Starting phenix.real_space_refine on Tue Mar 3 14:02:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qky_14057/03_2026/7qky_14057.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qky_14057/03_2026/7qky_14057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qky_14057/03_2026/7qky_14057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qky_14057/03_2026/7qky_14057.map" model { file = "/net/cci-nas-00/data/ceres_data/7qky_14057/03_2026/7qky_14057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qky_14057/03_2026/7qky_14057.cif" } resolution = 1.86 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 1776 2.51 5 N 504 2.21 5 O 612 1.98 5 H 2862 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5760 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 960 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "B" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 960 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "C" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 960 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "D" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 960 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "E" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 960 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "F" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 960 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Time building chain proxies: 1.10, per 1000 atoms: 0.19 Number of scatterers: 5760 At special positions: 0 Unit cell: (111.231, 82.878, 39.258, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 612 8.00 N 504 7.00 C 1776 6.00 H 2862 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 263.4 milliseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 47.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 386 removed outlier: 6.570A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU B 380 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ARG A 379 " --> pdb=" O GLU B 380 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ALA B 382 " --> pdb=" O ARG A 379 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN A 381 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ALA B 384 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS A 383 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR B 386 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS A 385 " --> pdb=" O THR B 386 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR B 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLU E 380 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG B 379 " --> pdb=" O GLU E 380 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ALA E 382 " --> pdb=" O ARG B 379 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN B 381 " --> pdb=" O ALA E 382 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ALA E 384 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS B 383 " --> pdb=" O ALA E 384 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N THR E 386 " --> pdb=" O LYS B 383 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS B 385 " --> pdb=" O THR E 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 394 removed outlier: 6.290A pdb=" N VAL A 393 " --> pdb=" O TYR B 394 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL B 393 " --> pdb=" O TYR E 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 398 through 399 removed outlier: 6.809A pdb=" N VAL A 398 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 398 " --> pdb=" O VAL E 399 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 406 through 414 removed outlier: 6.822A pdb=" N HIS A 407 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASN B 410 " --> pdb=" O HIS A 407 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER A 409 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N SER B 412 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 411 " --> pdb=" O SER B 412 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N THR B 414 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER A 413 " --> pdb=" O THR B 414 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N HIS B 407 " --> pdb=" O LEU E 408 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ASN E 410 " --> pdb=" O HIS B 407 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER B 409 " --> pdb=" O ASN E 410 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N SER E 412 " --> pdb=" O SER B 409 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 411 " --> pdb=" O SER E 412 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N THR E 414 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER B 413 " --> pdb=" O THR E 414 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 417 through 420 removed outlier: 6.310A pdb=" N ASP B 418 " --> pdb=" O MET E 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 424 through 429 removed outlier: 6.500A pdb=" N LEU A 425 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU B 428 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR A 427 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 425 " --> pdb=" O ALA E 426 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU E 428 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N THR B 427 " --> pdb=" O LEU E 428 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 432 through 433 Processing sheet with id=AA8, first strand: chain 'A' and resid 436 through 438 Processing sheet with id=AA9, first strand: chain 'C' and resid 377 through 386 removed outlier: 6.548A pdb=" N THR C 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N GLU D 380 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG C 379 " --> pdb=" O GLU D 380 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ALA D 382 " --> pdb=" O ARG C 379 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASN C 381 " --> pdb=" O ALA D 382 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA D 384 " --> pdb=" O ASN C 381 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS C 383 " --> pdb=" O ALA D 384 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N THR D 386 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS C 385 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR D 377 " --> pdb=" O PHE F 378 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N GLU F 380 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG D 379 " --> pdb=" O GLU F 380 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA F 382 " --> pdb=" O ARG D 379 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASN D 381 " --> pdb=" O ALA F 382 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ALA F 384 " --> pdb=" O ASN D 381 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LYS D 383 " --> pdb=" O ALA F 384 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N THR F 386 " --> pdb=" O LYS D 383 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS D 385 " --> pdb=" O THR F 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 392 through 394 removed outlier: 6.289A pdb=" N VAL C 393 " --> pdb=" O TYR D 394 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL D 393 " --> pdb=" O TYR F 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 398 through 399 removed outlier: 6.831A pdb=" N VAL C 398 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL D 398 " --> pdb=" O VAL F 399 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 406 through 414 removed outlier: 6.779A pdb=" N HIS C 407 " --> pdb=" O ARG D 406 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS D 407 " --> pdb=" O ARG F 406 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 417 through 420 Processing sheet with id=AB5, first strand: chain 'C' and resid 424 through 429 removed outlier: 6.520A pdb=" N LEU C 425 " --> pdb=" O ALA D 426 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU D 428 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N THR C 427 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU D 425 " --> pdb=" O ALA F 426 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU F 428 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N THR D 427 " --> pdb=" O LEU F 428 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 432 through 433 Processing sheet with id=AB7, first strand: chain 'C' and resid 436 through 438 35 hydrogen bonds defined for protein. 105 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 2862 1.12 - 1.29: 516 1.29 - 1.47: 956 1.47 - 1.64: 1450 1.64 - 1.81: 12 Bond restraints: 5796 Sorted by residual: bond pdb=" CE1 PHE A 378 " pdb=" HE1 PHE A 378 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N LYS E 383 " pdb=" H LYS E 383 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CE2 TYR E 394 " pdb=" HE2 TYR E 394 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE ARG A 379 " pdb=" HE ARG A 379 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N ALA C 384 " pdb=" H ALA C 384 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 5791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 7559 1.82 - 3.64: 2072 3.64 - 5.45: 563 5.45 - 7.27: 289 7.27 - 9.09: 11 Bond angle restraints: 10494 Sorted by residual: angle pdb=" CB HIS A 407 " pdb=" CG HIS A 407 " pdb=" CD2 HIS A 407 " ideal model delta sigma weight residual 131.20 125.26 5.94 1.30e+00 5.92e-01 2.09e+01 angle pdb=" N ALA B 429 " pdb=" CA ALA B 429 " pdb=" C ALA B 429 " ideal model delta sigma weight residual 108.99 116.02 -7.03 1.57e+00 4.06e-01 2.01e+01 angle pdb=" CB HIS E 407 " pdb=" CG HIS E 407 " pdb=" CD2 HIS E 407 " ideal model delta sigma weight residual 131.20 125.39 5.81 1.30e+00 5.92e-01 2.00e+01 angle pdb=" CB HIS C 407 " pdb=" CG HIS C 407 " pdb=" CD2 HIS C 407 " ideal model delta sigma weight residual 131.20 125.44 5.76 1.30e+00 5.92e-01 1.96e+01 angle pdb=" CB HIS D 407 " pdb=" CG HIS D 407 " pdb=" CD2 HIS D 407 " ideal model delta sigma weight residual 131.20 125.50 5.70 1.30e+00 5.92e-01 1.92e+01 ... (remaining 10489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.18: 2403 14.18 - 28.36: 238 28.36 - 42.54: 26 42.54 - 56.72: 43 56.72 - 70.89: 44 Dihedral angle restraints: 2754 sinusoidal: 1524 harmonic: 1230 Sorted by residual: dihedral pdb=" CA HIS C 388 " pdb=" C HIS C 388 " pdb=" N GLY C 389 " pdb=" CA GLY C 389 " ideal model delta harmonic sigma weight residual 180.00 151.24 28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA HIS B 388 " pdb=" C HIS B 388 " pdb=" N GLY B 389 " pdb=" CA GLY B 389 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA HIS D 388 " pdb=" C HIS D 388 " pdb=" N GLY D 389 " pdb=" CA GLY D 389 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 2751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 305 0.079 - 0.157: 151 0.157 - 0.235: 24 0.235 - 0.313: 1 0.313 - 0.392: 5 Chirality restraints: 486 Sorted by residual: chirality pdb=" CA HIS D 388 " pdb=" N HIS D 388 " pdb=" C HIS D 388 " pdb=" CB HIS D 388 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA HIS C 388 " pdb=" N HIS C 388 " pdb=" C HIS C 388 " pdb=" CB HIS C 388 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA HIS B 388 " pdb=" N HIS B 388 " pdb=" C HIS B 388 " pdb=" CB HIS B 388 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 ... (remaining 483 not shown) Planarity restraints: 888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 378 " -0.227 2.00e-02 2.50e+03 9.08e-02 2.47e+02 pdb=" CG PHE C 378 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE C 378 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 PHE C 378 " 0.073 2.00e-02 2.50e+03 pdb=" CE1 PHE C 378 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE C 378 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE C 378 " -0.036 2.00e-02 2.50e+03 pdb=" HD1 PHE C 378 " 0.113 2.00e-02 2.50e+03 pdb=" HD2 PHE C 378 " 0.053 2.00e-02 2.50e+03 pdb=" HE1 PHE C 378 " -0.025 2.00e-02 2.50e+03 pdb=" HE2 PHE C 378 " 0.024 2.00e-02 2.50e+03 pdb=" HZ PHE C 378 " -0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 378 " -0.200 2.00e-02 2.50e+03 8.24e-02 2.04e+02 pdb=" CG PHE D 378 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 PHE D 378 " 0.065 2.00e-02 2.50e+03 pdb=" CD2 PHE D 378 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 PHE D 378 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE D 378 " 0.041 2.00e-02 2.50e+03 pdb=" CZ PHE D 378 " -0.042 2.00e-02 2.50e+03 pdb=" HD1 PHE D 378 " 0.109 2.00e-02 2.50e+03 pdb=" HD2 PHE D 378 " 0.045 2.00e-02 2.50e+03 pdb=" HE1 PHE D 378 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 PHE D 378 " 0.039 2.00e-02 2.50e+03 pdb=" HZ PHE D 378 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 388 " -0.039 2.00e-02 2.50e+03 7.06e-02 4.99e+01 pdb=" N GLY D 389 " 0.122 2.00e-02 2.50e+03 pdb=" CA GLY D 389 " -0.035 2.00e-02 2.50e+03 pdb=" H GLY D 389 " -0.047 2.00e-02 2.50e+03 ... (remaining 885 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 551 2.17 - 2.78: 9561 2.78 - 3.39: 15847 3.39 - 3.99: 21842 3.99 - 4.60: 29797 Nonbonded interactions: 77598 Sorted by model distance: nonbonded pdb=" HG SER F 413 " pdb=" OD2 ASP F 418 " model vdw 1.568 2.450 nonbonded pdb=" HG SER E 413 " pdb=" OD2 ASP E 418 " model vdw 1.574 2.450 nonbonded pdb=" HG SER B 413 " pdb=" OD2 ASP B 418 " model vdw 1.579 2.450 nonbonded pdb=" HG SER D 413 " pdb=" OD2 ASP D 418 " model vdw 1.592 2.450 nonbonded pdb=" HG SER A 413 " pdb=" OD2 ASP A 418 " model vdw 1.639 2.450 ... (remaining 77593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 6.060 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: 0.030 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.520 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.034 2934 Z= 0.697 Angle : 1.746 7.133 3978 Z= 1.129 Chirality : 0.092 0.392 486 Planarity : 0.011 0.081 516 Dihedral : 12.756 70.894 1068 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.61 % Allowed : 3.03 % Favored : 96.36 % Cbeta Deviations : 0.81 % 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: -3.08 (0.30), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.23), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 406 TYR 0.027 0.009 TYR D 394 PHE 0.125 0.035 PHE C 378 HIS 0.003 0.001 HIS E 388 Details of bonding type rmsd covalent geometry : bond 0.01112 ( 2934) covalent geometry : angle 1.74615 ( 3978) hydrogen bonds : bond 0.09766 ( 35) hydrogen bonds : angle 8.57351 ( 105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.181 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: B 406 ARG cc_start: 0.7410 (mmt90) cc_final: 0.7174 (mmt-90) outliers start: 2 outliers final: 0 residues processed: 140 average time/residue: 0.9449 time to fit residues: 135.8147 Evaluate side-chains 117 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.223422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.190657 restraints weight = 5656.628| |-----------------------------------------------------------------------------| r_work (start): 0.4606 rms_B_bonded: 1.36 r_work: 0.4491 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.4411 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2934 Z= 0.145 Angle : 0.670 7.170 3978 Z= 0.346 Chirality : 0.048 0.134 486 Planarity : 0.003 0.016 516 Dihedral : 8.271 29.941 408 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.21 % Allowed : 12.73 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.98 (0.31), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.23), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 406 TYR 0.013 0.002 TYR C 394 PHE 0.015 0.003 PHE C 378 HIS 0.006 0.002 HIS D 407 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 2934) covalent geometry : angle 0.66950 ( 3978) hydrogen bonds : bond 0.03282 ( 35) hydrogen bonds : angle 6.19039 ( 105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7515 (mp0) REVERT: B 385 LYS cc_start: 0.7393 (tttt) cc_final: 0.7026 (mtpp) REVERT: B 431 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7366 (mp0) REVERT: C 431 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7583 (mp0) REVERT: D 431 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7475 (mp0) REVERT: E 380 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7683 (tm-30) REVERT: F 376 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.6084 (mt) outliers start: 4 outliers final: 0 residues processed: 123 average time/residue: 1.0434 time to fit residues: 131.5279 Evaluate side-chains 112 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.4848 r_free = 0.4848 target = 0.221434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.187675 restraints weight = 5429.377| |-----------------------------------------------------------------------------| r_work (start): 0.4564 rms_B_bonded: 1.38 r_work: 0.4443 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.4361 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2934 Z= 0.124 Angle : 0.623 6.799 3978 Z= 0.316 Chirality : 0.047 0.133 486 Planarity : 0.002 0.011 516 Dihedral : 7.487 27.046 408 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.30 % Allowed : 17.58 % Favored : 82.12 % 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: -3.00 (0.31), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.24), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 406 TYR 0.012 0.002 TYR C 394 PHE 0.009 0.002 PHE C 378 HIS 0.005 0.001 HIS D 407 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 2934) covalent geometry : angle 0.62276 ( 3978) hydrogen bonds : bond 0.02934 ( 35) hydrogen bonds : angle 5.60871 ( 105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7744 (tm-30) REVERT: B 380 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7634 (tm-30) REVERT: B 385 LYS cc_start: 0.7522 (tttt) cc_final: 0.7215 (mtpp) REVERT: B 431 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7421 (mp0) REVERT: C 385 LYS cc_start: 0.7608 (tttt) cc_final: 0.7301 (ttpp) REVERT: C 431 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7651 (mp0) REVERT: D 379 ARG cc_start: 0.7269 (mtt180) cc_final: 0.7007 (mtt180) REVERT: D 431 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7479 (mp0) REVERT: E 380 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7762 (tm-30) outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 1.0989 time to fit residues: 132.7619 Evaluate side-chains 107 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 386 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.218842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.185425 restraints weight = 5532.037| |-----------------------------------------------------------------------------| r_work (start): 0.4532 rms_B_bonded: 1.47 r_work: 0.4415 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.4334 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2934 Z= 0.155 Angle : 0.643 6.143 3978 Z= 0.325 Chirality : 0.047 0.128 486 Planarity : 0.002 0.014 516 Dihedral : 7.431 26.845 408 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.91 % Allowed : 17.88 % Favored : 81.21 % 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: -3.01 (0.32), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.24), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 406 TYR 0.012 0.002 TYR C 394 PHE 0.010 0.003 PHE C 378 HIS 0.006 0.002 HIS D 407 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 2934) covalent geometry : angle 0.64252 ( 3978) hydrogen bonds : bond 0.03227 ( 35) hydrogen bonds : angle 5.50696 ( 105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7787 (tm-30) REVERT: A 383 LYS cc_start: 0.7343 (mttm) cc_final: 0.6759 (mmmt) REVERT: A 406 ARG cc_start: 0.8464 (mtt180) cc_final: 0.8020 (mmt180) REVERT: B 385 LYS cc_start: 0.7483 (tttt) cc_final: 0.7176 (mtpp) REVERT: B 431 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7483 (mp0) REVERT: C 383 LYS cc_start: 0.7704 (ptpp) cc_final: 0.7155 (mmmt) REVERT: C 385 LYS cc_start: 0.7601 (tttt) cc_final: 0.7254 (ttpp) REVERT: C 431 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7663 (mp0) REVERT: D 379 ARG cc_start: 0.7275 (mtt180) cc_final: 0.7030 (mtt180) REVERT: D 431 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7502 (mp0) REVERT: E 380 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7759 (tm-30) outliers start: 3 outliers final: 3 residues processed: 112 average time/residue: 1.1318 time to fit residues: 129.5591 Evaluate side-chains 110 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.221441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.189676 restraints weight = 5617.706| |-----------------------------------------------------------------------------| r_work (start): 0.4586 rms_B_bonded: 1.37 r_work: 0.4459 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.4380 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2934 Z= 0.110 Angle : 0.601 5.933 3978 Z= 0.301 Chirality : 0.047 0.127 486 Planarity : 0.002 0.010 516 Dihedral : 7.007 25.072 408 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.91 % Allowed : 18.18 % Favored : 80.91 % 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: -2.99 (0.33), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.25), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 406 TYR 0.013 0.002 TYR C 394 PHE 0.007 0.002 PHE C 378 HIS 0.004 0.001 HIS D 407 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 2934) covalent geometry : angle 0.60078 ( 3978) hydrogen bonds : bond 0.02435 ( 35) hydrogen bonds : angle 4.81814 ( 105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7772 (tm-30) REVERT: A 383 LYS cc_start: 0.7428 (mttm) cc_final: 0.6782 (mmmt) REVERT: B 385 LYS cc_start: 0.7458 (tttt) cc_final: 0.7153 (mtpp) REVERT: B 431 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7427 (mp0) REVERT: C 383 LYS cc_start: 0.7722 (ptpp) cc_final: 0.7106 (mmmt) REVERT: C 385 LYS cc_start: 0.7581 (tttt) cc_final: 0.7227 (ttpp) REVERT: C 431 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7654 (mp0) REVERT: D 379 ARG cc_start: 0.7244 (mtt180) cc_final: 0.7007 (mtt180) REVERT: D 431 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7490 (mp0) REVERT: E 380 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7754 (tm-30) outliers start: 3 outliers final: 2 residues processed: 113 average time/residue: 1.1438 time to fit residues: 132.2175 Evaluate side-chains 110 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.4837 r_free = 0.4837 target = 0.219951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.186649 restraints weight = 5463.977| |-----------------------------------------------------------------------------| r_work (start): 0.4538 rms_B_bonded: 1.36 r_work: 0.4415 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.4334 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2934 Z= 0.152 Angle : 0.633 5.613 3978 Z= 0.320 Chirality : 0.047 0.128 486 Planarity : 0.002 0.013 516 Dihedral : 7.106 25.224 408 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.21 % Allowed : 18.18 % Favored : 80.61 % 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: -3.00 (0.32), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.25), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.013 0.002 TYR C 394 PHE 0.009 0.003 PHE C 378 HIS 0.006 0.002 HIS D 407 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 2934) covalent geometry : angle 0.63345 ( 3978) hydrogen bonds : bond 0.02993 ( 35) hydrogen bonds : angle 4.81072 ( 105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7811 (tm-30) REVERT: A 383 LYS cc_start: 0.7462 (mttm) cc_final: 0.6785 (mmmt) REVERT: A 406 ARG cc_start: 0.8476 (mtt180) cc_final: 0.8055 (mmm160) REVERT: B 385 LYS cc_start: 0.7474 (tttt) cc_final: 0.7156 (mtpp) REVERT: B 431 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7375 (mp0) REVERT: C 383 LYS cc_start: 0.7768 (ptpp) cc_final: 0.7139 (mmmt) REVERT: C 385 LYS cc_start: 0.7596 (tttt) cc_final: 0.7334 (mtpp) REVERT: C 431 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7632 (mp0) REVERT: D 379 ARG cc_start: 0.7261 (mtt180) cc_final: 0.7020 (mtt180) REVERT: D 431 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7536 (mp0) REVERT: E 380 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7735 (tm-30) outliers start: 4 outliers final: 3 residues processed: 110 average time/residue: 1.1585 time to fit residues: 130.2648 Evaluate side-chains 110 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.4834 r_free = 0.4834 target = 0.220127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.185894 restraints weight = 5413.670| |-----------------------------------------------------------------------------| r_work (start): 0.4546 rms_B_bonded: 1.40 r_work: 0.4424 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.4344 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2934 Z= 0.153 Angle : 0.648 5.885 3978 Z= 0.325 Chirality : 0.046 0.127 486 Planarity : 0.002 0.014 516 Dihedral : 7.041 24.097 408 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.52 % Allowed : 18.18 % Favored : 80.30 % 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: -2.99 (0.33), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.25), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 406 TYR 0.014 0.002 TYR C 394 PHE 0.009 0.003 PHE C 378 HIS 0.005 0.002 HIS D 407 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 2934) covalent geometry : angle 0.64760 ( 3978) hydrogen bonds : bond 0.02991 ( 35) hydrogen bonds : angle 4.73167 ( 105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7807 (tm-30) REVERT: A 383 LYS cc_start: 0.7464 (mttm) cc_final: 0.6829 (mmmt) REVERT: A 385 LYS cc_start: 0.7791 (ttpt) cc_final: 0.7301 (tttm) REVERT: A 406 ARG cc_start: 0.8469 (mtt180) cc_final: 0.8031 (mmt180) REVERT: B 385 LYS cc_start: 0.7467 (tttt) cc_final: 0.7155 (mtpp) REVERT: B 431 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7452 (mp0) REVERT: C 383 LYS cc_start: 0.7751 (ptpp) cc_final: 0.7081 (mmmt) REVERT: C 385 LYS cc_start: 0.7607 (tttt) cc_final: 0.7331 (mtpp) REVERT: C 406 ARG cc_start: 0.8315 (mmt-90) cc_final: 0.7515 (mmt180) REVERT: C 431 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7611 (mp0) REVERT: D 379 ARG cc_start: 0.7276 (mtt180) cc_final: 0.7035 (mtt180) REVERT: D 431 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7517 (mp0) REVERT: E 380 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7711 (tm-30) outliers start: 5 outliers final: 4 residues processed: 113 average time/residue: 1.1667 time to fit residues: 134.8292 Evaluate side-chains 112 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.4839 r_free = 0.4839 target = 0.220047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.186554 restraints weight = 5375.147| |-----------------------------------------------------------------------------| r_work (start): 0.4560 rms_B_bonded: 1.36 r_work: 0.4435 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.4356 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2934 Z= 0.138 Angle : 0.625 5.344 3978 Z= 0.315 Chirality : 0.047 0.127 486 Planarity : 0.002 0.013 516 Dihedral : 6.946 23.860 408 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.82 % Allowed : 18.18 % Favored : 80.00 % 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: -2.99 (0.33), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.25), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 406 TYR 0.015 0.002 TYR C 394 PHE 0.008 0.002 PHE C 378 HIS 0.005 0.001 HIS D 407 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 2934) covalent geometry : angle 0.62482 ( 3978) hydrogen bonds : bond 0.02727 ( 35) hydrogen bonds : angle 4.56489 ( 105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7824 (tm-30) REVERT: A 383 LYS cc_start: 0.7503 (mttm) cc_final: 0.6884 (mmmt) REVERT: A 385 LYS cc_start: 0.7787 (ttpt) cc_final: 0.7316 (tttm) REVERT: A 406 ARG cc_start: 0.8486 (mtt180) cc_final: 0.8058 (mmt180) REVERT: B 385 LYS cc_start: 0.7489 (tttt) cc_final: 0.7197 (mtpp) REVERT: B 431 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7446 (mp0) REVERT: C 383 LYS cc_start: 0.7770 (ptpp) cc_final: 0.7086 (mmmt) REVERT: C 385 LYS cc_start: 0.7586 (tttt) cc_final: 0.7331 (mtpp) REVERT: C 406 ARG cc_start: 0.8300 (mmt-90) cc_final: 0.7528 (mmt180) REVERT: C 431 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7611 (mp0) REVERT: D 379 ARG cc_start: 0.7277 (mtt180) cc_final: 0.7047 (mtt180) REVERT: D 431 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7522 (mp0) REVERT: E 380 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7719 (tm-30) outliers start: 6 outliers final: 4 residues processed: 113 average time/residue: 1.1286 time to fit residues: 130.4549 Evaluate side-chains 112 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain F residue 386 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.218402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.185495 restraints weight = 5404.121| |-----------------------------------------------------------------------------| r_work (start): 0.4549 rms_B_bonded: 1.47 r_work: 0.4426 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.4341 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2934 Z= 0.176 Angle : 0.665 5.738 3978 Z= 0.336 Chirality : 0.047 0.127 486 Planarity : 0.003 0.015 516 Dihedral : 7.103 24.394 408 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.21 % Allowed : 18.18 % Favored : 80.61 % 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: -3.01 (0.32), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.25), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.016 0.002 TYR C 394 PHE 0.009 0.003 PHE C 378 HIS 0.006 0.002 HIS D 407 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 2934) covalent geometry : angle 0.66528 ( 3978) hydrogen bonds : bond 0.03136 ( 35) hydrogen bonds : angle 4.75874 ( 105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7787 (tm-30) REVERT: A 385 LYS cc_start: 0.7787 (ttpt) cc_final: 0.7373 (ttpp) REVERT: A 406 ARG cc_start: 0.8478 (mtt180) cc_final: 0.8041 (mmt180) REVERT: B 385 LYS cc_start: 0.7484 (tttt) cc_final: 0.7174 (mtpp) REVERT: B 431 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7343 (mp0) REVERT: C 383 LYS cc_start: 0.7793 (ptpp) cc_final: 0.7094 (mmmt) REVERT: C 385 LYS cc_start: 0.7597 (tttt) cc_final: 0.7332 (mtpp) REVERT: C 406 ARG cc_start: 0.8311 (mmt-90) cc_final: 0.7524 (mmt180) REVERT: C 431 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7607 (mp0) REVERT: D 379 ARG cc_start: 0.7330 (mtt180) cc_final: 0.7093 (mtt180) REVERT: D 431 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7514 (mp0) REVERT: E 380 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7711 (tm-30) outliers start: 4 outliers final: 3 residues processed: 109 average time/residue: 1.1886 time to fit residues: 132.3575 Evaluate side-chains 111 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN B 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.217814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.184487 restraints weight = 5457.937| |-----------------------------------------------------------------------------| r_work (start): 0.4522 rms_B_bonded: 1.37 r_work: 0.4395 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.4313 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2934 Z= 0.226 Angle : 0.713 5.634 3978 Z= 0.362 Chirality : 0.047 0.126 486 Planarity : 0.003 0.022 516 Dihedral : 7.338 26.388 408 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.91 % Allowed : 19.39 % Favored : 79.70 % 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: -3.08 (0.32), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.25), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 379 TYR 0.017 0.003 TYR C 394 PHE 0.011 0.004 PHE C 378 HIS 0.007 0.002 HIS C 407 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 2934) covalent geometry : angle 0.71274 ( 3978) hydrogen bonds : bond 0.03634 ( 35) hydrogen bonds : angle 5.06171 ( 105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7800 (tm-30) REVERT: A 383 LYS cc_start: 0.7570 (mttm) cc_final: 0.6939 (mmmt) REVERT: A 406 ARG cc_start: 0.8478 (mtt180) cc_final: 0.8034 (mmm160) REVERT: B 385 LYS cc_start: 0.7508 (tttt) cc_final: 0.7214 (mtpp) REVERT: B 431 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7372 (mp0) REVERT: C 383 LYS cc_start: 0.7805 (ptpp) cc_final: 0.7103 (mmmt) REVERT: C 385 LYS cc_start: 0.7578 (tttt) cc_final: 0.7330 (mtpp) REVERT: C 406 ARG cc_start: 0.8343 (mmt-90) cc_final: 0.7551 (mmt180) REVERT: C 431 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7618 (mp0) REVERT: D 379 ARG cc_start: 0.7368 (mtt180) cc_final: 0.7132 (mtt180) REVERT: D 431 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7507 (mp0) REVERT: E 380 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7695 (tm-30) outliers start: 3 outliers final: 3 residues processed: 103 average time/residue: 1.1995 time to fit residues: 126.2211 Evaluate side-chains 106 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN B 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.220907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.187742 restraints weight = 5465.270| |-----------------------------------------------------------------------------| r_work (start): 0.4571 rms_B_bonded: 1.37 r_work: 0.4447 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.4367 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2934 Z= 0.128 Angle : 0.622 5.546 3978 Z= 0.312 Chirality : 0.047 0.129 486 Planarity : 0.002 0.013 516 Dihedral : 6.950 23.911 408 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.61 % Allowed : 19.70 % Favored : 79.70 % 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: -3.04 (0.33), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.25), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 406 TYR 0.016 0.002 TYR C 394 PHE 0.008 0.002 PHE E 378 HIS 0.004 0.001 HIS D 407 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 2934) covalent geometry : angle 0.62222 ( 3978) hydrogen bonds : bond 0.02599 ( 35) hydrogen bonds : angle 4.55286 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4298.96 seconds wall clock time: 73 minutes 12.87 seconds (4392.87 seconds total)