Starting phenix.real_space_refine on Mon Jul 28 23:28:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x1g_32940/07_2025/7x1g_32940.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x1g_32940/07_2025/7x1g_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_32940/07_2025/7x1g_32940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x1g_32940/07_2025/7x1g_32940.map" model { file = "/net/cci-nas-00/data/ceres_data/7x1g_32940/07_2025/7x1g_32940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x1g_32940/07_2025/7x1g_32940.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.83, per 1000 atoms: 0.63 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: 2.62 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.06 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: 3.22 Time building geometry restraints manager: 3.11 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: 0.05 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: 5.540 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: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.130 Process input model: 26.650 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:19.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.990 ------------------------------------------------------------------------------- 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 : 4.15 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.008 0.001 TRP B 240 HIS 0.003 0.001 HIS B 192 PHE 0.019 0.001 PHE A 846 TYR 0.006 0.001 TYR B 357 ARG 0.006 0.000 ARG A 823 Details of bonding type rmsd hydrogen bonds : bond 0.12348 ( 688) hydrogen bonds : angle 4.60317 ( 1962) covalent geometry : bond 0.00294 (11004) covalent geometry : angle 0.55447 (14934) *********************** 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 : 1.135 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: 0.7679 (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: 0.7664 (mp) outliers start: 4 outliers final: 1 residues processed: 250 average time/residue: 1.4332 time to fit residues: 385.2210 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 : 1.142 ------------------------------------------------------------------------------- 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 113 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 0.0870 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 121 optimal weight: 0.0030 overall best weight: 0.7170 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.129208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.102641 restraints weight = 12640.261| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.77 r_work: 0.2982 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11004 Z= 0.156 Angle : 0.545 8.173 14934 Z= 0.278 Chirality : 0.041 0.164 1764 Planarity : 0.004 0.033 1828 Dihedral : 3.827 15.782 1464 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.83 % Allowed : 10.19 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.23), residues: 1324 helix: 2.09 (0.18), residues: 858 sheet: 0.29 (0.43), residues: 108 loop : 0.06 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 515 HIS 0.006 0.001 HIS B 719 PHE 0.017 0.002 PHE B 486 TYR 0.015 0.001 TYR A 441 ARG 0.005 0.001 ARG A 157 Details of bonding type rmsd hydrogen bonds : bond 0.04374 ( 688) hydrogen bonds : angle 3.97818 ( 1962) covalent geometry : bond 0.00369 (11004) covalent geometry : angle 0.54523 (14934) *********************** 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 176 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 2.227 Fit side-chains REVERT: A 176 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6582 (tmm) REVERT: A 596 LYS cc_start: 0.7851 (mttt) cc_final: 0.7324 (mtpt) REVERT: A 734 LEU cc_start: 0.7719 (mt) cc_final: 0.7352 (mp) REVERT: A 750 ASN cc_start: 0.7497 (p0) cc_final: 0.7236 (p0) REVERT: B 106 VAL cc_start: 0.7973 (m) cc_final: 0.7747 (p) REVERT: B 242 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6577 (pm20) REVERT: B 596 LYS cc_start: 0.7778 (mttt) cc_final: 0.7230 (mtpt) REVERT: B 734 LEU cc_start: 0.7734 (mt) cc_final: 0.7376 (mp) REVERT: B 750 ASN cc_start: 0.7509 (p0) cc_final: 0.7264 (p0) REVERT: B 809 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7775 (mt) outliers start: 33 outliers final: 12 residues processed: 164 average time/residue: 1.4575 time to fit residues: 258.8482 Evaluate side-chains 143 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET 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 15 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN B 443 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.125476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.099357 restraints weight = 12760.074| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.71 r_work: 0.2937 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11004 Z= 0.158 Angle : 0.526 5.842 14934 Z= 0.269 Chirality : 0.040 0.156 1764 Planarity : 0.004 0.039 1828 Dihedral : 3.905 28.516 1464 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.91 % Allowed : 11.99 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.23), residues: 1324 helix: 2.00 (0.18), residues: 856 sheet: 0.35 (0.43), residues: 108 loop : -0.06 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 515 HIS 0.006 0.001 HIS B 719 PHE 0.016 0.002 PHE B 620 TYR 0.015 0.001 TYR A 441 ARG 0.006 0.001 ARG B 347 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 688) hydrogen bonds : angle 3.92015 ( 1962) covalent geometry : bond 0.00380 (11004) covalent geometry : angle 0.52614 (14934) *********************** 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 179 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.393 Fit side-chains REVERT: A 176 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6689 (tmm) REVERT: A 596 LYS cc_start: 0.8209 (mttt) cc_final: 0.7703 (mtpt) REVERT: A 734 LEU cc_start: 0.7939 (mt) cc_final: 0.7701 (mp) REVERT: B 242 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6854 (pm20) REVERT: B 596 LYS cc_start: 0.8142 (mttt) cc_final: 0.7611 (mtpt) REVERT: B 734 LEU cc_start: 0.7954 (mt) cc_final: 0.7712 (mp) outliers start: 34 outliers final: 14 residues processed: 164 average time/residue: 1.6620 time to fit residues: 296.2931 Evaluate side-chains 145 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET 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 434 THR Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 687 GLU 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 242 GLU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 687 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 83 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.126601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.100937 restraints weight = 12679.500| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.69 r_work: 0.2938 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11004 Z= 0.148 Angle : 0.512 6.331 14934 Z= 0.262 Chirality : 0.040 0.157 1764 Planarity : 0.004 0.042 1828 Dihedral : 3.858 15.748 1462 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.85 % Allowed : 12.50 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.23), residues: 1324 helix: 1.99 (0.18), residues: 856 sheet: 0.04 (0.43), residues: 114 loop : -0.15 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 515 HIS 0.006 0.001 HIS A 719 PHE 0.016 0.002 PHE A 620 TYR 0.015 0.001 TYR A 441 ARG 0.007 0.000 ARG A 157 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 688) hydrogen bonds : angle 3.91646 ( 1962) covalent geometry : bond 0.00356 (11004) covalent geometry : angle 0.51154 (14934) *********************** 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 183 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 1.183 Fit side-chains REVERT: A 176 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6664 (tmm) REVERT: A 363 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7718 (m-30) REVERT: A 479 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7985 (mp) REVERT: A 596 LYS cc_start: 0.8112 (mttt) cc_final: 0.7597 (mtpt) REVERT: A 734 LEU cc_start: 0.7939 (mt) cc_final: 0.7702 (mp) REVERT: B 242 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6677 (pm20) REVERT: B 363 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7710 (m-30) REVERT: B 479 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7964 (mp) REVERT: B 508 LYS cc_start: 0.7376 (mttt) cc_final: 0.7050 (mttp) REVERT: B 596 LYS cc_start: 0.8048 (mttt) cc_final: 0.7503 (mtpt) REVERT: B 734 LEU cc_start: 0.7947 (mt) cc_final: 0.7699 (mp) outliers start: 45 outliers final: 19 residues processed: 166 average time/residue: 1.3466 time to fit residues: 242.0728 Evaluate side-chains 154 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 191 VAL 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 266 MET Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 191 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 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 797 ASP Chi-restraints excluded: chain B residue 880 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 87 optimal weight: 0.3980 chunk 110 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 72 optimal weight: 0.0060 chunk 95 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.127379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.101895 restraints weight = 12657.890| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.75 r_work: 0.2963 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11004 Z= 0.126 Angle : 0.490 6.733 14934 Z= 0.250 Chirality : 0.039 0.154 1764 Planarity : 0.004 0.044 1828 Dihedral : 3.803 15.012 1462 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.42 % Allowed : 13.96 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.23), residues: 1324 helix: 2.03 (0.18), residues: 856 sheet: 0.10 (0.43), residues: 114 loop : -0.15 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 515 HIS 0.005 0.001 HIS A 719 PHE 0.016 0.001 PHE B 620 TYR 0.014 0.001 TYR B 441 ARG 0.005 0.000 ARG A 157 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 688) hydrogen bonds : angle 3.86521 ( 1962) covalent geometry : bond 0.00294 (11004) covalent geometry : angle 0.49046 (14934) *********************** 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 184 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 1.255 Fit side-chains REVERT: A 176 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6501 (tmm) REVERT: A 363 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: A 479 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7858 (mp) REVERT: A 596 LYS cc_start: 0.7962 (mttt) cc_final: 0.7474 (mtpt) REVERT: A 734 LEU cc_start: 0.7840 (mt) cc_final: 0.7586 (mp) REVERT: B 106 VAL cc_start: 0.8191 (m) cc_final: 0.7813 (p) REVERT: B 242 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6531 (pm20) REVERT: B 479 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7825 (mp) REVERT: B 508 LYS cc_start: 0.7147 (mttt) cc_final: 0.6742 (mtpt) REVERT: B 596 LYS cc_start: 0.7887 (mttt) cc_final: 0.7358 (mtpt) REVERT: B 734 LEU cc_start: 0.7828 (mt) cc_final: 0.7574 (mp) outliers start: 40 outliers final: 16 residues processed: 169 average time/residue: 1.1709 time to fit residues: 215.3994 Evaluate side-chains 155 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 266 MET 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 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 191 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 266 MET Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 479 LEU 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 29 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.131759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.107654 restraints weight = 12735.630| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.63 r_work: 0.2984 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11004 Z= 0.148 Angle : 0.514 6.932 14934 Z= 0.261 Chirality : 0.040 0.158 1764 Planarity : 0.004 0.045 1828 Dihedral : 3.854 15.403 1462 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.68 % Allowed : 14.30 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.23), residues: 1324 helix: 1.98 (0.18), residues: 856 sheet: 0.16 (0.44), residues: 114 loop : -0.22 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 515 HIS 0.005 0.001 HIS B 719 PHE 0.015 0.002 PHE A 620 TYR 0.014 0.001 TYR B 441 ARG 0.005 0.000 ARG B 157 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 688) hydrogen bonds : angle 3.92447 ( 1962) covalent geometry : bond 0.00356 (11004) covalent geometry : angle 0.51360 (14934) *********************** 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 180 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 1.195 Fit side-chains REVERT: A 363 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7696 (m-30) REVERT: A 479 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7897 (mp) REVERT: A 596 LYS cc_start: 0.8053 (mttt) cc_final: 0.7573 (mtpt) REVERT: A 734 LEU cc_start: 0.7948 (mt) cc_final: 0.7708 (mp) REVERT: A 854 MET cc_start: 0.8135 (ttm) cc_final: 0.7874 (ptp) REVERT: B 106 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.7849 (p) REVERT: B 242 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6742 (pm20) REVERT: B 363 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7714 (m-30) REVERT: B 479 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7922 (mp) REVERT: B 508 LYS cc_start: 0.7275 (mttt) cc_final: 0.6953 (mttp) REVERT: B 596 LYS cc_start: 0.7998 (mttt) cc_final: 0.7468 (mtpt) REVERT: B 734 LEU cc_start: 0.7931 (mt) cc_final: 0.7690 (mp) REVERT: B 878 GLU cc_start: 0.7143 (mp0) cc_final: 0.6595 (tt0) outliers start: 43 outliers final: 17 residues processed: 161 average time/residue: 1.2042 time to fit residues: 210.9812 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 : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 266 MET 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 479 LEU 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 191 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 81 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.131198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.106931 restraints weight = 12882.022| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.65 r_work: 0.2958 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2552 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= 0.160 Angle : 0.521 7.285 14934 Z= 0.265 Chirality : 0.040 0.159 1764 Planarity : 0.004 0.047 1828 Dihedral : 3.920 15.888 1462 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.08 % Allowed : 15.84 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.23), residues: 1324 helix: 1.93 (0.18), residues: 856 sheet: 0.23 (0.44), residues: 114 loop : -0.26 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 515 HIS 0.006 0.001 HIS A 719 PHE 0.016 0.002 PHE B 620 TYR 0.016 0.001 TYR B 441 ARG 0.008 0.000 ARG B 347 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 688) hydrogen bonds : angle 3.93716 ( 1962) covalent geometry : bond 0.00388 (11004) covalent geometry : angle 0.52122 (14934) *********************** 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 176 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 1.263 Fit side-chains REVERT: A 363 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7615 (m-30) REVERT: A 479 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7868 (mp) REVERT: A 596 LYS cc_start: 0.8012 (mttt) cc_final: 0.7546 (mtpt) REVERT: A 734 LEU cc_start: 0.7978 (mt) cc_final: 0.7722 (mp) REVERT: B 106 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7821 (p) REVERT: B 363 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: B 479 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7887 (mp) REVERT: B 596 LYS cc_start: 0.7968 (mttt) cc_final: 0.7446 (mtpt) REVERT: B 734 LEU cc_start: 0.7977 (mt) cc_final: 0.7718 (mp) REVERT: B 878 GLU cc_start: 0.7118 (mp0) cc_final: 0.6531 (tt0) outliers start: 36 outliers final: 20 residues processed: 163 average time/residue: 1.4222 time to fit residues: 253.1896 Evaluate side-chains 157 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL 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 266 MET 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 191 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 31 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 111 optimal weight: 0.0670 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.134882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110852 restraints weight = 12527.887| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.65 r_work: 0.2989 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11004 Z= 0.127 Angle : 0.502 7.059 14934 Z= 0.255 Chirality : 0.039 0.156 1764 Planarity : 0.004 0.047 1828 Dihedral : 3.848 15.065 1462 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.74 % Allowed : 16.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.23), residues: 1324 helix: 1.98 (0.18), residues: 856 sheet: 0.30 (0.45), residues: 114 loop : -0.24 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 515 HIS 0.004 0.001 HIS A 719 PHE 0.016 0.001 PHE B 620 TYR 0.014 0.001 TYR B 441 ARG 0.009 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 688) hydrogen bonds : angle 3.90692 ( 1962) covalent geometry : bond 0.00297 (11004) covalent geometry : angle 0.50187 (14934) *********************** 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 171 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 3.327 Fit side-chains REVERT: A 363 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7620 (m-30) REVERT: A 504 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7552 (tp) REVERT: A 596 LYS cc_start: 0.8042 (mttt) cc_final: 0.7520 (mtpt) REVERT: A 734 LEU cc_start: 0.7974 (mt) cc_final: 0.7731 (mp) REVERT: B 106 VAL cc_start: 0.8227 (OUTLIER) cc_final: 0.7822 (p) REVERT: B 363 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: B 479 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7735 (mp) REVERT: B 482 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8515 (p) REVERT: B 596 LYS cc_start: 0.8029 (mttt) cc_final: 0.7521 (mtpt) REVERT: B 734 LEU cc_start: 0.7976 (mt) cc_final: 0.7731 (mp) REVERT: B 878 GLU cc_start: 0.7078 (mp0) cc_final: 0.6524 (tt0) outliers start: 32 outliers final: 15 residues processed: 158 average time/residue: 1.4570 time to fit residues: 252.1290 Evaluate side-chains 157 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL 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 266 MET 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 B residue 106 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 122 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 chunk 52 optimal weight: 0.0170 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.128333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.102756 restraints weight = 12799.709| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.79 r_work: 0.2948 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11004 Z= 0.135 Angle : 0.511 7.170 14934 Z= 0.260 Chirality : 0.039 0.156 1764 Planarity : 0.004 0.046 1828 Dihedral : 3.858 14.952 1462 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.23 % Allowed : 18.15 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.23), residues: 1324 helix: 1.97 (0.18), residues: 856 sheet: 0.37 (0.46), residues: 114 loop : -0.25 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 515 HIS 0.005 0.001 HIS A 719 PHE 0.015 0.001 PHE A 620 TYR 0.014 0.001 TYR B 441 ARG 0.010 0.000 ARG B 347 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 688) hydrogen bonds : angle 3.89652 ( 1962) covalent geometry : bond 0.00322 (11004) covalent geometry : angle 0.51112 (14934) *********************** 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 165 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 1.148 Fit side-chains REVERT: A 242 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6795 (pm20) REVERT: A 363 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7534 (m-30) REVERT: A 504 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7454 (tp) REVERT: A 596 LYS cc_start: 0.7882 (mttt) cc_final: 0.7376 (mtpt) REVERT: A 734 LEU cc_start: 0.7860 (mt) cc_final: 0.7604 (mp) REVERT: A 848 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7393 (mtm) REVERT: A 878 GLU cc_start: 0.7165 (mp0) cc_final: 0.6517 (tt0) REVERT: B 106 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7856 (p) REVERT: B 363 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7518 (m-30) REVERT: B 508 LYS cc_start: 0.7207 (mttm) cc_final: 0.6688 (mtmt) REVERT: B 596 LYS cc_start: 0.7851 (mttt) cc_final: 0.7345 (mtpt) REVERT: B 734 LEU cc_start: 0.7864 (mt) cc_final: 0.7610 (mp) REVERT: B 878 GLU cc_start: 0.7016 (mp0) cc_final: 0.6453 (tt0) outliers start: 26 outliers final: 17 residues processed: 153 average time/residue: 1.3002 time to fit residues: 216.7392 Evaluate side-chains 157 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL 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 266 MET 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 A residue 848 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 191 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 337 LYS Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 434 THR 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 125 optimal weight: 1.9990 chunk 93 optimal weight: 0.0370 chunk 21 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 17 optimal weight: 0.0000 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.4064 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.134935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.111045 restraints weight = 12548.605| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.63 r_work: 0.3025 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11004 Z= 0.119 Angle : 0.499 7.463 14934 Z= 0.254 Chirality : 0.039 0.159 1764 Planarity : 0.004 0.046 1828 Dihedral : 3.790 14.851 1462 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.14 % Allowed : 18.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.23), residues: 1324 helix: 2.02 (0.18), residues: 856 sheet: 0.40 (0.46), residues: 114 loop : -0.27 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 515 HIS 0.005 0.001 HIS A 192 PHE 0.015 0.001 PHE B 620 TYR 0.013 0.001 TYR B 441 ARG 0.011 0.000 ARG B 347 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 688) hydrogen bonds : angle 3.83486 ( 1962) covalent geometry : bond 0.00274 (11004) covalent geometry : angle 0.49881 (14934) ********************** 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 164 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 1.286 Fit side-chains REVERT: A 242 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6933 (pm20) REVERT: A 363 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: A 596 LYS cc_start: 0.8002 (mttt) cc_final: 0.7521 (mtpt) REVERT: A 734 LEU cc_start: 0.7935 (mt) cc_final: 0.7695 (mp) REVERT: A 878 GLU cc_start: 0.7197 (mp0) cc_final: 0.6583 (tt0) REVERT: B 106 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7948 (p) REVERT: B 363 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7602 (m-30) REVERT: B 504 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7520 (tp) REVERT: B 596 LYS cc_start: 0.7997 (mttt) cc_final: 0.7507 (mtpt) REVERT: B 734 LEU cc_start: 0.7938 (mt) cc_final: 0.7695 (mp) REVERT: B 878 GLU cc_start: 0.7122 (mp0) cc_final: 0.6569 (tt0) outliers start: 25 outliers final: 17 residues processed: 153 average time/residue: 1.1947 time to fit residues: 199.9236 Evaluate side-chains 156 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL 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 266 MET 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 797 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 191 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 337 LYS Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 434 THR 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 122 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.133927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.109937 restraints weight = 12540.821| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.64 r_work: 0.2989 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11004 Z= 0.160 Angle : 0.529 7.701 14934 Z= 0.269 Chirality : 0.040 0.160 1764 Planarity : 0.004 0.047 1828 Dihedral : 3.909 15.631 1462 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.14 % Allowed : 18.58 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.23), residues: 1324 helix: 1.92 (0.18), residues: 856 sheet: 0.35 (0.47), residues: 112 loop : -0.29 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 515 HIS 0.006 0.001 HIS A 719 PHE 0.016 0.002 PHE A 620 TYR 0.015 0.001 TYR B 441 ARG 0.011 0.000 ARG B 347 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 688) hydrogen bonds : angle 3.91585 ( 1962) covalent geometry : bond 0.00388 (11004) covalent geometry : angle 0.52890 (14934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9026.65 seconds wall clock time: 166 minutes 19.39 seconds (9979.39 seconds total)