Starting phenix.real_space_refine on Wed Feb 12 00:01:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qkx_14056/02_2025/7qkx_14056.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkx_14056/02_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_14056/02_2025/7qkx_14056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkx_14056/02_2025/7qkx_14056.map" model { file = "/net/cci-nas-00/data/ceres_data/7qkx_14056/02_2025/7qkx_14056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkx_14056/02_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-5592/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: 4.65, per 1000 atoms: 0.68 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: 1.69 Conformation dependent library (CDL) restraints added in 539.1 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: 0.70 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: 2.10 Time building geometry restraints manager: 2.04 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: 4.000 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: 0.120 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.040 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- 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= 0.736 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 *********************** 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 : 0.539 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: 0.5866 time to fit residues: 79.1584 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 : 0.636 ------------------------------------------------------------------------------- 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 = 0.148615 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 = 12024.713| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 2.06 r_work: 0.4308 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4219 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.4219 ------------------------------------------------------------------------------- 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= 0.193 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 *********************** 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 : 0.554 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: 0.7997 (ttpt) cc_final: 0.7504 (mttm) REVERT: A 348 ASP cc_start: 0.8353 (t0) cc_final: 0.8106 (t0) REVERT: A 369 LYS cc_start: 0.8224 (mttt) cc_final: 0.7801 (mtpt) REVERT: C 311 LYS cc_start: 0.8879 (ttpt) cc_final: 0.8266 (mmtt) REVERT: C 321 LYS cc_start: 0.7959 (ttpt) cc_final: 0.7609 (mttt) REVERT: C 349 ARG cc_start: 0.7898 (mtt180) cc_final: 0.6147 (mmm160) REVERT: C 369 LYS cc_start: 0.8077 (mttt) cc_final: 0.7793 (mtpt) REVERT: E 321 LYS cc_start: 0.8409 (ttpt) cc_final: 0.8176 (mttm) REVERT: E 349 ARG cc_start: 0.7179 (mtt180) cc_final: 0.6324 (pmt-80) REVERT: E 369 LYS cc_start: 0.8155 (mttt) cc_final: 0.7746 (mtpt) REVERT: E 375 LYS cc_start: 0.8417 (tttt) cc_final: 0.7928 (ttmm) REVERT: G 369 LYS cc_start: 0.8078 (mttt) cc_final: 0.7627 (mtpt) REVERT: B 311 LYS cc_start: 0.8732 (ttpt) cc_final: 0.8163 (mmtt) REVERT: B 317 LYS cc_start: 0.8018 (pttt) cc_final: 0.7626 (pttp) REVERT: B 321 LYS cc_start: 0.7854 (ttpt) cc_final: 0.7478 (mttm) REVERT: B 349 ARG cc_start: 0.8045 (mtt180) cc_final: 0.6155 (mmm160) REVERT: B 369 LYS cc_start: 0.7949 (mttt) cc_final: 0.7574 (mtpt) REVERT: D 321 LYS cc_start: 0.8323 (ttpt) cc_final: 0.8054 (mttp) REVERT: D 349 ARG cc_start: 0.7413 (mtt180) cc_final: 0.6553 (pmt-80) REVERT: D 369 LYS cc_start: 0.8117 (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: 0.6483 time to fit residues: 54.0737 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 : 0.610 ------------------------------------------------------------------------------- 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: 0.9980 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: 5.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4516 r_free = 0.4516 target = 0.143557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.129507 restraints weight = 12551.653| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 2.11 r_work: 0.4303 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4216 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3396 Z= 0.166 Angle : 0.544 5.359 4548 Z= 0.278 Chirality : 0.052 0.138 516 Planarity : 0.002 0.018 576 Dihedral : 5.409 15.087 444 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.26 % Allowed : 10.68 % Favored : 89.06 % 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: -1.47 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 330 PHE 0.007 0.001 PHE B 378 TYR 0.012 0.002 TYR G 310 ARG 0.002 0.000 ARG G 349 *********************** 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: 1 poor density : 65 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8034 (ttpt) cc_final: 0.7587 (mttm) REVERT: A 348 ASP cc_start: 0.7989 (t0) cc_final: 0.7771 (t0) REVERT: A 369 LYS cc_start: 0.8185 (mttt) cc_final: 0.7754 (mtpt) REVERT: A 375 LYS cc_start: 0.8129 (tttt) cc_final: 0.7562 (ttmm) REVERT: C 311 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8323 (mmtt) REVERT: C 321 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7806 (mttm) REVERT: C 349 ARG cc_start: 0.7934 (mtt180) cc_final: 0.6250 (mmm160) REVERT: C 369 LYS cc_start: 0.8069 (mttt) cc_final: 0.7761 (mtpt) REVERT: E 321 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8217 (mttp) REVERT: E 342 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8142 (tt0) REVERT: E 349 ARG cc_start: 0.7312 (mtt180) cc_final: 0.6397 (pmt-80) REVERT: E 369 LYS cc_start: 0.8155 (mttt) cc_final: 0.7751 (mtpt) REVERT: E 375 LYS cc_start: 0.8439 (tttt) cc_final: 0.7973 (ttmm) REVERT: G 369 LYS cc_start: 0.8104 (mttt) cc_final: 0.7735 (mtpt) REVERT: B 311 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8188 (mmtt) REVERT: B 349 ARG cc_start: 0.8063 (mtt180) cc_final: 0.6177 (mmm160) REVERT: B 369 LYS cc_start: 0.8068 (mttt) cc_final: 0.7686 (mtpt) REVERT: D 321 LYS cc_start: 0.8370 (ttpt) cc_final: 0.8082 (mttp) REVERT: D 349 ARG cc_start: 0.7448 (mtt180) cc_final: 0.6430 (pmt-80) REVERT: D 358 ASP cc_start: 0.8660 (m-30) cc_final: 0.8451 (m-30) REVERT: D 375 LYS cc_start: 0.8470 (tttt) cc_final: 0.7953 (ttmm) outliers start: 1 outliers final: 1 residues processed: 66 average time/residue: 0.6332 time to fit residues: 47.0510 Evaluate side-chains 62 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 3 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 28 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.4481 r_free = 0.4481 target = 0.139577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.125322 restraints weight = 12884.817| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 2.23 r_work: 0.4257 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4169 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3396 Z= 0.162 Angle : 0.518 4.895 4548 Z= 0.262 Chirality : 0.051 0.139 516 Planarity : 0.002 0.017 576 Dihedral : 5.030 13.148 444 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.26 % Allowed : 11.46 % Favored : 88.28 % 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: -1.61 (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 0.002 0.001 HIS E 330 PHE 0.006 0.001 PHE B 378 TYR 0.011 0.002 TYR G 310 ARG 0.002 0.000 ARG G 349 *********************** 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 67 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7970 (ttpt) cc_final: 0.7514 (mttm) REVERT: A 348 ASP cc_start: 0.7827 (t0) cc_final: 0.7620 (t0) REVERT: A 369 LYS cc_start: 0.8171 (mttt) cc_final: 0.7675 (mtpt) REVERT: A 375 LYS cc_start: 0.8039 (tttt) cc_final: 0.7445 (ttmm) REVERT: C 311 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8257 (mmtt) REVERT: C 321 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7718 (mttm) REVERT: C 349 ARG cc_start: 0.7899 (mtt180) cc_final: 0.6119 (mmm160) REVERT: C 369 LYS cc_start: 0.8029 (mttt) cc_final: 0.7668 (mtpt) REVERT: E 321 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8180 (mttp) REVERT: E 342 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8120 (tt0) REVERT: E 349 ARG cc_start: 0.7389 (mtt180) cc_final: 0.6282 (pmt-80) REVERT: E 369 LYS cc_start: 0.8165 (mttt) cc_final: 0.7703 (mtpt) REVERT: E 375 LYS cc_start: 0.8472 (tttt) cc_final: 0.7954 (ttmm) REVERT: G 308 ILE cc_start: 0.8553 (mt) cc_final: 0.8348 (mp) REVERT: B 307 GLN cc_start: 0.7770 (tt0) cc_final: 0.7517 (tt0) REVERT: B 311 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8106 (mmtt) REVERT: B 349 ARG cc_start: 0.7999 (mtt180) cc_final: 0.6057 (mmm160) REVERT: B 369 LYS cc_start: 0.8028 (mttt) cc_final: 0.7599 (mtpt) REVERT: D 321 LYS cc_start: 0.8391 (ttpt) cc_final: 0.8024 (mttp) REVERT: D 349 ARG cc_start: 0.7465 (mtt180) cc_final: 0.6462 (pmt-80) REVERT: D 358 ASP cc_start: 0.8669 (m-30) cc_final: 0.8385 (m-30) REVERT: D 375 LYS cc_start: 0.8504 (tttt) cc_final: 0.7932 (ttmm) outliers start: 1 outliers final: 1 residues processed: 67 average time/residue: 0.5849 time to fit residues: 43.7916 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 : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 36 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4469 r_free = 0.4469 target = 0.139551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.125395 restraints weight = 12876.676| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 2.20 r_work: 0.4247 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4158 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3396 Z= 0.143 Angle : 0.495 5.625 4548 Z= 0.248 Chirality : 0.051 0.138 516 Planarity : 0.002 0.016 576 Dihedral : 4.673 12.751 444 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.26 % Allowed : 11.46 % Favored : 88.28 % 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: -1.61 (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 0.002 0.001 HIS D 330 PHE 0.005 0.001 PHE B 378 TYR 0.010 0.002 TYR G 310 ARG 0.002 0.000 ARG E 349 *********************** 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 62 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7686 (mttm) REVERT: A 369 LYS cc_start: 0.8166 (mttt) cc_final: 0.7684 (mtpt) REVERT: A 375 LYS cc_start: 0.8067 (tttt) cc_final: 0.7461 (ttmm) REVERT: C 311 LYS cc_start: 0.8902 (ttpt) cc_final: 0.8309 (mmtt) REVERT: C 321 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7774 (mttm) REVERT: C 349 ARG cc_start: 0.7932 (mtt180) cc_final: 0.6203 (mmm160) REVERT: C 369 LYS cc_start: 0.8042 (mttt) cc_final: 0.7683 (mtpt) REVERT: E 321 LYS cc_start: 0.8475 (ttpt) cc_final: 0.8170 (mttp) REVERT: E 349 ARG cc_start: 0.7552 (mtt180) cc_final: 0.6343 (pmt-80) REVERT: E 369 LYS cc_start: 0.8232 (mttt) cc_final: 0.7766 (mtpt) REVERT: E 375 LYS cc_start: 0.8528 (tttt) cc_final: 0.8012 (ttmm) REVERT: B 311 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8190 (mmtt) REVERT: B 349 ARG cc_start: 0.8052 (mtt180) cc_final: 0.6150 (mmm160) REVERT: D 321 LYS cc_start: 0.8443 (ttpt) cc_final: 0.8074 (mttp) REVERT: D 348 ASP cc_start: 0.8306 (t0) cc_final: 0.8046 (t0) REVERT: D 349 ARG cc_start: 0.7604 (mtt180) cc_final: 0.6583 (pmt-80) REVERT: D 358 ASP cc_start: 0.8625 (m-30) cc_final: 0.8346 (m-30) REVERT: D 375 LYS cc_start: 0.8530 (tttt) cc_final: 0.7974 (ttmm) outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 0.6074 time to fit residues: 42.2611 Evaluate side-chains 54 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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: 1.9990 chunk 6 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.130101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.115920 restraints weight = 13507.591| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 2.18 r_work: 0.4142 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4054 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4468 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= 0.151 Angle : 0.496 5.414 4548 Z= 0.252 Chirality : 0.050 0.138 516 Planarity : 0.002 0.016 576 Dihedral : 4.565 11.892 444 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: -1.65 (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 0.002 0.001 HIS A 329 PHE 0.005 0.001 PHE B 378 TYR 0.011 0.002 TYR G 310 ARG 0.002 0.000 ARG E 349 *********************** 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 60 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8027 (ttpt) cc_final: 0.7690 (mttp) REVERT: A 369 LYS cc_start: 0.8141 (mttt) cc_final: 0.7652 (mtpt) REVERT: A 375 LYS cc_start: 0.8055 (tttt) cc_final: 0.7429 (ttmm) REVERT: C 321 LYS cc_start: 0.8104 (ttpt) cc_final: 0.7727 (mttm) REVERT: C 349 ARG cc_start: 0.7892 (mtt180) cc_final: 0.6218 (mmm160) REVERT: C 369 LYS cc_start: 0.8035 (mttt) cc_final: 0.7632 (mtpt) REVERT: E 321 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8176 (mttp) REVERT: E 349 ARG cc_start: 0.7617 (mtt180) cc_final: 0.6385 (pmt-80) REVERT: E 369 LYS cc_start: 0.8210 (mttt) cc_final: 0.7717 (mtpt) REVERT: E 375 LYS cc_start: 0.8547 (tttt) cc_final: 0.8004 (ttmm) REVERT: B 311 LYS cc_start: 0.8755 (ttpt) cc_final: 0.8162 (mmtt) REVERT: B 349 ARG cc_start: 0.8039 (mtt180) cc_final: 0.6235 (mmm160) REVERT: D 321 LYS cc_start: 0.8452 (ttpt) cc_final: 0.8072 (mttm) REVERT: D 349 ARG cc_start: 0.7681 (mtt180) cc_final: 0.6582 (pmt-80) REVERT: D 358 ASP cc_start: 0.8603 (m-30) cc_final: 0.8303 (m-30) REVERT: D 375 LYS cc_start: 0.8557 (tttt) cc_final: 0.7976 (ttmm) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.5797 time to fit residues: 39.2274 Evaluate side-chains 54 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.4494 r_free = 0.4494 target = 0.140289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.126427 restraints weight = 12668.349| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 2.17 r_work: 0.4270 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4180 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4617 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= 0.112 Angle : 0.492 5.257 4548 Z= 0.243 Chirality : 0.051 0.137 516 Planarity : 0.002 0.016 576 Dihedral : 4.304 10.920 444 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.26 % Allowed : 13.28 % 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 (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 0.002 0.001 HIS G 330 PHE 0.002 0.000 PHE B 378 TYR 0.007 0.001 TYR G 310 ARG 0.001 0.000 ARG A 349 *********************** 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 57 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8035 (ttpt) cc_final: 0.7671 (mttp) REVERT: A 369 LYS cc_start: 0.8159 (mttt) cc_final: 0.7665 (mtpt) REVERT: A 375 LYS cc_start: 0.8046 (tttt) cc_final: 0.7438 (ttmm) REVERT: C 321 LYS cc_start: 0.8116 (ttpt) cc_final: 0.7736 (mttm) REVERT: C 349 ARG cc_start: 0.7854 (mtt180) cc_final: 0.6175 (mmm160) REVERT: C 369 LYS cc_start: 0.8078 (mttt) cc_final: 0.7697 (mtpt) REVERT: E 321 LYS cc_start: 0.8470 (ttpt) cc_final: 0.8128 (mttp) REVERT: E 349 ARG cc_start: 0.7643 (mtt180) cc_final: 0.6420 (pmt-80) REVERT: E 369 LYS cc_start: 0.8169 (mttt) cc_final: 0.7686 (mtpt) REVERT: E 375 LYS cc_start: 0.8549 (tttt) cc_final: 0.8008 (ttmm) REVERT: B 311 LYS cc_start: 0.8767 (ttpt) cc_final: 0.8137 (mmtt) REVERT: B 349 ARG cc_start: 0.8002 (mtt180) cc_final: 0.6180 (mmm160) REVERT: D 321 LYS cc_start: 0.8466 (ttpt) cc_final: 0.8049 (mttp) REVERT: D 349 ARG cc_start: 0.7731 (mtt180) cc_final: 0.6602 (pmt-80) REVERT: D 375 LYS cc_start: 0.8557 (tttt) cc_final: 0.7979 (ttmm) outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.6431 time to fit residues: 40.4038 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 : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 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: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.123801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.109545 restraints weight = 14483.852| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 2.14 r_work: 0.4027 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3939 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3396 Z= 0.328 Angle : 0.580 4.271 4548 Z= 0.303 Chirality : 0.051 0.143 516 Planarity : 0.003 0.019 576 Dihedral : 4.838 11.653 444 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: -1.76 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 329 PHE 0.010 0.002 PHE B 378 TYR 0.020 0.004 TYR G 310 ARG 0.002 0.001 ARG D 349 *********************** 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 : 0.566 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8054 (ttpt) cc_final: 0.7712 (mttp) REVERT: A 375 LYS cc_start: 0.8128 (tttt) cc_final: 0.7508 (ttmm) REVERT: C 321 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7616 (mttm) REVERT: C 349 ARG cc_start: 0.8055 (mtt180) cc_final: 0.6294 (mmm160) REVERT: C 369 LYS cc_start: 0.8059 (mttt) cc_final: 0.7647 (mtpt) REVERT: E 321 LYS cc_start: 0.8484 (ttpt) cc_final: 0.8123 (mttp) REVERT: E 349 ARG cc_start: 0.7795 (mtt180) cc_final: 0.6405 (pmt-80) REVERT: E 369 LYS cc_start: 0.8287 (mttt) cc_final: 0.7778 (mtpt) REVERT: B 349 ARG cc_start: 0.8111 (mtt180) cc_final: 0.6393 (mmm160) REVERT: D 321 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8065 (mttp) REVERT: D 358 ASP cc_start: 0.8687 (m-30) cc_final: 0.8417 (m-30) REVERT: D 375 LYS cc_start: 0.8605 (tttt) cc_final: 0.7996 (ttmm) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.4993 time to fit residues: 30.2305 Evaluate side-chains 50 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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: 0.7980 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.4317 r_free = 0.4317 target = 0.126832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.112386 restraints weight = 14240.819| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 2.21 r_work: 0.4071 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3983 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.4733 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= 0.213 Angle : 0.543 5.046 4548 Z= 0.277 Chirality : 0.051 0.140 516 Planarity : 0.003 0.019 576 Dihedral : 4.733 11.252 444 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 15.10 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.004 0.001 PHE B 378 TYR 0.013 0.002 TYR G 310 ARG 0.002 0.000 ARG G 349 *********************** 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: 0 poor density : 52 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8096 (ttpt) cc_final: 0.7747 (mttp) REVERT: A 375 LYS cc_start: 0.8106 (tttt) cc_final: 0.7519 (ttmm) REVERT: C 321 LYS cc_start: 0.8141 (ttpt) cc_final: 0.7640 (mttm) REVERT: C 349 ARG cc_start: 0.8000 (mtt180) cc_final: 0.6264 (mmm160) REVERT: C 369 LYS cc_start: 0.8085 (mttt) cc_final: 0.7700 (mtpt) REVERT: E 349 ARG cc_start: 0.7880 (mtt180) cc_final: 0.6445 (pmt-80) REVERT: E 369 LYS cc_start: 0.8235 (mttt) cc_final: 0.7749 (mtpt) REVERT: B 349 ARG cc_start: 0.8077 (mtt180) cc_final: 0.6367 (mmm160) REVERT: D 321 LYS cc_start: 0.8534 (ttpt) cc_final: 0.8062 (mttp) REVERT: D 349 ARG cc_start: 0.7894 (mtt180) cc_final: 0.6568 (pmt-80) REVERT: D 358 ASP cc_start: 0.8621 (m-30) cc_final: 0.8364 (m-30) REVERT: D 375 LYS cc_start: 0.8595 (tttt) cc_final: 0.7986 (ttmm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.5659 time to fit residues: 33.3406 Evaluate side-chains 50 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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: 2.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4408 r_free = 0.4408 target = 0.133958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.120365 restraints weight = 13532.972| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 2.22 r_work: 0.4192 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4103 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3396 Z= 0.149 Angle : 0.520 4.468 4548 Z= 0.264 Chirality : 0.050 0.138 516 Planarity : 0.003 0.029 576 Dihedral : 4.496 10.917 444 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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 G 330 PHE 0.003 0.001 PHE B 378 TYR 0.009 0.002 TYR G 310 ARG 0.001 0.000 ARG E 349 ********************** 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 50 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7639 (mttp) REVERT: A 375 LYS cc_start: 0.8005 (tttt) cc_final: 0.7410 (ttmm) REVERT: C 321 LYS cc_start: 0.8069 (ttpt) cc_final: 0.7560 (mttp) REVERT: C 349 ARG cc_start: 0.7927 (mtt180) cc_final: 0.6177 (mmm160) REVERT: C 369 LYS cc_start: 0.8003 (mttt) cc_final: 0.7609 (mtpt) REVERT: E 349 ARG cc_start: 0.7836 (mtt180) cc_final: 0.6393 (pmt-80) REVERT: E 369 LYS cc_start: 0.8178 (mttt) cc_final: 0.7673 (mtpt) REVERT: B 349 ARG cc_start: 0.7931 (mtt180) cc_final: 0.6109 (mmm160) REVERT: D 321 LYS cc_start: 0.8511 (ttpt) cc_final: 0.7969 (mttm) REVERT: D 349 ARG cc_start: 0.7816 (mtt180) cc_final: 0.6422 (pmt-80) REVERT: D 358 ASP cc_start: 0.8639 (m-30) cc_final: 0.8331 (m-30) REVERT: D 375 LYS cc_start: 0.8588 (tttt) cc_final: 0.7975 (ttmm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.5656 time to fit residues: 32.6381 Evaluate side-chains 50 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.132013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.118497 restraints weight = 13557.642| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 2.18 r_work: 0.4159 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4072 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4839 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= 0.187 Angle : 0.533 4.185 4548 Z= 0.274 Chirality : 0.051 0.140 516 Planarity : 0.003 0.032 576 Dihedral : 4.533 11.181 444 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: -1.86 (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 HIS 0.002 0.001 HIS A 329 PHE 0.005 0.001 PHE B 378 TYR 0.012 0.002 TYR G 310 ARG 0.001 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4201.37 seconds wall clock time: 74 minutes 40.08 seconds (4480.08 seconds total)