Starting phenix.real_space_refine on Sun Aug 24 17:11:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgj_36236/08_2025/8jgj_36236_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgj_36236/08_2025/8jgj_36236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jgj_36236/08_2025/8jgj_36236_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgj_36236/08_2025/8jgj_36236_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jgj_36236/08_2025/8jgj_36236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgj_36236/08_2025/8jgj_36236.map" } resolution = 3.3 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= 0.002 sd= 0.033 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 S 72 5.16 5 Cl 6 4.86 5 C 7060 2.51 5 N 1780 2.21 5 O 1894 1.98 5 H 10850 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21668 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 10798 Classifications: {'peptide': 684} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 655} Chain breaks: 4 Chain: "B" Number of atoms: 10798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 10798 Classifications: {'peptide': 684} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 655} Chain breaks: 4 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CL': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CL': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.96, per 1000 atoms: 0.18 Number of scatterers: 21668 At special positions: 0 Unit cell: (90.21, 119.97, 109.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 6 17.00 S 72 16.00 P 6 15.00 O 1894 8.00 N 1780 7.00 C 7060 6.00 H 10850 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 161 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 161 " - pdb=" SG CYS B 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 562 " - pdb=" SG CYS B 568 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 618.5 milliseconds Enol-peptide restraints added in 1.4 microseconds 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 6 sheets defined 68.1% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 92 through 112 removed outlier: 3.855A pdb=" N LYS A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 157 removed outlier: 4.521A pdb=" N GLY A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TRP A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 203 through 233 Processing helix chain 'A' and resid 234 through 237 removed outlier: 3.787A pdb=" N CYS A 237 " --> pdb=" O PRO A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 237' Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 254 through 257 removed outlier: 4.191A pdb=" N LEU A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 257' Processing helix chain 'A' and resid 258 through 274 Processing helix chain 'A' and resid 283 through 298 removed outlier: 4.201A pdb=" N HIS A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.538A pdb=" N THR A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 327 Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 347 through 366 removed outlier: 3.993A pdb=" N ARG A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 391 through 420 removed outlier: 3.673A pdb=" N GLY A 397 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 426 through 443 removed outlier: 3.501A pdb=" N PHE A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 469 through 473 removed outlier: 3.749A pdb=" N ASP A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 516 removed outlier: 3.718A pdb=" N TYR A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 505 " --> pdb=" O TRP A 501 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 552 Processing helix chain 'A' and resid 555 through 560 removed outlier: 3.998A pdb=" N GLU A 560 " --> pdb=" O PHE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 588 Processing helix chain 'A' and resid 590 through 601 removed outlier: 3.683A pdb=" N VAL A 594 " --> pdb=" O THR A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 622 Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 653 through 658 removed outlier: 3.909A pdb=" N VAL A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 709 through 722 Processing helix chain 'A' and resid 767 through 779 removed outlier: 4.003A pdb=" N VAL A 771 " --> pdb=" O PRO A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 805 removed outlier: 4.085A pdb=" N LEU A 801 " --> pdb=" O LYS A 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 112 removed outlier: 3.833A pdb=" N LYS B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 157 removed outlier: 4.510A pdb=" N GLY B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TRP B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 203 through 233 Processing helix chain 'B' and resid 234 through 237 removed outlier: 3.786A pdb=" N CYS B 237 " --> pdb=" O PRO B 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 234 through 237' Processing helix chain 'B' and resid 240 through 249 Processing helix chain 'B' and resid 254 through 257 removed outlier: 4.184A pdb=" N LEU B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 254 through 257' Processing helix chain 'B' and resid 258 through 274 Processing helix chain 'B' and resid 283 through 298 removed outlier: 4.235A pdb=" N HIS B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 removed outlier: 3.551A pdb=" N THR B 305 " --> pdb=" O PRO B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 327 Processing helix chain 'B' and resid 328 through 339 Processing helix chain 'B' and resid 347 through 366 removed outlier: 3.983A pdb=" N ARG B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 391 through 420 removed outlier: 3.963A pdb=" N ILE B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 426 through 443 removed outlier: 3.522A pdb=" N PHE B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 469 through 473 removed outlier: 3.844A pdb=" N ASP B 473 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 516 removed outlier: 3.536A pdb=" N TYR B 497 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 505 " --> pdb=" O TRP B 501 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 515 " --> pdb=" O ILE B 511 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE B 516 " --> pdb=" O ILE B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 555 through 560 removed outlier: 3.956A pdb=" N GLU B 560 " --> pdb=" O PHE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 588 Processing helix chain 'B' and resid 590 through 601 removed outlier: 3.737A pdb=" N VAL B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 622 Processing helix chain 'B' and resid 623 through 625 No H-bonds generated for 'chain 'B' and resid 623 through 625' Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 653 through 658 removed outlier: 3.932A pdb=" N VAL B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 686 Processing helix chain 'B' and resid 709 through 722 Processing helix chain 'B' and resid 767 through 779 removed outlier: 3.983A pdb=" N VAL B 771 " --> pdb=" O PRO B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 805 removed outlier: 4.080A pdb=" N LEU B 801 " --> pdb=" O LYS B 797 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 691 through 695 removed outlier: 6.544A pdb=" N PHE A 692 " --> pdb=" O PHE A 706 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE A 706 " --> pdb=" O PHE A 692 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 694 " --> pdb=" O VAL A 704 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 782 through 786 Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA5, first strand: chain 'B' and resid 691 through 695 Processing sheet with id=AA6, first strand: chain 'B' and resid 782 through 786 645 hydrogen bonds defined for protein. 1908 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: 4.86 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 10826 1.02 - 1.22: 31 1.22 - 1.42: 4608 1.42 - 1.61: 6367 1.61 - 1.81: 108 Bond restraints: 21940 Sorted by residual: bond pdb=" NZ LYS B 281 " pdb=" HZ3 LYS B 281 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" NZ LYS B 245 " pdb=" HZ3 LYS B 245 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" NZ LYS A 281 " pdb=" HZ3 LYS A 281 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" NZ LYS A 281 " pdb=" HZ2 LYS A 281 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" NZ LYS B 281 " pdb=" HZ1 LYS B 281 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 21935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 39063 1.54 - 3.08: 518 3.08 - 4.63: 59 4.63 - 6.17: 10 6.17 - 7.71: 8 Bond angle restraints: 39658 Sorted by residual: angle pdb=" N GLU B 339 " pdb=" CA GLU B 339 " pdb=" C GLU B 339 " ideal model delta sigma weight residual 112.45 120.02 -7.57 1.39e+00 5.18e-01 2.96e+01 angle pdb=" N GLU A 339 " pdb=" CA GLU A 339 " pdb=" C GLU A 339 " ideal model delta sigma weight residual 112.04 119.75 -7.71 1.44e+00 4.82e-01 2.87e+01 angle pdb=" N GLU A 282 " pdb=" CA GLU A 282 " pdb=" C GLU A 282 " ideal model delta sigma weight residual 112.45 105.31 7.14 1.39e+00 5.18e-01 2.64e+01 angle pdb=" N GLU B 282 " pdb=" CA GLU B 282 " pdb=" C GLU B 282 " ideal model delta sigma weight residual 112.45 105.65 6.80 1.39e+00 5.18e-01 2.39e+01 angle pdb=" C GLU A 339 " pdb=" CA GLU A 339 " pdb=" CB GLU A 339 " ideal model delta sigma weight residual 110.56 104.31 6.25 1.83e+00 2.99e-01 1.16e+01 ... (remaining 39653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 9196 16.94 - 33.87: 789 33.87 - 50.81: 227 50.81 - 67.75: 118 67.75 - 84.69: 20 Dihedral angle restraints: 10350 sinusoidal: 5518 harmonic: 4832 Sorted by residual: dihedral pdb=" CA ILE A 253 " pdb=" C ILE A 253 " pdb=" N ARG A 254 " pdb=" CA ARG A 254 " ideal model delta harmonic sigma weight residual -180.00 -161.59 -18.41 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ILE B 253 " pdb=" C ILE B 253 " pdb=" N ARG B 254 " pdb=" CA ARG B 254 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CB GLU B 599 " pdb=" CG GLU B 599 " pdb=" CD GLU B 599 " pdb=" OE1 GLU B 599 " ideal model delta sinusoidal sigma weight residual 0.00 -84.69 84.69 1 3.00e+01 1.11e-03 9.68e+00 ... (remaining 10347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1509 0.061 - 0.121: 174 0.121 - 0.182: 9 0.182 - 0.242: 2 0.242 - 0.303: 4 Chirality restraints: 1698 Sorted by residual: chirality pdb=" C2' ATP B 901 " pdb=" C1' ATP B 901 " pdb=" C3' ATP B 901 " pdb=" O2' ATP B 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C2' ATP A 901 " pdb=" C1' ATP A 901 " pdb=" C3' ATP A 901 " pdb=" O2' ATP A 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3' ATP B 901 " pdb=" C2' ATP B 901 " pdb=" C4' ATP B 901 " pdb=" O3' ATP B 901 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1695 not shown) Planarity restraints: 3144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 283 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO A 284 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 283 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO B 284 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 245 " -0.010 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" N THR A 246 " 0.032 2.00e-02 2.50e+03 pdb=" CA THR A 246 " -0.008 2.00e-02 2.50e+03 pdb=" H THR A 246 " -0.014 2.00e-02 2.50e+03 ... (remaining 3141 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1923 2.22 - 2.81: 47095 2.81 - 3.41: 61251 3.41 - 4.00: 79424 4.00 - 4.60: 124746 Nonbonded interactions: 314439 Sorted by model distance: nonbonded pdb=" O MET A 683 " pdb=" HG1 THR A 687 " model vdw 1.623 2.450 nonbonded pdb=" O PHE A 443 " pdb="HH11 ARG A 449 " model vdw 1.625 2.450 nonbonded pdb=" O PHE B 518 " pdb=" HG SER B 524 " model vdw 1.640 2.450 nonbonded pdb=" O PHE A 518 " pdb=" HG SER A 524 " model vdw 1.644 2.450 nonbonded pdb=" HZ3 LYS A 798 " pdb=" O3G ATP A 901 " model vdw 1.651 2.450 ... (remaining 314434 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: 0.03 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: 1.080 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: 0.140 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.590 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 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 : 0.009 0.892 11097 Z= 0.866 Angle : 0.558 7.711 15078 Z= 0.308 Chirality : 0.040 0.303 1698 Planarity : 0.004 0.052 1844 Dihedral : 14.575 84.686 3966 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.23 (0.23), residues: 1348 helix: 0.95 (0.18), residues: 830 sheet: -2.07 (1.04), residues: 30 loop : -1.03 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 418 TYR 0.017 0.001 TYR A 211 PHE 0.014 0.001 PHE A 300 TRP 0.008 0.001 TRP A 403 HIS 0.003 0.001 HIS B 553 Details of bonding type rmsd covalent geometry : bond 0.00357 (11090) covalent geometry : angle 0.55817 (15066) SS BOND : bond 0.00227 ( 6) SS BOND : angle 0.45043 ( 12) hydrogen bonds : bond 0.13708 ( 645) hydrogen bonds : angle 6.77670 ( 1908) Misc. bond : bond 0.89152 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 683 MET cc_start: 0.7682 (ppp) cc_final: 0.7278 (ptt) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2649 time to fit residues: 57.7563 Evaluate side-chains 131 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.186555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.145384 restraints weight = 34894.830| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.11 r_work: 0.3482 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 11097 Z= 0.304 Angle : 0.627 6.243 15078 Z= 0.335 Chirality : 0.042 0.150 1698 Planarity : 0.005 0.055 1844 Dihedral : 8.987 86.765 1544 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.58 % Allowed : 6.51 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: -0.11 (0.23), residues: 1348 helix: 0.75 (0.18), residues: 842 sheet: -2.07 (1.00), residues: 30 loop : -1.37 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 539 TYR 0.023 0.002 TYR A 211 PHE 0.019 0.002 PHE B 251 TRP 0.015 0.001 TRP A 403 HIS 0.003 0.001 HIS B 787 Details of bonding type rmsd covalent geometry : bond 0.00716 (11090) covalent geometry : angle 0.62647 (15066) SS BOND : bond 0.00440 ( 6) SS BOND : angle 0.80277 ( 12) hydrogen bonds : bond 0.04991 ( 645) hydrogen bonds : angle 5.20519 ( 1908) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.8491 (ttp-110) cc_final: 0.8264 (ttp-170) REVERT: A 598 PHE cc_start: 0.6298 (t80) cc_final: 0.6074 (t80) outliers start: 18 outliers final: 17 residues processed: 144 average time/residue: 0.2288 time to fit residues: 46.9711 Evaluate side-chains 148 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 787 HIS Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 774 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 37 optimal weight: 0.1980 chunk 132 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.191462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.151639 restraints weight = 34282.151| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.99 r_work: 0.3567 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11097 Z= 0.125 Angle : 0.488 4.724 15078 Z= 0.259 Chirality : 0.037 0.144 1698 Planarity : 0.004 0.051 1844 Dihedral : 8.368 89.595 1544 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.06 % Allowed : 7.75 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.50 (0.23), residues: 1348 helix: 1.23 (0.18), residues: 842 sheet: -1.90 (1.00), residues: 30 loop : -1.11 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 106 TYR 0.016 0.001 TYR A 211 PHE 0.010 0.001 PHE B 406 TRP 0.011 0.001 TRP A 403 HIS 0.004 0.001 HIS B 787 Details of bonding type rmsd covalent geometry : bond 0.00278 (11090) covalent geometry : angle 0.48816 (15066) SS BOND : bond 0.00149 ( 6) SS BOND : angle 0.38324 ( 12) hydrogen bonds : bond 0.04160 ( 645) hydrogen bonds : angle 4.81537 ( 1908) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.8478 (ttp-110) cc_final: 0.8172 (ttp-170) REVERT: A 683 MET cc_start: 0.7916 (ptt) cc_final: 0.7708 (ptt) outliers start: 12 outliers final: 12 residues processed: 143 average time/residue: 0.2179 time to fit residues: 44.9704 Evaluate side-chains 140 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 774 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.195352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.155669 restraints weight = 34306.014| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.00 r_work: 0.3596 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11097 Z= 0.134 Angle : 0.473 4.947 15078 Z= 0.248 Chirality : 0.036 0.143 1698 Planarity : 0.004 0.050 1844 Dihedral : 7.973 89.884 1544 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.67 % Allowed : 8.27 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.75 (0.23), residues: 1348 helix: 1.45 (0.18), residues: 842 sheet: -1.98 (1.01), residues: 30 loop : -1.04 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 106 TYR 0.016 0.001 TYR A 211 PHE 0.009 0.001 PHE B 377 TRP 0.011 0.001 TRP A 403 HIS 0.004 0.001 HIS B 787 Details of bonding type rmsd covalent geometry : bond 0.00306 (11090) covalent geometry : angle 0.47317 (15066) SS BOND : bond 0.00176 ( 6) SS BOND : angle 0.35197 ( 12) hydrogen bonds : bond 0.03903 ( 645) hydrogen bonds : angle 4.62176 ( 1908) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 PHE cc_start: 0.6025 (t80) cc_final: 0.5811 (t80) REVERT: A 683 MET cc_start: 0.7914 (ptt) cc_final: 0.7697 (ptt) outliers start: 19 outliers final: 16 residues processed: 144 average time/residue: 0.2159 time to fit residues: 44.6497 Evaluate side-chains 145 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 787 HIS Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 774 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.193072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.153037 restraints weight = 34048.961| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.98 r_work: 0.3565 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11097 Z= 0.141 Angle : 0.473 4.481 15078 Z= 0.249 Chirality : 0.037 0.144 1698 Planarity : 0.004 0.050 1844 Dihedral : 7.767 87.379 1544 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.32 % Allowed : 9.51 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.83 (0.23), residues: 1348 helix: 1.51 (0.18), residues: 842 sheet: -1.98 (1.03), residues: 30 loop : -1.02 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 106 TYR 0.017 0.001 TYR A 211 PHE 0.008 0.001 PHE B 377 TRP 0.011 0.001 TRP A 403 HIS 0.004 0.001 HIS B 787 Details of bonding type rmsd covalent geometry : bond 0.00321 (11090) covalent geometry : angle 0.47276 (15066) SS BOND : bond 0.00194 ( 6) SS BOND : angle 0.43561 ( 12) hydrogen bonds : bond 0.03867 ( 645) hydrogen bonds : angle 4.56386 ( 1908) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 PHE cc_start: 0.6072 (t80) cc_final: 0.5859 (t80) REVERT: A 683 MET cc_start: 0.7958 (ptt) cc_final: 0.7724 (ptt) REVERT: B 598 PHE cc_start: 0.6112 (t80) cc_final: 0.5888 (t80) outliers start: 15 outliers final: 15 residues processed: 143 average time/residue: 0.2262 time to fit residues: 46.5042 Evaluate side-chains 147 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 774 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.191359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.150017 restraints weight = 34393.526| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.10 r_work: 0.3512 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11097 Z= 0.166 Angle : 0.493 4.716 15078 Z= 0.259 Chirality : 0.037 0.148 1698 Planarity : 0.004 0.051 1844 Dihedral : 7.803 85.770 1544 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.76 % Allowed : 9.95 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.70 (0.23), residues: 1348 helix: 1.41 (0.18), residues: 842 sheet: -1.97 (1.04), residues: 30 loop : -1.07 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 106 TYR 0.019 0.001 TYR A 211 PHE 0.010 0.001 PHE B 251 TRP 0.012 0.001 TRP A 403 HIS 0.003 0.001 HIS B 787 Details of bonding type rmsd covalent geometry : bond 0.00385 (11090) covalent geometry : angle 0.49268 (15066) SS BOND : bond 0.00236 ( 6) SS BOND : angle 0.53239 ( 12) hydrogen bonds : bond 0.03976 ( 645) hydrogen bonds : angle 4.57793 ( 1908) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 PHE cc_start: 0.6099 (t80) cc_final: 0.5871 (t80) REVERT: A 683 MET cc_start: 0.7943 (ptt) cc_final: 0.7712 (ptt) REVERT: A 711 ASP cc_start: 0.6353 (m-30) cc_final: 0.5905 (m-30) REVERT: B 598 PHE cc_start: 0.6083 (t80) cc_final: 0.5861 (t80) REVERT: B 675 MET cc_start: 0.4064 (ptp) cc_final: 0.3824 (ptp) REVERT: B 711 ASP cc_start: 0.6451 (m-30) cc_final: 0.6124 (m-30) outliers start: 20 outliers final: 17 residues processed: 143 average time/residue: 0.2348 time to fit residues: 48.3247 Evaluate side-chains 146 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 787 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 774 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.190647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.150577 restraints weight = 34185.229| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.02 r_work: 0.3565 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11097 Z= 0.151 Angle : 0.478 4.671 15078 Z= 0.251 Chirality : 0.037 0.146 1698 Planarity : 0.004 0.051 1844 Dihedral : 7.528 88.514 1544 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.67 % Allowed : 10.48 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.82 (0.24), residues: 1348 helix: 1.50 (0.18), residues: 842 sheet: -1.84 (1.06), residues: 30 loop : -1.03 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 752 TYR 0.019 0.001 TYR A 211 PHE 0.008 0.001 PHE B 377 TRP 0.012 0.001 TRP A 403 HIS 0.004 0.001 HIS B 787 Details of bonding type rmsd covalent geometry : bond 0.00348 (11090) covalent geometry : angle 0.47780 (15066) SS BOND : bond 0.00208 ( 6) SS BOND : angle 0.48948 ( 12) hydrogen bonds : bond 0.03846 ( 645) hydrogen bonds : angle 4.51811 ( 1908) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 PHE cc_start: 0.6095 (t80) cc_final: 0.5867 (t80) REVERT: A 683 MET cc_start: 0.7982 (ptt) cc_final: 0.7733 (ptt) REVERT: A 782 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.6563 (pp30) REVERT: B 598 PHE cc_start: 0.6068 (t80) cc_final: 0.5838 (t80) REVERT: B 782 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.6647 (pp30) outliers start: 19 outliers final: 17 residues processed: 139 average time/residue: 0.2495 time to fit residues: 50.1890 Evaluate side-chains 145 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 782 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 55 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.197307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.158428 restraints weight = 33841.765| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.07 r_work: 0.3546 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11097 Z= 0.133 Angle : 0.468 6.546 15078 Z= 0.244 Chirality : 0.036 0.145 1698 Planarity : 0.004 0.050 1844 Dihedral : 7.314 88.792 1544 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.50 % Allowed : 10.74 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.92 (0.24), residues: 1348 helix: 1.59 (0.18), residues: 842 sheet: -1.79 (1.07), residues: 30 loop : -0.99 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 106 TYR 0.017 0.001 TYR A 211 PHE 0.007 0.001 PHE A 406 TRP 0.011 0.001 TRP A 403 HIS 0.004 0.001 HIS B 787 Details of bonding type rmsd covalent geometry : bond 0.00303 (11090) covalent geometry : angle 0.46783 (15066) SS BOND : bond 0.00184 ( 6) SS BOND : angle 0.41780 ( 12) hydrogen bonds : bond 0.03732 ( 645) hydrogen bonds : angle 4.46397 ( 1908) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 PHE cc_start: 0.6139 (t80) cc_final: 0.5919 (t80) REVERT: A 683 MET cc_start: 0.8043 (ptt) cc_final: 0.7801 (ptt) REVERT: A 711 ASP cc_start: 0.6452 (m-30) cc_final: 0.6052 (m-30) REVERT: A 782 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.6526 (pp30) REVERT: B 598 PHE cc_start: 0.6069 (t80) cc_final: 0.5847 (t80) REVERT: B 711 ASP cc_start: 0.6606 (m-30) cc_final: 0.6268 (m-30) REVERT: B 782 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.6628 (pp30) outliers start: 17 outliers final: 14 residues processed: 150 average time/residue: 0.2538 time to fit residues: 54.2392 Evaluate side-chains 151 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 782 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 128 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 0.0070 chunk 96 optimal weight: 4.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.192863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.149215 restraints weight = 34331.918| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.97 r_work: 0.3476 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11097 Z= 0.154 Angle : 0.483 5.018 15078 Z= 0.253 Chirality : 0.037 0.147 1698 Planarity : 0.004 0.059 1844 Dihedral : 7.368 89.650 1544 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.50 % Allowed : 10.74 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.85 (0.24), residues: 1348 helix: 1.54 (0.18), residues: 842 sheet: -1.81 (1.06), residues: 30 loop : -1.03 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 106 TYR 0.019 0.001 TYR A 211 PHE 0.009 0.001 PHE A 706 TRP 0.012 0.001 TRP A 403 HIS 0.004 0.001 HIS B 787 Details of bonding type rmsd covalent geometry : bond 0.00356 (11090) covalent geometry : angle 0.48284 (15066) SS BOND : bond 0.00221 ( 6) SS BOND : angle 0.50524 ( 12) hydrogen bonds : bond 0.03816 ( 645) hydrogen bonds : angle 4.47712 ( 1908) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 PHE cc_start: 0.6160 (t80) cc_final: 0.5928 (t80) REVERT: A 683 MET cc_start: 0.8023 (ptt) cc_final: 0.7796 (ptt) REVERT: A 782 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.6517 (pp30) REVERT: B 447 TYR cc_start: 0.8394 (m-80) cc_final: 0.8137 (m-10) REVERT: B 598 PHE cc_start: 0.6120 (t80) cc_final: 0.5889 (t80) REVERT: B 782 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.6675 (pp30) outliers start: 17 outliers final: 15 residues processed: 148 average time/residue: 0.2582 time to fit residues: 54.1366 Evaluate side-chains 153 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 782 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 81 optimal weight: 0.4980 chunk 106 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 0.0070 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.195045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.153189 restraints weight = 34161.907| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.19 r_work: 0.3513 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11097 Z= 0.107 Angle : 0.450 4.929 15078 Z= 0.235 Chirality : 0.036 0.140 1698 Planarity : 0.004 0.050 1844 Dihedral : 6.889 82.065 1544 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.50 % Allowed : 10.65 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 1.17 (0.24), residues: 1348 helix: 1.82 (0.18), residues: 840 sheet: -1.84 (1.06), residues: 30 loop : -0.94 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 106 TYR 0.015 0.001 TYR A 211 PHE 0.011 0.001 PHE B 300 TRP 0.009 0.001 TRP B 93 HIS 0.004 0.001 HIS B 787 Details of bonding type rmsd covalent geometry : bond 0.00237 (11090) covalent geometry : angle 0.45045 (15066) SS BOND : bond 0.00130 ( 6) SS BOND : angle 0.33080 ( 12) hydrogen bonds : bond 0.03534 ( 645) hydrogen bonds : angle 4.34172 ( 1908) Misc. bond : bond 0.00009 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 TYR cc_start: 0.8361 (m-80) cc_final: 0.8148 (m-10) REVERT: A 502 GLN cc_start: 0.8539 (pt0) cc_final: 0.8119 (pt0) REVERT: A 598 PHE cc_start: 0.6123 (t80) cc_final: 0.5899 (t80) REVERT: A 683 MET cc_start: 0.7995 (ptt) cc_final: 0.7786 (ptt) REVERT: B 447 TYR cc_start: 0.8318 (m-80) cc_final: 0.8081 (m-10) REVERT: B 598 PHE cc_start: 0.6048 (t80) cc_final: 0.5832 (t80) REVERT: B 782 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.6586 (pp30) outliers start: 17 outliers final: 15 residues processed: 156 average time/residue: 0.2683 time to fit residues: 58.9775 Evaluate side-chains 151 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 782 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 104 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.193248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.151167 restraints weight = 34079.741| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.91 r_work: 0.3494 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11097 Z= 0.166 Angle : 0.490 4.568 15078 Z= 0.258 Chirality : 0.037 0.148 1698 Planarity : 0.004 0.050 1844 Dihedral : 7.173 87.019 1544 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.58 % Allowed : 10.39 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.98 (0.24), residues: 1348 helix: 1.65 (0.18), residues: 842 sheet: -1.90 (1.06), residues: 30 loop : -0.99 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 106 TYR 0.019 0.001 TYR B 211 PHE 0.010 0.001 PHE A 393 TRP 0.013 0.001 TRP A 403 HIS 0.004 0.001 HIS B 787 Details of bonding type rmsd covalent geometry : bond 0.00384 (11090) covalent geometry : angle 0.49039 (15066) SS BOND : bond 0.00226 ( 6) SS BOND : angle 0.50803 ( 12) hydrogen bonds : bond 0.03834 ( 645) hydrogen bonds : angle 4.42986 ( 1908) Misc. bond : bond 0.00016 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5179.09 seconds wall clock time: 88 minutes 37.99 seconds (5317.99 seconds total)