Starting phenix.real_space_refine on Wed Mar 5 20:18:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9c_18276/03_2025/8q9c_18276.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9c_18276/03_2025/8q9c_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/cci-nas-00/data/ceres_data/8q9c_18276/03_2025/8q9c_18276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9c_18276/03_2025/8q9c_18276.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9c_18276/03_2025/8q9c_18276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9c_18276/03_2025/8q9c_18276.cif" } 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. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.13, per 1000 atoms: 0.91 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 421.2 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: 0.96 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: 0.79 Time building geometry restraints manager: 0.95 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: 0.00 - 1.65: 2970 1.65 - 3.31: 1261 3.31 - 4.96: 354 4.96 - 6.62: 87 6.62 - 8.27: 8 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 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.525 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.549 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.556 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.583 3.040 ... (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 Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.590 Find NCS groups from input model: 0.140 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.190 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.397 Fit side-chains REVERT: B 311 LYS cc_start: 0.7501 (mttt) cc_final: 0.7125 (mmtm) REVERT: C 327 ASN cc_start: 0.7032 (m-40) cc_final: 0.6417 (m110) REVERT: D 369 LYS cc_start: 0.7708 (tttt) cc_final: 0.7443 (tttp) REVERT: D 375 LYS cc_start: 0.7107 (tttt) cc_final: 0.6848 (tttm) REVERT: E 351 GLN cc_start: 0.8023 (tt0) cc_final: 0.7243 (mt0) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.3117 time to fit residues: 24.5777 Evaluate side-chains 37 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN C 327 ASN D 327 ASN A 327 ASN A 368 ASN E 327 ASN F 327 ASN F 329 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.087750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.077237 restraints weight = 6261.823| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.70 r_work: 0.3531 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2459 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= 0.210 Angle : 0.686 7.442 4680 Z= 0.331 Chirality : 0.052 0.130 528 Planarity : 0.004 0.032 594 Dihedral : 5.158 15.243 462 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.01 % Allowed : 6.31 % Favored : 92.68 % 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: -2.15 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.012 0.002 PHE A 378 TYR 0.013 0.003 TYR D 310 ARG 0.003 0.001 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 43 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.415 Fit side-chains REVERT: B 311 LYS cc_start: 0.8032 (mttt) cc_final: 0.7557 (mmtt) REVERT: B 342 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7331 (mp0) REVERT: C 327 ASN cc_start: 0.7540 (m110) cc_final: 0.7111 (m110) REVERT: D 327 ASN cc_start: 0.8044 (m110) cc_final: 0.7838 (m-40) REVERT: E 351 GLN cc_start: 0.8354 (tt0) cc_final: 0.7917 (mt0) outliers start: 4 outliers final: 2 residues processed: 42 average time/residue: 0.2906 time to fit residues: 13.9832 Evaluate side-chains 35 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain A residue 327 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.0070 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 overall best weight: 5.6006 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.081623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.071769 restraints weight = 6619.772| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.64 r_work: 0.3424 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 3498 Z= 0.447 Angle : 0.712 6.293 4680 Z= 0.356 Chirality : 0.053 0.154 528 Planarity : 0.004 0.038 594 Dihedral : 5.563 15.210 462 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.02 % Allowed : 8.33 % Favored : 89.65 % 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: -1.95 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 329 PHE 0.011 0.003 PHE A 346 TYR 0.023 0.005 TYR F 310 ARG 0.002 0.001 ARG B 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 52 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.344 Fit side-chains REVERT: B 311 LYS cc_start: 0.8364 (mttt) cc_final: 0.7779 (mmtt) REVERT: B 342 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7409 (mp0) REVERT: C 342 GLU cc_start: 0.8185 (mp0) cc_final: 0.7891 (mp0) REVERT: C 375 LYS cc_start: 0.8453 (tttt) cc_final: 0.8075 (tttp) REVERT: A 311 LYS cc_start: 0.4939 (mmtt) cc_final: 0.4475 (mmtm) REVERT: A 321 LYS cc_start: 0.8118 (mttt) cc_final: 0.7876 (mttp) REVERT: E 351 GLN cc_start: 0.8361 (tt0) cc_final: 0.7888 (mt0) outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 0.2750 time to fit residues: 15.9184 Evaluate side-chains 43 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain E residue 320 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 11 optimal weight: 0.3980 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.081562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.071712 restraints weight = 6674.240| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.64 r_work: 0.3420 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 3498 Z= 0.431 Angle : 0.685 5.627 4680 Z= 0.340 Chirality : 0.052 0.145 528 Planarity : 0.004 0.046 594 Dihedral : 5.572 15.608 462 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.02 % Allowed : 9.34 % Favored : 88.64 % 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: -1.92 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 329 PHE 0.009 0.002 PHE E 346 TYR 0.019 0.005 TYR E 310 ARG 0.003 0.001 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 49 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.390 Fit side-chains REVERT: B 311 LYS cc_start: 0.8449 (mttt) cc_final: 0.8058 (mttm) REVERT: B 342 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7524 (mp0) REVERT: C 372 GLU cc_start: 0.8710 (tt0) cc_final: 0.8450 (mt-10) REVERT: C 375 LYS cc_start: 0.8564 (tttt) cc_final: 0.8211 (tttm) REVERT: E 351 GLN cc_start: 0.8391 (tt0) cc_final: 0.7821 (mt0) REVERT: F 311 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8193 (ptpt) outliers start: 8 outliers final: 6 residues processed: 47 average time/residue: 0.3175 time to fit residues: 16.8751 Evaluate side-chains 41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 25 optimal weight: 0.2980 chunk 6 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 1 optimal weight: 0.3980 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.081309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.071142 restraints weight = 6597.176| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.74 r_work: 0.3407 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3498 Z= 0.351 Angle : 0.634 5.497 4680 Z= 0.313 Chirality : 0.050 0.137 528 Planarity : 0.004 0.037 594 Dihedral : 5.354 15.135 462 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.02 % Allowed : 10.10 % Favored : 87.88 % 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: -1.79 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 329 PHE 0.007 0.002 PHE E 346 TYR 0.016 0.004 TYR E 310 ARG 0.002 0.000 ARG B 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 43 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.412 Fit side-chains REVERT: B 311 LYS cc_start: 0.8494 (mttt) cc_final: 0.8033 (mmtm) REVERT: B 342 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7517 (mp0) REVERT: C 372 GLU cc_start: 0.8751 (tt0) cc_final: 0.8487 (mt-10) REVERT: E 351 GLN cc_start: 0.8369 (tt0) cc_final: 0.7804 (mt0) outliers start: 8 outliers final: 6 residues processed: 40 average time/residue: 0.2794 time to fit residues: 12.9142 Evaluate side-chains 40 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.078988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.068834 restraints weight = 6881.624| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.78 r_work: 0.3362 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.007 0.055 3498 Z= 0.478 Angle : 0.690 6.039 4680 Z= 0.348 Chirality : 0.053 0.137 528 Planarity : 0.005 0.054 594 Dihedral : 5.667 15.175 462 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.02 % Allowed : 10.61 % Favored : 87.37 % 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: -1.99 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 329 PHE 0.010 0.002 PHE E 378 TYR 0.022 0.005 TYR E 310 ARG 0.003 0.001 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 to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.403 Fit side-chains REVERT: B 311 LYS cc_start: 0.8558 (mttt) cc_final: 0.8015 (mmtm) REVERT: B 342 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7515 (mp0) REVERT: B 348 ASP cc_start: 0.7571 (t70) cc_final: 0.7259 (t70) REVERT: C 372 GLU cc_start: 0.8811 (tt0) cc_final: 0.8581 (mt-10) REVERT: A 311 LYS cc_start: 0.4706 (mmtt) cc_final: 0.3441 (tppt) REVERT: E 351 GLN cc_start: 0.8389 (tt0) cc_final: 0.7851 (mt0) outliers start: 8 outliers final: 6 residues processed: 41 average time/residue: 0.2545 time to fit residues: 12.2585 Evaluate side-chains 40 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.082060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.072028 restraints weight = 6590.466| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.75 r_work: 0.3423 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3498 Z= 0.320 Angle : 0.632 6.715 4680 Z= 0.310 Chirality : 0.050 0.131 528 Planarity : 0.004 0.037 594 Dihedral : 5.368 14.967 462 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.02 % Allowed : 11.62 % Favored : 86.36 % 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 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.006 0.001 PHE E 346 TYR 0.015 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 42 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.374 Fit side-chains REVERT: B 311 LYS cc_start: 0.8557 (mttt) cc_final: 0.7987 (mmtm) REVERT: B 342 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7520 (mp0) REVERT: B 348 ASP cc_start: 0.7536 (t70) cc_final: 0.7200 (t70) REVERT: C 372 GLU cc_start: 0.8763 (tt0) cc_final: 0.8529 (mt-10) REVERT: A 311 LYS cc_start: 0.4870 (mmtt) cc_final: 0.3849 (tppt) REVERT: E 351 GLN cc_start: 0.8384 (tt0) cc_final: 0.7818 (mt0) outliers start: 8 outliers final: 6 residues processed: 40 average time/residue: 0.2520 time to fit residues: 11.8801 Evaluate side-chains 39 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.083204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.073124 restraints weight = 6498.417| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.74 r_work: 0.3444 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3498 Z= 0.256 Angle : 0.608 8.238 4680 Z= 0.291 Chirality : 0.049 0.126 528 Planarity : 0.003 0.031 594 Dihedral : 5.097 14.215 462 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.03 % Allowed : 10.86 % Favored : 86.11 % 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: -1.77 (0.39), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.006 0.001 PHE E 346 TYR 0.013 0.003 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 44 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.416 Fit side-chains REVERT: B 311 LYS cc_start: 0.8514 (mttt) cc_final: 0.7871 (mmtm) REVERT: B 342 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7505 (mp0) REVERT: B 348 ASP cc_start: 0.7528 (t70) cc_final: 0.7180 (t70) REVERT: C 372 GLU cc_start: 0.8748 (tt0) cc_final: 0.8512 (mt-10) REVERT: A 311 LYS cc_start: 0.4862 (mmtt) cc_final: 0.3866 (tppt) REVERT: A 379 ARG cc_start: 0.3881 (OUTLIER) cc_final: 0.2081 (ttp-170) REVERT: E 351 GLN cc_start: 0.8385 (tt0) cc_final: 0.7807 (mt0) outliers start: 12 outliers final: 9 residues processed: 40 average time/residue: 0.2595 time to fit residues: 12.1331 Evaluate side-chains 41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 37 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.082541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.072496 restraints weight = 6473.428| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.72 r_work: 0.3433 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3498 Z= 0.311 Angle : 0.619 7.522 4680 Z= 0.300 Chirality : 0.049 0.128 528 Planarity : 0.003 0.038 594 Dihedral : 5.140 14.108 462 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.53 % Allowed : 11.36 % Favored : 86.11 % 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 (0.39), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.006 0.001 PHE E 346 TYR 0.016 0.004 TYR D 310 ARG 0.002 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: B 311 LYS cc_start: 0.8520 (mttt) cc_final: 0.7869 (mmtm) REVERT: B 342 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7492 (mp0) REVERT: C 372 GLU cc_start: 0.8756 (tt0) cc_final: 0.8540 (mt-10) REVERT: A 351 GLN cc_start: 0.7795 (tt0) cc_final: 0.7191 (mt0) REVERT: A 379 ARG cc_start: 0.3610 (OUTLIER) cc_final: 0.1235 (ttp80) REVERT: E 351 GLN cc_start: 0.8407 (tt0) cc_final: 0.7802 (mt0) outliers start: 10 outliers final: 9 residues processed: 40 average time/residue: 0.2472 time to fit residues: 11.5643 Evaluate side-chains 43 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.081409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.071383 restraints weight = 6677.939| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.74 r_work: 0.3412 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4031 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= 0.373 Angle : 0.645 7.473 4680 Z= 0.317 Chirality : 0.050 0.130 528 Planarity : 0.004 0.046 594 Dihedral : 5.292 14.647 462 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.78 % Allowed : 10.86 % Favored : 86.36 % 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: -1.85 (0.39), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 329 PHE 0.008 0.002 PHE E 346 TYR 0.019 0.004 TYR E 310 ARG 0.002 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 42 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.435 Fit side-chains REVERT: B 311 LYS cc_start: 0.8564 (mttt) cc_final: 0.7986 (mmtm) REVERT: B 342 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7492 (mp0) REVERT: C 372 GLU cc_start: 0.8759 (tt0) cc_final: 0.8538 (mt-10) REVERT: A 311 LYS cc_start: 0.4843 (mmtt) cc_final: 0.3552 (tppt) REVERT: A 351 GLN cc_start: 0.7831 (tt0) cc_final: 0.7219 (mt0) REVERT: A 379 ARG cc_start: 0.3679 (OUTLIER) cc_final: 0.1293 (ttp80) REVERT: E 351 GLN cc_start: 0.8475 (tt0) cc_final: 0.7803 (mt0) outliers start: 11 outliers final: 10 residues processed: 39 average time/residue: 0.2529 time to fit residues: 11.5690 Evaluate side-chains 42 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 22 optimal weight: 0.3980 chunk 40 optimal weight: 9.9990 chunk 23 optimal weight: 0.0970 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 overall best weight: 2.6982 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.083292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.073157 restraints weight = 6513.667| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.75 r_work: 0.3447 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3498 Z= 0.245 Angle : 0.601 7.687 4680 Z= 0.288 Chirality : 0.049 0.126 528 Planarity : 0.003 0.030 594 Dihedral : 4.993 13.891 462 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.78 % Allowed : 10.86 % Favored : 86.36 % 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: -1.75 (0.39), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.005 0.001 PHE E 346 TYR 0.013 0.003 TYR D 310 ARG 0.002 0.000 ARG F 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2474.26 seconds wall clock time: 43 minutes 17.30 seconds (2597.30 seconds total)