Starting phenix.real_space_refine on Tue Sep 24 04:18:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkx_14056/09_2024/7qkx_14056.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkx_14056/09_2024/7qkx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkx_14056/09_2024/7qkx_14056.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkx_14056/09_2024/7qkx_14056.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkx_14056/09_2024/7qkx_14056.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkx_14056/09_2024/7qkx_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-5461/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: 4.31, 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: 1.41 Conformation dependent library (CDL) restraints added in 525.7 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: 0.63 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.442A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.925A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 321 removed outlier: 6.307A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330 removed outlier: 5.913A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN A 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342 Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.430A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 357 removed outlier: 6.521A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N SER E 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLY A 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.427A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 377 removed outlier: 6.597A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 307 through 310 removed outlier: 6.495A pdb=" N ILE G 308 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN G 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N TYR D 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL G 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.923A pdb=" N VAL G 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 317 through 321 Processing sheet with id=AB4, first strand: chain 'B' and resid 325 through 330 removed outlier: 5.930A pdb=" N GLY G 326 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N HIS B 329 " --> pdb=" O GLY G 326 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE G 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY D 326 " --> pdb=" O LEU G 325 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN G 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 337 through 342 removed outlier: 6.560A pdb=" N VAL G 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LYS B 340 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL G 339 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLU B 342 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER G 341 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.472A pdb=" N ASP G 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 350 through 357 removed outlier: 6.344A pdb=" N VAL G 350 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LYS B 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER G 352 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N GLY B 355 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE G 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU B 357 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER G 356 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN G 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE D 354 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS G 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N SER D 356 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY G 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.446A pdb=" N THR G 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 369 through 377 removed outlier: 6.626A pdb=" N LYS G 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLU D 372 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE G 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N HIS D 374 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR G 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N LEU D 376 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS G 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) 64 hydrogen bonds defined for protein. 192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 3474 1.11 - 1.29: 558 1.29 - 1.46: 941 1.46 - 1.64: 1897 1.64 - 1.81: 6 Bond restraints: 6876 Sorted by residual: bond pdb=" N ASP C 345 " pdb=" H ASP C 345 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" N ARG C 349 " pdb=" H ARG C 349 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" N SER A 352 " pdb=" H SER A 352 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" N ILE D 360 " pdb=" H ILE D 360 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" N HIS B 329 " pdb=" H HIS B 329 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 ... (remaining 6871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 10520 2.47 - 4.95: 1561 4.95 - 7.42: 444 7.42 - 9.89: 15 9.89 - 12.36: 6 Bond angle restraints: 12546 Sorted by residual: angle pdb=" CA ASP G 345 " pdb=" CB ASP G 345 " pdb=" CG ASP G 345 " ideal model delta sigma weight residual 112.60 117.62 -5.02 1.00e+00 1.00e+00 2.52e+01 angle pdb=" OE1 GLN G 336 " pdb=" CD GLN G 336 " pdb=" NE2 GLN G 336 " ideal model delta sigma weight residual 122.60 117.64 4.96 1.00e+00 1.00e+00 2.46e+01 angle pdb=" CA ASP E 345 " pdb=" CB ASP E 345 " pdb=" CG ASP E 345 " ideal model delta sigma weight residual 112.60 117.54 -4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" CA ASP A 345 " pdb=" CB ASP A 345 " pdb=" CG ASP A 345 " ideal model delta sigma weight residual 112.60 117.47 -4.87 1.00e+00 1.00e+00 2.37e+01 angle pdb=" N GLY G 326 " pdb=" CA GLY G 326 " pdb=" C GLY G 326 " ideal model delta sigma weight residual 110.69 117.16 -6.47 1.33e+00 5.65e-01 2.36e+01 ... (remaining 12541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.51: 2745 13.51 - 27.02: 207 27.02 - 40.52: 84 40.52 - 54.03: 54 54.03 - 67.54: 78 Dihedral angle restraints: 3168 sinusoidal: 1806 harmonic: 1362 Sorted by residual: dihedral pdb=" CA LYS G 375 " pdb=" C LYS G 375 " pdb=" N LEU G 376 " pdb=" CA LEU G 376 " ideal model delta harmonic sigma weight residual 180.00 151.10 28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA THR B 377 " pdb=" C THR B 377 " pdb=" N PHE B 378 " pdb=" CA PHE B 378 " ideal model delta harmonic sigma weight residual -180.00 -152.40 -27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA LYS G 369 " pdb=" C LYS G 369 " pdb=" N LYS G 370 " pdb=" CA LYS G 370 " ideal model delta harmonic sigma weight residual 180.00 157.11 22.89 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 3165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 286 0.067 - 0.133: 165 0.133 - 0.199: 48 0.199 - 0.265: 13 0.265 - 0.332: 4 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA LEU G 376 " pdb=" N LEU G 376 " pdb=" C LEU G 376 " pdb=" CB LEU G 376 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA LYS C 343 " pdb=" N LYS C 343 " pdb=" C LYS C 343 " pdb=" CB LYS C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA LYS A 317 " pdb=" N LYS A 317 " pdb=" C LYS A 317 " pdb=" CB LYS A 317 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 513 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.076 2.00e-02 2.50e+03 3.17e-02 3.02e+01 pdb=" CG TYR C 310 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.045 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " 0.007 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 362 " 0.057 2.00e-02 2.50e+03 3.62e-02 2.95e+01 pdb=" CG HIS A 362 " -0.050 2.00e-02 2.50e+03 pdb=" ND1 HIS A 362 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS A 362 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 HIS A 362 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 HIS A 362 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 HIS A 362 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 HIS A 362 " 0.035 2.00e-02 2.50e+03 pdb=" HE2 HIS A 362 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 359 " 0.004 2.00e-02 2.50e+03 4.08e-02 2.50e+01 pdb=" CG ASN A 359 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 359 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 359 " -0.082 2.00e-02 2.50e+03 pdb="HD21 ASN A 359 " 0.046 2.00e-02 2.50e+03 pdb="HD22 ASN A 359 " 0.023 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 447 2.17 - 2.78: 11789 2.78 - 3.39: 17717 3.39 - 3.99: 24010 3.99 - 4.60: 33554 Nonbonded interactions: 87517 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.566 2.450 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.570 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.573 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.577 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.593 2.450 ... (remaining 87512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 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: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.650 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.170 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.581 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: 0.5708 time to fit residues: 76.9031 Evaluate side-chains 81 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.710 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: 0.7834 (ttpt) cc_final: 0.7276 (mttm) REVERT: A 369 LYS cc_start: 0.7509 (mttt) cc_final: 0.7106 (mtpt) REVERT: C 311 LYS cc_start: 0.7380 (ttpt) cc_final: 0.6794 (mmtt) REVERT: C 321 LYS cc_start: 0.7866 (ttpt) cc_final: 0.7456 (mttt) REVERT: C 349 ARG cc_start: 0.8155 (mtt180) cc_final: 0.6306 (mmm160) REVERT: C 369 LYS cc_start: 0.7406 (mttt) cc_final: 0.7131 (mtpt) REVERT: E 321 LYS cc_start: 0.8424 (ttpt) cc_final: 0.8044 (mttm) REVERT: E 349 ARG cc_start: 0.7380 (mtt180) cc_final: 0.6487 (pmt-80) REVERT: E 369 LYS cc_start: 0.7896 (mttt) cc_final: 0.7386 (mtpt) REVERT: E 375 LYS cc_start: 0.7296 (tttt) cc_final: 0.6851 (ttmm) REVERT: G 369 LYS cc_start: 0.7362 (mttt) cc_final: 0.6878 (mtpt) REVERT: B 311 LYS cc_start: 0.7549 (ttpt) cc_final: 0.6914 (mmtt) REVERT: B 317 LYS cc_start: 0.6585 (pttt) cc_final: 0.6350 (pttp) REVERT: B 321 LYS cc_start: 0.7775 (ttpt) cc_final: 0.7295 (mttm) REVERT: B 349 ARG cc_start: 0.8284 (mtt180) cc_final: 0.6318 (mmm160) REVERT: B 369 LYS cc_start: 0.7291 (mttt) cc_final: 0.6901 (mtpt) REVERT: D 321 LYS cc_start: 0.8322 (ttpt) cc_final: 0.7888 (mttp) REVERT: D 349 ARG cc_start: 0.7612 (mtt180) cc_final: 0.6661 (pmt-80) REVERT: D 369 LYS cc_start: 0.7776 (mttt) cc_final: 0.7294 (mtpt) REVERT: D 375 LYS cc_start: 0.7150 (tttt) cc_final: 0.6625 (ttmm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.6085 time to fit residues: 51.1119 Evaluate side-chains 68 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3396 Z= 0.353 Angle : 0.635 6.445 4548 Z= 0.332 Chirality : 0.053 0.139 516 Planarity : 0.003 0.023 576 Dihedral : 5.933 16.962 444 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: -1.56 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 329 PHE 0.012 0.002 PHE B 378 TYR 0.023 0.004 TYR G 310 ARG 0.003 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 64 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7928 (ttpt) cc_final: 0.7367 (mttm) REVERT: A 369 LYS cc_start: 0.7336 (mttt) cc_final: 0.6914 (mtpt) REVERT: A 375 LYS cc_start: 0.5915 (tttt) cc_final: 0.5544 (ttmm) REVERT: C 306 VAL cc_start: 0.4837 (t) cc_final: 0.4485 (t) REVERT: C 321 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7631 (mttm) REVERT: C 349 ARG cc_start: 0.8231 (mtt180) cc_final: 0.6458 (mmm160) REVERT: C 369 LYS cc_start: 0.7243 (mttt) cc_final: 0.6903 (mtpt) REVERT: E 321 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8053 (mttm) REVERT: E 349 ARG cc_start: 0.7690 (mtt180) cc_final: 0.6480 (pmt-80) REVERT: E 369 LYS cc_start: 0.7917 (mttt) cc_final: 0.7389 (mtpt) REVERT: E 375 LYS cc_start: 0.7361 (tttt) cc_final: 0.6853 (ttmm) REVERT: G 308 ILE cc_start: 0.5834 (mt) cc_final: 0.5618 (mp) REVERT: G 369 LYS cc_start: 0.7302 (mttt) cc_final: 0.6807 (mtpt) REVERT: B 349 ARG cc_start: 0.8337 (mtt180) cc_final: 0.6529 (mmm160) REVERT: B 369 LYS cc_start: 0.7289 (mttt) cc_final: 0.6866 (mtpt) REVERT: D 321 LYS cc_start: 0.8410 (ttpt) cc_final: 0.7955 (mttm) REVERT: D 349 ARG cc_start: 0.7816 (mtt180) cc_final: 0.6710 (pmt-80) REVERT: D 375 LYS cc_start: 0.7319 (tttt) cc_final: 0.6715 (ttmm) outliers start: 1 outliers final: 1 residues processed: 64 average time/residue: 0.4927 time to fit residues: 35.4302 Evaluate side-chains 57 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 4 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4308 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= 0.354 Angle : 0.622 5.890 4548 Z= 0.322 Chirality : 0.052 0.142 516 Planarity : 0.003 0.021 576 Dihedral : 5.777 15.822 444 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.26 % Allowed : 12.76 % 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: -1.74 (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 0.004 0.001 HIS A 329 PHE 0.010 0.002 PHE B 378 TYR 0.020 0.003 TYR G 310 ARG 0.003 0.001 ARG A 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 55 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.544 Fit side-chains REVERT: A 321 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7420 (mttp) REVERT: A 375 LYS cc_start: 0.5984 (tttt) cc_final: 0.5630 (ttmm) REVERT: C 321 LYS cc_start: 0.8046 (ttpt) cc_final: 0.7554 (mttp) REVERT: C 349 ARG cc_start: 0.8284 (mtt180) cc_final: 0.6455 (mmm160) REVERT: C 369 LYS cc_start: 0.7365 (mttt) cc_final: 0.7004 (mtpt) REVERT: E 321 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8056 (mttp) REVERT: E 349 ARG cc_start: 0.7909 (mtt180) cc_final: 0.6452 (pmt-80) REVERT: E 375 LYS cc_start: 0.7434 (tttt) cc_final: 0.6898 (ttmm) REVERT: B 349 ARG cc_start: 0.8337 (mtt180) cc_final: 0.6658 (mmp-170) REVERT: D 321 LYS cc_start: 0.8430 (ttpt) cc_final: 0.7915 (mttp) REVERT: D 349 ARG cc_start: 0.7954 (mtt180) cc_final: 0.6576 (pmt-80) REVERT: D 375 LYS cc_start: 0.7292 (tttt) cc_final: 0.6665 (ttmm) outliers start: 1 outliers final: 1 residues processed: 55 average time/residue: 0.5039 time to fit residues: 31.6210 Evaluate side-chains 52 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 30 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3396 Z= 0.320 Angle : 0.596 5.883 4548 Z= 0.309 Chirality : 0.052 0.140 516 Planarity : 0.003 0.020 576 Dihedral : 5.547 15.088 444 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.52 % Allowed : 11.98 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.81 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.009 0.001 PHE B 378 TYR 0.017 0.003 TYR G 310 ARG 0.002 0.000 ARG G 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 53 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.637 Fit side-chains REVERT: A 321 LYS cc_start: 0.7970 (ttpt) cc_final: 0.7536 (mttp) REVERT: A 349 ARG cc_start: 0.7733 (mtp85) cc_final: 0.7189 (mtt-85) REVERT: A 375 LYS cc_start: 0.5963 (tttt) cc_final: 0.5613 (ttmm) REVERT: C 321 LYS cc_start: 0.8075 (ttpt) cc_final: 0.7560 (mttp) REVERT: C 349 ARG cc_start: 0.8290 (mtt180) cc_final: 0.6495 (mmm160) REVERT: C 369 LYS cc_start: 0.7384 (mttt) cc_final: 0.7003 (mtpt) REVERT: E 321 LYS cc_start: 0.8510 (ttpt) cc_final: 0.8034 (mttp) REVERT: E 349 ARG cc_start: 0.7983 (mtt180) cc_final: 0.6386 (pmt-80) REVERT: G 349 ARG cc_start: 0.7669 (mtp85) cc_final: 0.7342 (mtt-85) REVERT: B 349 ARG cc_start: 0.8336 (mtt180) cc_final: 0.6681 (mmp-170) REVERT: D 321 LYS cc_start: 0.8465 (ttpt) cc_final: 0.7931 (mttp) REVERT: D 375 LYS cc_start: 0.7253 (tttt) cc_final: 0.6619 (ttmm) outliers start: 2 outliers final: 2 residues processed: 52 average time/residue: 0.5008 time to fit residues: 29.8719 Evaluate side-chains 52 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 overall best weight: 1.8126 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4608 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= 0.160 Angle : 0.528 4.959 4548 Z= 0.267 Chirality : 0.051 0.139 516 Planarity : 0.002 0.017 576 Dihedral : 5.063 13.653 444 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.52 % Allowed : 11.20 % 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: -1.83 (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 0.003 0.001 HIS G 330 PHE 0.004 0.001 PHE B 378 TYR 0.009 0.002 TYR G 310 ARG 0.001 0.000 ARG G 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 56 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7950 (ttpt) cc_final: 0.7540 (mttp) REVERT: A 349 ARG cc_start: 0.7728 (mtp85) cc_final: 0.7352 (mtt-85) REVERT: A 375 LYS cc_start: 0.5937 (tttt) cc_final: 0.5586 (ttmm) REVERT: C 321 LYS cc_start: 0.7980 (ttpt) cc_final: 0.7473 (mttp) REVERT: C 349 ARG cc_start: 0.8251 (mtt180) cc_final: 0.6391 (mmm160) REVERT: C 369 LYS cc_start: 0.7376 (mttt) cc_final: 0.7008 (mtpt) REVERT: E 321 LYS cc_start: 0.8427 (ttpt) cc_final: 0.7964 (mttm) REVERT: E 349 ARG cc_start: 0.7979 (mtt180) cc_final: 0.6445 (pmt-80) REVERT: G 349 ARG cc_start: 0.7650 (mtp85) cc_final: 0.7348 (mtt-85) REVERT: B 349 ARG cc_start: 0.8315 (mtt180) cc_final: 0.6526 (mmm160) REVERT: D 321 LYS cc_start: 0.8425 (ttpt) cc_final: 0.7885 (mttm) REVERT: D 375 LYS cc_start: 0.7301 (tttt) cc_final: 0.6700 (ttmm) outliers start: 2 outliers final: 2 residues processed: 55 average time/residue: 0.5076 time to fit residues: 32.1240 Evaluate side-chains 51 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.0970 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4719 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= 0.176 Angle : 0.518 4.782 4548 Z= 0.264 Chirality : 0.051 0.139 516 Planarity : 0.002 0.016 576 Dihedral : 4.868 13.125 444 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.52 % Allowed : 12.50 % 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: -1.87 (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 E 329 PHE 0.006 0.001 PHE B 378 TYR 0.011 0.002 TYR G 310 ARG 0.001 0.000 ARG G 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 55 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7512 (mttp) REVERT: A 349 ARG cc_start: 0.7718 (mtp85) cc_final: 0.7170 (mtt-85) REVERT: A 375 LYS cc_start: 0.5876 (tttt) cc_final: 0.5537 (ttmm) REVERT: C 321 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7447 (mttp) REVERT: C 349 ARG cc_start: 0.8282 (mtt180) cc_final: 0.6397 (mmm160) REVERT: C 369 LYS cc_start: 0.7382 (mttt) cc_final: 0.7012 (mtpt) REVERT: E 349 ARG cc_start: 0.8010 (mtt180) cc_final: 0.6488 (pmt-80) REVERT: G 349 ARG cc_start: 0.7683 (mtp85) cc_final: 0.6977 (mtt-85) REVERT: B 349 ARG cc_start: 0.8303 (mtt180) cc_final: 0.6534 (mmm160) REVERT: D 321 LYS cc_start: 0.8393 (ttpt) cc_final: 0.7849 (mttp) REVERT: D 349 ARG cc_start: 0.8035 (mtt180) cc_final: 0.6538 (pmt-80) outliers start: 2 outliers final: 2 residues processed: 54 average time/residue: 0.5339 time to fit residues: 32.9633 Evaluate side-chains 52 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4818 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= 0.135 Angle : 0.505 4.454 4548 Z= 0.255 Chirality : 0.051 0.138 516 Planarity : 0.002 0.015 576 Dihedral : 4.669 12.366 444 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.52 % Allowed : 12.50 % 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: -1.85 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 330 PHE 0.003 0.001 PHE B 378 TYR 0.008 0.002 TYR G 310 ARG 0.002 0.000 ARG A 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 53 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7957 (ttpt) cc_final: 0.7467 (mttp) REVERT: A 349 ARG cc_start: 0.7724 (mtp85) cc_final: 0.7507 (mtp85) REVERT: A 375 LYS cc_start: 0.5872 (tttt) cc_final: 0.5525 (ttmm) REVERT: C 321 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7350 (mttm) REVERT: C 349 ARG cc_start: 0.8245 (mtt180) cc_final: 0.6382 (mmm160) REVERT: C 369 LYS cc_start: 0.7373 (mttt) cc_final: 0.7017 (mtpt) REVERT: E 349 ARG cc_start: 0.8035 (mtt180) cc_final: 0.6589 (pmt-80) REVERT: G 349 ARG cc_start: 0.7681 (mtp85) cc_final: 0.7340 (mtt-85) REVERT: B 349 ARG cc_start: 0.8280 (mtt180) cc_final: 0.6452 (mmm160) REVERT: D 321 LYS cc_start: 0.8391 (ttpt) cc_final: 0.7847 (mttm) REVERT: D 349 ARG cc_start: 0.8055 (mtt180) cc_final: 0.6613 (pmt-80) outliers start: 2 outliers final: 2 residues processed: 52 average time/residue: 0.5110 time to fit residues: 30.5122 Evaluate side-chains 51 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3396 Z= 0.170 Angle : 0.516 4.540 4548 Z= 0.263 Chirality : 0.051 0.139 516 Planarity : 0.002 0.016 576 Dihedral : 4.639 12.339 444 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.26 % Allowed : 13.54 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.87 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.005 0.001 PHE B 378 TYR 0.011 0.002 TYR G 310 ARG 0.001 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 50 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7459 (mttp) REVERT: A 349 ARG cc_start: 0.7767 (mtp85) cc_final: 0.7556 (mtp85) REVERT: A 375 LYS cc_start: 0.5846 (tttt) cc_final: 0.5509 (ttmm) REVERT: C 321 LYS cc_start: 0.7879 (ttpt) cc_final: 0.7344 (mttm) REVERT: C 349 ARG cc_start: 0.8259 (mtt180) cc_final: 0.6380 (mmm160) REVERT: C 369 LYS cc_start: 0.7370 (mttt) cc_final: 0.7021 (mtpt) REVERT: E 349 ARG cc_start: 0.8065 (mtt180) cc_final: 0.6581 (pmt-80) REVERT: G 349 ARG cc_start: 0.7715 (mtp85) cc_final: 0.7364 (mtt-85) REVERT: B 349 ARG cc_start: 0.8293 (mtt180) cc_final: 0.6508 (mmm160) REVERT: D 321 LYS cc_start: 0.8383 (ttpt) cc_final: 0.7842 (mttp) REVERT: D 349 ARG cc_start: 0.8075 (mtt180) cc_final: 0.6596 (pmt-80) outliers start: 1 outliers final: 1 residues processed: 50 average time/residue: 0.5369 time to fit residues: 30.6610 Evaluate side-chains 49 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4935 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= 0.129 Angle : 0.506 4.720 4548 Z= 0.256 Chirality : 0.051 0.136 516 Planarity : 0.002 0.015 576 Dihedral : 4.508 11.932 444 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.52 % Allowed : 13.54 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.003 0.000 PHE B 378 TYR 0.008 0.002 TYR G 310 ARG 0.001 0.000 ARG G 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 49 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.508 Fit side-chains REVERT: A 321 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7452 (mttp) REVERT: A 375 LYS cc_start: 0.5825 (tttt) cc_final: 0.5494 (ttmm) REVERT: C 349 ARG cc_start: 0.8216 (mtt180) cc_final: 0.6359 (mmm160) REVERT: C 369 LYS cc_start: 0.7354 (mttt) cc_final: 0.7015 (mtpt) REVERT: E 349 ARG cc_start: 0.8084 (mtt180) cc_final: 0.6616 (pmt-80) REVERT: G 349 ARG cc_start: 0.7728 (mtp85) cc_final: 0.7400 (mtt-85) REVERT: B 349 ARG cc_start: 0.8259 (mtt180) cc_final: 0.6444 (mmm160) REVERT: D 321 LYS cc_start: 0.8368 (ttpt) cc_final: 0.7827 (mttm) REVERT: D 349 ARG cc_start: 0.8081 (mtt180) cc_final: 0.6603 (pmt-80) outliers start: 2 outliers final: 1 residues processed: 48 average time/residue: 0.4776 time to fit residues: 26.5767 Evaluate side-chains 45 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 0.0980 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 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 = 0.4399 r_free = 0.4399 target = 0.178797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.140149 restraints weight = 12252.536| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 1.70 r_work: 0.4330 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.4262 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4955 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= 0.143 Angle : 0.506 4.246 4548 Z= 0.259 Chirality : 0.051 0.137 516 Planarity : 0.002 0.015 576 Dihedral : 4.451 11.629 444 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.26 % Allowed : 13.54 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (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 0.009 0.002 TYR G 310 ARG 0.001 0.000 ARG G 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2636.86 seconds wall clock time: 51 minutes 31.96 seconds (3091.96 seconds total)