Starting phenix.real_space_refine on Wed Mar 4 04:19:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x1g_32940/03_2026/7x1g_32940.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x1g_32940/03_2026/7x1g_32940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x1g_32940/03_2026/7x1g_32940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x1g_32940/03_2026/7x1g_32940.map" model { file = "/net/cci-nas-00/data/ceres_data/7x1g_32940/03_2026/7x1g_32940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x1g_32940/03_2026/7x1g_32940.cif" } resolution = 2.94 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= 0.026 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 7084 2.51 5 N 1770 2.21 5 O 1846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s 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: 10760 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5380 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 28, 'TRANS': 647} Chain breaks: 6 Chain: "B" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5380 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 28, 'TRANS': 647} Chain breaks: 6 Time building chain proxies: 2.35, per 1000 atoms: 0.22 Number of scatterers: 10760 At special positions: 0 Unit cell: (122.329, 87.847, 102.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1846 8.00 N 1770 7.00 C 7084 6.00 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: 0.88 Conformation dependent library (CDL) restraints added in 437.4 milliseconds 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 5 sheets defined 66.8% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 147 through 160 removed outlier: 3.701A pdb=" N PHE A 159 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 278 through 288 removed outlier: 3.603A pdb=" N GLN A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 343 through 354 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 371 through 401 Proline residue: A 389 - end of helix Processing helix chain 'A' and resid 406 through 424 Processing helix chain 'A' and resid 435 through 453 Processing helix chain 'A' and resid 455 through 477 Processing helix chain 'A' and resid 478 through 486 removed outlier: 3.614A pdb=" N LEU A 481 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 518 removed outlier: 3.501A pdb=" N GLU A 491 " --> pdb=" O LYS A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 594 Processing helix chain 'A' and resid 595 through 597 No H-bonds generated for 'chain 'A' and resid 595 through 597' Processing helix chain 'A' and resid 601 through 611 removed outlier: 3.710A pdb=" N SER A 609 " --> pdb=" O ARG A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 626 removed outlier: 3.531A pdb=" N ILE A 615 " --> pdb=" O CYS A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 684 Processing helix chain 'A' and resid 685 through 689 Processing helix chain 'A' and resid 696 through 713 removed outlier: 3.624A pdb=" N PHE A 713 " --> pdb=" O GLY A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 732 removed outlier: 3.820A pdb=" N LEU A 727 " --> pdb=" O PRO A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 768 Processing helix chain 'A' and resid 769 through 772 Processing helix chain 'A' and resid 780 through 795 Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'A' and resid 825 through 848 Processing helix chain 'A' and resid 851 through 856 Processing helix chain 'A' and resid 857 through 877 removed outlier: 3.581A pdb=" N ILE A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE A 866 " --> pdb=" O MET A 862 " (cutoff:3.500A) Proline residue: A 867 - end of helix removed outlier: 4.297A pdb=" N LEU A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) Proline residue: A 874 - end of helix Processing helix chain 'A' and resid 878 through 887 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 147 through 160 removed outlier: 3.652A pdb=" N PHE B 159 " --> pdb=" O MET B 155 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 265 through 277 Processing helix chain 'B' and resid 278 through 288 removed outlier: 3.604A pdb=" N GLN B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 306 Processing helix chain 'B' and resid 343 through 354 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 371 through 401 Proline residue: B 389 - end of helix Processing helix chain 'B' and resid 406 through 424 Processing helix chain 'B' and resid 435 through 453 Processing helix chain 'B' and resid 455 through 477 Processing helix chain 'B' and resid 478 through 486 removed outlier: 3.612A pdb=" N LEU B 481 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 518 Processing helix chain 'B' and resid 570 through 594 Processing helix chain 'B' and resid 595 through 597 No H-bonds generated for 'chain 'B' and resid 595 through 597' Processing helix chain 'B' and resid 601 through 611 Processing helix chain 'B' and resid 612 through 626 Processing helix chain 'B' and resid 654 through 684 Processing helix chain 'B' and resid 685 through 689 Processing helix chain 'B' and resid 696 through 713 removed outlier: 3.624A pdb=" N PHE B 713 " --> pdb=" O GLY B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 732 removed outlier: 3.826A pdb=" N LEU B 727 " --> pdb=" O PRO B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 768 Processing helix chain 'B' and resid 769 through 772 Processing helix chain 'B' and resid 780 through 795 Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 811 through 815 Processing helix chain 'B' and resid 819 through 824 Processing helix chain 'B' and resid 825 through 848 Processing helix chain 'B' and resid 851 through 856 Processing helix chain 'B' and resid 857 through 877 removed outlier: 3.572A pdb=" N ILE B 861 " --> pdb=" O ILE B 857 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE B 866 " --> pdb=" O MET B 862 " (cutoff:3.500A) Proline residue: B 867 - end of helix removed outlier: 4.310A pdb=" N LEU B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) Proline residue: B 874 - end of helix Processing helix chain 'B' and resid 878 through 887 Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 143 removed outlier: 5.469A pdb=" N VAL A 235 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG A 248 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 13.208A pdb=" N VAL A 247 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 11.908A pdb=" N GLN A 211 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N PHE A 249 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N SER A 213 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ILE A 251 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A 215 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL A 253 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 217 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA A 255 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N CYS A 219 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY A 200 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N SER A 213 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 11.850A pdb=" N ILE A 198 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N LEU A 215 " --> pdb=" O ASP A 196 " (cutoff:3.500A) removed outlier: 10.948A pdb=" N ASP A 196 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 107 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 107 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N ASP B 196 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 9.747A pdb=" N LEU B 215 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 11.824A pdb=" N ILE B 198 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N SER B 213 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY B 200 " --> pdb=" O GLN B 211 " (cutoff:3.500A) removed outlier: 13.180A pdb=" N VAL B 247 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N GLN B 211 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N PHE B 249 " --> pdb=" O GLN B 211 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N SER B 213 " --> pdb=" O PHE B 249 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE B 251 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU B 215 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL B 253 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE B 217 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ALA B 255 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N CYS B 219 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG B 248 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL B 235 " --> pdb=" O ASN B 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 432 through 433 Processing sheet with id=AA3, first strand: chain 'A' and resid 733 through 740 removed outlier: 6.742A pdb=" N LEU A 734 " --> pdb=" O VAL A 749 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 432 through 433 Processing sheet with id=AA5, first strand: chain 'B' and resid 733 through 740 removed outlier: 6.746A pdb=" N LEU B 734 " --> pdb=" O VAL B 749 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 1962 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: 1.75 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1633 1.31 - 1.43: 2986 1.43 - 1.56: 6287 1.56 - 1.68: 0 1.68 - 1.81: 98 Bond restraints: 11004 Sorted by residual: bond pdb=" CA TRP B 240 " pdb=" C TRP B 240 " ideal model delta sigma weight residual 1.525 1.477 0.047 1.11e-02 8.12e+03 1.82e+01 bond pdb=" C ASN B 239 " pdb=" O ASN B 239 " ideal model delta sigma weight residual 1.234 1.185 0.049 1.19e-02 7.06e+03 1.70e+01 bond pdb=" CA GLU B 242 " pdb=" C GLU B 242 " ideal model delta sigma weight residual 1.519 1.469 0.050 1.22e-02 6.72e+03 1.70e+01 bond pdb=" C TYR B 357 " pdb=" N PRO B 358 " ideal model delta sigma weight residual 1.335 1.381 -0.046 1.36e-02 5.41e+03 1.13e+01 bond pdb=" C TYR A 357 " pdb=" N PRO A 358 " ideal model delta sigma weight residual 1.335 1.381 -0.045 1.36e-02 5.41e+03 1.11e+01 ... (remaining 10999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 14827 2.77 - 5.54: 95 5.54 - 8.31: 9 8.31 - 11.08: 1 11.08 - 13.85: 2 Bond angle restraints: 14934 Sorted by residual: angle pdb=" N TRP B 240 " pdb=" CA TRP B 240 " pdb=" C TRP B 240 " ideal model delta sigma weight residual 113.50 103.04 10.46 1.65e+00 3.67e-01 4.02e+01 angle pdb=" C TYR A 357 " pdb=" N PRO A 358 " pdb=" CA PRO A 358 " ideal model delta sigma weight residual 119.05 112.38 6.67 1.11e+00 8.12e-01 3.61e+01 angle pdb=" C TYR B 357 " pdb=" N PRO B 358 " pdb=" CA PRO B 358 " ideal model delta sigma weight residual 119.05 112.43 6.62 1.11e+00 8.12e-01 3.56e+01 angle pdb=" N GLU B 242 " pdb=" CA GLU B 242 " pdb=" C GLU B 242 " ideal model delta sigma weight residual 113.55 107.02 6.53 1.26e+00 6.30e-01 2.69e+01 angle pdb=" N ASN B 243 " pdb=" CA ASN B 243 " pdb=" C ASN B 243 " ideal model delta sigma weight residual 111.87 104.96 6.91 1.41e+00 5.03e-01 2.40e+01 ... (remaining 14929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 5806 16.27 - 32.54: 581 32.54 - 48.80: 116 48.80 - 65.07: 15 65.07 - 81.34: 8 Dihedral angle restraints: 6526 sinusoidal: 2574 harmonic: 3952 Sorted by residual: dihedral pdb=" CB LYS B 512 " pdb=" CG LYS B 512 " pdb=" CD LYS B 512 " pdb=" CE LYS B 512 " ideal model delta sinusoidal sigma weight residual -60.00 -119.58 59.58 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB LYS A 512 " pdb=" CG LYS A 512 " pdb=" CD LYS A 512 " pdb=" CE LYS A 512 " ideal model delta sinusoidal sigma weight residual -60.00 -119.53 59.53 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ASN B 239 " pdb=" C ASN B 239 " pdb=" CA ASN B 239 " pdb=" CB ASN B 239 " ideal model delta harmonic sigma weight residual 122.80 115.21 7.59 0 2.50e+00 1.60e-01 9.22e+00 ... (remaining 6523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1440 0.044 - 0.087: 243 0.087 - 0.131: 75 0.131 - 0.175: 4 0.175 - 0.219: 2 Chirality restraints: 1764 Sorted by residual: chirality pdb=" CA ARG A 822 " pdb=" N ARG A 822 " pdb=" C ARG A 822 " pdb=" CB ARG A 822 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASN B 239 " pdb=" N ASN B 239 " pdb=" C ASN B 239 " pdb=" CB ASN B 239 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA GLU A 242 " pdb=" N GLU A 242 " pdb=" C GLU A 242 " pdb=" CB GLU A 242 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 1761 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 774 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO B 775 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 775 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 775 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 774 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.17e+00 pdb=" N PRO A 775 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 775 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 775 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 239 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" CG ASN B 239 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 239 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 239 " 0.009 2.00e-02 2.50e+03 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1403 2.75 - 3.29: 10666 3.29 - 3.83: 18274 3.83 - 4.36: 21620 4.36 - 4.90: 37999 Nonbonded interactions: 89962 Sorted by model distance: nonbonded pdb=" O CYS B 386 " pdb=" OG1 THR B 390 " model vdw 2.218 3.040 nonbonded pdb=" O CYS A 386 " pdb=" OG1 THR A 390 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR B 357 " pdb=" O LEU B 423 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR A 357 " pdb=" O LEU A 423 " model vdw 2.237 3.040 nonbonded pdb=" O LEU A 600 " pdb=" NH1 ARG A 605 " model vdw 2.261 3.120 ... (remaining 89957 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.350 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:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.003 0.050 11004 Z= 0.185 Angle : 0.554 13.851 14934 Z= 0.314 Chirality : 0.038 0.219 1764 Planarity : 0.003 0.058 1828 Dihedral : 13.159 81.339 3970 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.34 % Allowed : 0.34 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.38 (0.24), residues: 1324 helix: 2.30 (0.18), residues: 862 sheet: -0.00 (0.41), residues: 108 loop : 0.37 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 823 TYR 0.006 0.001 TYR B 357 PHE 0.019 0.001 PHE A 846 TRP 0.008 0.001 TRP B 240 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00294 (11004) covalent geometry : angle 0.55447 (14934) hydrogen bonds : bond 0.12348 ( 688) hydrogen bonds : angle 4.60317 ( 1962) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 246 time to evaluate : 0.316 Fit side-chains REVERT: A 596 LYS cc_start: 0.8402 (mttt) cc_final: 0.8099 (mtpt) REVERT: A 734 LEU cc_start: 0.7972 (mt) cc_final: 0.7680 (mp) REVERT: B 106 VAL cc_start: 0.8196 (m) cc_final: 0.7909 (p) REVERT: B 596 LYS cc_start: 0.8383 (mttt) cc_final: 0.8061 (mtpt) REVERT: B 734 LEU cc_start: 0.7978 (mt) cc_final: 0.7663 (mp) outliers start: 4 outliers final: 1 residues processed: 250 average time/residue: 0.5886 time to fit residues: 158.1068 Evaluate side-chains 149 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 857 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN A 467 ASN A 741 ASN B 239 ASN B 443 GLN B 467 ASN B 741 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.127227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.101478 restraints weight = 12808.570| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.66 r_work: 0.2931 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11004 Z= 0.209 Angle : 0.594 8.268 14934 Z= 0.302 Chirality : 0.043 0.169 1764 Planarity : 0.005 0.037 1828 Dihedral : 3.987 16.889 1464 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.91 % Allowed : 10.36 % Favored : 86.73 % 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: 1.95 (0.23), residues: 1324 helix: 2.05 (0.18), residues: 846 sheet: 0.31 (0.43), residues: 108 loop : -0.11 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 347 TYR 0.017 0.001 TYR A 441 PHE 0.018 0.002 PHE B 486 TRP 0.012 0.002 TRP B 515 HIS 0.008 0.002 HIS B 719 Details of bonding type rmsd covalent geometry : bond 0.00507 (11004) covalent geometry : angle 0.59388 (14934) hydrogen bonds : bond 0.04735 ( 688) hydrogen bonds : angle 4.09130 ( 1962) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.475 Fit side-chains REVERT: A 596 LYS cc_start: 0.8034 (mttt) cc_final: 0.7482 (mtpt) REVERT: A 734 LEU cc_start: 0.7905 (mt) cc_final: 0.7581 (mp) REVERT: B 242 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6743 (pm20) REVERT: B 596 LYS cc_start: 0.7963 (mttt) cc_final: 0.7396 (mtpt) REVERT: B 734 LEU cc_start: 0.7910 (mt) cc_final: 0.7568 (mp) REVERT: B 750 ASN cc_start: 0.7815 (p0) cc_final: 0.7614 (p0) REVERT: B 809 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7873 (mt) outliers start: 34 outliers final: 12 residues processed: 165 average time/residue: 0.5943 time to fit residues: 105.6091 Evaluate side-chains 146 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 630 GLU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 797 ASP Chi-restraints excluded: chain B residue 809 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 124 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.125802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.099951 restraints weight = 12839.813| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.69 r_work: 0.2936 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11004 Z= 0.153 Angle : 0.521 5.918 14934 Z= 0.267 Chirality : 0.040 0.156 1764 Planarity : 0.004 0.039 1828 Dihedral : 3.965 28.120 1464 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.17 % Allowed : 11.56 % Favored : 85.27 % 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: 1.91 (0.23), residues: 1324 helix: 2.04 (0.18), residues: 844 sheet: 0.35 (0.44), residues: 108 loop : -0.19 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 157 TYR 0.016 0.001 TYR B 441 PHE 0.016 0.002 PHE A 620 TRP 0.014 0.001 TRP A 515 HIS 0.006 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00367 (11004) covalent geometry : angle 0.52134 (14934) hydrogen bonds : bond 0.04267 ( 688) hydrogen bonds : angle 3.94914 ( 1962) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.307 Fit side-chains REVERT: A 479 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7991 (mp) REVERT: A 596 LYS cc_start: 0.8071 (mttt) cc_final: 0.7556 (mtpt) REVERT: A 734 LEU cc_start: 0.7946 (mt) cc_final: 0.7705 (mp) REVERT: B 242 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6775 (pm20) REVERT: B 596 LYS cc_start: 0.8011 (mttt) cc_final: 0.7469 (mtpt) REVERT: B 734 LEU cc_start: 0.7930 (mt) cc_final: 0.7672 (mp) outliers start: 37 outliers final: 13 residues processed: 169 average time/residue: 0.5592 time to fit residues: 102.0947 Evaluate side-chains 145 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 797 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 40 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 63 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.122219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.095983 restraints weight = 12924.287| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.73 r_work: 0.2878 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11004 Z= 0.212 Angle : 0.570 6.560 14934 Z= 0.291 Chirality : 0.042 0.164 1764 Planarity : 0.005 0.045 1828 Dihedral : 4.116 17.956 1462 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.02 % Allowed : 12.76 % Favored : 83.22 % 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: 1.64 (0.23), residues: 1324 helix: 1.81 (0.18), residues: 852 sheet: 0.38 (0.43), residues: 108 loop : -0.34 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 157 TYR 0.019 0.002 TYR A 441 PHE 0.017 0.002 PHE A 858 TRP 0.016 0.002 TRP B 515 HIS 0.008 0.002 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00526 (11004) covalent geometry : angle 0.57029 (14934) hydrogen bonds : bond 0.04676 ( 688) hydrogen bonds : angle 4.08760 ( 1962) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 145 time to evaluate : 0.446 Fit side-chains REVERT: A 242 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6841 (mm-30) REVERT: A 363 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7781 (m-30) REVERT: A 508 LYS cc_start: 0.7513 (mttt) cc_final: 0.7188 (mttp) REVERT: A 596 LYS cc_start: 0.8227 (mttt) cc_final: 0.7689 (mtpt) REVERT: A 734 LEU cc_start: 0.8133 (mt) cc_final: 0.7877 (mp) REVERT: A 741 ASN cc_start: 0.8044 (t0) cc_final: 0.7818 (t0) REVERT: B 242 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6000 (tm-30) REVERT: B 363 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7747 (m-30) REVERT: B 479 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8050 (mp) REVERT: B 508 LYS cc_start: 0.7508 (mttt) cc_final: 0.7185 (mttp) REVERT: B 596 LYS cc_start: 0.8190 (mttt) cc_final: 0.7639 (mtpt) REVERT: B 734 LEU cc_start: 0.8131 (mt) cc_final: 0.7875 (mp) REVERT: B 741 ASN cc_start: 0.8044 (t0) cc_final: 0.7831 (t0) outliers start: 47 outliers final: 17 residues processed: 175 average time/residue: 0.5471 time to fit residues: 103.4899 Evaluate side-chains 159 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 797 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.126011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.100442 restraints weight = 12794.825| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.68 r_work: 0.2913 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11004 Z= 0.143 Angle : 0.508 6.626 14934 Z= 0.260 Chirality : 0.040 0.158 1764 Planarity : 0.004 0.046 1828 Dihedral : 3.971 16.526 1462 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.25 % Allowed : 15.33 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.77 (0.23), residues: 1324 helix: 1.96 (0.18), residues: 844 sheet: 0.11 (0.43), residues: 114 loop : -0.28 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 157 TYR 0.015 0.001 TYR A 441 PHE 0.016 0.001 PHE A 620 TRP 0.016 0.001 TRP B 515 HIS 0.005 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00340 (11004) covalent geometry : angle 0.50778 (14934) hydrogen bonds : bond 0.04173 ( 688) hydrogen bonds : angle 3.96316 ( 1962) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.403 Fit side-chains REVERT: A 242 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6753 (mm-30) REVERT: A 363 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7618 (m-30) REVERT: A 479 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7957 (mp) REVERT: A 508 LYS cc_start: 0.7303 (mttt) cc_final: 0.7005 (mttp) REVERT: A 596 LYS cc_start: 0.8107 (mttt) cc_final: 0.7601 (mtpt) REVERT: A 734 LEU cc_start: 0.8051 (mt) cc_final: 0.7800 (mp) REVERT: B 106 VAL cc_start: 0.8287 (OUTLIER) cc_final: 0.7912 (p) REVERT: B 242 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.5861 (tm-30) REVERT: B 363 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7641 (m-30) REVERT: B 370 LYS cc_start: 0.7842 (mmtp) cc_final: 0.7496 (mmtm) REVERT: B 479 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7931 (mp) REVERT: B 508 LYS cc_start: 0.7312 (mttt) cc_final: 0.7020 (mttp) REVERT: B 596 LYS cc_start: 0.8050 (mttt) cc_final: 0.7515 (mtpt) REVERT: B 734 LEU cc_start: 0.8040 (mt) cc_final: 0.7793 (mp) outliers start: 38 outliers final: 15 residues processed: 161 average time/residue: 0.5360 time to fit residues: 93.4105 Evaluate side-chains 154 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 797 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.121490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.095329 restraints weight = 12990.600| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.71 r_work: 0.2858 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11004 Z= 0.236 Angle : 0.589 7.135 14934 Z= 0.299 Chirality : 0.043 0.168 1764 Planarity : 0.005 0.048 1828 Dihedral : 4.214 18.608 1462 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.02 % Allowed : 15.58 % Favored : 80.39 % 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: 1.53 (0.23), residues: 1324 helix: 1.79 (0.18), residues: 840 sheet: 0.07 (0.43), residues: 114 loop : -0.40 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 157 TYR 0.019 0.002 TYR A 441 PHE 0.017 0.002 PHE B 858 TRP 0.018 0.002 TRP B 515 HIS 0.008 0.002 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00586 (11004) covalent geometry : angle 0.58874 (14934) hydrogen bonds : bond 0.04793 ( 688) hydrogen bonds : angle 4.13709 ( 1962) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 0.358 Fit side-chains REVERT: A 363 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7714 (m-30) REVERT: A 370 LYS cc_start: 0.7967 (mmtp) cc_final: 0.7635 (mmtm) REVERT: A 479 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8001 (mp) REVERT: A 596 LYS cc_start: 0.8162 (mttt) cc_final: 0.7650 (mtpt) REVERT: A 734 LEU cc_start: 0.8138 (mt) cc_final: 0.7739 (mp) REVERT: B 242 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6757 (pm20) REVERT: B 363 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: B 370 LYS cc_start: 0.7960 (mmtp) cc_final: 0.7620 (mmtm) REVERT: B 479 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7984 (mp) REVERT: B 596 LYS cc_start: 0.8137 (mttt) cc_final: 0.7620 (mtpt) REVERT: B 734 LEU cc_start: 0.8136 (mt) cc_final: 0.7737 (mp) REVERT: B 809 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7947 (mt) outliers start: 47 outliers final: 19 residues processed: 167 average time/residue: 0.5346 time to fit residues: 96.8920 Evaluate side-chains 156 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 809 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 118 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 GLN B 593 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.132880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.108761 restraints weight = 12598.584| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.64 r_work: 0.2947 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11004 Z= 0.142 Angle : 0.516 6.906 14934 Z= 0.264 Chirality : 0.040 0.156 1764 Planarity : 0.004 0.047 1828 Dihedral : 4.037 16.917 1462 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.25 % Allowed : 17.38 % Favored : 79.37 % 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: 1.68 (0.23), residues: 1324 helix: 1.91 (0.18), residues: 844 sheet: 0.09 (0.44), residues: 114 loop : -0.36 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 157 TYR 0.015 0.001 TYR B 441 PHE 0.017 0.001 PHE B 620 TRP 0.014 0.001 TRP B 515 HIS 0.005 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00336 (11004) covalent geometry : angle 0.51559 (14934) hydrogen bonds : bond 0.04184 ( 688) hydrogen bonds : angle 3.99676 ( 1962) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.343 Fit side-chains REVERT: A 187 MET cc_start: 0.5264 (mpp) cc_final: 0.5051 (mpp) REVERT: A 363 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: A 479 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7906 (mp) REVERT: A 596 LYS cc_start: 0.8039 (mttt) cc_final: 0.7574 (mtpt) REVERT: A 734 LEU cc_start: 0.8042 (mt) cc_final: 0.7797 (mp) REVERT: B 106 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.7841 (p) REVERT: B 187 MET cc_start: 0.5242 (mpp) cc_final: 0.5029 (mpp) REVERT: B 242 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.5754 (tm-30) REVERT: B 363 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7637 (m-30) REVERT: B 479 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7917 (mp) REVERT: B 596 LYS cc_start: 0.7999 (mttt) cc_final: 0.7488 (mtpt) REVERT: B 734 LEU cc_start: 0.8036 (mt) cc_final: 0.7796 (mp) REVERT: B 878 GLU cc_start: 0.7232 (mp0) cc_final: 0.6599 (tt0) outliers start: 38 outliers final: 16 residues processed: 160 average time/residue: 0.5231 time to fit residues: 91.0343 Evaluate side-chains 158 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 606 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 71 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 87 optimal weight: 0.0070 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.124937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.099329 restraints weight = 12877.483| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.69 r_work: 0.2915 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11004 Z= 0.143 Angle : 0.514 6.983 14934 Z= 0.263 Chirality : 0.039 0.157 1764 Planarity : 0.004 0.047 1828 Dihedral : 4.004 16.608 1462 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.91 % Allowed : 17.55 % Favored : 79.54 % 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: 1.70 (0.23), residues: 1324 helix: 1.92 (0.18), residues: 844 sheet: 0.10 (0.44), residues: 114 loop : -0.34 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 347 TYR 0.015 0.001 TYR A 441 PHE 0.016 0.001 PHE B 620 TRP 0.013 0.001 TRP B 515 HIS 0.005 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00342 (11004) covalent geometry : angle 0.51427 (14934) hydrogen bonds : bond 0.04165 ( 688) hydrogen bonds : angle 3.96565 ( 1962) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.435 Fit side-chains REVERT: A 187 MET cc_start: 0.5173 (mpp) cc_final: 0.4956 (mpp) REVERT: A 363 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7618 (m-30) REVERT: A 479 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7929 (mp) REVERT: A 596 LYS cc_start: 0.8090 (mttt) cc_final: 0.7608 (mtpt) REVERT: A 734 LEU cc_start: 0.8074 (mt) cc_final: 0.7834 (mp) REVERT: B 106 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.7895 (p) REVERT: B 187 MET cc_start: 0.5155 (mpp) cc_final: 0.4933 (mpp) REVERT: B 242 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6677 (pm20) REVERT: B 292 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7033 (mp0) REVERT: B 363 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: B 479 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7952 (mp) REVERT: B 596 LYS cc_start: 0.8074 (mttt) cc_final: 0.7567 (mtpt) REVERT: B 734 LEU cc_start: 0.8081 (mt) cc_final: 0.7850 (mp) REVERT: B 878 GLU cc_start: 0.7195 (mp0) cc_final: 0.6567 (tt0) outliers start: 34 outliers final: 19 residues processed: 162 average time/residue: 0.5246 time to fit residues: 92.2753 Evaluate side-chains 159 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 797 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 48 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 46 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 0.0570 chunk 110 optimal weight: 0.0970 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.126066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.100668 restraints weight = 12689.642| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.64 r_work: 0.2950 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11004 Z= 0.120 Angle : 0.499 7.213 14934 Z= 0.256 Chirality : 0.039 0.152 1764 Planarity : 0.004 0.046 1828 Dihedral : 3.889 15.314 1462 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.40 % Allowed : 18.07 % Favored : 79.54 % 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: 1.83 (0.23), residues: 1324 helix: 2.02 (0.18), residues: 844 sheet: 0.20 (0.45), residues: 114 loop : -0.30 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 347 TYR 0.013 0.001 TYR B 441 PHE 0.016 0.001 PHE B 620 TRP 0.012 0.001 TRP B 515 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00278 (11004) covalent geometry : angle 0.49894 (14934) hydrogen bonds : bond 0.03895 ( 688) hydrogen bonds : angle 3.90280 ( 1962) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.416 Fit side-chains REVERT: A 187 MET cc_start: 0.5210 (mpp) cc_final: 0.5001 (mpp) REVERT: A 363 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: A 504 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7827 (tp) REVERT: A 596 LYS cc_start: 0.8293 (mttt) cc_final: 0.7858 (mtpt) REVERT: A 734 LEU cc_start: 0.8113 (mt) cc_final: 0.7901 (mp) REVERT: A 878 GLU cc_start: 0.7322 (mp0) cc_final: 0.6792 (tt0) REVERT: B 187 MET cc_start: 0.5203 (mpp) cc_final: 0.4987 (mpp) REVERT: B 292 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7115 (mp0) REVERT: B 363 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7664 (m-30) REVERT: B 504 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7843 (tp) REVERT: B 596 LYS cc_start: 0.8262 (mttt) cc_final: 0.7789 (mtpt) REVERT: B 734 LEU cc_start: 0.8129 (mt) cc_final: 0.7912 (mp) REVERT: B 878 GLU cc_start: 0.7266 (mp0) cc_final: 0.6752 (mt-10) outliers start: 28 outliers final: 16 residues processed: 158 average time/residue: 0.5233 time to fit residues: 89.8014 Evaluate side-chains 155 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 797 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 93 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.125345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.099178 restraints weight = 12599.590| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.72 r_work: 0.2925 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11004 Z= 0.136 Angle : 0.512 7.291 14934 Z= 0.261 Chirality : 0.039 0.155 1764 Planarity : 0.004 0.048 1828 Dihedral : 3.898 15.553 1462 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.97 % Allowed : 19.43 % Favored : 78.60 % 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: 1.76 (0.23), residues: 1324 helix: 1.89 (0.18), residues: 856 sheet: 0.18 (0.46), residues: 112 loop : -0.21 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 347 TYR 0.014 0.001 TYR A 441 PHE 0.016 0.001 PHE B 620 TRP 0.012 0.001 TRP A 515 HIS 0.004 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00326 (11004) covalent geometry : angle 0.51197 (14934) hydrogen bonds : bond 0.04016 ( 688) hydrogen bonds : angle 3.90792 ( 1962) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.388 Fit side-chains REVERT: A 187 MET cc_start: 0.5204 (mpp) cc_final: 0.4988 (mpp) REVERT: A 242 GLU cc_start: 0.7251 (mm-30) cc_final: 0.7025 (pm20) REVERT: A 292 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7095 (mp0) REVERT: A 363 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7624 (m-30) REVERT: A 504 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7677 (tp) REVERT: A 596 LYS cc_start: 0.8218 (mttt) cc_final: 0.7779 (mtpt) REVERT: A 734 LEU cc_start: 0.8084 (mt) cc_final: 0.7849 (mp) REVERT: A 878 GLU cc_start: 0.7327 (mp0) cc_final: 0.6711 (tt0) REVERT: B 187 MET cc_start: 0.5195 (mpp) cc_final: 0.4981 (mpp) REVERT: B 292 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7072 (mp0) REVERT: B 363 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: B 504 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7672 (tp) REVERT: B 596 LYS cc_start: 0.8192 (mttt) cc_final: 0.7714 (mtpt) REVERT: B 734 LEU cc_start: 0.8090 (mt) cc_final: 0.7860 (mp) REVERT: B 878 GLU cc_start: 0.7265 (mp0) cc_final: 0.6690 (mt-10) outliers start: 23 outliers final: 17 residues processed: 150 average time/residue: 0.5202 time to fit residues: 84.3870 Evaluate side-chains 158 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 797 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 114 optimal weight: 0.4980 chunk 132 optimal weight: 0.0770 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 110 optimal weight: 0.4980 chunk 60 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.126544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.100430 restraints weight = 12658.834| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.71 r_work: 0.2924 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11004 Z= 0.123 Angle : 0.500 7.202 14934 Z= 0.255 Chirality : 0.039 0.153 1764 Planarity : 0.004 0.048 1828 Dihedral : 3.840 14.969 1462 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.14 % Allowed : 19.35 % Favored : 78.51 % 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: 1.81 (0.23), residues: 1324 helix: 1.93 (0.18), residues: 856 sheet: 0.23 (0.45), residues: 112 loop : -0.19 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 347 TYR 0.013 0.001 TYR A 441 PHE 0.015 0.001 PHE B 620 TRP 0.012 0.001 TRP A 515 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00290 (11004) covalent geometry : angle 0.50030 (14934) hydrogen bonds : bond 0.03871 ( 688) hydrogen bonds : angle 3.84583 ( 1962) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3504.59 seconds wall clock time: 60 minutes 24.19 seconds (3624.19 seconds total)