Starting phenix.real_space_refine on Tue Feb 11 01:07:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qk1_14028/02_2025/7qk1_14028.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qk1_14028/02_2025/7qk1_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_14028/02_2025/7qk1_14028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qk1_14028/02_2025/7qk1_14028.map" model { file = "/net/cci-nas-00/data/ceres_data/7qk1_14028/02_2025/7qk1_14028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qk1_14028/02_2025/7qk1_14028.cif" } resolution = 3.03 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= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 2.70, per 1000 atoms: 0.78 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: 0.84 Conformation dependent library (CDL) restraints added in 507.6 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: 0.57 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: 0.94 Time building geometry restraints manager: 0.99 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: 0.01 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: 0.290 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.500 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.930 ------------------------------------------------------------------------------- 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= 0.722 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 (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: -1.61 (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 HIS 0.019 0.005 HIS D 362 PHE 0.066 0.013 PHE A 346 TYR 0.062 0.016 TYR D 310 ARG 0.005 0.001 ARG A 349 *********************** 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 : 0.397 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: 0.6033 (pmt-80) REVERT: F 340 LYS cc_start: 0.8171 (mttm) cc_final: 0.7949 (mmtp) REVERT: F 359 ASN cc_start: 0.9004 (t0) cc_final: 0.8763 (t0) REVERT: F 369 LYS cc_start: 0.8093 (pttt) cc_final: 0.7600 (tptp) REVERT: B 321 LYS cc_start: 0.8578 (mmtp) cc_final: 0.7920 (pttt) REVERT: B 347 LYS cc_start: 0.9049 (mttt) cc_final: 0.7809 (pttm) REVERT: D 331 LYS cc_start: 0.7993 (mtpt) cc_final: 0.7016 (mmtm) REVERT: D 342 GLU cc_start: 0.8097 (tt0) cc_final: 0.7822 (tt0) REVERT: D 347 LYS cc_start: 0.8754 (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: 0.2779 time to fit residues: 56.4824 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 : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.112506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101335 restraints weight = 5211.893| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.44 r_work: 0.3436 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3498 Z= 0.278 Angle : 0.681 6.909 4680 Z= 0.345 Chirality : 0.052 0.147 528 Planarity : 0.004 0.033 594 Dihedral : 7.063 30.242 462 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.02 % Allowed : 15.91 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.36 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.011 0.002 PHE B 378 TYR 0.018 0.002 TYR C 310 ARG 0.002 0.000 ARG C 349 *********************** 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 155 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.408 Fit side-chains REVERT: C 310 TYR cc_start: 0.9420 (t80) cc_final: 0.9053 (t80) REVERT: C 315 LEU cc_start: 0.9374 (mt) cc_final: 0.9165 (mt) REVERT: E 314 ASP cc_start: 0.8708 (t0) cc_final: 0.8422 (t0) REVERT: E 368 ASN cc_start: 0.8707 (m110) cc_final: 0.8405 (m-40) REVERT: F 331 LYS cc_start: 0.7703 (mmmt) cc_final: 0.6438 (ttmt) REVERT: F 338 GLU cc_start: 0.8248 (tt0) cc_final: 0.7728 (tm-30) REVERT: F 359 ASN cc_start: 0.9333 (t0) cc_final: 0.9121 (t0) REVERT: F 369 LYS cc_start: 0.8406 (pttt) cc_final: 0.7089 (tppt) REVERT: A 317 LYS cc_start: 0.8306 (mtmt) cc_final: 0.7651 (mttm) REVERT: A 338 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8259 (tm-30) REVERT: A 340 LYS cc_start: 0.8554 (mttm) cc_final: 0.8068 (mtpt) REVERT: A 349 ARG cc_start: 0.8066 (ptp-170) cc_final: 0.7764 (ptm160) REVERT: A 351 GLN cc_start: 0.8565 (tt0) cc_final: 0.8102 (mt0) REVERT: B 319 THR cc_start: 0.9184 (m) cc_final: 0.8743 (p) REVERT: B 321 LYS cc_start: 0.8713 (mmtp) cc_final: 0.7257 (pttt) REVERT: B 327 ASN cc_start: 0.8951 (t0) cc_final: 0.8523 (t0) REVERT: B 338 GLU cc_start: 0.8708 (tt0) cc_final: 0.8229 (tm-30) REVERT: B 340 LYS cc_start: 0.8979 (mtpt) cc_final: 0.8395 (mttm) REVERT: B 347 LYS cc_start: 0.8988 (mttt) cc_final: 0.7702 (pttm) REVERT: B 348 ASP cc_start: 0.8838 (t0) cc_final: 0.7527 (p0) REVERT: B 349 ARG cc_start: 0.8569 (ptp-170) cc_final: 0.6855 (pmt-80) REVERT: B 372 GLU cc_start: 0.4829 (mm-30) cc_final: 0.3954 (mm-30) REVERT: D 307 GLN cc_start: 0.4060 (tp-100) cc_final: 0.3839 (tp-100) REVERT: D 331 LYS cc_start: 0.8142 (mtpt) cc_final: 0.6471 (mmmt) REVERT: D 347 LYS cc_start: 0.8762 (mttt) cc_final: 0.8374 (mmmt) REVERT: D 349 ARG cc_start: 0.8382 (pmm-80) cc_final: 0.5618 (mmp80) REVERT: D 370 LYS cc_start: 0.9055 (tttm) cc_final: 0.8676 (tptm) outliers start: 8 outliers final: 5 residues processed: 148 average time/residue: 0.2201 time to fit residues: 37.1208 Evaluate side-chains 139 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 19 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.110861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.100134 restraints weight = 5610.726| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.39 r_work: 0.3409 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 0.031 3498 Z= 0.395 Angle : 0.691 7.150 4680 Z= 0.347 Chirality : 0.052 0.137 528 Planarity : 0.004 0.041 594 Dihedral : 6.663 30.246 462 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.29 % Allowed : 15.66 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.51 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 362 PHE 0.016 0.002 PHE B 378 TYR 0.014 0.002 TYR C 310 ARG 0.003 0.000 ARG D 379 *********************** 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 150 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.428 Fit side-chains REVERT: C 310 TYR cc_start: 0.9409 (t80) cc_final: 0.9106 (t80) REVERT: E 314 ASP cc_start: 0.8634 (t0) cc_final: 0.8300 (t0) REVERT: F 331 LYS cc_start: 0.6719 (mmmt) cc_final: 0.5447 (ttmt) REVERT: F 359 ASN cc_start: 0.9322 (t0) cc_final: 0.9088 (t0) REVERT: F 369 LYS cc_start: 0.8529 (pttt) cc_final: 0.7102 (tptt) REVERT: A 338 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8231 (tm-30) REVERT: A 340 LYS cc_start: 0.8439 (mttm) cc_final: 0.8128 (mtpt) REVERT: A 349 ARG cc_start: 0.8250 (ptp-170) cc_final: 0.7940 (ptm160) REVERT: A 351 GLN cc_start: 0.8597 (tt0) cc_final: 0.8151 (mt0) REVERT: A 372 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: B 321 LYS cc_start: 0.8782 (mmtp) cc_final: 0.7075 (pttm) REVERT: B 338 GLU cc_start: 0.8742 (tt0) cc_final: 0.8223 (tm-30) REVERT: B 340 LYS cc_start: 0.8914 (mtpt) cc_final: 0.8544 (mtpp) REVERT: B 347 LYS cc_start: 0.8991 (mttt) cc_final: 0.7780 (pttm) REVERT: B 348 ASP cc_start: 0.8571 (t0) cc_final: 0.7274 (p0) REVERT: B 349 ARG cc_start: 0.8691 (ptp-170) cc_final: 0.6673 (pmt-80) REVERT: B 372 GLU cc_start: 0.4311 (mm-30) cc_final: 0.3413 (pt0) REVERT: D 317 LYS cc_start: 0.5200 (mmmt) cc_final: 0.4321 (mmmt) REVERT: D 347 LYS cc_start: 0.8676 (mttt) cc_final: 0.8291 (mmmt) REVERT: D 349 ARG cc_start: 0.8288 (pmm-80) cc_final: 0.5353 (mmm160) REVERT: D 370 LYS cc_start: 0.9052 (tttm) cc_final: 0.8647 (tptm) outliers start: 17 outliers final: 12 residues processed: 138 average time/residue: 0.2222 time to fit residues: 34.7405 Evaluate side-chains 141 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 26 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 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 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 = 0.3723 r_free = 0.3723 target = 0.112135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.101106 restraints weight = 5606.074| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.44 r_work: 0.3447 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4129 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= 0.239 Angle : 0.602 6.086 4680 Z= 0.299 Chirality : 0.050 0.133 528 Planarity : 0.004 0.040 594 Dihedral : 5.993 26.980 462 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.78 % Allowed : 18.69 % Favored : 78.54 % 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: -1.43 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.010 0.002 PHE E 378 TYR 0.014 0.002 TYR C 310 ARG 0.001 0.000 ARG F 379 *********************** 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 152 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.439 Fit side-chains REVERT: C 310 TYR cc_start: 0.9408 (t80) cc_final: 0.9103 (t80) REVERT: C 342 GLU cc_start: 0.8494 (tt0) cc_final: 0.8286 (tt0) REVERT: E 314 ASP cc_start: 0.8603 (t0) cc_final: 0.8254 (t0) REVERT: E 368 ASN cc_start: 0.8693 (m110) cc_final: 0.8361 (m-40) REVERT: F 359 ASN cc_start: 0.9269 (t0) cc_final: 0.9062 (t0) REVERT: F 369 LYS cc_start: 0.8382 (pttt) cc_final: 0.7127 (tptp) REVERT: A 308 ILE cc_start: 0.8658 (mt) cc_final: 0.8441 (mt) REVERT: A 321 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7869 (mmtp) REVERT: A 338 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8160 (tm-30) REVERT: A 340 LYS cc_start: 0.8362 (mttm) cc_final: 0.8096 (mtpt) REVERT: A 351 GLN cc_start: 0.8508 (tt0) cc_final: 0.8136 (mt0) REVERT: B 321 LYS cc_start: 0.8590 (mmtp) cc_final: 0.6998 (pttm) REVERT: B 327 ASN cc_start: 0.9374 (t0) cc_final: 0.8966 (t0) REVERT: B 338 GLU cc_start: 0.8740 (tt0) cc_final: 0.8214 (tm-30) REVERT: B 340 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8560 (mtpp) REVERT: B 347 LYS cc_start: 0.9006 (mttt) cc_final: 0.7776 (pttm) REVERT: B 348 ASP cc_start: 0.8483 (t0) cc_final: 0.7336 (p0) REVERT: B 372 GLU cc_start: 0.3898 (mm-30) cc_final: 0.2904 (pt0) REVERT: D 317 LYS cc_start: 0.5591 (mmmt) cc_final: 0.4300 (mtmt) REVERT: D 347 LYS cc_start: 0.8674 (mttt) cc_final: 0.8374 (mmmt) REVERT: D 349 ARG cc_start: 0.8129 (pmm-80) cc_final: 0.5281 (mmm160) REVERT: D 370 LYS cc_start: 0.9107 (tttm) cc_final: 0.8802 (tptm) outliers start: 11 outliers final: 8 residues processed: 144 average time/residue: 0.2246 time to fit residues: 36.9797 Evaluate side-chains 139 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 347 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 321 LYS 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 41 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** D 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.109618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.098334 restraints weight = 5680.751| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.55 r_work: 0.3388 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 3498 Z= 0.405 Angle : 0.680 6.879 4680 Z= 0.336 Chirality : 0.051 0.133 528 Planarity : 0.004 0.040 594 Dihedral : 6.225 26.390 462 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.04 % Allowed : 19.44 % Favored : 76.52 % 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: -1.59 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 362 PHE 0.016 0.002 PHE B 378 TYR 0.011 0.002 TYR C 310 ARG 0.002 0.000 ARG F 379 *********************** 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 149 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.412 Fit side-chains REVERT: C 310 TYR cc_start: 0.9415 (t80) cc_final: 0.9112 (t80) REVERT: C 348 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8423 (t70) REVERT: E 314 ASP cc_start: 0.8549 (t0) cc_final: 0.8214 (t0) REVERT: F 369 LYS cc_start: 0.8498 (pttt) cc_final: 0.7153 (tptt) REVERT: A 338 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8222 (tm-30) REVERT: A 351 GLN cc_start: 0.8624 (tt0) cc_final: 0.8204 (mt0) REVERT: B 321 LYS cc_start: 0.8806 (mmtp) cc_final: 0.7062 (pttm) REVERT: B 338 GLU cc_start: 0.8778 (tt0) cc_final: 0.8230 (tm-30) REVERT: B 347 LYS cc_start: 0.9044 (mttt) cc_final: 0.7820 (pttm) REVERT: B 348 ASP cc_start: 0.8556 (t0) cc_final: 0.7337 (p0) REVERT: B 372 GLU cc_start: 0.4525 (mm-30) cc_final: 0.2672 (pt0) REVERT: D 317 LYS cc_start: 0.5327 (mmmt) cc_final: 0.4510 (mmtt) REVERT: D 347 LYS cc_start: 0.8674 (mttt) cc_final: 0.8318 (mmmt) REVERT: D 349 ARG cc_start: 0.8370 (pmm-80) cc_final: 0.5347 (mmm160) REVERT: D 370 LYS cc_start: 0.9102 (tttm) cc_final: 0.8785 (tptm) outliers start: 16 outliers final: 13 residues processed: 136 average time/residue: 0.2190 time to fit residues: 34.0888 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 : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 316 SER 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 319 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 0.4980 chunk 2 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 overall best weight: 5.8988 ------------------------------------------------------------------------------- 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** D 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.107685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.096303 restraints weight = 5835.802| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.57 r_work: 0.3372 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4365 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= 0.473 Angle : 0.709 7.111 4680 Z= 0.351 Chirality : 0.052 0.135 528 Planarity : 0.005 0.043 594 Dihedral : 6.318 26.708 462 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.30 % Allowed : 20.20 % 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 (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: -1.76 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 374 PHE 0.017 0.002 PHE B 378 TYR 0.011 0.002 TYR D 310 ARG 0.002 0.000 ARG F 379 *********************** 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 153 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.468 Fit side-chains REVERT: C 310 TYR cc_start: 0.9434 (t80) cc_final: 0.9134 (t80) REVERT: C 342 GLU cc_start: 0.8657 (tt0) cc_final: 0.8453 (tt0) REVERT: C 348 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8423 (t70) REVERT: E 314 ASP cc_start: 0.8530 (t0) cc_final: 0.8210 (t0) REVERT: F 369 LYS cc_start: 0.8568 (pttt) cc_final: 0.7230 (tptt) REVERT: A 338 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8113 (tm-30) REVERT: A 351 GLN cc_start: 0.8616 (tt0) cc_final: 0.8124 (mt0) REVERT: B 321 LYS cc_start: 0.8879 (mmtp) cc_final: 0.7097 (pttm) REVERT: B 338 GLU cc_start: 0.8795 (tt0) cc_final: 0.8221 (tm-30) REVERT: B 347 LYS cc_start: 0.9037 (mttt) cc_final: 0.7840 (pttm) REVERT: D 317 LYS cc_start: 0.5506 (mmmt) cc_final: 0.4866 (mmtt) REVERT: D 347 LYS cc_start: 0.8702 (mttt) cc_final: 0.8332 (mmmt) REVERT: D 349 ARG cc_start: 0.8422 (pmm-80) cc_final: 0.5428 (mmm160) REVERT: D 370 LYS cc_start: 0.9034 (tttm) cc_final: 0.8504 (tptt) outliers start: 21 outliers final: 17 residues processed: 137 average time/residue: 0.2193 time to fit residues: 34.5284 Evaluate side-chains 145 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 316 SER 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 A residue 344 LEU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 377 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 16 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 0.1980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN B 327 ASN D 307 GLN D 330 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.116121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.105224 restraints weight = 5548.078| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.48 r_work: 0.3513 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3498 Z= 0.123 Angle : 0.569 7.840 4680 Z= 0.272 Chirality : 0.050 0.142 528 Planarity : 0.004 0.046 594 Dihedral : 5.230 23.932 462 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.77 % Allowed : 24.24 % 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 (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: -1.57 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 362 PHE 0.009 0.001 PHE E 378 TYR 0.012 0.001 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** 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 144 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.427 Fit side-chains REVERT: C 310 TYR cc_start: 0.9388 (t80) cc_final: 0.9137 (t80) REVERT: C 348 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8347 (t70) REVERT: E 314 ASP cc_start: 0.8507 (t0) cc_final: 0.8223 (t0) REVERT: F 340 LYS cc_start: 0.7982 (mmtp) cc_final: 0.7732 (mmtp) REVERT: F 369 LYS cc_start: 0.8215 (pttt) cc_final: 0.6927 (tppt) REVERT: A 314 ASP cc_start: 0.8180 (t0) cc_final: 0.7831 (t0) REVERT: A 338 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8155 (tm-30) REVERT: A 351 GLN cc_start: 0.8474 (tt0) cc_final: 0.8193 (mt0) REVERT: B 321 LYS cc_start: 0.8345 (mmtp) cc_final: 0.6670 (pttm) REVERT: B 327 ASN cc_start: 0.9004 (t0) cc_final: 0.8586 (t0) REVERT: B 338 GLU cc_start: 0.8780 (tt0) cc_final: 0.8257 (tm-30) REVERT: B 347 LYS cc_start: 0.9051 (mttt) cc_final: 0.7805 (pttm) REVERT: B 348 ASP cc_start: 0.8508 (t0) cc_final: 0.6967 (p0) REVERT: B 349 ARG cc_start: 0.8573 (ptp-170) cc_final: 0.6442 (pmt-80) REVERT: B 377 THR cc_start: 0.9048 (m) cc_final: 0.8819 (p) REVERT: D 317 LYS cc_start: 0.5663 (mmmt) cc_final: 0.4667 (mmtt) REVERT: D 349 ARG cc_start: 0.8008 (pmm-80) cc_final: 0.5223 (mmm160) REVERT: D 370 LYS cc_start: 0.9229 (tttm) cc_final: 0.8922 (tptm) outliers start: 7 outliers final: 2 residues processed: 139 average time/residue: 0.2244 time to fit residues: 35.6229 Evaluate side-chains 133 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain A residue 315 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 0.0970 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.111317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.100087 restraints weight = 5671.495| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.55 r_work: 0.3441 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4642 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= 0.244 Angle : 0.616 6.616 4680 Z= 0.298 Chirality : 0.050 0.133 528 Planarity : 0.005 0.065 594 Dihedral : 5.414 22.096 462 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.02 % Allowed : 23.48 % 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 (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: -1.61 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.011 0.002 PHE B 378 TYR 0.010 0.002 TYR C 310 ARG 0.008 0.001 ARG C 349 *********************** 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 140 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.413 Fit side-chains REVERT: C 310 TYR cc_start: 0.9413 (t80) cc_final: 0.9125 (t80) REVERT: C 348 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8399 (t70) REVERT: E 314 ASP cc_start: 0.8532 (t0) cc_final: 0.8193 (t0) REVERT: F 340 LYS cc_start: 0.7954 (mmtp) cc_final: 0.7725 (mmtp) REVERT: F 369 LYS cc_start: 0.8445 (pttt) cc_final: 0.7131 (tptt) REVERT: A 314 ASP cc_start: 0.8310 (t0) cc_final: 0.7957 (t0) REVERT: A 338 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8153 (tm-30) REVERT: A 351 GLN cc_start: 0.8527 (tt0) cc_final: 0.8216 (mt0) REVERT: B 321 LYS cc_start: 0.8534 (mmtp) cc_final: 0.6999 (pttm) REVERT: B 327 ASN cc_start: 0.9444 (t0) cc_final: 0.9088 (t0) REVERT: B 338 GLU cc_start: 0.8773 (tt0) cc_final: 0.8211 (tm-30) REVERT: B 340 LYS cc_start: 0.8956 (mtpt) cc_final: 0.8259 (mttm) REVERT: B 347 LYS cc_start: 0.9060 (mttt) cc_final: 0.7822 (pttm) REVERT: B 348 ASP cc_start: 0.8536 (t0) cc_final: 0.6873 (p0) REVERT: B 349 ARG cc_start: 0.8644 (ptp-170) cc_final: 0.6622 (pmt-80) REVERT: B 377 THR cc_start: 0.9019 (m) cc_final: 0.8817 (p) REVERT: D 317 LYS cc_start: 0.5762 (mmmt) cc_final: 0.5240 (mmtt) REVERT: D 349 ARG cc_start: 0.8146 (pmm-80) cc_final: 0.5301 (mmp80) REVERT: D 370 LYS cc_start: 0.9056 (tttm) cc_final: 0.8543 (tptt) outliers start: 8 outliers final: 6 residues processed: 133 average time/residue: 0.2266 time to fit residues: 34.3142 Evaluate side-chains 137 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 357 LEU 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 A residue 315 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 20.0000 chunk 8 optimal weight: 0.0670 chunk 27 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.116018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.104973 restraints weight = 5510.968| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.55 r_work: 0.3514 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3498 Z= 0.144 Angle : 0.568 6.851 4680 Z= 0.270 Chirality : 0.049 0.145 528 Planarity : 0.005 0.052 594 Dihedral : 4.923 20.741 462 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.77 % Allowed : 23.23 % 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 (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: -1.50 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.007 0.001 PHE E 378 TYR 0.011 0.001 TYR C 310 ARG 0.005 0.000 ARG C 349 *********************** 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 141 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.446 Fit side-chains REVERT: C 310 TYR cc_start: 0.9385 (t80) cc_final: 0.9155 (t80) REVERT: C 348 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8287 (t70) REVERT: E 314 ASP cc_start: 0.8578 (t0) cc_final: 0.8217 (t0) REVERT: F 331 LYS cc_start: 0.6660 (tppt) cc_final: 0.6230 (tppt) REVERT: F 369 LYS cc_start: 0.8294 (pttt) cc_final: 0.7088 (tppt) REVERT: A 314 ASP cc_start: 0.8208 (t0) cc_final: 0.7846 (t0) REVERT: A 338 GLU cc_start: 0.8641 (tm-30) cc_final: 0.7907 (tm-30) REVERT: A 349 ARG cc_start: 0.8254 (ptm160) cc_final: 0.7968 (ptp-110) REVERT: A 351 GLN cc_start: 0.8414 (tt0) cc_final: 0.8199 (mt0) REVERT: B 321 LYS cc_start: 0.8332 (mmtp) cc_final: 0.6804 (pttm) REVERT: B 327 ASN cc_start: 0.9414 (t0) cc_final: 0.8977 (t0) REVERT: B 338 GLU cc_start: 0.8766 (tt0) cc_final: 0.8278 (tm-30) REVERT: B 340 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8172 (mttm) REVERT: B 347 LYS cc_start: 0.9048 (mttt) cc_final: 0.7861 (pttm) REVERT: B 349 ARG cc_start: 0.8566 (ptp-170) cc_final: 0.6433 (pmt-80) REVERT: B 375 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8297 (ttpt) REVERT: D 317 LYS cc_start: 0.5843 (mmmt) cc_final: 0.5373 (mmtt) REVERT: D 349 ARG cc_start: 0.7930 (pmm-80) cc_final: 0.5100 (mmm160) REVERT: D 351 GLN cc_start: 0.8618 (tt0) cc_final: 0.8015 (mt0) REVERT: D 370 LYS cc_start: 0.9114 (tttm) cc_final: 0.8741 (tptt) outliers start: 7 outliers final: 4 residues processed: 135 average time/residue: 0.2097 time to fit residues: 32.4113 Evaluate side-chains 135 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 357 LEU Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain A residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS B 330 HIS D 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.110561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.099352 restraints weight = 5690.557| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.54 r_work: 0.3432 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3498 Z= 0.305 Angle : 0.669 8.828 4680 Z= 0.320 Chirality : 0.050 0.136 528 Planarity : 0.005 0.052 594 Dihedral : 5.425 22.120 462 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.52 % Allowed : 23.23 % Favored : 75.25 % 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: -1.55 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.012 0.002 PHE B 378 TYR 0.009 0.002 TYR C 310 ARG 0.008 0.001 ARG C 349 ********************** 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 139 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.446 Fit side-chains REVERT: C 310 TYR cc_start: 0.9418 (t80) cc_final: 0.9132 (t80) REVERT: C 348 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8381 (t70) REVERT: E 314 ASP cc_start: 0.8524 (t0) cc_final: 0.8182 (t0) REVERT: F 331 LYS cc_start: 0.6759 (tppt) cc_final: 0.6272 (tppt) REVERT: F 369 LYS cc_start: 0.8484 (pttt) cc_final: 0.7200 (tptt) REVERT: A 338 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8144 (tm-30) REVERT: A 351 GLN cc_start: 0.8533 (tt0) cc_final: 0.8215 (mt0) REVERT: B 321 LYS cc_start: 0.8603 (mmtp) cc_final: 0.7086 (pttm) REVERT: B 338 GLU cc_start: 0.8780 (tt0) cc_final: 0.8211 (tm-30) REVERT: B 340 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8276 (mttm) REVERT: B 347 LYS cc_start: 0.9054 (mttt) cc_final: 0.7833 (pttm) REVERT: B 349 ARG cc_start: 0.8632 (ptp-170) cc_final: 0.6568 (pmt-80) REVERT: D 317 LYS cc_start: 0.5939 (mmmt) cc_final: 0.5468 (mmtt) REVERT: D 349 ARG cc_start: 0.8252 (pmm-80) cc_final: 0.5362 (mmm160) REVERT: D 370 LYS cc_start: 0.9066 (tttm) cc_final: 0.8551 (tptt) outliers start: 6 outliers final: 5 residues processed: 133 average time/residue: 0.2148 time to fit residues: 32.7603 Evaluate side-chains 137 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 357 LEU Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 0.0570 chunk 22 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 overall best weight: 5.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN D 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.109137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.097954 restraints weight = 5742.292| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.47 r_work: 0.3406 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3498 Z= 0.440 Angle : 0.726 8.517 4680 Z= 0.354 Chirality : 0.052 0.139 528 Planarity : 0.005 0.054 594 Dihedral : 5.924 25.777 462 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.53 % Allowed : 22.47 % 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 (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: -1.74 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 374 PHE 0.016 0.002 PHE B 378 TYR 0.012 0.002 TYR D 310 ARG 0.009 0.001 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2278.64 seconds wall clock time: 41 minutes 19.85 seconds (2479.85 seconds total)