Starting phenix.real_space_refine on Mon Nov 13 17:33:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk1_14028/11_2023/7qk1_14028.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk1_14028/11_2023/7qk1_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_14028/11_2023/7qk1_14028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk1_14028/11_2023/7qk1_14028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk1_14028/11_2023/7qk1_14028.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk1_14028/11_2023/7qk1_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-1.21rc1-5144/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: 2.30, per 1000 atoms: 0.67 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: 1.24 Conformation dependent library (CDL) restraints added in 634.4 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: 0.46 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: 0.78 Time building geometry restraints manager: 1.35 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: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.670 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.900 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.950 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.457 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2575 time to fit residues: 52.4761 Evaluate side-chains 144 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.441 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5916 ------------------------------------------------------------------------------- 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: 6.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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: 0.8041 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3498 Z= 0.259 Angle : 0.672 6.601 4680 Z= 0.341 Chirality : 0.051 0.145 528 Planarity : 0.004 0.033 594 Dihedral : 7.036 30.279 462 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.03 % Allowed : 15.66 % Favored : 81.31 % 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: -1.35 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.27), residues: 438 *********************** 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: 12 poor density : 143 time to evaluate : 0.455 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 145 average time/residue: 0.2363 time to fit residues: 38.9675 Evaluate side-chains 146 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 139 time to evaluate : 0.446 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0723 time to fit residues: 1.2923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 10 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 34 optimal weight: 0.0570 chunk 37 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 overall best weight: 3.0504 ------------------------------------------------------------------------------- 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** B 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4389 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= 0.257 Angle : 0.638 6.220 4680 Z= 0.316 Chirality : 0.050 0.133 528 Planarity : 0.004 0.043 594 Dihedral : 6.231 27.898 462 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.28 % Allowed : 17.68 % 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: -1.43 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.27), residues: 438 *********************** 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: 13 poor density : 145 time to evaluate : 0.400 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 149 average time/residue: 0.2413 time to fit residues: 40.5662 Evaluate side-chains 148 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 0.442 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0651 time to fit residues: 1.3326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 0.0370 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 7.4066 ------------------------------------------------------------------------------- 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 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: 0.8153 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 3498 Z= 0.576 Angle : 0.781 7.706 4680 Z= 0.391 Chirality : 0.054 0.145 528 Planarity : 0.005 0.048 594 Dihedral : 6.835 29.894 462 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.28 % Allowed : 17.93 % Favored : 78.79 % 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 *********************** 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 161 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 0.433 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 152 average time/residue: 0.2369 time to fit residues: 40.6290 Evaluate side-chains 146 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0600 time to fit residues: 1.2918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 23 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 351 GLN B 368 ASN D 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3498 Z= 0.410 Angle : 0.711 6.729 4680 Z= 0.355 Chirality : 0.051 0.144 528 Planarity : 0.005 0.049 594 Dihedral : 6.494 29.077 462 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.52 % Allowed : 20.96 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.27), residues: 438 *********************** 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 146 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 0.430 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 142 average time/residue: 0.2191 time to fit residues: 35.4778 Evaluate side-chains 137 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2033 time to fit residues: 1.3088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN B 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3498 Z= 0.429 Angle : 0.722 7.463 4680 Z= 0.359 Chirality : 0.052 0.143 528 Planarity : 0.005 0.047 594 Dihedral : 6.468 27.458 462 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.03 % Allowed : 21.97 % 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: -1.89 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.27), residues: 438 *********************** 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 147 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 0.432 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 139 average time/residue: 0.2177 time to fit residues: 34.6922 Evaluate side-chains 139 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 0.444 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0374 time to fit residues: 1.3083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 40 optimal weight: 0.0040 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 overall best weight: 2.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3498 Z= 0.256 Angle : 0.644 6.980 4680 Z= 0.319 Chirality : 0.050 0.147 528 Planarity : 0.005 0.045 594 Dihedral : 5.970 25.830 462 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.51 % Allowed : 22.22 % Favored : 77.27 % 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: -1.82 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.28), residues: 438 *********************** 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 135 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 0.397 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 134 average time/residue: 0.2025 time to fit residues: 31.3546 Evaluate side-chains 131 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1739 time to fit residues: 1.0009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN E 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3498 Z= 0.325 Angle : 0.682 7.715 4680 Z= 0.336 Chirality : 0.050 0.152 528 Planarity : 0.005 0.048 594 Dihedral : 5.981 25.425 462 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.77 % Allowed : 23.23 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.28), residues: 438 *********************** 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 138 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 0.448 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 133 average time/residue: 0.2186 time to fit residues: 33.5734 Evaluate side-chains 132 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1523 time to fit residues: 1.4890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 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 307 GLN C 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.5207 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= 0.278 Angle : 0.670 7.540 4680 Z= 0.329 Chirality : 0.050 0.139 528 Planarity : 0.005 0.048 594 Dihedral : 5.837 25.737 462 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.25 % Allowed : 25.00 % 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: -1.83 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.28), residues: 438 *********************** 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: 1 poor density : 135 time to evaluate : 0.390 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.2162 time to fit residues: 33.7419 Evaluate side-chains 133 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 0.446 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0463 time to fit residues: 0.7788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 0.0170 chunk 30 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 0.2980 chunk 6 optimal weight: 4.9990 overall best weight: 3.0624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.5290 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= 0.275 Angle : 0.661 7.556 4680 Z= 0.325 Chirality : 0.050 0.136 528 Planarity : 0.005 0.048 594 Dihedral : 5.731 25.025 462 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.25 % Allowed : 25.76 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.28), residues: 438 ********************** 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 132 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.2074 time to fit residues: 31.3515 Evaluate side-chains 130 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.448 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0345 time to fit residues: 0.6470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN C 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.117707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.106279 restraints weight = 5501.900| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.37 r_work: 0.3559 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5272 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= 0.279 Angle : 0.666 7.518 4680 Z= 0.327 Chirality : 0.050 0.137 528 Planarity : 0.005 0.049 594 Dihedral : 5.717 25.119 462 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.25 % Allowed : 26.01 % 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: -1.82 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.28), residues: 438 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1354.56 seconds wall clock time: 25 minutes 15.33 seconds (1515.33 seconds total)