Starting phenix.real_space_refine on Tue Mar 3 16:02:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qkx_14056/03_2026/7qkx_14056.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkx_14056/03_2026/7qkx_14056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qkx_14056/03_2026/7qkx_14056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkx_14056/03_2026/7qkx_14056.map" model { file = "/net/cci-nas-00/data/ceres_data/7qkx_14056/03_2026/7qkx_14056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkx_14056/03_2026/7qkx_14056.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2106 2.51 5 N 606 2.21 5 O 624 1.98 5 H 3480 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6822 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "G" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "B" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 1.10, per 1000 atoms: 0.16 Number of scatterers: 6822 At special positions: 0 Unit cell: (86.52, 146.672, 36.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 624 8.00 N 606 7.00 C 2106 6.00 H 3480 1.00 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: 0.48 Conformation dependent library (CDL) restraints added in 303.1 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.442A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.925A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 321 removed outlier: 6.307A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330 removed outlier: 5.913A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN A 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342 Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.430A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 357 removed outlier: 6.521A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N SER E 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLY A 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.427A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 377 removed outlier: 6.597A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 307 through 310 removed outlier: 6.495A pdb=" N ILE G 308 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN G 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N TYR D 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL G 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.923A pdb=" N VAL G 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 317 through 321 Processing sheet with id=AB4, first strand: chain 'B' and resid 325 through 330 removed outlier: 5.930A pdb=" N GLY G 326 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N HIS B 329 " --> pdb=" O GLY G 326 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE G 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY D 326 " --> pdb=" O LEU G 325 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN G 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 337 through 342 removed outlier: 6.560A pdb=" N VAL G 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LYS B 340 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL G 339 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLU B 342 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER G 341 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.472A pdb=" N ASP G 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 350 through 357 removed outlier: 6.344A pdb=" N VAL G 350 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LYS B 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER G 352 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N GLY B 355 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE G 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU B 357 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER G 356 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN G 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE D 354 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS G 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N SER D 356 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY G 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.446A pdb=" N THR G 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 369 through 377 removed outlier: 6.626A pdb=" N LYS G 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLU D 372 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE G 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N HIS D 374 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR G 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N LEU D 376 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS G 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) 64 hydrogen bonds defined for protein. 192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 3474 1.11 - 1.29: 558 1.29 - 1.46: 941 1.46 - 1.64: 1897 1.64 - 1.81: 6 Bond restraints: 6876 Sorted by residual: bond pdb=" N ASP C 345 " pdb=" H ASP C 345 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" N ARG C 349 " pdb=" H ARG C 349 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" N SER A 352 " pdb=" H SER A 352 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" N ILE D 360 " pdb=" H ILE D 360 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" N HIS B 329 " pdb=" H HIS B 329 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 ... (remaining 6871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 10520 2.47 - 4.95: 1561 4.95 - 7.42: 444 7.42 - 9.89: 15 9.89 - 12.36: 6 Bond angle restraints: 12546 Sorted by residual: angle pdb=" CA ASP G 345 " pdb=" CB ASP G 345 " pdb=" CG ASP G 345 " ideal model delta sigma weight residual 112.60 117.62 -5.02 1.00e+00 1.00e+00 2.52e+01 angle pdb=" OE1 GLN G 336 " pdb=" CD GLN G 336 " pdb=" NE2 GLN G 336 " ideal model delta sigma weight residual 122.60 117.64 4.96 1.00e+00 1.00e+00 2.46e+01 angle pdb=" CA ASP E 345 " pdb=" CB ASP E 345 " pdb=" CG ASP E 345 " ideal model delta sigma weight residual 112.60 117.54 -4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" CA ASP A 345 " pdb=" CB ASP A 345 " pdb=" CG ASP A 345 " ideal model delta sigma weight residual 112.60 117.47 -4.87 1.00e+00 1.00e+00 2.37e+01 angle pdb=" N GLY G 326 " pdb=" CA GLY G 326 " pdb=" C GLY G 326 " ideal model delta sigma weight residual 110.69 117.16 -6.47 1.33e+00 5.65e-01 2.36e+01 ... (remaining 12541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.51: 2745 13.51 - 27.02: 207 27.02 - 40.52: 84 40.52 - 54.03: 54 54.03 - 67.54: 78 Dihedral angle restraints: 3168 sinusoidal: 1806 harmonic: 1362 Sorted by residual: dihedral pdb=" CA LYS G 375 " pdb=" C LYS G 375 " pdb=" N LEU G 376 " pdb=" CA LEU G 376 " ideal model delta harmonic sigma weight residual 180.00 151.10 28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA THR B 377 " pdb=" C THR B 377 " pdb=" N PHE B 378 " pdb=" CA PHE B 378 " ideal model delta harmonic sigma weight residual -180.00 -152.40 -27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA LYS G 369 " pdb=" C LYS G 369 " pdb=" N LYS G 370 " pdb=" CA LYS G 370 " ideal model delta harmonic sigma weight residual 180.00 157.11 22.89 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 3165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 286 0.067 - 0.133: 165 0.133 - 0.199: 48 0.199 - 0.265: 13 0.265 - 0.332: 4 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA LEU G 376 " pdb=" N LEU G 376 " pdb=" C LEU G 376 " pdb=" CB LEU G 376 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA LYS C 343 " pdb=" N LYS C 343 " pdb=" C LYS C 343 " pdb=" CB LYS C 343 " 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 LYS A 317 " pdb=" N LYS A 317 " pdb=" C LYS A 317 " pdb=" CB LYS A 317 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 513 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.076 2.00e-02 2.50e+03 3.17e-02 3.02e+01 pdb=" CG TYR C 310 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.045 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " 0.007 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 362 " 0.057 2.00e-02 2.50e+03 3.62e-02 2.95e+01 pdb=" CG HIS A 362 " -0.050 2.00e-02 2.50e+03 pdb=" ND1 HIS A 362 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS A 362 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 HIS A 362 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 HIS A 362 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 HIS A 362 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 HIS A 362 " 0.035 2.00e-02 2.50e+03 pdb=" HE2 HIS A 362 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 359 " 0.004 2.00e-02 2.50e+03 4.08e-02 2.50e+01 pdb=" CG ASN A 359 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 359 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 359 " -0.082 2.00e-02 2.50e+03 pdb="HD21 ASN A 359 " 0.046 2.00e-02 2.50e+03 pdb="HD22 ASN A 359 " 0.023 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 447 2.17 - 2.78: 11789 2.78 - 3.39: 17717 3.39 - 3.99: 24010 3.99 - 4.60: 33554 Nonbonded interactions: 87517 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.566 2.450 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.570 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.573 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.577 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.593 2.450 ... (remaining 87512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' } 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: 4.080 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: 0.040 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.490 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.010 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 0.037 3396 Z= 0.676 Angle : 1.820 6.465 4548 Z= 1.209 Chirality : 0.091 0.332 516 Planarity : 0.010 0.061 576 Dihedral : 10.510 53.065 1296 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 349 TYR 0.069 0.020 TYR C 310 PHE 0.032 0.011 PHE D 346 HIS 0.016 0.004 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.01089 ( 3396) covalent geometry : angle 1.81992 ( 4548) hydrogen bonds : bond 0.10610 ( 64) hydrogen bonds : angle 7.24467 ( 192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 VAL cc_start: 0.2146 (t) cc_final: 0.1679 (t) REVERT: A 321 LYS cc_start: 0.7775 (ttpt) cc_final: 0.7229 (mttt) REVERT: A 369 LYS cc_start: 0.7304 (mttt) cc_final: 0.6679 (mtpt) REVERT: C 311 LYS cc_start: 0.7178 (ttpt) cc_final: 0.6637 (mmtt) REVERT: C 321 LYS cc_start: 0.7729 (ttpt) cc_final: 0.7232 (mttt) REVERT: C 349 ARG cc_start: 0.8240 (mtt180) cc_final: 0.6396 (mmm160) REVERT: C 369 LYS cc_start: 0.7273 (mttt) cc_final: 0.6941 (mtpt) REVERT: E 321 LYS cc_start: 0.8467 (ttpt) cc_final: 0.7984 (mttp) REVERT: E 349 ARG cc_start: 0.7507 (mtt180) cc_final: 0.6724 (pmt-80) REVERT: E 369 LYS cc_start: 0.7898 (mttt) cc_final: 0.7469 (mtpt) REVERT: E 375 LYS cc_start: 0.7042 (tttt) cc_final: 0.6662 (ttmm) REVERT: G 321 LYS cc_start: 0.7458 (ttmt) cc_final: 0.7081 (mttp) REVERT: G 369 LYS cc_start: 0.7227 (mttt) cc_final: 0.6697 (mtpt) REVERT: B 311 LYS cc_start: 0.7520 (ttpt) cc_final: 0.6908 (mmtt) REVERT: B 317 LYS cc_start: 0.6545 (pttt) cc_final: 0.6340 (pttp) REVERT: B 321 LYS cc_start: 0.7680 (ttpt) cc_final: 0.7144 (mttt) REVERT: B 349 ARG cc_start: 0.8213 (mtt180) cc_final: 0.6483 (mmm160) REVERT: B 369 LYS cc_start: 0.7323 (mttt) cc_final: 0.6984 (mtpt) REVERT: D 306 VAL cc_start: 0.3383 (t) cc_final: 0.3178 (t) REVERT: D 321 LYS cc_start: 0.8424 (ttpt) cc_final: 0.7906 (mttp) REVERT: D 349 ARG cc_start: 0.7720 (mtt180) cc_final: 0.6679 (pmt-80) REVERT: D 369 LYS cc_start: 0.7872 (mttt) cc_final: 0.7381 (mtpt) REVERT: D 375 LYS cc_start: 0.6926 (tttt) cc_final: 0.6421 (ttmm) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2629 time to fit residues: 35.4108 Evaluate side-chains 83 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 362 HIS E 362 HIS G 362 HIS B 362 HIS D 362 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.149385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.135296 restraints weight = 12138.522| |-----------------------------------------------------------------------------| r_work (start): 0.4409 rms_B_bonded: 2.02 r_work: 0.4320 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4234 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3396 Z= 0.115 Angle : 0.616 6.824 4548 Z= 0.322 Chirality : 0.054 0.144 516 Planarity : 0.003 0.024 576 Dihedral : 6.539 20.142 444 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 0.26 % Allowed : 11.72 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 349 TYR 0.013 0.002 TYR G 310 PHE 0.018 0.002 PHE B 378 HIS 0.004 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 3396) covalent geometry : angle 0.61605 ( 4548) hydrogen bonds : bond 0.02654 ( 64) hydrogen bonds : angle 4.95805 ( 192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7590 (mttm) REVERT: A 348 ASP cc_start: 0.8409 (t0) cc_final: 0.8201 (t0) REVERT: A 375 LYS cc_start: 0.8046 (tttt) cc_final: 0.7492 (ttmm) REVERT: C 311 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8307 (mmtt) REVERT: C 321 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7666 (mttt) REVERT: C 349 ARG cc_start: 0.7940 (mtt180) cc_final: 0.6252 (mmm160) REVERT: C 369 LYS cc_start: 0.8110 (mttt) cc_final: 0.7849 (mtpt) REVERT: E 321 LYS cc_start: 0.8387 (ttpt) cc_final: 0.8161 (mttp) REVERT: E 349 ARG cc_start: 0.7215 (mtt180) cc_final: 0.6445 (pmt-80) REVERT: E 369 LYS cc_start: 0.8154 (mttt) cc_final: 0.7767 (mtpt) REVERT: E 375 LYS cc_start: 0.8418 (tttt) cc_final: 0.7942 (ttmm) REVERT: G 321 LYS cc_start: 0.7646 (ttmt) cc_final: 0.7376 (mttp) REVERT: G 349 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7390 (mtp85) REVERT: G 369 LYS cc_start: 0.8083 (mttt) cc_final: 0.7666 (mtpt) REVERT: B 311 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8186 (mmtt) REVERT: B 317 LYS cc_start: 0.8042 (pttt) cc_final: 0.7654 (pttp) REVERT: B 321 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7527 (mttm) REVERT: B 349 ARG cc_start: 0.7969 (mtt180) cc_final: 0.6222 (mmm160) REVERT: B 369 LYS cc_start: 0.7957 (mttt) cc_final: 0.7596 (mtpt) REVERT: D 321 LYS cc_start: 0.8308 (ttpt) cc_final: 0.8072 (mttp) REVERT: D 375 LYS cc_start: 0.8410 (tttt) cc_final: 0.7891 (ttmm) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.2822 time to fit residues: 23.6736 Evaluate side-chains 67 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 = 0.4480 r_free = 0.4480 target = 0.140304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.126015 restraints weight = 12715.051| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 2.10 r_work: 0.4258 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4173 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3396 Z= 0.114 Angle : 0.543 5.378 4548 Z= 0.279 Chirality : 0.052 0.138 516 Planarity : 0.003 0.020 576 Dihedral : 5.400 15.044 444 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.52 % Allowed : 10.16 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.013 0.002 TYR G 310 PHE 0.007 0.001 PHE B 378 HIS 0.003 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 3396) covalent geometry : angle 0.54343 ( 4548) hydrogen bonds : bond 0.02066 ( 64) hydrogen bonds : angle 4.27742 ( 192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8028 (ttpt) cc_final: 0.7591 (mttm) REVERT: A 348 ASP cc_start: 0.7978 (t0) cc_final: 0.7749 (t0) REVERT: A 375 LYS cc_start: 0.8155 (tttt) cc_final: 0.7575 (ttmm) REVERT: C 311 LYS cc_start: 0.8902 (ttpt) cc_final: 0.8343 (mmtt) REVERT: C 321 LYS cc_start: 0.8149 (ttpt) cc_final: 0.7829 (mttm) REVERT: C 349 ARG cc_start: 0.7965 (mtt180) cc_final: 0.6283 (mmm160) REVERT: C 369 LYS cc_start: 0.8095 (mttt) cc_final: 0.7796 (mtpt) REVERT: E 321 LYS cc_start: 0.8476 (ttpt) cc_final: 0.8218 (mttp) REVERT: E 349 ARG cc_start: 0.7400 (mtt180) cc_final: 0.6446 (pmt-80) REVERT: E 369 LYS cc_start: 0.8146 (mttt) cc_final: 0.7736 (mtpt) REVERT: E 375 LYS cc_start: 0.8400 (tttt) cc_final: 0.7919 (ttmm) REVERT: G 349 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7423 (mtp85) REVERT: G 369 LYS cc_start: 0.8102 (mttt) cc_final: 0.7733 (mtpt) REVERT: B 311 LYS cc_start: 0.8763 (ttpt) cc_final: 0.8238 (mmtt) REVERT: B 349 ARG cc_start: 0.8014 (mtt180) cc_final: 0.6221 (mmm160) REVERT: B 369 LYS cc_start: 0.8084 (mttt) cc_final: 0.7717 (mtpt) REVERT: D 321 LYS cc_start: 0.8393 (ttpt) cc_final: 0.8099 (mttp) REVERT: D 349 ARG cc_start: 0.7590 (mtp85) cc_final: 0.6395 (pmt-80) REVERT: D 358 ASP cc_start: 0.8686 (m-30) cc_final: 0.8481 (m-30) REVERT: D 375 LYS cc_start: 0.8462 (tttt) cc_final: 0.7939 (ttmm) outliers start: 2 outliers final: 1 residues processed: 65 average time/residue: 0.2837 time to fit residues: 20.5317 Evaluate side-chains 58 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 = 0.4384 r_free = 0.4384 target = 0.131772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.118311 restraints weight = 13491.120| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 2.16 r_work: 0.4165 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4076 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3396 Z= 0.166 Angle : 0.559 5.142 4548 Z= 0.287 Chirality : 0.052 0.140 516 Planarity : 0.003 0.018 576 Dihedral : 5.307 13.951 444 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.52 % Allowed : 11.46 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 349 TYR 0.015 0.003 TYR G 310 PHE 0.009 0.001 PHE B 378 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 3396) covalent geometry : angle 0.55942 ( 4548) hydrogen bonds : bond 0.02035 ( 64) hydrogen bonds : angle 4.14652 ( 192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8014 (ttpt) cc_final: 0.7551 (mttm) REVERT: A 375 LYS cc_start: 0.8116 (tttt) cc_final: 0.7513 (ttmm) REVERT: C 321 LYS cc_start: 0.8148 (ttpt) cc_final: 0.7753 (mttm) REVERT: C 349 ARG cc_start: 0.8004 (mtt180) cc_final: 0.6271 (mmm160) REVERT: C 369 LYS cc_start: 0.8007 (mttt) cc_final: 0.7660 (mtpt) REVERT: E 321 LYS cc_start: 0.8466 (ttpt) cc_final: 0.8154 (mttp) REVERT: E 349 ARG cc_start: 0.7517 (mtt180) cc_final: 0.6385 (pmt-80) REVERT: E 369 LYS cc_start: 0.8263 (mttt) cc_final: 0.7795 (mtpt) REVERT: E 375 LYS cc_start: 0.8509 (tttt) cc_final: 0.7992 (ttmm) REVERT: G 349 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7553 (mtp85) REVERT: B 311 LYS cc_start: 0.8770 (ttpt) cc_final: 0.8190 (mmtt) REVERT: B 349 ARG cc_start: 0.7973 (mtt180) cc_final: 0.6240 (mmm160) REVERT: B 369 LYS cc_start: 0.7996 (mttt) cc_final: 0.7562 (mtpt) REVERT: D 321 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8088 (mttp) REVERT: D 349 ARG cc_start: 0.7734 (mtp85) cc_final: 0.6363 (pmt-80) REVERT: D 358 ASP cc_start: 0.8661 (m-30) cc_final: 0.8408 (m-30) REVERT: D 375 LYS cc_start: 0.8532 (tttt) cc_final: 0.7977 (ttmm) outliers start: 2 outliers final: 1 residues processed: 64 average time/residue: 0.2517 time to fit residues: 17.9713 Evaluate side-chains 57 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.4453 r_free = 0.4453 target = 0.136567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.122733 restraints weight = 13132.757| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 2.21 r_work: 0.4231 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4143 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3396 Z= 0.105 Angle : 0.513 5.734 4548 Z= 0.258 Chirality : 0.051 0.138 516 Planarity : 0.002 0.016 576 Dihedral : 4.870 13.177 444 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.52 % Allowed : 12.24 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.010 0.002 TYR G 310 PHE 0.005 0.001 PHE B 378 HIS 0.002 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 3396) covalent geometry : angle 0.51269 ( 4548) hydrogen bonds : bond 0.01790 ( 64) hydrogen bonds : angle 3.94751 ( 192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8023 (ttpt) cc_final: 0.7681 (mttm) REVERT: A 375 LYS cc_start: 0.8030 (tttt) cc_final: 0.7412 (ttmm) REVERT: C 321 LYS cc_start: 0.8090 (ttpt) cc_final: 0.7724 (mttm) REVERT: C 349 ARG cc_start: 0.7944 (mtt180) cc_final: 0.6212 (mmm160) REVERT: C 369 LYS cc_start: 0.8027 (mttt) cc_final: 0.7663 (mtpt) REVERT: E 321 LYS cc_start: 0.8487 (ttpt) cc_final: 0.8179 (mttp) REVERT: E 349 ARG cc_start: 0.7500 (mtt180) cc_final: 0.6389 (pmt-80) REVERT: E 369 LYS cc_start: 0.8256 (mttt) cc_final: 0.7780 (mtpt) REVERT: E 375 LYS cc_start: 0.8534 (tttt) cc_final: 0.8002 (ttmm) REVERT: G 349 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7359 (mtp85) REVERT: B 311 LYS cc_start: 0.8771 (ttpt) cc_final: 0.8148 (mmtt) REVERT: B 349 ARG cc_start: 0.7883 (mtt180) cc_final: 0.6154 (mmm160) REVERT: B 369 LYS cc_start: 0.8032 (mttt) cc_final: 0.7629 (mtpt) REVERT: D 321 LYS cc_start: 0.8436 (ttpt) cc_final: 0.8034 (mttp) REVERT: D 348 ASP cc_start: 0.8303 (t0) cc_final: 0.8059 (t0) REVERT: D 349 ARG cc_start: 0.7772 (mtp85) cc_final: 0.6303 (pmt-80) REVERT: D 358 ASP cc_start: 0.8676 (m-30) cc_final: 0.8363 (m-30) REVERT: D 375 LYS cc_start: 0.8525 (tttt) cc_final: 0.7924 (ttmm) outliers start: 2 outliers final: 1 residues processed: 58 average time/residue: 0.2744 time to fit residues: 17.8421 Evaluate side-chains 56 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 ARG Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 37 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.4500 r_free = 0.4500 target = 0.140786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.127210 restraints weight = 13039.421| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 2.23 r_work: 0.4286 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4196 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3396 Z= 0.076 Angle : 0.486 5.826 4548 Z= 0.241 Chirality : 0.051 0.138 516 Planarity : 0.002 0.014 576 Dihedral : 4.452 11.214 444 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.52 % Allowed : 11.98 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.006 0.001 TYR G 310 PHE 0.003 0.000 PHE B 378 HIS 0.002 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00172 ( 3396) covalent geometry : angle 0.48640 ( 4548) hydrogen bonds : bond 0.01625 ( 64) hydrogen bonds : angle 3.80000 ( 192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8028 (ttpt) cc_final: 0.7662 (mttp) REVERT: A 349 ARG cc_start: 0.7625 (mtp85) cc_final: 0.6975 (mtt-85) REVERT: A 375 LYS cc_start: 0.8049 (tttt) cc_final: 0.7434 (ttmm) REVERT: C 321 LYS cc_start: 0.8102 (ttpt) cc_final: 0.7739 (mttm) REVERT: C 349 ARG cc_start: 0.7889 (mtt180) cc_final: 0.6081 (mmm160) REVERT: C 369 LYS cc_start: 0.8075 (mttt) cc_final: 0.7705 (mtpt) REVERT: E 321 LYS cc_start: 0.8463 (ttpt) cc_final: 0.8100 (mttp) REVERT: E 349 ARG cc_start: 0.7547 (mtt180) cc_final: 0.6411 (pmt-80) REVERT: E 369 LYS cc_start: 0.8165 (mttt) cc_final: 0.7678 (mtpt) REVERT: E 375 LYS cc_start: 0.8522 (tttt) cc_final: 0.7972 (ttmm) REVERT: G 349 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7421 (mtp85) REVERT: B 311 LYS cc_start: 0.8759 (ttpt) cc_final: 0.8114 (mmtt) REVERT: B 349 ARG cc_start: 0.7856 (mtt180) cc_final: 0.6179 (mmm160) REVERT: D 321 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8040 (mttp) REVERT: D 348 ASP cc_start: 0.8288 (t0) cc_final: 0.8086 (t0) REVERT: D 349 ARG cc_start: 0.7831 (mtp85) cc_final: 0.6350 (pmt-80) REVERT: D 375 LYS cc_start: 0.8538 (tttt) cc_final: 0.7968 (ttmm) outliers start: 2 outliers final: 0 residues processed: 57 average time/residue: 0.2837 time to fit residues: 18.0814 Evaluate side-chains 53 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.4314 r_free = 0.4314 target = 0.126660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.112733 restraints weight = 14288.751| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 2.13 r_work: 0.4065 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3974 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3396 Z= 0.171 Angle : 0.534 4.875 4548 Z= 0.276 Chirality : 0.051 0.141 516 Planarity : 0.003 0.017 576 Dihedral : 4.730 11.762 444 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.26 % Allowed : 12.50 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 349 TYR 0.018 0.003 TYR G 310 PHE 0.009 0.001 PHE B 378 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 3396) covalent geometry : angle 0.53363 ( 4548) hydrogen bonds : bond 0.01762 ( 64) hydrogen bonds : angle 3.85089 ( 192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8056 (ttpt) cc_final: 0.7758 (mttp) REVERT: A 375 LYS cc_start: 0.8127 (tttt) cc_final: 0.7507 (ttmm) REVERT: C 321 LYS cc_start: 0.8090 (ttpt) cc_final: 0.7629 (mttm) REVERT: C 349 ARG cc_start: 0.8044 (mtt180) cc_final: 0.6251 (mmm160) REVERT: C 369 LYS cc_start: 0.8055 (mttt) cc_final: 0.7654 (mtpt) REVERT: E 321 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8093 (mttp) REVERT: E 349 ARG cc_start: 0.7697 (mtt180) cc_final: 0.6426 (pmt-80) REVERT: E 369 LYS cc_start: 0.8283 (mttt) cc_final: 0.7779 (mtpt) REVERT: E 375 LYS cc_start: 0.8590 (tttt) cc_final: 0.8023 (ttmm) REVERT: G 349 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7547 (mtp85) REVERT: B 349 ARG cc_start: 0.7973 (mtt180) cc_final: 0.6370 (mmm160) REVERT: D 321 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8056 (mttp) REVERT: D 349 ARG cc_start: 0.7961 (mtp85) cc_final: 0.6452 (pmt-80) REVERT: D 358 ASP cc_start: 0.8711 (m-30) cc_final: 0.8437 (m-30) REVERT: D 375 LYS cc_start: 0.8584 (tttt) cc_final: 0.7988 (ttmm) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.2939 time to fit residues: 17.6995 Evaluate side-chains 52 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.127625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.113638 restraints weight = 14485.011| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.18 r_work: 0.4067 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3975 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3396 Z= 0.152 Angle : 0.539 5.180 4548 Z= 0.273 Chirality : 0.051 0.141 516 Planarity : 0.002 0.017 576 Dihedral : 4.737 11.377 444 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.26 % Allowed : 13.80 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 349 TYR 0.014 0.003 TYR G 310 PHE 0.004 0.001 PHE B 378 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 3396) covalent geometry : angle 0.53873 ( 4548) hydrogen bonds : bond 0.01729 ( 64) hydrogen bonds : angle 3.77919 ( 192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7808 (mttp) REVERT: A 375 LYS cc_start: 0.8102 (tttt) cc_final: 0.7523 (ttmm) REVERT: C 321 LYS cc_start: 0.8148 (ttpt) cc_final: 0.7669 (mttm) REVERT: C 349 ARG cc_start: 0.8043 (mtt180) cc_final: 0.6296 (mmm160) REVERT: C 369 LYS cc_start: 0.8082 (mttt) cc_final: 0.7697 (mtpt) REVERT: E 349 ARG cc_start: 0.7821 (mtt180) cc_final: 0.6438 (pmt-80) REVERT: E 369 LYS cc_start: 0.8258 (mttt) cc_final: 0.7778 (mtpt) REVERT: G 349 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7568 (mtp85) REVERT: B 349 ARG cc_start: 0.7975 (mtt180) cc_final: 0.6385 (mmm160) REVERT: D 321 LYS cc_start: 0.8536 (ttpt) cc_final: 0.8077 (mttm) REVERT: D 349 ARG cc_start: 0.7938 (mtp85) cc_final: 0.6399 (pmt-80) REVERT: D 358 ASP cc_start: 0.8646 (m-30) cc_final: 0.8397 (m-30) REVERT: D 375 LYS cc_start: 0.8602 (tttt) cc_final: 0.8012 (ttmm) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.2864 time to fit residues: 16.3844 Evaluate side-chains 51 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 1 optimal weight: 0.0050 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- 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 = 0.4333 r_free = 0.4333 target = 0.128344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.114398 restraints weight = 14303.256| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 2.15 r_work: 0.4088 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3997 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3396 Z= 0.130 Angle : 0.521 4.551 4548 Z= 0.266 Chirality : 0.051 0.139 516 Planarity : 0.003 0.025 576 Dihedral : 4.629 11.273 444 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.26 % Allowed : 13.02 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 349 TYR 0.013 0.002 TYR G 310 PHE 0.005 0.001 PHE B 378 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3396) covalent geometry : angle 0.52103 ( 4548) hydrogen bonds : bond 0.01663 ( 64) hydrogen bonds : angle 3.69999 ( 192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8096 (ttpt) cc_final: 0.7739 (mttp) REVERT: A 375 LYS cc_start: 0.8090 (tttt) cc_final: 0.7501 (ttmm) REVERT: C 321 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7617 (mttm) REVERT: C 349 ARG cc_start: 0.8010 (mtt180) cc_final: 0.6292 (mmm160) REVERT: C 369 LYS cc_start: 0.8040 (mttt) cc_final: 0.7657 (mtpt) REVERT: E 349 ARG cc_start: 0.7871 (mtt180) cc_final: 0.6410 (pmt-80) REVERT: E 369 LYS cc_start: 0.8239 (mttt) cc_final: 0.7737 (mtpt) REVERT: G 349 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7642 (mtp85) REVERT: B 349 ARG cc_start: 0.7979 (mtt180) cc_final: 0.6359 (mmm160) REVERT: D 321 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8047 (mttm) REVERT: D 349 ARG cc_start: 0.7927 (mtp85) cc_final: 0.6428 (pmt-80) REVERT: D 358 ASP cc_start: 0.8622 (m-30) cc_final: 0.8340 (m-30) REVERT: D 375 LYS cc_start: 0.8598 (tttt) cc_final: 0.7992 (ttmm) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.2765 time to fit residues: 15.7698 Evaluate side-chains 52 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 8 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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 = 0.4295 r_free = 0.4295 target = 0.123701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.110016 restraints weight = 14185.927| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.16 r_work: 0.4065 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3976 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3396 Z= 0.154 Angle : 0.545 5.474 4548 Z= 0.280 Chirality : 0.051 0.141 516 Planarity : 0.003 0.031 576 Dihedral : 4.712 11.355 444 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.26 % Allowed : 13.54 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.015 0.003 TYR G 310 PHE 0.006 0.001 PHE B 378 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 3396) covalent geometry : angle 0.54508 ( 4548) hydrogen bonds : bond 0.01718 ( 64) hydrogen bonds : angle 3.70118 ( 192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7755 (mttp) REVERT: A 349 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7365 (mtt180) REVERT: A 375 LYS cc_start: 0.8086 (tttt) cc_final: 0.7507 (ttmm) REVERT: C 321 LYS cc_start: 0.8130 (ttpt) cc_final: 0.7601 (mttm) REVERT: C 349 ARG cc_start: 0.8029 (mtt180) cc_final: 0.6318 (mmm160) REVERT: C 369 LYS cc_start: 0.8057 (mttt) cc_final: 0.7663 (mtpt) REVERT: E 349 ARG cc_start: 0.7921 (mtt180) cc_final: 0.6495 (pmt-80) REVERT: E 369 LYS cc_start: 0.8211 (mttt) cc_final: 0.7714 (mtpt) REVERT: B 349 ARG cc_start: 0.7966 (mtt180) cc_final: 0.6402 (mmm160) REVERT: D 321 LYS cc_start: 0.8518 (ttpt) cc_final: 0.8042 (mttm) REVERT: D 349 ARG cc_start: 0.7922 (mtp85) cc_final: 0.6391 (pmt-80) REVERT: D 358 ASP cc_start: 0.8646 (m-30) cc_final: 0.8388 (m-30) outliers start: 1 outliers final: 0 residues processed: 50 average time/residue: 0.2762 time to fit residues: 15.4435 Evaluate side-chains 49 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.0170 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.3624 ------------------------------------------------------------------------------- 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 = 0.4414 r_free = 0.4414 target = 0.134066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.120792 restraints weight = 13504.521| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 2.19 r_work: 0.4193 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4106 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3396 Z= 0.096 Angle : 0.505 4.601 4548 Z= 0.257 Chirality : 0.051 0.136 516 Planarity : 0.003 0.035 576 Dihedral : 4.446 11.005 444 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 13.54 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.009 0.002 TYR G 310 PHE 0.002 0.000 PHE D 346 HIS 0.002 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 3396) covalent geometry : angle 0.50451 ( 4548) hydrogen bonds : bond 0.01518 ( 64) hydrogen bonds : angle 3.53238 ( 192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2171.16 seconds wall clock time: 37 minutes 38.17 seconds (2258.17 seconds total)