Starting phenix.real_space_refine on Mon Sep 23 15:10:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk1_14028/09_2024/7qk1_14028.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk1_14028/09_2024/7qk1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk1_14028/09_2024/7qk1_14028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk1_14028/09_2024/7qk1_14028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk1_14028/09_2024/7qk1_14028.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk1_14028/09_2024/7qk1_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-5461/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: 2.62, per 1000 atoms: 0.76 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: 0.72 Conformation dependent library (CDL) restraints added in 420.1 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: 0.63 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: 1.03 Time building geometry restraints manager: 0.88 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: 0.360 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.770 Find NCS groups from input model: 0.130 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.560 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.424 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: 0.2500 time to fit residues: 50.9050 Evaluate side-chains 139 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 fitting. rotamer outliers: 8 poor density : 147 time to evaluate : 0.516 Fit side-chains REVERT: F 331 LYS cc_start: 0.7497 (mmmt) cc_final: 0.7064 (ttmt) REVERT: F 359 ASN cc_start: 0.9125 (t0) cc_final: 0.8894 (t0) REVERT: F 369 LYS cc_start: 0.7800 (pttt) cc_final: 0.7463 (tppt) REVERT: A 340 LYS cc_start: 0.8456 (mttm) cc_final: 0.8227 (mtpt) REVERT: A 349 ARG cc_start: 0.8597 (ptp-170) cc_final: 0.8392 (ptm160) REVERT: B 319 THR cc_start: 0.9148 (m) cc_final: 0.8881 (p) REVERT: B 321 LYS cc_start: 0.8218 (mmtp) cc_final: 0.7591 (pttt) REVERT: B 327 ASN cc_start: 0.8864 (t0) cc_final: 0.8362 (t0) REVERT: B 347 LYS cc_start: 0.9144 (mttt) cc_final: 0.7996 (pttm) REVERT: B 348 ASP cc_start: 0.8926 (t0) cc_final: 0.7842 (p0) REVERT: B 349 ARG cc_start: 0.8886 (ptp-170) cc_final: 0.7357 (pmt-80) REVERT: B 372 GLU cc_start: 0.5221 (mm-30) cc_final: 0.4323 (mm-30) REVERT: D 331 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7027 (mmmt) REVERT: D 349 ARG cc_start: 0.8611 (pmm-80) cc_final: 0.6081 (mmp80) REVERT: D 370 LYS cc_start: 0.8456 (tttm) cc_final: 0.8212 (tptm) outliers start: 8 outliers final: 5 residues processed: 148 average time/residue: 0.2207 time to fit residues: 37.3074 Evaluate side-chains 138 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 31 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 A 327 ASN A 359 ASN B 359 ASN B 368 ASN D 327 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3917 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= 0.242 Angle : 0.650 6.669 4680 Z= 0.322 Chirality : 0.050 0.134 528 Planarity : 0.004 0.037 594 Dihedral : 6.274 27.695 462 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.78 % Allowed : 18.18 % Favored : 79.04 % 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: -1.41 (0.36), 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 HIS 0.005 0.001 HIS C 362 PHE 0.012 0.002 PHE E 378 TYR 0.018 0.002 TYR C 310 ARG 0.001 0.000 ARG F 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 145 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 0.420 Fit side-chains REVERT: F 331 LYS cc_start: 0.7477 (mmmt) cc_final: 0.7072 (ttmt) REVERT: F 340 LYS cc_start: 0.8511 (mmtp) cc_final: 0.8268 (mmtp) REVERT: F 359 ASN cc_start: 0.9071 (t0) cc_final: 0.8808 (t0) REVERT: F 369 LYS cc_start: 0.7758 (pttt) cc_final: 0.7535 (tppt) REVERT: B 321 LYS cc_start: 0.8072 (mmtp) cc_final: 0.7314 (pttm) REVERT: B 327 ASN cc_start: 0.8896 (t0) cc_final: 0.8406 (t0) REVERT: B 347 LYS cc_start: 0.9145 (mttt) cc_final: 0.8056 (pttm) REVERT: B 348 ASP cc_start: 0.8673 (t0) cc_final: 0.7536 (p0) REVERT: B 349 ARG cc_start: 0.8960 (ptp-170) cc_final: 0.7352 (pmt-80) REVERT: D 317 LYS cc_start: 0.5349 (mmmt) cc_final: 0.5127 (mtmt) REVERT: D 331 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7191 (mmpt) REVERT: D 349 ARG cc_start: 0.8481 (pmm-80) cc_final: 0.6049 (mmm160) REVERT: D 351 GLN cc_start: 0.8717 (tt0) cc_final: 0.8400 (mt0) REVERT: D 370 LYS cc_start: 0.8484 (tttm) cc_final: 0.8160 (tptm) outliers start: 11 outliers final: 8 residues processed: 137 average time/residue: 0.2240 time to fit residues: 34.9364 Evaluate side-chains 139 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 360 ILE 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 377 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 6.1186 ------------------------------------------------------------------------------- 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** F 327 ASN B 327 ASN B 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 3498 Z= 0.488 Angle : 0.739 7.565 4680 Z= 0.369 Chirality : 0.052 0.146 528 Planarity : 0.005 0.043 594 Dihedral : 6.614 28.788 462 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.80 % Allowed : 16.67 % 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: -1.59 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 374 PHE 0.014 0.002 PHE B 378 TYR 0.011 0.002 TYR D 310 ARG 0.003 0.001 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 159 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 0.425 Fit side-chains REVERT: C 348 ASP cc_start: 0.9147 (OUTLIER) cc_final: 0.8875 (t70) REVERT: F 369 LYS cc_start: 0.8153 (pttt) cc_final: 0.7630 (tptt) REVERT: B 321 LYS cc_start: 0.8427 (mmtp) cc_final: 0.7409 (pttm) REVERT: B 347 LYS cc_start: 0.9192 (mttt) cc_final: 0.8104 (pttm) REVERT: D 317 LYS cc_start: 0.5694 (mmmt) cc_final: 0.4855 (mmmt) REVERT: D 349 ARG cc_start: 0.8511 (pmm-80) cc_final: 0.5772 (mmm160) REVERT: D 370 LYS cc_start: 0.8454 (tttm) cc_final: 0.8248 (tptm) outliers start: 19 outliers final: 15 residues processed: 145 average time/residue: 0.2159 time to fit residues: 35.7048 Evaluate side-chains 142 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 340 LYS Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 377 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 3498 Z= 0.385 Angle : 0.705 6.945 4680 Z= 0.349 Chirality : 0.051 0.146 528 Planarity : 0.005 0.043 594 Dihedral : 6.346 27.258 462 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.79 % Allowed : 19.70 % 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: -1.68 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 374 PHE 0.010 0.002 PHE A 378 TYR 0.018 0.002 TYR C 310 ARG 0.002 0.000 ARG D 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 144 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 0.439 Fit side-chains REVERT: F 340 LYS cc_start: 0.8176 (mmtp) cc_final: 0.7920 (mmtp) REVERT: F 369 LYS cc_start: 0.7995 (pttt) cc_final: 0.7456 (tptt) REVERT: B 321 LYS cc_start: 0.8322 (mmtp) cc_final: 0.7291 (pttm) REVERT: B 347 LYS cc_start: 0.9189 (mttt) cc_final: 0.8112 (pttm) REVERT: B 349 ARG cc_start: 0.8978 (ptp-170) cc_final: 0.7397 (pmt-80) REVERT: D 317 LYS cc_start: 0.5655 (mmmt) cc_final: 0.5232 (mtmt) REVERT: D 349 ARG cc_start: 0.8466 (pmm-80) cc_final: 0.5649 (mmm160) outliers start: 15 outliers final: 14 residues processed: 133 average time/residue: 0.2045 time to fit residues: 31.3934 Evaluate side-chains 138 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 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 10 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 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 351 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4492 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= 0.420 Angle : 0.723 7.949 4680 Z= 0.357 Chirality : 0.051 0.146 528 Planarity : 0.005 0.040 594 Dihedral : 6.348 26.049 462 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.29 % Allowed : 19.44 % Favored : 76.26 % 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: -1.80 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 374 PHE 0.012 0.002 PHE B 378 TYR 0.010 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 141 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 0.407 Fit side-chains REVERT: C 348 ASP cc_start: 0.9131 (OUTLIER) cc_final: 0.8854 (t70) REVERT: F 369 LYS cc_start: 0.8038 (pttt) cc_final: 0.7497 (tptt) REVERT: B 321 LYS cc_start: 0.8488 (mmtp) cc_final: 0.7427 (pttm) REVERT: B 340 LYS cc_start: 0.8618 (mmtt) cc_final: 0.7484 (pttm) REVERT: B 347 LYS cc_start: 0.9186 (mttt) cc_final: 0.8109 (pttm) REVERT: B 349 ARG cc_start: 0.8997 (ptp-170) cc_final: 0.7384 (pmt-80) REVERT: D 317 LYS cc_start: 0.5778 (mmmt) cc_final: 0.4923 (mmtt) REVERT: D 349 ARG cc_start: 0.8490 (pmm-80) cc_final: 0.5685 (mmm160) outliers start: 17 outliers final: 15 residues processed: 129 average time/residue: 0.1933 time to fit residues: 28.9663 Evaluate side-chains 137 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 340 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4599 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= 0.246 Angle : 0.649 7.241 4680 Z= 0.319 Chirality : 0.050 0.138 528 Planarity : 0.004 0.041 594 Dihedral : 5.863 25.650 462 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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 (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: -1.72 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.009 0.001 PHE A 378 TYR 0.020 0.002 TYR C 310 ARG 0.001 0.000 ARG D 379 *********************** 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 141 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 0.392 Fit side-chains REVERT: C 348 ASP cc_start: 0.9083 (OUTLIER) cc_final: 0.8801 (t70) REVERT: F 369 LYS cc_start: 0.7917 (pttt) cc_final: 0.7507 (tptp) REVERT: B 321 LYS cc_start: 0.8126 (mmtp) cc_final: 0.7222 (pttm) REVERT: B 347 LYS cc_start: 0.9173 (mttt) cc_final: 0.8091 (pttm) REVERT: B 349 ARG cc_start: 0.8952 (ptp-170) cc_final: 0.7331 (pmt-80) REVERT: D 317 LYS cc_start: 0.5729 (mmmt) cc_final: 0.4047 (mmmt) REVERT: D 349 ARG cc_start: 0.8319 (pmm-80) cc_final: 0.5595 (mmm160) outliers start: 12 outliers final: 8 residues processed: 131 average time/residue: 0.2068 time to fit residues: 31.4469 Evaluate side-chains 130 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 377 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 3 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 34 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3498 Z= 0.417 Angle : 0.729 7.558 4680 Z= 0.358 Chirality : 0.052 0.153 528 Planarity : 0.005 0.048 594 Dihedral : 6.148 25.243 462 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.04 % Allowed : 21.72 % Favored : 74.24 % 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: -1.84 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.012 0.002 PHE B 378 TYR 0.010 0.002 TYR D 310 ARG 0.002 0.000 ARG F 379 *********************** 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 fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 0.438 Fit side-chains REVERT: C 348 ASP cc_start: 0.9121 (OUTLIER) cc_final: 0.8845 (t70) REVERT: F 369 LYS cc_start: 0.8056 (pttt) cc_final: 0.7452 (tptt) REVERT: B 321 LYS cc_start: 0.8486 (mmtp) cc_final: 0.7438 (pttm) REVERT: B 347 LYS cc_start: 0.9186 (mttt) cc_final: 0.8101 (pttm) REVERT: B 349 ARG cc_start: 0.8985 (ptp-170) cc_final: 0.7341 (pmt-80) REVERT: D 317 LYS cc_start: 0.5549 (mmmt) cc_final: 0.5031 (mmtt) REVERT: D 349 ARG cc_start: 0.8483 (pmm-80) cc_final: 0.5714 (mmm160) outliers start: 16 outliers final: 15 residues processed: 128 average time/residue: 0.1979 time to fit residues: 29.7700 Evaluate side-chains 139 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 357 LEU 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 341 SER Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.0050 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.9800 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3498 Z= 0.208 Angle : 0.647 7.481 4680 Z= 0.315 Chirality : 0.050 0.145 528 Planarity : 0.004 0.044 594 Dihedral : 5.651 24.771 462 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.03 % Allowed : 22.22 % 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 (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: -1.72 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.008 0.001 PHE D 378 TYR 0.020 0.002 TYR C 310 ARG 0.001 0.000 ARG A 379 *********************** 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 136 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 0.397 Fit side-chains REVERT: C 348 ASP cc_start: 0.9058 (OUTLIER) cc_final: 0.8778 (t70) REVERT: F 340 LYS cc_start: 0.8234 (mmtp) cc_final: 0.7331 (mmmt) REVERT: F 369 LYS cc_start: 0.7888 (pttt) cc_final: 0.7480 (tptp) REVERT: B 321 LYS cc_start: 0.8128 (mmtp) cc_final: 0.7219 (pttm) REVERT: B 340 LYS cc_start: 0.8642 (mmtt) cc_final: 0.8441 (mmtm) REVERT: B 347 LYS cc_start: 0.9158 (mttt) cc_final: 0.8086 (pttm) REVERT: B 349 ARG cc_start: 0.8897 (ptp-170) cc_final: 0.7250 (pmt-80) REVERT: D 317 LYS cc_start: 0.5433 (mmmt) cc_final: 0.3939 (mmmt) REVERT: D 349 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.5546 (mmm160) outliers start: 12 outliers final: 8 residues processed: 127 average time/residue: 0.1967 time to fit residues: 28.9412 Evaluate side-chains 130 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 348 ASP 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 D residue 324 SER 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 20 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3498 Z= 0.285 Angle : 0.689 7.712 4680 Z= 0.335 Chirality : 0.050 0.142 528 Planarity : 0.005 0.049 594 Dihedral : 5.724 23.443 462 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.03 % Allowed : 22.73 % Favored : 74.24 % 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: -1.72 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.009 0.002 PHE B 378 TYR 0.007 0.001 TYR F 310 ARG 0.001 0.000 ARG F 379 ********************** 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 138 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 0.372 Fit side-chains REVERT: C 348 ASP cc_start: 0.9076 (OUTLIER) cc_final: 0.8798 (t70) REVERT: F 369 LYS cc_start: 0.7989 (pttt) cc_final: 0.7408 (tptt) REVERT: B 321 LYS cc_start: 0.8217 (mmtp) cc_final: 0.7297 (pttm) REVERT: B 347 LYS cc_start: 0.9154 (mttt) cc_final: 0.8090 (pttm) REVERT: B 349 ARG cc_start: 0.8905 (ptp-170) cc_final: 0.7278 (pmt-80) REVERT: D 317 LYS cc_start: 0.5479 (mmmt) cc_final: 0.4579 (mmtt) REVERT: D 349 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.5712 (mmm160) outliers start: 12 outliers final: 10 residues processed: 128 average time/residue: 0.1880 time to fit residues: 27.9658 Evaluate side-chains 135 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 348 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.0470 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.111894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.100619 restraints weight = 5642.757| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.48 r_work: 0.3452 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3498 Z= 0.227 Angle : 0.665 8.673 4680 Z= 0.320 Chirality : 0.050 0.156 528 Planarity : 0.004 0.047 594 Dihedral : 5.457 23.199 462 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.78 % Allowed : 23.48 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.65 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.008 0.001 PHE D 378 TYR 0.021 0.002 TYR C 310 ARG 0.002 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1255.82 seconds wall clock time: 23 minutes 24.40 seconds (1404.40 seconds total)