Starting phenix.real_space_refine on Sat Mar 7 12:27:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tfk_10493/03_2026/6tfk_10493.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tfk_10493/03_2026/6tfk_10493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tfk_10493/03_2026/6tfk_10493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tfk_10493/03_2026/6tfk_10493.map" model { file = "/net/cci-nas-00/data/ceres_data/6tfk_10493/03_2026/6tfk_10493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tfk_10493/03_2026/6tfk_10493.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians Mg 1 5.21 5 S 56 5.16 5 C 13760 2.51 5 N 3532 2.21 5 O 4344 1.98 5 H 21544 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43237 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 10809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 10809 Classifications: {'peptide': 681} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 663} Chain breaks: 1 Chain: "B" Number of atoms: 10809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 10809 Classifications: {'peptide': 681} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 663} Chain breaks: 1 Chain: "C" Number of atoms: 10809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 10809 Classifications: {'peptide': 681} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 663} Chain breaks: 1 Chain: "D" Number of atoms: 10809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 10809 Classifications: {'peptide': 681} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 663} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.00, per 1000 atoms: 0.19 Number of scatterers: 43237 At special positions: 0 Unit cell: (150.865, 150.865, 155.085, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 Mg 1 11.99 O 4344 8.00 N 3532 7.00 C 13760 6.00 H 21544 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: 3.96 Conformation dependent library (CDL) restraints added in 1.2 seconds 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5136 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 40 sheets defined 27.6% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 95 through 182 Proline residue: A 119 - end of helix Proline residue: A 171 - end of helix Processing helix chain 'A' and resid 204 through 219 Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 248 through 258 Processing helix chain 'A' and resid 267 through 296 Processing helix chain 'A' and resid 304 through 321 Processing helix chain 'A' and resid 396 through 399 No H-bonds generated for 'chain 'A' and resid 396 through 399' Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'B' and resid 95 through 182 Proline residue: B 119 - end of helix Proline residue: B 171 - end of helix Processing helix chain 'B' and resid 204 through 219 Processing helix chain 'B' and resid 227 through 239 Processing helix chain 'B' and resid 248 through 258 Processing helix chain 'B' and resid 267 through 296 Processing helix chain 'B' and resid 304 through 321 Processing helix chain 'B' and resid 396 through 399 No H-bonds generated for 'chain 'B' and resid 396 through 399' Processing helix chain 'B' and resid 511 through 518 Processing helix chain 'C' and resid 95 through 182 Proline residue: C 119 - end of helix Proline residue: C 171 - end of helix Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.504A pdb=" N LEU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 248 through 258 Processing helix chain 'C' and resid 267 through 296 Processing helix chain 'C' and resid 304 through 321 Processing helix chain 'C' and resid 396 through 399 No H-bonds generated for 'chain 'C' and resid 396 through 399' Processing helix chain 'C' and resid 511 through 518 Processing helix chain 'D' and resid 95 through 182 Proline residue: D 119 - end of helix Proline residue: D 171 - end of helix Processing helix chain 'D' and resid 204 through 219 Processing helix chain 'D' and resid 227 through 239 Processing helix chain 'D' and resid 248 through 258 Processing helix chain 'D' and resid 267 through 296 Processing helix chain 'D' and resid 304 through 321 Processing helix chain 'D' and resid 396 through 399 No H-bonds generated for 'chain 'D' and resid 396 through 399' Processing helix chain 'D' and resid 511 through 518 Processing sheet with id=A, first strand: chain 'A' and resid 329 through 331 Processing sheet with id=B, first strand: chain 'A' and resid 334 through 338 Processing sheet with id=C, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.667A pdb=" N THR A 439 " --> pdb=" O THR A 423 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE A 425 " --> pdb=" O GLU A 437 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A 437 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE A 427 " --> pdb=" O ARG A 435 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG A 435 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ASN A 453 " --> pdb=" O PHE A 442 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'A' and resid 479 through 482 removed outlier: 5.570A pdb=" N LEU A 357 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA A 375 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY A 359 " --> pdb=" O TYR A 373 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'A' and resid 407 through 409 Processing sheet with id=F, first strand: chain 'A' and resid 573 through 575 Processing sheet with id=G, first strand: chain 'A' and resid 581 through 584 removed outlier: 4.059A pdb=" N TYR A 619 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ASP A 611 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE A 617 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'A' and resid 596 through 598 Processing sheet with id=I, first strand: chain 'A' and resid 685 through 687 Processing sheet with id=J, first strand: chain 'A' and resid 690 through 693 Processing sheet with id=K, first strand: chain 'B' and resid 329 through 331 Processing sheet with id=L, first strand: chain 'B' and resid 334 through 338 Processing sheet with id=M, first strand: chain 'B' and resid 346 through 350 removed outlier: 6.666A pdb=" N THR B 439 " --> pdb=" O THR B 423 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE B 425 " --> pdb=" O GLU B 437 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU B 437 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE B 427 " --> pdb=" O ARG B 435 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG B 435 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ASN B 453 " --> pdb=" O PHE B 442 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'B' and resid 479 through 482 removed outlier: 5.578A pdb=" N LEU B 357 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA B 375 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY B 359 " --> pdb=" O TYR B 373 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'B' and resid 407 through 409 Processing sheet with id=P, first strand: chain 'B' and resid 573 through 575 Processing sheet with id=Q, first strand: chain 'B' and resid 581 through 584 removed outlier: 4.065A pdb=" N TYR B 619 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ASP B 611 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE B 617 " --> pdb=" O ASP B 611 " (cutoff:3.500A) Processing sheet with id=R, first strand: chain 'B' and resid 596 through 598 Processing sheet with id=S, first strand: chain 'B' and resid 685 through 687 Processing sheet with id=T, first strand: chain 'B' and resid 690 through 693 Processing sheet with id=U, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=V, first strand: chain 'C' and resid 334 through 338 Processing sheet with id=W, first strand: chain 'C' and resid 346 through 350 removed outlier: 6.687A pdb=" N THR C 439 " --> pdb=" O THR C 423 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE C 425 " --> pdb=" O GLU C 437 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLU C 437 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE C 427 " --> pdb=" O ARG C 435 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG C 435 " --> pdb=" O PHE C 427 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ASN C 453 " --> pdb=" O PHE C 442 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'C' and resid 479 through 482 removed outlier: 5.596A pdb=" N LEU C 357 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA C 375 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY C 359 " --> pdb=" O TYR C 373 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'C' and resid 407 through 409 Processing sheet with id=Z, first strand: chain 'C' and resid 573 through 575 Processing sheet with id=AA, first strand: chain 'C' and resid 581 through 584 removed outlier: 4.056A pdb=" N TYR C 619 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ASP C 611 " --> pdb=" O ILE C 617 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE C 617 " --> pdb=" O ASP C 611 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'C' and resid 596 through 598 Processing sheet with id=AC, first strand: chain 'C' and resid 685 through 687 Processing sheet with id=AD, first strand: chain 'C' and resid 690 through 693 Processing sheet with id=AE, first strand: chain 'D' and resid 329 through 331 Processing sheet with id=AF, first strand: chain 'D' and resid 334 through 338 Processing sheet with id=AG, first strand: chain 'D' and resid 346 through 350 removed outlier: 6.682A pdb=" N THR D 439 " --> pdb=" O THR D 423 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE D 425 " --> pdb=" O GLU D 437 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU D 437 " --> pdb=" O ILE D 425 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE D 427 " --> pdb=" O ARG D 435 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG D 435 " --> pdb=" O PHE D 427 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN D 453 " --> pdb=" O PHE D 442 " (cutoff:3.500A) Processing sheet with id=AH, first strand: chain 'D' and resid 479 through 482 removed outlier: 5.588A pdb=" N LEU D 357 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA D 375 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY D 359 " --> pdb=" O TYR D 373 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain 'D' and resid 407 through 409 Processing sheet with id=AJ, first strand: chain 'D' and resid 573 through 575 Processing sheet with id=AK, first strand: chain 'D' and resid 581 through 584 removed outlier: 4.050A pdb=" N TYR D 619 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ASP D 611 " --> pdb=" O ILE D 617 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE D 617 " --> pdb=" O ASP D 611 " (cutoff:3.500A) Processing sheet with id=AL, first strand: chain 'D' and resid 596 through 598 Processing sheet with id=AM, first strand: chain 'D' and resid 685 through 687 Processing sheet with id=AN, first strand: chain 'D' and resid 690 through 693 1071 hydrogen bonds defined for protein. 2961 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: 11.43 Time building geometry restraints manager: 5.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 21532 1.03 - 1.23: 14 1.23 - 1.42: 9114 1.42 - 1.62: 12840 1.62 - 1.81: 100 Bond restraints: 43600 Sorted by residual: bond pdb=" C GLN D 404 " pdb=" N SER D 405 " ideal model delta sigma weight residual 1.328 1.346 -0.018 1.25e-02 6.40e+03 2.03e+00 bond pdb=" N ASP C 403 " pdb=" CA ASP C 403 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.46e+00 bond pdb=" N MET A 746 " pdb=" CA MET A 746 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.06e+00 bond pdb=" N MET B 746 " pdb=" CA MET B 746 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.06e+00 bond pdb=" CA MET B 746 " pdb=" CB MET B 746 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.69e-02 3.50e+03 8.35e-01 ... (remaining 43595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 76790 1.25 - 2.51: 1945 2.51 - 3.76: 94 3.76 - 5.01: 17 5.01 - 6.26: 6 Bond angle restraints: 78852 Sorted by residual: angle pdb=" C ASP C 403 " pdb=" CA ASP C 403 " pdb=" CB ASP C 403 " ideal model delta sigma weight residual 110.42 116.68 -6.26 1.99e+00 2.53e-01 9.91e+00 angle pdb=" N SER D 405 " pdb=" CA SER D 405 " pdb=" C SER D 405 " ideal model delta sigma weight residual 108.54 112.48 -3.94 1.41e+00 5.03e-01 7.81e+00 angle pdb=" C ASP D 403 " pdb=" CA ASP D 403 " pdb=" CB ASP D 403 " ideal model delta sigma weight residual 110.42 115.89 -5.47 1.99e+00 2.53e-01 7.55e+00 angle pdb=" N ILE C 358 " pdb=" CA ILE C 358 " pdb=" C ILE C 358 " ideal model delta sigma weight residual 113.71 111.37 2.34 9.50e-01 1.11e+00 6.07e+00 angle pdb=" N ILE A 358 " pdb=" CA ILE A 358 " pdb=" C ILE A 358 " ideal model delta sigma weight residual 113.71 111.39 2.32 9.50e-01 1.11e+00 5.96e+00 ... (remaining 78847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.77: 18778 13.77 - 27.54: 1221 27.54 - 41.31: 272 41.31 - 55.07: 154 55.07 - 68.84: 51 Dihedral angle restraints: 20476 sinusoidal: 11216 harmonic: 9260 Sorted by residual: dihedral pdb=" CA GLN D 404 " pdb=" C GLN D 404 " pdb=" N SER D 405 " pdb=" CA SER D 405 " ideal model delta harmonic sigma weight residual -180.00 -159.77 -20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA SER B 405 " pdb=" C SER B 405 " pdb=" N GLU B 406 " pdb=" CA GLU B 406 " ideal model delta harmonic sigma weight residual 180.00 163.18 16.82 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA GLN C 404 " pdb=" C GLN C 404 " pdb=" N SER C 405 " pdb=" CA SER C 405 " ideal model delta harmonic sigma weight residual -180.00 -163.52 -16.48 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 20473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2262 0.031 - 0.062: 796 0.062 - 0.094: 178 0.094 - 0.125: 167 0.125 - 0.156: 33 Chirality restraints: 3436 Sorted by residual: chirality pdb=" CA ILE B 788 " pdb=" N ILE B 788 " pdb=" C ILE B 788 " pdb=" CB ILE B 788 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA ILE A 733 " pdb=" N ILE A 733 " pdb=" C ILE A 733 " pdb=" CB ILE A 733 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE C 733 " pdb=" N ILE C 733 " pdb=" C ILE C 733 " pdb=" CB ILE C 733 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 3433 not shown) Planarity restraints: 6484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS D 401 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO D 402 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 402 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 402 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 675 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.49e+00 pdb=" N PRO B 676 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 676 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 676 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 675 " 0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO A 676 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 676 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 676 " 0.015 5.00e-02 4.00e+02 ... (remaining 6481 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1696 2.17 - 2.78: 90255 2.78 - 3.39: 118702 3.39 - 3.99: 155600 3.99 - 4.60: 247341 Nonbonded interactions: 613594 Sorted by model distance: nonbonded pdb=" H ASN C 490 " pdb=" O LYS C 508 " model vdw 1.569 2.450 nonbonded pdb=" H ASN A 490 " pdb=" O LYS A 508 " model vdw 1.569 2.450 nonbonded pdb=" H ASN B 490 " pdb=" O LYS B 508 " model vdw 1.570 2.450 nonbonded pdb=" H ASN D 490 " pdb=" O LYS D 508 " model vdw 1.572 2.450 nonbonded pdb=" HG1 THR D 685 " pdb=" O LYS D 708 " model vdw 1.625 2.450 ... (remaining 613589 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' and resid 95 through 789) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.180 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: 0.270 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 41.270 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 0.002 0.035 22056 Z= 0.111 Angle : 0.469 6.264 29856 Z= 0.264 Chirality : 0.041 0.156 3436 Planarity : 0.002 0.031 3836 Dihedral : 9.645 68.843 8216 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 0.24 % Allowed : 2.93 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.15), residues: 2708 helix: 0.49 (0.17), residues: 804 sheet: -1.88 (0.17), residues: 720 loop : -3.08 (0.15), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 175 TYR 0.008 0.001 TYR C 475 PHE 0.007 0.001 PHE C 765 TRP 0.004 0.001 TRP D 552 HIS 0.003 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00220 (22056) covalent geometry : angle 0.46914 (29856) hydrogen bonds : bond 0.03948 ( 1071) hydrogen bonds : angle 4.74514 ( 2961) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 349 time to evaluate : 1.081 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 THR cc_start: 0.8624 (m) cc_final: 0.8407 (m) REVERT: A 679 ILE cc_start: 0.2914 (OUTLIER) cc_final: 0.2491 (pp) REVERT: A 756 PHE cc_start: 0.7794 (p90) cc_final: 0.7559 (p90) REVERT: B 635 ARG cc_start: 0.8211 (mtp180) cc_final: 0.7958 (mtp180) REVERT: B 756 PHE cc_start: 0.7794 (p90) cc_final: 0.7514 (p90) REVERT: C 679 ILE cc_start: 0.2863 (OUTLIER) cc_final: 0.2516 (mt) REVERT: C 756 PHE cc_start: 0.7855 (p90) cc_final: 0.7644 (p90) REVERT: D 598 GLN cc_start: 0.8104 (tt0) cc_final: 0.7822 (tt0) outliers start: 6 outliers final: 2 residues processed: 355 average time/residue: 1.2212 time to fit residues: 501.7935 Evaluate side-chains 194 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 190 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 788 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 548 ASN B 624 ASN B 773 ASN C 624 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.208872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.129814 restraints weight = 76202.831| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.52 r_work: 0.3355 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22056 Z= 0.161 Angle : 0.550 6.061 29856 Z= 0.293 Chirality : 0.042 0.144 3436 Planarity : 0.003 0.040 3836 Dihedral : 4.744 42.469 2932 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.20 % Favored : 92.73 % Rotamer: Outliers : 1.67 % Allowed : 8.82 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.15), residues: 2708 helix: 1.60 (0.17), residues: 804 sheet: -1.63 (0.17), residues: 828 loop : -2.90 (0.16), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 435 TYR 0.014 0.001 TYR C 410 PHE 0.011 0.001 PHE D 636 TRP 0.005 0.001 TRP D 684 HIS 0.003 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00374 (22056) covalent geometry : angle 0.55009 (29856) hydrogen bonds : bond 0.04010 ( 1071) hydrogen bonds : angle 4.80429 ( 2961) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 1.426 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: symmetry clash 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: 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 257 THR cc_start: 0.8704 (m) cc_final: 0.8444 (m) REVERT: A 347 MET cc_start: 0.7980 (ttm) cc_final: 0.7736 (ttm) REVERT: A 458 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7444 (tm-30) REVERT: A 519 ASP cc_start: 0.7966 (t70) cc_final: 0.7601 (t0) REVERT: A 562 ASP cc_start: 0.5328 (OUTLIER) cc_final: 0.4599 (p0) REVERT: A 635 ARG cc_start: 0.7818 (mtp180) cc_final: 0.7581 (mtp180) REVERT: A 679 ILE cc_start: 0.2667 (OUTLIER) cc_final: 0.2418 (mt) REVERT: B 519 ASP cc_start: 0.7958 (t70) cc_final: 0.7600 (t0) REVERT: B 562 ASP cc_start: 0.5419 (OUTLIER) cc_final: 0.4778 (OUTLIER) REVERT: B 756 PHE cc_start: 0.7674 (p90) cc_final: 0.7466 (p90) REVERT: C 519 ASP cc_start: 0.7883 (t70) cc_final: 0.7533 (t0) REVERT: C 562 ASP cc_start: 0.5363 (OUTLIER) cc_final: 0.4712 (OUTLIER) REVERT: C 635 ARG cc_start: 0.7857 (mtp180) cc_final: 0.7616 (mtp180) REVERT: C 679 ILE cc_start: 0.2576 (OUTLIER) cc_final: 0.2313 (mt) REVERT: D 137 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8567 (mp) REVERT: D 347 MET cc_start: 0.7987 (ttm) cc_final: 0.7726 (ttm) REVERT: D 519 ASP cc_start: 0.7916 (t70) cc_final: 0.7570 (t0) REVERT: D 562 ASP cc_start: 0.5097 (OUTLIER) cc_final: 0.4315 (p0) REVERT: D 679 ILE cc_start: 0.2565 (OUTLIER) cc_final: 0.2088 (mt) outliers start: 41 outliers final: 13 residues processed: 230 average time/residue: 1.0803 time to fit residues: 296.9319 Evaluate side-chains 183 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 679 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 49 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 196 optimal weight: 7.9990 chunk 263 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 548 ASN D 548 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.208120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.133059 restraints weight = 76628.334| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.30 r_work: 0.3317 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22056 Z= 0.149 Angle : 0.511 5.745 29856 Z= 0.274 Chirality : 0.042 0.159 3436 Planarity : 0.003 0.036 3836 Dihedral : 4.677 40.452 2930 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.83 % Favored : 92.10 % Rotamer: Outliers : 2.40 % Allowed : 8.90 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.16), residues: 2708 helix: 2.04 (0.17), residues: 804 sheet: -1.45 (0.17), residues: 824 loop : -2.69 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 435 TYR 0.013 0.001 TYR D 410 PHE 0.009 0.001 PHE D 636 TRP 0.004 0.001 TRP D 552 HIS 0.002 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00347 (22056) covalent geometry : angle 0.51058 (29856) hydrogen bonds : bond 0.04050 ( 1071) hydrogen bonds : angle 4.77392 ( 2961) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 174 time to evaluate : 1.145 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: symmetry clash 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: symmetry clash 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 144 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7969 (mttt) REVERT: A 347 MET cc_start: 0.8025 (ttm) cc_final: 0.7754 (ttm) REVERT: A 458 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: A 519 ASP cc_start: 0.8141 (t70) cc_final: 0.7606 (m-30) REVERT: A 562 ASP cc_start: 0.5357 (OUTLIER) cc_final: 0.4622 (p0) REVERT: A 635 ARG cc_start: 0.7796 (mtp180) cc_final: 0.7423 (ttp80) REVERT: B 124 MET cc_start: 0.7205 (mmm) cc_final: 0.6978 (mtp) REVERT: B 144 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7988 (mttt) REVERT: B 519 ASP cc_start: 0.8162 (t70) cc_final: 0.7581 (m-30) REVERT: B 562 ASP cc_start: 0.5445 (OUTLIER) cc_final: 0.4798 (p0) REVERT: C 519 ASP cc_start: 0.8139 (t70) cc_final: 0.7633 (m-30) REVERT: C 562 ASP cc_start: 0.5395 (OUTLIER) cc_final: 0.4743 (p0) REVERT: C 635 ARG cc_start: 0.7821 (mtp180) cc_final: 0.7450 (ttp80) REVERT: C 679 ILE cc_start: 0.2271 (OUTLIER) cc_final: 0.2055 (mt) REVERT: D 137 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8578 (mp) REVERT: D 347 MET cc_start: 0.8034 (ttm) cc_final: 0.7780 (ttm) REVERT: D 519 ASP cc_start: 0.8135 (t70) cc_final: 0.7616 (m-30) REVERT: D 562 ASP cc_start: 0.4999 (OUTLIER) cc_final: 0.4244 (OUTLIER) REVERT: D 635 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7838 (ttp80) REVERT: D 679 ILE cc_start: 0.2322 (OUTLIER) cc_final: 0.2096 (mt) outliers start: 59 outliers final: 22 residues processed: 220 average time/residue: 1.2039 time to fit residues: 310.5450 Evaluate side-chains 187 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 715 SER Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 635 ARG Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 715 SER Chi-restraints excluded: chain D residue 788 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 271 optimal weight: 9.9990 chunk 221 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 chunk 224 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 249 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN B 548 ASN C 548 ASN C 691 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.205479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.128109 restraints weight = 76658.598| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.62 r_work: 0.3279 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 22056 Z= 0.207 Angle : 0.545 5.595 29856 Z= 0.295 Chirality : 0.043 0.139 3436 Planarity : 0.004 0.036 3836 Dihedral : 4.820 39.441 2928 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.12 % Favored : 91.80 % Rotamer: Outliers : 2.52 % Allowed : 10.00 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.16), residues: 2708 helix: 1.98 (0.17), residues: 804 sheet: -1.45 (0.17), residues: 828 loop : -2.65 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 246 TYR 0.016 0.001 TYR D 410 PHE 0.008 0.001 PHE D 636 TRP 0.004 0.001 TRP D 684 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00496 (22056) covalent geometry : angle 0.54543 (29856) hydrogen bonds : bond 0.04485 ( 1071) hydrogen bonds : angle 4.89472 ( 2961) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 162 time to evaluate : 1.116 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.8610 (mmm) cc_final: 0.8058 (mmt) REVERT: A 144 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8034 (mttt) REVERT: A 347 MET cc_start: 0.8073 (ttm) cc_final: 0.7860 (ttm) REVERT: A 470 ASN cc_start: 0.7617 (t0) cc_final: 0.7406 (t0) REVERT: A 504 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8101 (p) REVERT: A 562 ASP cc_start: 0.5254 (OUTLIER) cc_final: 0.4561 (p0) REVERT: A 635 ARG cc_start: 0.7788 (mtp180) cc_final: 0.7493 (mtp180) REVERT: B 144 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7981 (mttt) REVERT: B 368 THR cc_start: 0.8197 (m) cc_final: 0.7957 (m) REVERT: B 504 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8096 (p) REVERT: B 519 ASP cc_start: 0.8370 (t70) cc_final: 0.8161 (t70) REVERT: B 562 ASP cc_start: 0.5448 (OUTLIER) cc_final: 0.4836 (p0) REVERT: C 129 MET cc_start: 0.8694 (mmm) cc_final: 0.8148 (mmt) REVERT: C 465 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7396 (mtm180) REVERT: C 504 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8096 (p) REVERT: C 519 ASP cc_start: 0.8344 (t70) cc_final: 0.7661 (m-30) REVERT: C 562 ASP cc_start: 0.5423 (OUTLIER) cc_final: 0.4760 (p0) REVERT: C 635 ARG cc_start: 0.7848 (mtp180) cc_final: 0.7540 (mtp180) REVERT: C 679 ILE cc_start: 0.2411 (OUTLIER) cc_final: 0.2162 (mt) REVERT: D 129 MET cc_start: 0.8687 (mmm) cc_final: 0.8166 (mmt) REVERT: D 137 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8572 (mp) REVERT: D 347 MET cc_start: 0.8027 (ttm) cc_final: 0.7790 (ttm) REVERT: D 504 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8081 (p) REVERT: D 519 ASP cc_start: 0.8350 (t70) cc_final: 0.8139 (t70) REVERT: D 635 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7796 (ttp80) REVERT: D 679 ILE cc_start: 0.2370 (OUTLIER) cc_final: 0.2132 (mt) outliers start: 62 outliers final: 24 residues processed: 212 average time/residue: 1.1838 time to fit residues: 295.6999 Evaluate side-chains 192 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 715 SER Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 635 ARG Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 715 SER Chi-restraints excluded: chain D residue 788 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 133 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 26 optimal weight: 0.6980 chunk 266 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 269 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN A 691 ASN B 691 ASN D 548 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.203691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.124227 restraints weight = 76316.229| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.21 r_work: 0.3295 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 22056 Z= 0.248 Angle : 0.561 6.127 29856 Z= 0.306 Chirality : 0.044 0.157 3436 Planarity : 0.004 0.038 3836 Dihedral : 4.928 39.694 2928 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.53 % Favored : 91.32 % Rotamer: Outliers : 2.11 % Allowed : 11.34 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.16), residues: 2708 helix: 1.87 (0.17), residues: 804 sheet: -1.39 (0.18), residues: 780 loop : -2.70 (0.16), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 246 TYR 0.016 0.001 TYR D 410 PHE 0.007 0.001 PHE A 492 TRP 0.004 0.001 TRP D 552 HIS 0.003 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00593 (22056) covalent geometry : angle 0.56052 (29856) hydrogen bonds : bond 0.04725 ( 1071) hydrogen bonds : angle 4.93789 ( 2961) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 164 time to evaluate : 1.453 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: symmetry clash 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: symmetry clash REVERT: A 129 MET cc_start: 0.8615 (mmm) cc_final: 0.8110 (mmt) REVERT: A 144 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8021 (mttt) REVERT: A 347 MET cc_start: 0.8005 (ttm) cc_final: 0.7784 (ttm) REVERT: A 361 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: A 458 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7433 (tm-30) REVERT: A 465 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7366 (mtm180) REVERT: A 470 ASN cc_start: 0.7660 (t0) cc_final: 0.7450 (t0) REVERT: A 504 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8053 (p) REVERT: A 562 ASP cc_start: 0.5305 (OUTLIER) cc_final: 0.4612 (p0) REVERT: A 635 ARG cc_start: 0.7811 (mtp180) cc_final: 0.7523 (mtp180) REVERT: B 129 MET cc_start: 0.8681 (mmm) cc_final: 0.8177 (mmt) REVERT: B 144 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7950 (mttt) REVERT: B 465 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7331 (mtm180) REVERT: B 504 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8059 (p) REVERT: B 562 ASP cc_start: 0.5466 (OUTLIER) cc_final: 0.4868 (p0) REVERT: C 129 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8122 (mmt) REVERT: C 361 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: C 465 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7332 (mtm180) REVERT: C 504 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8059 (p) REVERT: C 562 ASP cc_start: 0.5427 (OUTLIER) cc_final: 0.4787 (p0) REVERT: C 635 ARG cc_start: 0.7849 (mtp180) cc_final: 0.7556 (mtp180) REVERT: C 679 ILE cc_start: 0.2378 (OUTLIER) cc_final: 0.2140 (mt) REVERT: D 124 MET cc_start: 0.7374 (mmm) cc_final: 0.7157 (mtp) REVERT: D 129 MET cc_start: 0.8638 (mmm) cc_final: 0.8163 (mmt) REVERT: D 137 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8553 (mp) REVERT: D 347 MET cc_start: 0.7972 (ttm) cc_final: 0.7732 (ttm) REVERT: D 361 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: D 504 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8052 (p) REVERT: D 562 ASP cc_start: 0.5087 (OUTLIER) cc_final: 0.4363 (p0) REVERT: D 635 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7888 (ttp80) REVERT: D 679 ILE cc_start: 0.2206 (OUTLIER) cc_final: 0.1973 (mt) outliers start: 52 outliers final: 22 residues processed: 207 average time/residue: 1.1241 time to fit residues: 275.2109 Evaluate side-chains 193 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 715 SER Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 635 ARG Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 715 SER Chi-restraints excluded: chain D residue 788 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 122 optimal weight: 10.0000 chunk 216 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 209 optimal weight: 0.8980 chunk 238 optimal weight: 2.9990 chunk 237 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 548 ASN C 548 ASN D 548 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.206170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.131631 restraints weight = 76125.484| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.61 r_work: 0.3320 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22056 Z= 0.112 Angle : 0.491 6.009 29856 Z= 0.264 Chirality : 0.041 0.155 3436 Planarity : 0.003 0.035 3836 Dihedral : 4.671 37.176 2928 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.72 % Favored : 93.17 % Rotamer: Outliers : 1.42 % Allowed : 12.40 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.16), residues: 2708 helix: 2.38 (0.18), residues: 804 sheet: -1.24 (0.18), residues: 760 loop : -2.65 (0.16), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 435 TYR 0.013 0.001 TYR D 410 PHE 0.022 0.001 PHE C 636 TRP 0.003 0.001 TRP A 658 HIS 0.002 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00251 (22056) covalent geometry : angle 0.49098 (29856) hydrogen bonds : bond 0.03940 ( 1071) hydrogen bonds : angle 4.71306 ( 2961) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.833 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.8579 (mmm) cc_final: 0.8080 (mmt) REVERT: A 144 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7973 (mttt) REVERT: A 168 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8393 (mt-10) REVERT: A 347 MET cc_start: 0.8006 (ttm) cc_final: 0.7771 (ttm) REVERT: A 635 ARG cc_start: 0.7848 (mtp180) cc_final: 0.7513 (ttp80) REVERT: B 129 MET cc_start: 0.8684 (mmm) cc_final: 0.8112 (mmt) REVERT: B 144 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7970 (mttt) REVERT: B 168 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8378 (mt-10) REVERT: B 465 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7262 (mtm180) REVERT: B 562 ASP cc_start: 0.5471 (OUTLIER) cc_final: 0.4844 (p0) REVERT: C 129 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8060 (mmt) REVERT: C 465 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7206 (mtm180) REVERT: C 635 ARG cc_start: 0.7877 (mtp180) cc_final: 0.7490 (ttp80) REVERT: D 129 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8123 (mmt) REVERT: D 137 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8520 (mp) REVERT: D 168 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8422 (mt-10) REVERT: D 347 MET cc_start: 0.7978 (ttm) cc_final: 0.7759 (ttm) REVERT: D 465 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7004 (mtm180) REVERT: D 562 ASP cc_start: 0.5047 (OUTLIER) cc_final: 0.4350 (p0) REVERT: D 679 ILE cc_start: 0.2753 (OUTLIER) cc_final: 0.2511 (mt) outliers start: 35 outliers final: 17 residues processed: 198 average time/residue: 1.2186 time to fit residues: 281.1372 Evaluate side-chains 180 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 465 ARG Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 788 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 266 optimal weight: 10.0000 chunk 234 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 198 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 chunk 171 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 189 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 548 ASN C 548 ASN C 691 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.199716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124094 restraints weight = 76454.246| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.33 r_work: 0.3230 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.109 22056 Z= 0.419 Angle : 0.694 7.791 29856 Z= 0.382 Chirality : 0.051 0.158 3436 Planarity : 0.005 0.040 3836 Dihedral : 5.381 40.994 2926 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.12 % Favored : 89.73 % Rotamer: Outliers : 2.80 % Allowed : 12.44 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.15), residues: 2708 helix: 1.35 (0.17), residues: 804 sheet: -1.62 (0.18), residues: 792 loop : -2.83 (0.16), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 246 TYR 0.021 0.002 TYR A 410 PHE 0.017 0.002 PHE C 636 TRP 0.008 0.002 TRP A 684 HIS 0.003 0.001 HIS B 576 Details of bonding type rmsd covalent geometry : bond 0.01015 (22056) covalent geometry : angle 0.69434 (29856) hydrogen bonds : bond 0.05809 ( 1071) hydrogen bonds : angle 5.20575 ( 2961) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 157 time to evaluate : 1.220 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8094 (mttt) REVERT: A 347 MET cc_start: 0.8039 (ttm) cc_final: 0.7837 (ttm) REVERT: A 361 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.7554 (tm-30) REVERT: A 465 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7402 (mtm180) REVERT: A 504 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8188 (p) REVERT: A 635 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7625 (mtp180) REVERT: A 679 ILE cc_start: 0.2136 (OUTLIER) cc_final: 0.1886 (mt) REVERT: B 129 MET cc_start: 0.8588 (mmm) cc_final: 0.8155 (mmt) REVERT: B 144 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8113 (mttt) REVERT: B 361 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: B 465 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7431 (mtm180) REVERT: B 504 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8180 (p) REVERT: B 562 ASP cc_start: 0.5448 (OUTLIER) cc_final: 0.4908 (p0) REVERT: B 634 LYS cc_start: 0.7248 (mmtp) cc_final: 0.6492 (mtpm) REVERT: C 361 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: C 465 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7498 (mtm180) REVERT: C 504 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8174 (p) REVERT: C 562 ASP cc_start: 0.5543 (OUTLIER) cc_final: 0.4958 (p0) REVERT: C 635 ARG cc_start: 0.7863 (mtp180) cc_final: 0.7528 (ttp80) REVERT: C 679 ILE cc_start: 0.2264 (OUTLIER) cc_final: 0.2032 (mt) REVERT: C 746 MET cc_start: 0.5544 (ttm) cc_final: 0.5213 (tpp) REVERT: D 137 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8500 (mp) REVERT: D 361 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: D 504 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8174 (p) REVERT: D 562 ASP cc_start: 0.5220 (OUTLIER) cc_final: 0.4451 (p0) REVERT: D 635 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7921 (ttp80) REVERT: D 679 ILE cc_start: 0.2346 (OUTLIER) cc_final: 0.2078 (mt) outliers start: 69 outliers final: 25 residues processed: 213 average time/residue: 1.2589 time to fit residues: 312.8953 Evaluate side-chains 201 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 682 ASN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 117 TYR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 715 SER Chi-restraints excluded: chain D residue 117 TYR Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 635 ARG Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 715 SER Chi-restraints excluded: chain D residue 788 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 147 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 188 optimal weight: 0.0870 chunk 201 optimal weight: 10.0000 chunk 76 optimal weight: 0.5980 chunk 208 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 548 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.205518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.127650 restraints weight = 76809.070| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.43 r_work: 0.3323 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22056 Z= 0.109 Angle : 0.510 8.340 29856 Z= 0.274 Chirality : 0.042 0.156 3436 Planarity : 0.003 0.031 3836 Dihedral : 4.820 37.512 2926 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.35 % Favored : 93.50 % Rotamer: Outliers : 1.06 % Allowed : 14.27 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.16), residues: 2708 helix: 2.16 (0.17), residues: 804 sheet: -1.39 (0.18), residues: 760 loop : -2.73 (0.16), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 635 TYR 0.016 0.001 TYR A 410 PHE 0.018 0.001 PHE C 636 TRP 0.002 0.000 TRP A 658 HIS 0.002 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00240 (22056) covalent geometry : angle 0.51023 (29856) hydrogen bonds : bond 0.04024 ( 1071) hydrogen bonds : angle 4.74652 ( 2961) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 1.160 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.8566 (mmm) cc_final: 0.8094 (mmt) REVERT: A 144 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7955 (mttt) REVERT: A 168 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8435 (mt-10) REVERT: A 465 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7263 (mtm180) REVERT: A 635 ARG cc_start: 0.7819 (mtp180) cc_final: 0.7387 (ttp80) REVERT: B 129 MET cc_start: 0.8631 (mmm) cc_final: 0.8094 (mmt) REVERT: B 144 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7942 (mttt) REVERT: B 168 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8431 (mt-10) REVERT: C 129 MET cc_start: 0.8605 (mmm) cc_final: 0.8091 (mmt) REVERT: C 168 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8463 (mt-10) REVERT: C 185 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7387 (mp0) REVERT: C 465 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7151 (mtm180) REVERT: C 635 ARG cc_start: 0.7829 (mtp180) cc_final: 0.7451 (ttp80) REVERT: D 168 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8497 (mt-10) REVERT: D 185 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7405 (mp0) REVERT: D 347 MET cc_start: 0.7989 (ttm) cc_final: 0.7732 (ttm) REVERT: D 465 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7061 (mtm180) REVERT: D 619 TYR cc_start: 0.6701 (t80) cc_final: 0.6477 (t80) REVERT: D 679 ILE cc_start: 0.2954 (OUTLIER) cc_final: 0.2740 (mt) outliers start: 26 outliers final: 10 residues processed: 186 average time/residue: 1.2222 time to fit residues: 265.7365 Evaluate side-chains 177 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 465 ARG Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 788 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 133 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 548 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.203986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126196 restraints weight = 76674.710| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.51 r_work: 0.3285 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22056 Z= 0.161 Angle : 0.520 8.880 29856 Z= 0.280 Chirality : 0.042 0.167 3436 Planarity : 0.003 0.031 3836 Dihedral : 4.802 36.549 2926 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.35 % Favored : 91.51 % Rotamer: Outliers : 1.10 % Allowed : 14.35 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.16), residues: 2708 helix: 2.21 (0.17), residues: 804 sheet: -1.38 (0.19), residues: 720 loop : -2.69 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 465 TYR 0.014 0.001 TYR A 410 PHE 0.026 0.001 PHE A 636 TRP 0.004 0.001 TRP C 684 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00384 (22056) covalent geometry : angle 0.52007 (29856) hydrogen bonds : bond 0.04275 ( 1071) hydrogen bonds : angle 4.75853 ( 2961) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 1.226 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7977 (mttt) REVERT: A 465 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7213 (mtm180) REVERT: A 635 ARG cc_start: 0.7828 (mtp180) cc_final: 0.7608 (mtp180) REVERT: B 129 MET cc_start: 0.8653 (mmm) cc_final: 0.8153 (mmt) REVERT: B 144 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7980 (mttt) REVERT: C 129 MET cc_start: 0.8647 (mmm) cc_final: 0.8122 (mmt) REVERT: C 185 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7461 (mp0) REVERT: C 465 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7174 (mtm180) REVERT: C 562 ASP cc_start: 0.5455 (OUTLIER) cc_final: 0.4828 (p0) REVERT: C 635 ARG cc_start: 0.7830 (mtp180) cc_final: 0.7450 (ttp80) REVERT: D 185 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7461 (mp0) REVERT: D 347 MET cc_start: 0.8011 (ttm) cc_final: 0.7774 (ttm) REVERT: D 619 TYR cc_start: 0.6687 (t80) cc_final: 0.6466 (t80) outliers start: 27 outliers final: 12 residues processed: 182 average time/residue: 1.0863 time to fit residues: 232.4287 Evaluate side-chains 170 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 788 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 17 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 241 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 238 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 chunk 245 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4429 r_free = 0.4429 target = 0.205470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126734 restraints weight = 76628.880| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.56 r_work: 0.3331 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22056 Z= 0.116 Angle : 0.507 13.115 29856 Z= 0.269 Chirality : 0.041 0.159 3436 Planarity : 0.003 0.032 3836 Dihedral : 4.609 19.810 2924 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.57 % Favored : 93.28 % Rotamer: Outliers : 0.77 % Allowed : 14.88 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.16), residues: 2708 helix: 2.39 (0.17), residues: 804 sheet: -1.33 (0.19), residues: 720 loop : -2.65 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 435 TYR 0.014 0.001 TYR A 410 PHE 0.025 0.001 PHE A 636 TRP 0.004 0.001 TRP D 658 HIS 0.003 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00264 (22056) covalent geometry : angle 0.50688 (29856) hydrogen bonds : bond 0.03958 ( 1071) hydrogen bonds : angle 4.63502 ( 2961) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.697 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.8693 (mmm) cc_final: 0.8137 (mmt) REVERT: A 144 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7948 (mttt) REVERT: A 168 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8391 (mt-10) REVERT: A 635 ARG cc_start: 0.7809 (mtp180) cc_final: 0.7386 (ttp80) REVERT: B 129 MET cc_start: 0.8669 (mmm) cc_final: 0.8093 (mmt) REVERT: B 144 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7953 (mttt) REVERT: C 635 ARG cc_start: 0.7825 (mtp180) cc_final: 0.7433 (ttp80) REVERT: D 185 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7450 (mp0) REVERT: D 347 MET cc_start: 0.8041 (ttm) cc_final: 0.7816 (ttm) outliers start: 19 outliers final: 10 residues processed: 173 average time/residue: 0.9863 time to fit residues: 200.3828 Evaluate side-chains 164 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 601 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 216 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.4413 r_free = 0.4413 target = 0.203847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124020 restraints weight = 77096.038| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.47 r_work: 0.3260 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22056 Z= 0.174 Angle : 0.524 9.458 29856 Z= 0.281 Chirality : 0.042 0.152 3436 Planarity : 0.003 0.033 3836 Dihedral : 4.684 20.826 2924 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.12 % Favored : 91.73 % Rotamer: Outliers : 0.85 % Allowed : 14.80 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.16), residues: 2708 helix: 2.28 (0.17), residues: 804 sheet: -1.36 (0.19), residues: 720 loop : -2.67 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 435 TYR 0.014 0.001 TYR A 410 PHE 0.025 0.001 PHE A 636 TRP 0.004 0.001 TRP C 684 HIS 0.003 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00416 (22056) covalent geometry : angle 0.52441 (29856) hydrogen bonds : bond 0.04299 ( 1071) hydrogen bonds : angle 4.70431 ( 2961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17469.97 seconds wall clock time: 295 minutes 40.56 seconds (17740.56 seconds total)