Starting phenix.real_space_refine on Thu Dec 7 18:27:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9c_18276/12_2023/8q9c_18276.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9c_18276/12_2023/8q9c_18276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9c_18276/12_2023/8q9c_18276.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9c_18276/12_2023/8q9c_18276.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9c_18276/12_2023/8q9c_18276.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9c_18276/12_2023/8q9c_18276.pdb" } resolution = 3.4 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= 0.001 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 "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3444 Number of models: 1 Model: "" Number of chains: 6 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: "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: "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} 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: "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} Time building chain proxies: 2.32, per 1000 atoms: 0.67 Number of scatterers: 3444 At special positions: 0 Unit cell: (108.768, 120.304, 51.088, 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: 1.04 Conformation dependent library (CDL) restraints added in 745.1 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 42.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.591A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.830A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 325 removed outlier: 6.303A pdb=" N VAL C 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LYS D 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER C 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N GLY D 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N CYS C 322 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU D 325 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER C 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 337 through 342 removed outlier: 6.506A pdb=" N GLU B 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N SER D 341 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS B 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLU D 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER C 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.478A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 362 removed outlier: 6.911A pdb=" N GLN D 351 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER B 352 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS D 353 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE B 354 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY D 355 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER B 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N GLN C 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 10.431A pdb=" N ILE D 354 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N LYS C 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 10.301A pdb=" N SER D 356 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLY C 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ASP D 358 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU C 357 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE D 360 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN C 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N HIS D 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 369 through 371 removed outlier: 6.343A pdb=" N LYS C 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 374 through 375 removed outlier: 6.442A pdb=" N HIS C 374 " --> pdb=" O LYS D 375 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.547A pdb=" N GLN A 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N TYR F 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.815A pdb=" N VAL A 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 318 through 320 removed outlier: 6.323A pdb=" N VAL E 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.670A pdb=" N SER E 324 " --> pdb=" O LEU F 325 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 337 through 342 removed outlier: 6.436A pdb=" N GLU A 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N SER F 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS A 340 " --> pdb=" O SER F 341 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.480A pdb=" N ASP A 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 350 through 362 removed outlier: 6.797A pdb=" N GLN F 351 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER A 352 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS F 353 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE A 354 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY F 355 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER A 356 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N GLN E 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N ILE F 354 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N LYS E 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 10.228A pdb=" N SER F 356 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLY E 355 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ASP F 358 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU E 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE F 360 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN E 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N HIS F 362 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR E 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.404A pdb=" N LYS E 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 374 through 375 removed outlier: 6.427A pdb=" N HIS E 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) 46 hydrogen bonds defined for protein. 138 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: 0.77 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1045 1.34 - 1.46: 386 1.46 - 1.57: 2061 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3498 Sorted by residual: bond pdb=" CA LYS A 331 " pdb=" C LYS A 331 " ideal model delta sigma weight residual 1.532 1.549 -0.017 6.50e-03 2.37e+04 7.14e+00 bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.97e+00 bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.91e+00 bond pdb=" CZ ARG E 379 " pdb=" NH2 ARG E 379 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.56e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.17e+00 ... (remaining 3493 not shown) Histogram of bond angle deviations from ideal: 100.63 - 106.68: 220 106.68 - 112.73: 1665 112.73 - 118.78: 984 118.78 - 124.83: 1659 124.83 - 130.88: 152 Bond angle restraints: 4680 Sorted by residual: angle pdb=" C LYS A 331 " pdb=" CA LYS A 331 " pdb=" CB LYS A 331 " ideal model delta sigma weight residual 110.71 115.43 -4.72 9.40e-01 1.13e+00 2.52e+01 angle pdb=" C ASP B 348 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " ideal model delta sigma weight residual 121.97 130.24 -8.27 1.73e+00 3.34e-01 2.29e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 117.30 -4.70 1.00e+00 1.00e+00 2.21e+01 angle pdb=" CD ARG B 349 " pdb=" NE ARG B 349 " pdb=" CZ ARG B 349 " ideal model delta sigma weight residual 124.40 130.88 -6.48 1.40e+00 5.10e-01 2.14e+01 angle pdb=" CA ASP D 358 " pdb=" CB ASP D 358 " pdb=" CG ASP D 358 " ideal model delta sigma weight residual 112.60 117.04 -4.44 1.00e+00 1.00e+00 1.97e+01 ... (remaining 4675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.89: 1775 7.89 - 15.79: 247 15.79 - 23.68: 65 23.68 - 31.58: 30 31.58 - 39.47: 19 Dihedral angle restraints: 2136 sinusoidal: 894 harmonic: 1242 Sorted by residual: dihedral pdb=" C LYS B 347 " pdb=" N LYS B 347 " pdb=" CA LYS B 347 " pdb=" CB LYS B 347 " ideal model delta harmonic sigma weight residual -122.60 -133.81 11.21 0 2.50e+00 1.60e-01 2.01e+01 dihedral pdb=" CA ASN A 359 " pdb=" C ASN A 359 " pdb=" N ILE A 360 " pdb=" CA ILE A 360 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLY A 333 " pdb=" C GLY A 333 " pdb=" N GLY A 334 " pdb=" CA GLY A 334 " ideal model delta harmonic sigma weight residual 180.00 161.03 18.97 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 2133 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.077: 317 0.077 - 0.154: 171 0.154 - 0.231: 34 0.231 - 0.307: 5 0.307 - 0.384: 1 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS B 347 " pdb=" N LYS B 347 " pdb=" C LYS B 347 " pdb=" CB LYS B 347 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA LYS A 347 " pdb=" N LYS A 347 " pdb=" C LYS A 347 " pdb=" CB LYS A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ASP E 348 " pdb=" N ASP E 348 " pdb=" C ASP E 348 " pdb=" CB ASP E 348 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 525 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " 0.141 2.00e-02 2.50e+03 7.56e-02 1.14e+02 pdb=" CG TYR B 310 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " -0.072 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " 0.136 2.00e-02 2.50e+03 7.27e-02 1.06e+02 pdb=" CG TYR D 310 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " -0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " -0.066 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.104 2.00e-02 2.50e+03 5.49e-02 6.02e+01 pdb=" CG TYR F 310 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.079 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 1667 3.00 - 3.47: 2854 3.47 - 3.95: 5200 3.95 - 4.42: 5227 4.42 - 4.90: 10821 Nonbonded interactions: 25769 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.524 2.440 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.525 2.440 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.549 2.440 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.556 2.440 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.583 2.440 ... (remaining 25764 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.060 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.870 Find NCS groups from input model: 0.230 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 0.034 3498 Z= 0.751 Angle : 1.964 8.274 4680 Z= 1.272 Chirality : 0.091 0.384 528 Planarity : 0.013 0.112 594 Dihedral : 9.222 39.470 1344 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.25 % 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: -2.98 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.004 HIS B 330 PHE 0.052 0.014 PHE A 346 TYR 0.141 0.041 TYR B 310 ARG 0.003 0.001 ARG F 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 71 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.419 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.3341 time to fit residues: 26.3447 Evaluate side-chains 40 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.424 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5937 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN D 327 ASN ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN E 327 ASN F 327 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3498 Z= 0.182 Angle : 0.677 7.362 4680 Z= 0.325 Chirality : 0.051 0.129 528 Planarity : 0.004 0.033 594 Dihedral : 5.119 15.550 462 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.01 % Allowed : 7.07 % Favored : 91.92 % 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: -2.18 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.011 0.002 PHE A 378 TYR 0.012 0.003 TYR E 310 ARG 0.003 0.000 ARG F 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 45 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.421 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 44 average time/residue: 0.3354 time to fit residues: 16.6567 Evaluate side-chains 37 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0328 time to fit residues: 0.6510 ------------------------------------------------------------------------------- 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: 5.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 13 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3498 Z= 0.354 Angle : 0.661 6.611 4680 Z= 0.323 Chirality : 0.051 0.140 528 Planarity : 0.004 0.029 594 Dihedral : 5.198 14.899 462 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.01 % Allowed : 9.09 % Favored : 89.90 % 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: -1.73 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 330 PHE 0.009 0.002 PHE F 346 TYR 0.019 0.005 TYR F 310 ARG 0.002 0.000 ARG A 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 47 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.409 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 45 average time/residue: 0.2910 time to fit residues: 14.9715 Evaluate side-chains 31 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0336 time to fit residues: 0.6688 ------------------------------------------------------------------------------- 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: 1.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3498 Z= 0.274 Angle : 0.617 6.588 4680 Z= 0.296 Chirality : 0.049 0.135 528 Planarity : 0.003 0.029 594 Dihedral : 5.084 15.626 462 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.52 % Allowed : 10.35 % Favored : 88.13 % 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: -1.40 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 329 PHE 0.006 0.001 PHE A 378 TYR 0.014 0.003 TYR D 310 ARG 0.002 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.414 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 36 average time/residue: 0.3253 time to fit residues: 13.3366 Evaluate side-chains 33 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2531 time to fit residues: 1.4191 ------------------------------------------------------------------------------- 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: 9.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 3498 Z= 0.469 Angle : 0.690 5.561 4680 Z= 0.348 Chirality : 0.052 0.140 528 Planarity : 0.004 0.030 594 Dihedral : 5.634 15.721 462 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.26 % Allowed : 11.11 % Favored : 87.63 % 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: -1.70 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 329 PHE 0.011 0.003 PHE E 346 TYR 0.025 0.006 TYR F 310 ARG 0.004 0.001 ARG A 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 47 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.373 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 0.3197 time to fit residues: 17.0207 Evaluate side-chains 37 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.452 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1101 time to fit residues: 1.2026 ------------------------------------------------------------------------------- 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: 9.9990 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3498 Z= 0.287 Angle : 0.604 5.862 4680 Z= 0.295 Chirality : 0.049 0.128 528 Planarity : 0.003 0.029 594 Dihedral : 5.183 15.575 462 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.01 % Allowed : 13.89 % Favored : 85.10 % 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 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 PHE 0.011 0.001 PHE D 378 TYR 0.015 0.003 TYR D 310 ARG 0.002 0.000 ARG B 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 43 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.403 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 43 average time/residue: 0.2957 time to fit residues: 14.5642 Evaluate side-chains 34 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1289 time to fit residues: 1.0711 ------------------------------------------------------------------------------- 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: 4.9990 chunk 34 optimal weight: 0.3980 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 0.0070 chunk 20 optimal weight: 9.9990 overall best weight: 2.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3498 Z= 0.209 Angle : 0.581 8.480 4680 Z= 0.276 Chirality : 0.048 0.124 528 Planarity : 0.003 0.024 594 Dihedral : 4.836 14.251 462 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.26 % Allowed : 13.89 % Favored : 84.85 % 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: -1.44 (0.39), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.008 0.001 PHE D 378 TYR 0.013 0.003 TYR D 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 40 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.434 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 39 average time/residue: 0.2687 time to fit residues: 12.3629 Evaluate side-chains 37 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1761 time to fit residues: 1.4274 ------------------------------------------------------------------------------- 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: 9.9990 chunk 31 optimal weight: 0.3980 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3498 Z= 0.174 Angle : 0.567 8.057 4680 Z= 0.263 Chirality : 0.048 0.121 528 Planarity : 0.002 0.021 594 Dihedral : 4.528 13.320 462 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 0.25 % Allowed : 14.65 % Favored : 85.10 % 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: -1.31 (0.40), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.004 0.001 PHE E 346 TYR 0.011 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 31 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.423 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 30 average time/residue: 0.2575 time to fit residues: 9.2032 Evaluate side-chains 31 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4627 time to fit residues: 1.1018 ------------------------------------------------------------------------------- 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: 10.0000 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 0.0270 chunk 39 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3498 Z= 0.374 Angle : 0.640 7.263 4680 Z= 0.312 Chirality : 0.050 0.127 528 Planarity : 0.003 0.033 594 Dihedral : 5.017 14.058 462 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.01 % Allowed : 14.14 % Favored : 84.85 % 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: -1.52 (0.40), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 330 PHE 0.009 0.002 PHE E 346 TYR 0.020 0.005 TYR C 310 ARG 0.002 0.000 ARG B 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 39 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.424 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 37 average time/residue: 0.2367 time to fit residues: 10.4812 Evaluate side-chains 33 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.430 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0383 time to fit residues: 0.6667 ------------------------------------------------------------------------------- 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: 8.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 3498 Z= 0.563 Angle : 0.746 8.248 4680 Z= 0.374 Chirality : 0.053 0.132 528 Planarity : 0.005 0.044 594 Dihedral : 5.561 15.583 462 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.76 % Allowed : 15.66 % Favored : 83.59 % 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: -1.98 (0.39), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS C 329 PHE 0.012 0.003 PHE F 378 TYR 0.029 0.007 TYR E 310 ARG 0.004 0.001 ARG B 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 39 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.376 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.2393 time to fit residues: 11.0763 Evaluate side-chains 35 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.420 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0360 time to fit residues: 0.7127 ------------------------------------------------------------------------------- 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: 6.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.0370 chunk 41 optimal weight: 0.8980 overall best weight: 2.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.081380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.070789 restraints weight = 6567.734| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.79 r_work: 0.3407 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3498 Z= 0.231 Angle : 0.621 8.097 4680 Z= 0.292 Chirality : 0.049 0.127 528 Planarity : 0.003 0.027 594 Dihedral : 4.977 14.176 462 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.00 % Allowed : 16.41 % Favored : 83.59 % 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: -1.71 (0.40), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.003 0.001 PHE E 346 TYR 0.011 0.003 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: 1303.38 seconds wall clock time: 24 minutes 38.67 seconds (1478.67 seconds total)