Starting phenix.real_space_refine on Sun Mar 10 17:24:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk1_14028/03_2024/7qk1_14028.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk1_14028/03_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_14028/03_2024/7qk1_14028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk1_14028/03_2024/7qk1_14028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk1_14028/03_2024/7qk1_14028.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk1_14028/03_2024/7qk1_14028.pdb" } 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 Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "E ARG 379": "NH1" <-> "NH2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ARG 379": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.25, per 1000 atoms: 0.65 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 621.5 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: 0.50 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: 0.80 Time building geometry restraints manager: 1.28 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: 101.43 - 107.18: 215 107.18 - 112.93: 1720 112.93 - 118.68: 888 118.68 - 124.43: 1647 124.43 - 130.18: 210 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 2.440 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.554 2.440 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.565 2.440 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 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.620 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.620 Find NCS groups from input model: 0.220 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.660 ------------------------------------------------------------------------------- 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 : 0.382 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: 0.2559 time to fit residues: 52.2174 Evaluate side-chains 139 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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: 20.0000 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 368 ASN F 329 HIS F 330 HIS A 327 ASN A 362 HIS A 374 HIS B 327 ASN D 327 ASN D 362 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3498 Z= 0.314 Angle : 0.682 6.795 4680 Z= 0.346 Chirality : 0.052 0.149 528 Planarity : 0.004 0.034 594 Dihedral : 7.150 30.905 462 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.28 % Allowed : 15.15 % Favored : 81.57 % 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 : -1.02 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 362 PHE 0.012 0.002 PHE B 378 TYR 0.019 0.002 TYR C 310 ARG 0.002 0.000 ARG D 379 *********************** 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 154 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 0.364 Fit side-chains REVERT: F 331 LYS cc_start: 0.7545 (mmmt) cc_final: 0.7078 (ttmt) REVERT: F 359 ASN cc_start: 0.9026 (t0) cc_final: 0.8795 (t0) REVERT: F 369 LYS cc_start: 0.7908 (pttt) cc_final: 0.7428 (tptp) REVERT: B 319 THR cc_start: 0.9199 (m) cc_final: 0.8860 (p) REVERT: B 321 LYS cc_start: 0.8157 (mmtp) cc_final: 0.7500 (pttt) REVERT: B 340 LYS cc_start: 0.8509 (mtpt) cc_final: 0.8305 (mttm) REVERT: B 347 LYS cc_start: 0.9156 (mttt) cc_final: 0.8033 (pttm) REVERT: B 348 ASP cc_start: 0.8950 (t0) cc_final: 0.7865 (p0) REVERT: B 349 ARG cc_start: 0.8863 (ptp-170) cc_final: 0.7361 (pmt-80) REVERT: B 372 GLU cc_start: 0.5239 (mm-30) cc_final: 0.4350 (mm-30) REVERT: D 331 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7010 (mmmt) REVERT: D 349 ARG cc_start: 0.8670 (pmm-80) cc_final: 0.6173 (mmm160) outliers start: 13 outliers final: 9 residues processed: 143 average time/residue: 0.2300 time to fit residues: 37.4887 Evaluate side-chains 137 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain E residue 316 SER 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 Chi-restraints excluded: chain D residue 377 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN B 359 ASN B 368 ASN B 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3498 Z= 0.440 Angle : 0.718 6.869 4680 Z= 0.361 Chirality : 0.053 0.145 528 Planarity : 0.005 0.045 594 Dihedral : 6.817 31.105 462 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.05 % Allowed : 17.68 % Favored : 77.27 % 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 0.017 0.002 PHE B 378 TYR 0.016 0.002 TYR C 310 ARG 0.002 0.001 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 158 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 0.408 Fit side-chains REVERT: C 338 GLU cc_start: 0.8244 (tt0) cc_final: 0.8000 (tm-30) REVERT: F 331 LYS cc_start: 0.6788 (mmmt) cc_final: 0.6285 (ttmt) REVERT: F 338 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7341 (tm-30) REVERT: F 369 LYS cc_start: 0.7955 (pttt) cc_final: 0.7434 (tptt) REVERT: B 321 LYS cc_start: 0.8366 (mmtp) cc_final: 0.7480 (pttm) REVERT: B 347 LYS cc_start: 0.9195 (mttt) cc_final: 0.8102 (pttm) REVERT: D 317 LYS cc_start: 0.5544 (mmmt) cc_final: 0.4903 (mmmt) REVERT: D 349 ARG cc_start: 0.8544 (pmm-80) cc_final: 0.5771 (mmm160) outliers start: 20 outliers final: 16 residues processed: 143 average time/residue: 0.2066 time to fit residues: 33.9358 Evaluate side-chains 139 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 358 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 327 ASN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 320 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: 8.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 3498 Z= 0.325 Angle : 0.654 8.165 4680 Z= 0.324 Chirality : 0.050 0.135 528 Planarity : 0.004 0.046 594 Dihedral : 6.313 28.601 462 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.05 % Allowed : 18.18 % Favored : 76.77 % 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: -1.58 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.27), 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 0.015 0.002 TYR C 310 ARG 0.001 0.000 ARG A 349 *********************** 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 148 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 0.351 Fit side-chains REVERT: F 369 LYS cc_start: 0.7885 (pttt) cc_final: 0.7493 (tptp) REVERT: B 321 LYS cc_start: 0.8216 (mmtp) cc_final: 0.7309 (pttm) REVERT: B 347 LYS cc_start: 0.9182 (mttt) cc_final: 0.8092 (pttm) REVERT: B 349 ARG cc_start: 0.8949 (ptp-170) cc_final: 0.7375 (pmt-80) REVERT: D 317 LYS cc_start: 0.5776 (mmmt) cc_final: 0.5226 (mtmt) REVERT: D 349 ARG cc_start: 0.8422 (pmm-80) cc_final: 0.5643 (mmm160) REVERT: D 370 LYS cc_start: 0.8057 (tttm) cc_final: 0.7745 (tptt) outliers start: 20 outliers final: 14 residues processed: 134 average time/residue: 0.1862 time to fit residues: 28.9239 Evaluate side-chains 137 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 316 SER 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 A residue 307 GLN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 320 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 30 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 0.0000 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4385 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= 0.283 Angle : 0.651 7.345 4680 Z= 0.318 Chirality : 0.050 0.138 528 Planarity : 0.004 0.044 594 Dihedral : 6.011 26.298 462 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.79 % Allowed : 19.95 % 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: -1.59 (0.36), 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 0.004 0.001 HIS C 362 PHE 0.010 0.002 PHE E 378 TYR 0.007 0.001 TYR F 310 ARG 0.001 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 145 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 0.470 Fit side-chains REVERT: F 340 LYS cc_start: 0.8317 (mmtp) cc_final: 0.8066 (mmtp) REVERT: F 369 LYS cc_start: 0.7879 (pttt) cc_final: 0.7506 (tptp) REVERT: B 321 LYS cc_start: 0.8158 (mmtp) cc_final: 0.7419 (pttm) REVERT: B 347 LYS cc_start: 0.9180 (mttt) cc_final: 0.8093 (pttm) REVERT: B 349 ARG cc_start: 0.8951 (ptp-170) cc_final: 0.7357 (pmt-80) REVERT: D 317 LYS cc_start: 0.5569 (OUTLIER) cc_final: 0.5079 (mtmt) REVERT: D 349 ARG cc_start: 0.8343 (pmm-80) cc_final: 0.5605 (mmm160) REVERT: D 351 GLN cc_start: 0.8668 (tt0) cc_final: 0.8329 (mt0) outliers start: 15 outliers final: 12 residues processed: 135 average time/residue: 0.2038 time to fit residues: 31.7500 Evaluate side-chains 135 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 316 SER 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 A residue 341 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 317 LYS 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 10 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 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** F 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3498 Z= 0.415 Angle : 0.695 7.422 4680 Z= 0.343 Chirality : 0.051 0.143 528 Planarity : 0.005 0.044 594 Dihedral : 6.226 25.945 462 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.29 % Allowed : 19.95 % Favored : 75.76 % 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: -1.78 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.013 0.002 PHE B 378 TYR 0.018 0.003 TYR C 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 142 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 0.449 Fit side-chains REVERT: F 340 LYS cc_start: 0.8284 (mmtp) cc_final: 0.7257 (mmmt) REVERT: F 369 LYS cc_start: 0.8092 (pttt) cc_final: 0.7543 (tptp) REVERT: B 321 LYS cc_start: 0.8327 (mmtp) cc_final: 0.7402 (pttm) REVERT: B 347 LYS cc_start: 0.9199 (mttt) cc_final: 0.8104 (pttm) REVERT: B 349 ARG cc_start: 0.8985 (ptp-170) cc_final: 0.7356 (pmt-80) REVERT: D 317 LYS cc_start: 0.5607 (OUTLIER) cc_final: 0.4608 (mmtt) REVERT: D 349 ARG cc_start: 0.8492 (pmm-80) cc_final: 0.5709 (mmm160) outliers start: 17 outliers final: 16 residues processed: 130 average time/residue: 0.1851 time to fit residues: 28.0642 Evaluate side-chains 142 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 358 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 319 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.8208 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3498 Z= 0.368 Angle : 0.683 7.006 4680 Z= 0.335 Chirality : 0.051 0.143 528 Planarity : 0.005 0.045 594 Dihedral : 6.093 26.021 462 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.80 % Allowed : 19.70 % 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: -1.83 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.011 0.002 PHE B 378 TYR 0.018 0.002 TYR C 310 ARG 0.002 0.000 ARG F 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 146 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.361 Fit side-chains REVERT: F 340 LYS cc_start: 0.8288 (mmtp) cc_final: 0.8079 (mmtp) REVERT: F 369 LYS cc_start: 0.8079 (pttt) cc_final: 0.7560 (tptp) REVERT: B 321 LYS cc_start: 0.8281 (mmtp) cc_final: 0.7532 (pttm) REVERT: B 347 LYS cc_start: 0.9190 (mttt) cc_final: 0.8095 (pttm) REVERT: B 349 ARG cc_start: 0.8969 (ptp-170) cc_final: 0.7342 (pmt-80) REVERT: D 317 LYS cc_start: 0.5612 (OUTLIER) cc_final: 0.4666 (mmtt) REVERT: D 349 ARG cc_start: 0.8470 (pmm-80) cc_final: 0.5705 (mmm160) outliers start: 19 outliers final: 17 residues processed: 133 average time/residue: 0.1938 time to fit residues: 29.9113 Evaluate side-chains 141 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 316 SER 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 319 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 3498 Z= 0.471 Angle : 0.725 7.084 4680 Z= 0.360 Chirality : 0.052 0.146 528 Planarity : 0.005 0.051 594 Dihedral : 6.234 26.427 462 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.30 % Allowed : 19.70 % 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: -1.96 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.015 0.002 PHE B 378 TYR 0.012 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 145 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 0.413 Fit side-chains REVERT: F 369 LYS cc_start: 0.8132 (pttt) cc_final: 0.7591 (tptp) REVERT: B 321 LYS cc_start: 0.8322 (mmtp) cc_final: 0.7581 (pttm) REVERT: B 347 LYS cc_start: 0.9190 (mttt) cc_final: 0.8118 (pttm) REVERT: B 349 ARG cc_start: 0.8982 (ptp-170) cc_final: 0.7354 (pmt-80) REVERT: D 317 LYS cc_start: 0.5601 (OUTLIER) cc_final: 0.5020 (mmtt) REVERT: D 349 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.6317 (mmm160) outliers start: 21 outliers final: 19 residues processed: 129 average time/residue: 0.1854 time to fit residues: 27.9959 Evaluate side-chains 144 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 358 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 E residue 376 LEU Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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: 0.8222 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 3498 Z= 0.457 Angle : 0.729 8.398 4680 Z= 0.359 Chirality : 0.052 0.149 528 Planarity : 0.005 0.051 594 Dihedral : 6.218 26.936 462 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.56 % Allowed : 20.20 % 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: -2.04 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.010 0.002 PHE B 378 TYR 0.010 0.002 TYR D 310 ARG 0.002 0.000 ARG F 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 146 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 0.448 Fit side-chains REVERT: F 340 LYS cc_start: 0.8170 (mmtp) cc_final: 0.7106 (mmmt) REVERT: F 369 LYS cc_start: 0.8125 (pttt) cc_final: 0.7571 (tptp) REVERT: B 321 LYS cc_start: 0.8304 (mmtp) cc_final: 0.7551 (pttm) REVERT: B 347 LYS cc_start: 0.9185 (mttt) cc_final: 0.8120 (pttm) REVERT: B 349 ARG cc_start: 0.8977 (ptp-170) cc_final: 0.7351 (pmt-80) REVERT: D 317 LYS cc_start: 0.5602 (OUTLIER) cc_final: 0.5069 (mmtt) REVERT: D 340 LYS cc_start: 0.5595 (OUTLIER) cc_final: 0.5137 (mttm) REVERT: D 349 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.6301 (mmm160) outliers start: 22 outliers final: 19 residues processed: 129 average time/residue: 0.1895 time to fit residues: 28.5116 Evaluate side-chains 145 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 358 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 E residue 376 LEU Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 353 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 30 optimal weight: 0.0050 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- 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: 0.8195 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3498 Z= 0.305 Angle : 0.686 8.314 4680 Z= 0.334 Chirality : 0.050 0.144 528 Planarity : 0.004 0.049 594 Dihedral : 5.918 26.349 462 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.80 % Allowed : 20.71 % 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: -1.91 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.009 0.001 PHE D 378 TYR 0.006 0.001 TYR D 310 ARG 0.002 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 146 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.410 Fit side-chains REVERT: F 331 LYS cc_start: 0.6865 (tppt) cc_final: 0.6494 (tppt) REVERT: F 369 LYS cc_start: 0.8074 (pttt) cc_final: 0.7516 (tptp) REVERT: B 321 LYS cc_start: 0.8283 (mmtp) cc_final: 0.7525 (pttm) REVERT: B 347 LYS cc_start: 0.9065 (mttt) cc_final: 0.7969 (pttm) REVERT: B 349 ARG cc_start: 0.8947 (ptp-170) cc_final: 0.7315 (pmt-80) REVERT: D 317 LYS cc_start: 0.5561 (OUTLIER) cc_final: 0.5037 (mmtt) REVERT: D 340 LYS cc_start: 0.5523 (OUTLIER) cc_final: 0.5176 (mttm) REVERT: D 349 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.6062 (mmm160) outliers start: 19 outliers final: 16 residues processed: 132 average time/residue: 0.2141 time to fit residues: 33.0596 Evaluate side-chains 144 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 316 SER 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 319 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.109026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.097501 restraints weight = 5646.070| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.51 r_work: 0.3385 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3498 Z= 0.341 Angle : 0.696 8.160 4680 Z= 0.340 Chirality : 0.051 0.146 528 Planarity : 0.005 0.050 594 Dihedral : 5.921 25.684 462 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.56 % Allowed : 20.71 % 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: -1.91 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.009 0.002 PHE D 378 TYR 0.008 0.002 TYR D 310 ARG 0.001 0.000 ARG F 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1222.09 seconds wall clock time: 22 minutes 49.93 seconds (1369.93 seconds total)