cc_start: 0.9000 (mttt) cc_final: 0.7782 (pttm) REVERT: B 349 ARG cc_start: 0.8696 (ptp-170) cc_final: 0.6583 (pmt-80) REVERT: B 372 GLU cc_start: 0.4259 (mm-30) cc_final: 0.3392 (pt0) REVERT: D 317 LYS cc_start: 0.5187 (mmmt) cc_final: 0.4322 (mmmt) REVERT: D 347 LYS cc_start: 0.8688 (mttt) cc_final: 0.8305 (mmmt) REVERT: D 349 ARG cc_start: 0.8296 (pmm-80) cc_final: 0.5358 (mmm160) REVERT: D 370 LYS cc_start: 0.9052 (tttm) cc_final: 0.8653 (tptm) outliers start: 18 outliers final: 15 residues processed: 139 average time/residue: 0.0971 time to fit residues: 15.4086 Evaluate side-chains 147 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 377 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.112285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.101353 restraints weight = 5634.179| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.43 r_work: 0.3438 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3498 Z= 0.167 Angle : 0.618 7.897 4680 Z= 0.304 Chirality : 0.050 0.132 528 Planarity : 0.004 0.040 594 Dihedral : 6.026 27.309 462 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.54 % Allowed : 18.43 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 379 TYR 0.013 0.002 TYR C 310 PHE 0.010 0.002 PHE B 378 HIS 0.004 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 3498) covalent geometry : angle 0.61849 ( 4680) hydrogen bonds : bond 0.01594 ( 70) hydrogen bonds : angle 4.36290 ( 207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.105 Fit side-chains REVERT: C 310 TYR cc_start: 0.9406 (t80) cc_final: 0.9108 (t80) REVERT: C 348 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8429 (t70) REVERT: E 314 ASP cc_start: 0.8599 (t0) cc_final: 0.8284 (t0) REVERT: E 368 ASN cc_start: 0.8705 (m110) cc_final: 0.8381 (m-40) REVERT: F 338 GLU cc_start: 0.7693 (tm-30) cc_final: 0.6875 (tm-30) REVERT: F 359 ASN cc_start: 0.9329 (t0) cc_final: 0.9073 (t0) REVERT: F 369 LYS cc_start: 0.8398 (pttt) cc_final: 0.7140 (tptt) REVERT: A 338 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8171 (tm-30) REVERT: A 340 LYS cc_start: 0.8390 (mttm) cc_final: 0.8134 (mtpt) REVERT: A 351 GLN cc_start: 0.8546 (tt0) cc_final: 0.8182 (mt0) REVERT: B 321 LYS cc_start: 0.8641 (mmtp) cc_final: 0.6958 (pttm) REVERT: B 327 ASN cc_start: 0.9388 (t0) cc_final: 0.8981 (t0) REVERT: B 338 GLU cc_start: 0.8732 (tt0) cc_final: 0.8226 (tm-30) REVERT: B 340 LYS cc_start: 0.8936 (mtpt) cc_final: 0.8573 (mtpp) REVERT: B 347 LYS cc_start: 0.8977 (mttt) cc_final: 0.7780 (pttm) REVERT: B 348 ASP cc_start: 0.8494 (t0) cc_final: 0.7266 (p0) REVERT: B 372 GLU cc_start: 0.3957 (mm-30) cc_final: 0.2973 (pt0) REVERT: D 317 LYS cc_start: 0.5641 (mmmt) cc_final: 0.4409 (mmmt) REVERT: D 347 LYS cc_start: 0.8653 (mttt) cc_final: 0.8322 (mmmt) REVERT: D 349 ARG cc_start: 0.8150 (pmm-80) cc_final: 0.5297 (mmm160) REVERT: D 351 GLN cc_start: 0.8443 (tt0) cc_final: 0.7882 (mt0) REVERT: D 370 LYS cc_start: 0.9107 (tttm) cc_final: 0.8797 (tptm) outliers start: 14 outliers final: 10 residues processed: 138 average time/residue: 0.1029 time to fit residues: 16.1530 Evaluate side-chains 139 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN C 351 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.105130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.094007 restraints weight = 5682.999| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.42 r_work: 0.3360 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.044 3498 Z= 0.388 Angle : 0.776 8.469 4680 Z= 0.388 Chirality : 0.054 0.144 528 Planarity : 0.005 0.040 594 Dihedral : 6.678 28.117 462 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.55 % Allowed : 19.44 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 379 TYR 0.013 0.003 TYR D 310 PHE 0.020 0.003 PHE B 378 HIS 0.006 0.002 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00885 ( 3498) covalent geometry : angle 0.77585 ( 4680) hydrogen bonds : bond 0.02393 ( 70) hydrogen bonds : angle 4.57829 ( 207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.147 Fit side-chains REVERT: C 310 TYR cc_start: 0.9435 (t80) cc_final: 0.9105 (t80) REVERT: C 348 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8511 (t70) REVERT: E 314 ASP cc_start: 0.8512 (t0) cc_final: 0.8216 (t0) REVERT: F 338 GLU cc_start: 0.7438 (tm-30) cc_final: 0.6887 (tm-30) REVERT: F 369 LYS cc_start: 0.8684 (pttt) cc_final: 0.7321 (tptt) REVERT: A 338 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8177 (tm-30) REVERT: A 351 GLN cc_start: 0.8708 (tt0) cc_final: 0.8217 (mt0) REVERT: B 321 LYS cc_start: 0.8938 (mmtp) cc_final: 0.7080 (pttm) REVERT: B 338 GLU cc_start: 0.8756 (tt0) cc_final: 0.8218 (tm-30) REVERT: B 347 LYS cc_start: 0.9038 (mttt) cc_final: 0.7860 (pttm) REVERT: B 349 ARG cc_start: 0.8771 (ptp-170) cc_final: 0.6863 (pmt-80) REVERT: D 317 LYS cc_start: 0.5077 (mmmt) cc_final: 0.4341 (mmtt) REVERT: D 347 LYS cc_start: 0.8650 (mttt) cc_final: 0.8323 (mmmt) REVERT: D 349 ARG cc_start: 0.8351 (pmm-80) cc_final: 0.5469 (mmm160) outliers start: 18 outliers final: 16 residues processed: 137 average time/residue: 0.0934 time to fit residues: 14.6738 Evaluate side-chains 147 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain D residue 377 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.111861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.100604 restraints weight = 5575.141| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.53 r_work: 0.3435 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3498 Z= 0.135 Angle : 0.619 7.325 4680 Z= 0.301 Chirality : 0.050 0.134 528 Planarity : 0.004 0.040 594 Dihedral : 5.805 26.216 462 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.03 % Allowed : 21.46 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.012 0.002 TYR C 310 PHE 0.009 0.001 PHE A 378 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3498) covalent geometry : angle 0.61897 ( 4680) hydrogen bonds : bond 0.01477 ( 70) hydrogen bonds : angle 4.19245 ( 207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.147 Fit side-chains REVERT: C 310 TYR cc_start: 0.9414 (t80) cc_final: 0.9103 (t80) REVERT: C 348 ASP cc_start: 0.8870 (OUTLIER) cc_final: 0.8431 (t70) REVERT: E 314 ASP cc_start: 0.8526 (t0) cc_final: 0.8210 (t0) REVERT: F 369 LYS cc_start: 0.8414 (pttt) cc_final: 0.7180 (tppt) REVERT: A 338 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8192 (tm-30) REVERT: A 351 GLN cc_start: 0.8556 (tt0) cc_final: 0.8154 (mt0) REVERT: B 321 LYS cc_start: 0.8648 (mmtp) cc_final: 0.6938 (pttm) REVERT: B 327 ASN cc_start: 0.9382 (t0) cc_final: 0.8988 (t0) REVERT: B 338 GLU cc_start: 0.8792 (tt0) cc_final: 0.8251 (tm-30) REVERT: B 347 LYS cc_start: 0.9030 (mttt) cc_final: 0.7792 (pttm) REVERT: B 349 ARG cc_start: 0.8697 (ptp-170) cc_final: 0.6724 (pmt-80) REVERT: B 377 THR cc_start: 0.9069 (m) cc_final: 0.8807 (p) REVERT: D 317 LYS cc_start: 0.5364 (mmmt) cc_final: 0.3857 (mtmt) REVERT: D 347 LYS cc_start: 0.8674 (mttt) cc_final: 0.8370 (mmmt) REVERT: D 349 ARG cc_start: 0.8222 (pmm-80) cc_final: 0.5352 (mmm160) REVERT: D 370 LYS cc_start: 0.9156 (tttm) cc_final: 0.8674 (tptt) outliers start: 12 outliers final: 9 residues processed: 133 average time/residue: 0.1011 time to fit residues: 15.3488 Evaluate side-chains 136 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 341 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.108773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.097732 restraints weight = 5854.966| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.45 r_work: 0.3390 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 3498 Z= 0.308 Angle : 0.730 7.719 4680 Z= 0.357 Chirality : 0.052 0.147 528 Planarity : 0.005 0.046 594 Dihedral : 6.225 25.455 462 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.79 % Allowed : 21.46 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 379 TYR 0.011 0.002 TYR D 310 PHE 0.017 0.002 PHE B 378 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00696 ( 3498) covalent geometry : angle 0.72972 ( 4680) hydrogen bonds : bond 0.02074 ( 70) hydrogen bonds : angle 4.38990 ( 207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.106 Fit side-chains REVERT: C 310 TYR cc_start: 0.9437 (t80) cc_final: 0.9132 (t80) REVERT: C 348 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8495 (t70) REVERT: E 314 ASP cc_start: 0.8484 (t0) cc_final: 0.8172 (t0) REVERT: F 338 GLU cc_start: 0.7472 (tm-30) cc_final: 0.6917 (tm-30) REVERT: F 369 LYS cc_start: 0.8576 (pttt) cc_final: 0.7244 (tptt) REVERT: A 338 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8143 (tm-30) REVERT: A 351 GLN cc_start: 0.8658 (tt0) cc_final: 0.8226 (mt0) REVERT: B 321 LYS cc_start: 0.8897 (mmtp) cc_final: 0.7120 (pttm) REVERT: B 338 GLU cc_start: 0.8770 (tt0) cc_final: 0.8223 (tm-30) REVERT: B 347 LYS cc_start: 0.9032 (mttt) cc_final: 0.7855 (pttm) REVERT: B 349 ARG cc_start: 0.8751 (ptp-170) cc_final: 0.6836 (pmt-80) REVERT: D 317 LYS cc_start: 0.5478 (mmmt) cc_final: 0.4850 (mmtt) REVERT: D 347 LYS cc_start: 0.8724 (mttt) cc_final: 0.8400 (mmmt) REVERT: D 349 ARG cc_start: 0.8421 (pmm-80) cc_final: 0.5462 (mmm160) outliers start: 15 outliers final: 13 residues processed: 131 average time/residue: 0.1029 time to fit residues: 15.3077 Evaluate side-chains 141 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN D 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.110421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.099341 restraints weight = 5742.095| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.49 r_work: 0.3431 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3498 Z= 0.160 Angle : 0.635 7.400 4680 Z= 0.307 Chirality : 0.050 0.139 528 Planarity : 0.005 0.047 594 Dihedral : 5.758 25.650 462 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.54 % Allowed : 21.46 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 379 TYR 0.011 0.002 TYR C 310 PHE 0.009 0.001 PHE D 378 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 3498) covalent geometry : angle 0.63489 ( 4680) hydrogen bonds : bond 0.01597 ( 70) hydrogen bonds : angle 4.19230 ( 207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.142 Fit side-chains REVERT: C 310 TYR cc_start: 0.9403 (t80) cc_final: 0.9099 (t80) REVERT: C 348 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8420 (t70) REVERT: E 314 ASP cc_start: 0.8501 (t0) cc_final: 0.8172 (t0) REVERT: F 340 LYS cc_start: 0.8059 (mmtp) cc_final: 0.6815 (mmmt) REVERT: F 369 LYS cc_start: 0.8456 (pttt) cc_final: 0.7117 (tptt) REVERT: A 338 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8168 (tm-30) REVERT: A 351 GLN cc_start: 0.8528 (tt0) cc_final: 0.8123 (mt0) REVERT: B 321 LYS cc_start: 0.8719 (mmtp) cc_final: 0.6990 (pttm) REVERT: B 338 GLU cc_start: 0.8794 (tt0) cc_final: 0.8216 (tm-30) REVERT: B 347 LYS cc_start: 0.9011 (mttt) cc_final: 0.7794 (pttm) REVERT: B 349 ARG cc_start: 0.8676 (ptp-170) cc_final: 0.6679 (pmt-80) REVERT: B 377 THR cc_start: 0.9070 (m) cc_final: 0.8806 (p) REVERT: D 317 LYS cc_start: 0.5369 (mmmt) cc_final: 0.4565 (mmtt) REVERT: D 347 LYS cc_start: 0.8693 (mttt) cc_final: 0.8299 (mmmt) REVERT: D 349 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.5400 (mmm160) REVERT: D 370 LYS cc_start: 0.8976 (tttm) cc_final: 0.8698 (tptt) outliers start: 14 outliers final: 11 residues processed: 135 average time/residue: 0.0985 time to fit residues: 15.2213 Evaluate side-chains 140 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.108881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097738 restraints weight = 5737.781| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.45 r_work: 0.3403 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3498 Z= 0.271 Angle : 0.705 8.121 4680 Z= 0.343 Chirality : 0.052 0.153 528 Planarity : 0.005 0.050 594 Dihedral : 6.042 24.837 462 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.04 % Allowed : 21.97 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 379 TYR 0.010 0.002 TYR D 310 PHE 0.010 0.002 PHE B 378 HIS 0.004 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00610 ( 3498) covalent geometry : angle 0.70546 ( 4680) hydrogen bonds : bond 0.01947 ( 70) hydrogen bonds : angle 4.34180 ( 207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.151 Fit side-chains REVERT: C 310 TYR cc_start: 0.9424 (t80) cc_final: 0.9117 (t80) REVERT: C 348 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8504 (t70) REVERT: E 314 ASP cc_start: 0.8492 (t0) cc_final: 0.8150 (t0) REVERT: F 338 GLU cc_start: 0.7420 (tm-30) cc_final: 0.6880 (tm-30) REVERT: F 340 LYS cc_start: 0.8078 (mmtp) cc_final: 0.6831 (mmmt) REVERT: F 369 LYS cc_start: 0.8561 (pttt) cc_final: 0.7208 (tptt) REVERT: A 314 ASP cc_start: 0.8430 (t0) cc_final: 0.8045 (t0) REVERT: A 338 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8100 (tm-30) REVERT: A 351 GLN cc_start: 0.8593 (tt0) cc_final: 0.8158 (mt0) REVERT: B 321 LYS cc_start: 0.8820 (mmtp) cc_final: 0.7202 (pttm) REVERT: B 338 GLU cc_start: 0.8789 (tt0) cc_final: 0.8215 (tm-30) REVERT: B 347 LYS cc_start: 0.9039 (mttt) cc_final: 0.7827 (pttm) REVERT: B 349 ARG cc_start: 0.8718 (ptp-170) cc_final: 0.6787 (pmt-80) REVERT: D 317 LYS cc_start: 0.5448 (mmmt) cc_final: 0.4938 (mmtt) REVERT: D 340 LYS cc_start: 0.5630 (OUTLIER) cc_final: 0.4403 (mttm) REVERT: D 347 LYS cc_start: 0.8738 (mttt) cc_final: 0.8352 (mmmt) REVERT: D 349 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.5453 (mmm160) outliers start: 16 outliers final: 12 residues processed: 131 average time/residue: 0.0981 time to fit residues: 14.6849 Evaluate side-chains 142 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.108568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.097263 restraints weight = 5800.200| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.54 r_work: 0.3403 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3498 Z= 0.254 Angle : 0.690 8.061 4680 Z= 0.336 Chirality : 0.052 0.147 528 Planarity : 0.005 0.050 594 Dihedral : 6.037 25.804 462 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.04 % Allowed : 21.46 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.010 0.002 TYR C 310 PHE 0.009 0.002 PHE B 378 HIS 0.003 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 3498) covalent geometry : angle 0.69022 ( 4680) hydrogen bonds : bond 0.01901 ( 70) hydrogen bonds : angle 4.35645 ( 207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.150 Fit side-chains REVERT: C 310 TYR cc_start: 0.9417 (t80) cc_final: 0.9108 (t80) REVERT: C 348 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8489 (t70) REVERT: E 314 ASP cc_start: 0.8504 (t0) cc_final: 0.8171 (t0) REVERT: F 338 GLU cc_start: 0.7374 (tm-30) cc_final: 0.6875 (tm-30) REVERT: F 340 LYS cc_start: 0.8086 (mmtp) cc_final: 0.6852 (mmmt) REVERT: F 369 LYS cc_start: 0.8555 (pttt) cc_final: 0.7195 (tptt) REVERT: A 314 ASP cc_start: 0.8451 (t0) cc_final: 0.8084 (t0) REVERT: A 338 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8131 (tm-30) REVERT: A 351 GLN cc_start: 0.8602 (tt0) cc_final: 0.8160 (mt0) REVERT: B 321 LYS cc_start: 0.8845 (mmtp) cc_final: 0.7152 (pttm) REVERT: B 338 GLU cc_start: 0.8816 (tt0) cc_final: 0.8245 (tm-30) REVERT: B 347 LYS cc_start: 0.8902 (mttt) cc_final: 0.7604 (pttm) REVERT: B 349 ARG cc_start: 0.8716 (ptp-170) cc_final: 0.6797 (pmt-80) REVERT: D 317 LYS cc_start: 0.5485 (mmmt) cc_final: 0.4998 (mmtt) REVERT: D 340 LYS cc_start: 0.5676 (OUTLIER) cc_final: 0.4441 (mttm) REVERT: D 347 LYS cc_start: 0.8742 (mttt) cc_final: 0.8349 (mmmt) REVERT: D 349 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.5459 (mmm160) outliers start: 16 outliers final: 13 residues processed: 131 average time/residue: 0.1050 time to fit residues: 15.6838 Evaluate side-chains 145 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 35 optimal weight: 0.0060 chunk 29 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 overall best weight: 3.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.110583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.099565 restraints weight = 5750.212| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.45 r_work: 0.3431 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3498 Z= 0.178 Angle : 0.646 8.085 4680 Z= 0.312 Chirality : 0.050 0.140 528 Planarity : 0.005 0.050 594 Dihedral : 5.727 24.927 462 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.79 % Allowed : 21.21 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 379 TYR 0.011 0.002 TYR C 310 PHE 0.008 0.001 PHE D 378 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 3498) covalent geometry : angle 0.64623 ( 4680) hydrogen bonds : bond 0.01653 ( 70) hydrogen bonds : angle 4.21130 ( 207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1118.13 seconds wall clock time: 19 minutes 51.70 seconds (1191.70 seconds total)