Starting phenix.real_space_refine on Thu Jun 5 23:17:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qkx_14056/06_2025/7qkx_14056.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkx_14056/06_2025/7qkx_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_14056/06_2025/7qkx_14056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkx_14056/06_2025/7qkx_14056.map" model { file = "/net/cci-nas-00/data/ceres_data/7qkx_14056/06_2025/7qkx_14056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkx_14056/06_2025/7qkx_14056.cif" } resolution = 3.16 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= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 4.28, per 1000 atoms: 0.63 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: 1.48 Conformation dependent library (CDL) restraints added in 544.9 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: 0.65 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: 2.21 Time building geometry restraints manager: 1.84 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: 0.01 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: 3.800 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: 0.100 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.360 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.430 ------------------------------------------------------------------------------- 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 (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: -1.48 (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 HIS 0.016 0.004 HIS A 330 PHE 0.032 0.011 PHE D 346 TYR 0.069 0.020 TYR C 310 ARG 0.002 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.10610 ( 64) hydrogen bonds : angle 7.24467 ( 192) covalent geometry : bond 0.01089 ( 3396) covalent geometry : angle 1.81992 ( 4548) *********************** 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 : 0.586 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: 0.1680 (t) REVERT: A 321 LYS cc_start: 0.7775 (ttpt) cc_final: 0.7228 (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: 0.7233 (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: 0.6942 (mtpt) REVERT: E 321 LYS cc_start: 0.8467 (ttpt) cc_final: 0.7985 (mttp) REVERT: E 349 ARG cc_start: 0.7507 (mtt180) cc_final: 0.6723 (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: 0.6663 (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: 0.6909 (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: 0.6507 (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: 0.7721 (mtt180) cc_final: 0.6687 (pmt-80) REVERT: D 369 LYS cc_start: 0.7872 (mttt) cc_final: 0.7380 (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: 0.5767 time to fit residues: 77.7355 Evaluate side-chains 81 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.4490 r_free = 0.4490 target = 0.148616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.134284 restraints weight = 12024.717| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 2.06 r_work: 0.4307 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4220 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3129 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= 0.123 Angle : 0.616 6.906 4548 Z= 0.320 Chirality : 0.054 0.143 516 Planarity : 0.003 0.025 576 Dihedral : 6.578 20.151 444 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (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 HIS 0.004 0.001 HIS G 330 PHE 0.018 0.001 PHE B 378 TYR 0.014 0.002 TYR G 310 ARG 0.003 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.02576 ( 64) hydrogen bonds : angle 4.96349 ( 192) covalent geometry : bond 0.00290 ( 3396) covalent geometry : angle 0.61596 ( 4548) *********************** 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 75 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.508 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: A 321 LYS cc_start: 0.7999 (ttpt) cc_final: 0.7508 (mttm) REVERT: A 348 ASP cc_start: 0.8355 (t0) cc_final: 0.8109 (t0) REVERT: A 369 LYS cc_start: 0.8223 (mttt) cc_final: 0.7800 (mtpt) REVERT: C 311 LYS cc_start: 0.8881 (ttpt) cc_final: 0.8266 (mmtt) REVERT: C 321 LYS cc_start: 0.7959 (ttpt) cc_final: 0.7612 (mttt) REVERT: C 349 ARG cc_start: 0.7899 (mtt180) cc_final: 0.6151 (mmm160) REVERT: C 369 LYS cc_start: 0.8076 (mttt) cc_final: 0.7793 (mtpt) REVERT: E 321 LYS cc_start: 0.8408 (ttpt) cc_final: 0.8178 (mttm) REVERT: E 349 ARG cc_start: 0.7182 (mtt180) cc_final: 0.6328 (pmt-80) REVERT: E 369 LYS cc_start: 0.8155 (mttt) cc_final: 0.7745 (mtpt) REVERT: E 375 LYS cc_start: 0.8416 (tttt) cc_final: 0.7928 (ttmm) REVERT: G 369 LYS cc_start: 0.8075 (mttt) cc_final: 0.7625 (mtpt) REVERT: B 311 LYS cc_start: 0.8733 (ttpt) cc_final: 0.8165 (mmtt) REVERT: B 317 LYS cc_start: 0.8018 (pttt) cc_final: 0.7626 (pttp) REVERT: B 321 LYS cc_start: 0.7851 (ttpt) cc_final: 0.7477 (mttm) REVERT: B 349 ARG cc_start: 0.8046 (mtt180) cc_final: 0.6158 (mmm160) REVERT: B 369 LYS cc_start: 0.7950 (mttt) cc_final: 0.7575 (mtpt) REVERT: D 321 LYS cc_start: 0.8321 (ttpt) cc_final: 0.8055 (mttp) REVERT: D 349 ARG cc_start: 0.7415 (mtt180) cc_final: 0.6556 (pmt-80) REVERT: D 369 LYS cc_start: 0.8116 (mttt) cc_final: 0.7720 (mtpt) REVERT: D 375 LYS cc_start: 0.8403 (tttt) cc_final: 0.7903 (ttmm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.6256 time to fit residues: 52.2724 Evaluate side-chains 69 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.4529 r_free = 0.4529 target = 0.146294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.131070 restraints weight = 12667.391| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 2.23 r_work: 0.4300 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4217 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3396 Z= 0.091 Angle : 0.518 4.874 4548 Z= 0.263 Chirality : 0.052 0.137 516 Planarity : 0.002 0.017 576 Dihedral : 5.145 14.100 444 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.26 % Allowed : 10.42 % 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 (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: -1.48 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.005 0.001 PHE B 378 TYR 0.009 0.002 TYR G 310 ARG 0.002 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.01908 ( 64) hydrogen bonds : angle 4.19113 ( 192) covalent geometry : bond 0.00209 ( 3396) covalent geometry : angle 0.51767 ( 4548) *********************** 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 72 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7639 (mttm) REVERT: A 348 ASP cc_start: 0.7808 (t0) cc_final: 0.7600 (t0) REVERT: A 369 LYS cc_start: 0.8181 (mttt) cc_final: 0.7709 (mtpt) REVERT: A 375 LYS cc_start: 0.8055 (tttt) cc_final: 0.7453 (ttmm) REVERT: C 311 LYS cc_start: 0.8876 (ttpt) cc_final: 0.8296 (mmtt) REVERT: C 321 LYS cc_start: 0.8108 (ttpt) cc_final: 0.7784 (mttm) REVERT: C 349 ARG cc_start: 0.7873 (mtt180) cc_final: 0.6171 (mmm160) REVERT: C 369 LYS cc_start: 0.8065 (mttt) cc_final: 0.7734 (mtpt) REVERT: E 321 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8155 (mttm) REVERT: E 349 ARG cc_start: 0.7220 (mtt180) cc_final: 0.6370 (pmt-80) REVERT: E 369 LYS cc_start: 0.8129 (mttt) cc_final: 0.7683 (mtpt) REVERT: E 375 LYS cc_start: 0.8399 (tttt) cc_final: 0.7897 (ttmm) REVERT: B 311 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8168 (mmtt) REVERT: B 349 ARG cc_start: 0.8004 (mtt180) cc_final: 0.6084 (mmm160) REVERT: B 369 LYS cc_start: 0.8054 (mttt) cc_final: 0.7663 (mtpt) REVERT: D 321 LYS cc_start: 0.8406 (ttpt) cc_final: 0.8074 (mttm) REVERT: D 349 ARG cc_start: 0.7335 (mtt180) cc_final: 0.6451 (pmt-80) REVERT: D 358 ASP cc_start: 0.8668 (m-30) cc_final: 0.8383 (m-30) REVERT: D 369 LYS cc_start: 0.8096 (mttt) cc_final: 0.7698 (mtpt) REVERT: D 375 LYS cc_start: 0.8441 (tttt) cc_final: 0.7897 (ttmm) outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 0.5863 time to fit residues: 46.7231 Evaluate side-chains 60 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.4337 r_free = 0.4337 target = 0.126123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.111743 restraints weight = 13918.301| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.19 r_work: 0.4086 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3998 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 0.031 3396 Z= 0.159 Angle : 0.548 4.448 4548 Z= 0.284 Chirality : 0.052 0.139 516 Planarity : 0.003 0.019 576 Dihedral : 5.169 13.499 444 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 12.50 % 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 (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: -1.62 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.009 0.002 PHE B 378 TYR 0.017 0.003 TYR G 310 ARG 0.002 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.01834 ( 64) hydrogen bonds : angle 4.07171 ( 192) covalent geometry : bond 0.00352 ( 3396) covalent geometry : angle 0.54823 ( 4548) *********************** 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 66 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8005 (ttpt) cc_final: 0.7575 (mttm) REVERT: A 369 LYS cc_start: 0.8125 (mttt) cc_final: 0.7621 (mtpt) REVERT: A 375 LYS cc_start: 0.8115 (tttt) cc_final: 0.7499 (ttmm) REVERT: C 321 LYS cc_start: 0.8148 (ttpt) cc_final: 0.7746 (mttm) REVERT: C 349 ARG cc_start: 0.8034 (mtt180) cc_final: 0.6274 (mmm160) REVERT: C 369 LYS cc_start: 0.8017 (mttt) cc_final: 0.7640 (mtpt) REVERT: E 321 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8209 (mttp) REVERT: E 349 ARG cc_start: 0.7559 (mtt180) cc_final: 0.6401 (pmt-80) REVERT: E 369 LYS cc_start: 0.8257 (mttt) cc_final: 0.7779 (mtpt) REVERT: E 375 LYS cc_start: 0.8517 (tttt) cc_final: 0.8001 (ttmm) REVERT: B 311 LYS cc_start: 0.8773 (ttpt) cc_final: 0.8198 (mmtt) REVERT: B 349 ARG cc_start: 0.8089 (mtt180) cc_final: 0.6266 (mmm160) REVERT: B 369 LYS cc_start: 0.7978 (mttt) cc_final: 0.7539 (mtpt) REVERT: D 321 LYS cc_start: 0.8435 (ttpt) cc_final: 0.8084 (mttp) REVERT: D 349 ARG cc_start: 0.7637 (mtt180) cc_final: 0.6552 (pmt-80) REVERT: D 358 ASP cc_start: 0.8662 (m-30) cc_final: 0.8405 (m-30) REVERT: D 375 LYS cc_start: 0.8537 (tttt) cc_final: 0.7974 (ttmm) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.6117 time to fit residues: 45.7130 Evaluate side-chains 58 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.129764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.115361 restraints weight = 14216.160| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 2.19 r_work: 0.4083 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3995 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4406 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= 0.147 Angle : 0.536 5.684 4548 Z= 0.272 Chirality : 0.051 0.140 516 Planarity : 0.003 0.017 576 Dihedral : 4.978 13.121 444 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 13.02 % Favored : 86.98 % 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: -1.65 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.006 0.001 PHE B 378 TYR 0.013 0.002 TYR G 310 ARG 0.002 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.01742 ( 64) hydrogen bonds : angle 3.92783 ( 192) covalent geometry : bond 0.00317 ( 3396) covalent geometry : angle 0.53608 ( 4548) *********************** 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: 0 poor density : 59 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8041 (ttpt) cc_final: 0.7680 (mttp) REVERT: A 349 ARG cc_start: 0.7486 (mtp85) cc_final: 0.7211 (mtp85) REVERT: A 369 LYS cc_start: 0.8139 (mttt) cc_final: 0.7646 (mtpt) REVERT: A 375 LYS cc_start: 0.8042 (tttt) cc_final: 0.7431 (ttmm) REVERT: C 321 LYS cc_start: 0.8067 (ttpt) cc_final: 0.7645 (mttm) REVERT: C 349 ARG cc_start: 0.8034 (mtt180) cc_final: 0.6306 (mmm160) REVERT: C 369 LYS cc_start: 0.8043 (mttt) cc_final: 0.7633 (mtpt) REVERT: E 321 LYS cc_start: 0.8455 (ttpt) cc_final: 0.8149 (mttp) REVERT: E 349 ARG cc_start: 0.7625 (mtt180) cc_final: 0.6425 (pmt-80) REVERT: E 369 LYS cc_start: 0.8288 (mttt) cc_final: 0.7789 (mtpt) REVERT: E 375 LYS cc_start: 0.8541 (tttt) cc_final: 0.8006 (ttmm) REVERT: B 311 LYS cc_start: 0.8761 (ttpt) cc_final: 0.8169 (mmtt) REVERT: B 349 ARG cc_start: 0.8049 (mtt180) cc_final: 0.6315 (mmm160) REVERT: D 321 LYS cc_start: 0.8460 (ttpt) cc_final: 0.8068 (mttm) REVERT: D 349 ARG cc_start: 0.7745 (mtt180) cc_final: 0.6593 (pmt-80) REVERT: D 358 ASP cc_start: 0.8619 (m-30) cc_final: 0.8328 (m-30) REVERT: D 375 LYS cc_start: 0.8546 (tttt) cc_final: 0.7941 (ttmm) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.6196 time to fit residues: 41.3780 Evaluate side-chains 57 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.4389 r_free = 0.4389 target = 0.132130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.117714 restraints weight = 14033.669| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 2.20 r_work: 0.4134 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4044 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3396 Z= 0.107 Angle : 0.501 5.432 4548 Z= 0.253 Chirality : 0.051 0.138 516 Planarity : 0.002 0.018 576 Dihedral : 4.694 12.676 444 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.004 0.001 PHE B 378 TYR 0.009 0.002 TYR G 310 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01558 ( 64) hydrogen bonds : angle 3.73821 ( 192) covalent geometry : bond 0.00233 ( 3396) covalent geometry : angle 0.50106 ( 4548) *********************** 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 61 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8042 (ttpt) cc_final: 0.7681 (mttp) REVERT: A 349 ARG cc_start: 0.7450 (mtp85) cc_final: 0.6967 (mtt-85) REVERT: A 369 LYS cc_start: 0.8151 (mttt) cc_final: 0.7644 (mtpt) REVERT: A 375 LYS cc_start: 0.8055 (tttt) cc_final: 0.7444 (ttmm) REVERT: C 321 LYS cc_start: 0.8060 (ttpt) cc_final: 0.7637 (mttp) REVERT: C 349 ARG cc_start: 0.8040 (mtt180) cc_final: 0.6339 (mmm160) REVERT: C 369 LYS cc_start: 0.8057 (mttt) cc_final: 0.7645 (mtpt) REVERT: E 321 LYS cc_start: 0.8438 (ttpt) cc_final: 0.8085 (mttp) REVERT: E 349 ARG cc_start: 0.7642 (mtt180) cc_final: 0.6408 (pmt-80) REVERT: E 369 LYS cc_start: 0.8237 (mttt) cc_final: 0.7734 (mtpt) REVERT: E 375 LYS cc_start: 0.8575 (tttt) cc_final: 0.8017 (ttmm) REVERT: B 349 ARG cc_start: 0.8027 (mtt180) cc_final: 0.6235 (mmm160) REVERT: D 321 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8021 (mttm) REVERT: D 349 ARG cc_start: 0.7787 (mtt180) cc_final: 0.6593 (pmt-80) REVERT: D 358 ASP cc_start: 0.8597 (m-30) cc_final: 0.8310 (m-30) REVERT: D 375 LYS cc_start: 0.8575 (tttt) cc_final: 0.7986 (ttmm) outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.6042 time to fit residues: 40.9927 Evaluate side-chains 54 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 342 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.136786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.123161 restraints weight = 13090.081| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 2.21 r_work: 0.4240 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4150 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4714 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= 0.089 Angle : 0.492 4.835 4548 Z= 0.247 Chirality : 0.051 0.137 516 Planarity : 0.002 0.018 576 Dihedral : 4.432 11.069 444 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.26 % Allowed : 14.32 % Favored : 85.42 % 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: -1.74 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 330 PHE 0.004 0.001 PHE B 378 TYR 0.008 0.002 TYR G 310 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01452 ( 64) hydrogen bonds : angle 3.58881 ( 192) covalent geometry : bond 0.00198 ( 3396) covalent geometry : angle 0.49238 ( 4548) *********************** 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 53 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7734 (mttp) REVERT: A 349 ARG cc_start: 0.7458 (mtp85) cc_final: 0.7025 (mtt-85) REVERT: A 375 LYS cc_start: 0.8072 (tttt) cc_final: 0.7460 (ttmm) REVERT: C 321 LYS cc_start: 0.8057 (ttpt) cc_final: 0.7636 (mttm) REVERT: C 349 ARG cc_start: 0.7997 (mtt180) cc_final: 0.6317 (mmm160) REVERT: C 369 LYS cc_start: 0.8050 (mttt) cc_final: 0.7667 (mtpt) REVERT: E 321 LYS cc_start: 0.8492 (ttpt) cc_final: 0.8110 (mttp) REVERT: E 349 ARG cc_start: 0.7683 (mtt180) cc_final: 0.6429 (pmt-80) REVERT: E 369 LYS cc_start: 0.8199 (mttt) cc_final: 0.7704 (mtpt) REVERT: E 375 LYS cc_start: 0.8556 (tttt) cc_final: 0.7979 (ttmm) REVERT: B 311 LYS cc_start: 0.8773 (ttpt) cc_final: 0.8204 (mmtt) REVERT: B 349 ARG cc_start: 0.8014 (mtt180) cc_final: 0.6199 (mmm160) REVERT: D 321 LYS cc_start: 0.8462 (ttpt) cc_final: 0.7991 (mttp) REVERT: D 349 ARG cc_start: 0.7806 (mtt180) cc_final: 0.6609 (pmt-80) REVERT: D 375 LYS cc_start: 0.8583 (tttt) cc_final: 0.7997 (ttmm) outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 0.6934 time to fit residues: 40.7327 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 : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 342 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.122614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.108876 restraints weight = 14180.109| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.13 r_work: 0.4042 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3952 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3396 Z= 0.206 Angle : 0.553 4.140 4548 Z= 0.289 Chirality : 0.051 0.142 516 Planarity : 0.003 0.018 576 Dihedral : 4.814 11.787 444 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 14.32 % Favored : 85.68 % 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: -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 HIS 0.004 0.001 HIS E 329 PHE 0.008 0.001 PHE B 378 TYR 0.018 0.004 TYR G 310 ARG 0.002 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01808 ( 64) hydrogen bonds : angle 3.72696 ( 192) covalent geometry : bond 0.00452 ( 3396) covalent geometry : angle 0.55253 ( 4548) *********************** 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: 0 poor density : 52 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8092 (ttpt) cc_final: 0.7762 (mttp) REVERT: A 349 ARG cc_start: 0.7602 (mtp85) cc_final: 0.7170 (mtt-85) REVERT: A 375 LYS cc_start: 0.8139 (tttt) cc_final: 0.7550 (ttmm) REVERT: C 321 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7673 (mttm) REVERT: C 349 ARG cc_start: 0.8130 (mtt180) cc_final: 0.6352 (mmm160) REVERT: C 369 LYS cc_start: 0.8105 (mttt) cc_final: 0.7703 (mtpt) REVERT: E 321 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8089 (mttp) REVERT: E 349 ARG cc_start: 0.7914 (mtt180) cc_final: 0.6465 (pmt-80) REVERT: E 369 LYS cc_start: 0.8299 (mttt) cc_final: 0.7792 (mtpt) REVERT: B 349 ARG cc_start: 0.8131 (mtt180) cc_final: 0.6421 (mmm160) REVERT: D 321 LYS cc_start: 0.8524 (ttpt) cc_final: 0.8077 (mttp) REVERT: D 358 ASP cc_start: 0.8683 (m-30) cc_final: 0.8437 (m-30) REVERT: D 375 LYS cc_start: 0.8613 (tttt) cc_final: 0.8019 (ttmm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.5587 time to fit residues: 33.8865 Evaluate side-chains 51 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.4386 r_free = 0.4386 target = 0.132199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.118631 restraints weight = 13530.359| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 2.19 r_work: 0.4159 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4073 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4775 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= 0.125 Angle : 0.518 5.335 4548 Z= 0.263 Chirality : 0.051 0.139 516 Planarity : 0.002 0.018 576 Dihedral : 4.660 12.061 444 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.26 % Allowed : 14.06 % Favored : 85.68 % 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: -1.84 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.003 0.001 PHE B 378 TYR 0.011 0.002 TYR G 310 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01578 ( 64) hydrogen bonds : angle 3.58401 ( 192) covalent geometry : bond 0.00270 ( 3396) covalent geometry : angle 0.51786 ( 4548) *********************** 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 54 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8085 (ttpt) cc_final: 0.7643 (mttp) REVERT: A 349 ARG cc_start: 0.7440 (mtp85) cc_final: 0.7008 (mtt-85) REVERT: A 375 LYS cc_start: 0.8023 (tttt) cc_final: 0.7418 (ttmm) REVERT: C 321 LYS cc_start: 0.8097 (ttpt) cc_final: 0.7565 (mttm) REVERT: C 349 ARG cc_start: 0.8015 (mtt180) cc_final: 0.6240 (mmm160) REVERT: C 369 LYS cc_start: 0.8030 (mttt) cc_final: 0.7633 (mtpt) REVERT: E 349 ARG cc_start: 0.7840 (mtt180) cc_final: 0.6359 (pmt-80) REVERT: E 369 LYS cc_start: 0.8185 (mttt) cc_final: 0.7665 (mtpt) REVERT: G 349 ARG cc_start: 0.7314 (mtp85) cc_final: 0.7032 (mtt-85) REVERT: B 349 ARG cc_start: 0.8012 (mtt180) cc_final: 0.6297 (mmm160) REVERT: D 321 LYS cc_start: 0.8514 (ttpt) cc_final: 0.7976 (mttp) REVERT: D 349 ARG cc_start: 0.7855 (mtt180) cc_final: 0.6431 (pmt-80) REVERT: D 358 ASP cc_start: 0.8653 (m-30) cc_final: 0.8355 (m-30) REVERT: D 375 LYS cc_start: 0.8598 (tttt) cc_final: 0.7984 (ttmm) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.5766 time to fit residues: 34.6603 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 : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.0060 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 overall best weight: 1.7000 ------------------------------------------------------------------------------- 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 = 0.4404 r_free = 0.4404 target = 0.133633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.119941 restraints weight = 13601.126| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 2.23 r_work: 0.4177 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4089 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4850 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= 0.107 Angle : 0.504 4.160 4548 Z= 0.258 Chirality : 0.051 0.139 516 Planarity : 0.002 0.017 576 Dihedral : 4.526 12.210 444 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 14.32 % Favored : 85.68 % 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: -1.84 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.004 0.001 PHE B 378 TYR 0.010 0.002 TYR G 310 ARG 0.001 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.01475 ( 64) hydrogen bonds : angle 3.50775 ( 192) covalent geometry : bond 0.00232 ( 3396) covalent geometry : angle 0.50415 ( 4548) ********************** 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: 0 poor density : 51 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8095 (ttpt) cc_final: 0.7678 (mttp) REVERT: A 349 ARG cc_start: 0.7461 (mtp85) cc_final: 0.7121 (mtt-85) REVERT: A 375 LYS cc_start: 0.7999 (tttt) cc_final: 0.7395 (ttmm) REVERT: C 321 LYS cc_start: 0.8073 (ttpt) cc_final: 0.7551 (mttp) REVERT: C 349 ARG cc_start: 0.7998 (mtt180) cc_final: 0.6237 (mmm160) REVERT: C 369 LYS cc_start: 0.8004 (mttt) cc_final: 0.7614 (mtpt) REVERT: E 349 ARG cc_start: 0.7874 (mtt180) cc_final: 0.6337 (pmt-80) REVERT: E 369 LYS cc_start: 0.8162 (mttt) cc_final: 0.7647 (mtpt) REVERT: G 349 ARG cc_start: 0.7336 (mtp85) cc_final: 0.6670 (mtt-85) REVERT: B 349 ARG cc_start: 0.7995 (mtt180) cc_final: 0.6275 (mmm160) REVERT: D 321 LYS cc_start: 0.8508 (ttpt) cc_final: 0.7968 (mttm) REVERT: D 349 ARG cc_start: 0.7861 (mtt180) cc_final: 0.6416 (pmt-80) REVERT: D 358 ASP cc_start: 0.8624 (m-30) cc_final: 0.8314 (m-30) REVERT: D 375 LYS cc_start: 0.8599 (tttt) cc_final: 0.7981 (ttmm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.5801 time to fit residues: 33.5947 Evaluate side-chains 51 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 15 optimal weight: 0.2980 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 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 = 0.4392 r_free = 0.4392 target = 0.132716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.119115 restraints weight = 13595.464| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 2.20 r_work: 0.4166 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4079 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4895 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 : 0.510 4.074 4548 Z= 0.261 Chirality : 0.051 0.140 516 Planarity : 0.002 0.017 576 Dihedral : 4.503 12.308 444 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % 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: -1.84 (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 HIS 0.002 0.001 HIS E 329 PHE 0.004 0.001 PHE B 378 TYR 0.011 0.002 TYR G 310 ARG 0.001 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.01486 ( 64) hydrogen bonds : angle 3.49638 ( 192) covalent geometry : bond 0.00250 ( 3396) covalent geometry : angle 0.50994 ( 4548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4334.03 seconds wall clock time: 75 minutes 49.62 seconds (4549.62 seconds total)